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Bradshaw, Catriona S.; Garland, Suzanne M.; Fairley, Christopher K.; Fethers, Katherine; Tabrizi, Sepehr N. title: The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis date: 2013-09-27 journal: PLoS One DOI: 10.1371/journal.pone.0076892 sha: doc_id: 1090 cord_uid: qg2r691d file: cache/cord-001397-nrq4ncdf.json key: cord-001397-nrq4ncdf authors: Mlera, Luwanika; Melik, Wessam; Bloom, Marshall E. title: The role of viral persistence in flavivirus biology date: 2014-05-12 journal: Pathogens and Disease DOI: 10.1111/2049-632x.12178 sha: doc_id: 1397 cord_uid: nrq4ncdf file: cache/cord-002015-s3tdllby.json key: cord-002015-s3tdllby authors: Burton, Aaron S.; Di Stefano, Marco; Lehman, Niles; Orland, Henri; Micheletti, Cristian title: The elusive quest for RNA knots date: 2016-02-01 journal: RNA Biol DOI: 10.1080/15476286.2015.1132069 sha: doc_id: 2015 cord_uid: s3tdllby file: cache/cord-002376-970934vm.json key: cord-002376-970934vm authors: Mikel, Pavel; 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F.; Andrejeva, J.; Li, X.; Inesta-Vaquera, F.; Dong, C.; Cowling, V. H.; Goodbourn, S.; Randall, R. E. title: Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family date: 2016-09-29 journal: J Virol DOI: 10.1128/jvi.01056-16 sha: doc_id: 2238 cord_uid: fyztb8d9 file: cache/cord-000822-iuglkdcp.json key: cord-000822-iuglkdcp authors: Sperschneider, Jana; Datta, Amitava; Wise, Michael J. title: Predicting pseudoknotted structures across two RNA sequences date: 2012-12-01 journal: Bioinformatics DOI: 10.1093/bioinformatics/bts575 sha: doc_id: 822 cord_uid: iuglkdcp file: cache/cord-000881-s90geszi.json key: cord-000881-s90geszi authors: Lang, Dorothy M.; Zemla, A. T.; Zhou, C. L. 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L. title: Stimulation of ribosomal frameshifting by antisense LNA date: 2010-08-06 journal: Nucleic Acids Res DOI: 10.1093/nar/gkq650 sha: doc_id: 293 cord_uid: pc4x5e24 file: cache/cord-000372-wzwpyvll.json key: cord-000372-wzwpyvll authors: Castelló, Alfredo; Álvarez, Enrique; Carrasco, Luis title: The Multifaceted Poliovirus 2A Protease: Regulation of Gene Expression by Picornavirus Proteases date: 2011-04-14 journal: J Biomed Biotechnol DOI: 10.1155/2011/369648 sha: doc_id: 372 cord_uid: wzwpyvll file: cache/cord-000937-8vk89i4h.json key: cord-000937-8vk89i4h authors: Law, John; Jovel, Juan; Patterson, Jordan; Ford, Glenn; O’keefe, Sandra; Wang, Weiwei; Meng, Bo; Song, Deyong; Zhang, Yong; Tian, Zhijian; Wasilenko, Shawn T.; Rahbari, Mandana; Mitchell, Troy; Jordan, Tracy; Carpenter, Eric; Mason, Andrew L.; Wong, Gane Ka-Shu title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date: 2013-04-17 journal: PLoS One DOI: 10.1371/journal.pone.0060595 sha: doc_id: 937 cord_uid: 8vk89i4h file: cache/cord-002990-7flusgus.json key: cord-002990-7flusgus authors: Kitano, Mitsutaka; Hosmillo, Myra; Emmott, Edward; Lu, Jia; Goodfellow, Ian title: Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro date: 2018-04-26 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.00201-18 sha: doc_id: 2990 cord_uid: 7flusgus file: cache/cord-002222-rgqwm3vb.json key: cord-002222-rgqwm3vb authors: Olarte-Castillo, Ximena A.; Hofer, Heribert; Goller, Katja V.; Martella, Vito; Moehlman, Patricia D.; East, Marion L. title: Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date: 2016-09-23 journal: PLoS One DOI: 10.1371/journal.pone.0163548 sha: doc_id: 2222 cord_uid: rgqwm3vb file: cache/cord-002720-lrkscs71.json key: cord-002720-lrkscs71 authors: Kurosaki, Yohei; Martins, Danyelly Bruneska Gondim; Kimura, Mayuko; Catena, Andriu dos Santos; Borba, Maria Amélia Carlos Souto Maior; Mattos, Sandra da Silva; Abe, Haruka; Yoshikawa, Rokusuke; de Lima Filho, José Luiz; Yasuda, Jiro title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification date: 2017-10-18 journal: Sci Rep DOI: 10.1038/s41598-017-13836-9 sha: doc_id: 2720 cord_uid: lrkscs71 file: cache/cord-000364-ikq38rm1.json key: cord-000364-ikq38rm1 authors: Rasmuson, J.; Andersson, C.; Norrman, E.; Haney, M.; Evander, M.; Ahlm, C. title: Time to revise the paradigm of hantavirus syndromes? Hantavirus pulmonary syndrome caused by European hantavirus date: 2011-01-15 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-010-1141-6 sha: doc_id: 364 cord_uid: ikq38rm1 file: cache/cord-002542-f7l4ty2j.json key: cord-002542-f7l4ty2j authors: Jaworski, Elizabeth; Routh, Andrew title: Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus date: 2017-05-05 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1006365 sha: doc_id: 2542 cord_uid: f7l4ty2j file: cache/cord-000729-iq30z094.json key: cord-000729-iq30z094 authors: Marsh, Glenn A.; de Jong, Carol; Barr, Jennifer A.; Tachedjian, Mary; Smith, Craig; Middleton, Deborah; Yu, Meng; Todd, Shawn; Foord, Adam J.; Haring, Volker; Payne, Jean; Robinson, Rachel; Broz, Ivano; Crameri, Gary; Field, Hume E.; Wang, Lin-Fa title: Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date: 2012-08-02 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1002836 sha: doc_id: 729 cord_uid: iq30z094 file: cache/cord-000979-cav9n18w.json key: cord-000979-cav9n18w authors: Hoppe, Sebastian; Bier, Frank F.; Nickisch-Rosenegk, Markus v. title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 journal: PLoS One DOI: 10.1371/journal.pone.0065837 sha: doc_id: 979 cord_uid: cav9n18w file: cache/cord-002102-0zbp3uqf.json key: cord-002102-0zbp3uqf authors: Rasche, Andrea; Saqib, Muhammad; Liljander, Anne M.; Bornstein, Set; Zohaib, Ali; Renneker, Stefanie; Steinhagen, Katja; Wernery, Renate; Younan, Mario; Gluecks, Ilona; Hilali, Mosaad; Musa, Bakri E.; Jores, Joerg; Wernery, Ulrich; Drexer, Jan Felix; Drosten, Christian; Corman, Victor Max title: Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015 date: 2016-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid2207.160168 sha: doc_id: 2102 cord_uid: 0zbp3uqf file: cache/cord-003254-yiqdsf9z.json key: cord-003254-yiqdsf9z authors: Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date: 2018-08-07 journal: Mol Biol Evol DOI: 10.1093/molbev/msy155 sha: doc_id: 3254 cord_uid: yiqdsf9z file: cache/cord-000981-6vloa2w3.json key: cord-000981-6vloa2w3 authors: Bálint, Zoltán; Zabini, Diana; Konya, Viktoria; Nagaraj, Chandran; Végh, Attila G.; Váró, György; Wilhelm, Imola; Fazakas, Csilla; Krizbai, István A.; Heinemann, Akos; Olschewski, Horst; Olschewski, Andrea title: Double-Stranded RNA Attenuates the Barrier Function of Human Pulmonary Artery Endothelial Cells date: 2013-06-03 journal: PLoS One DOI: 10.1371/journal.pone.0063776 sha: doc_id: 981 cord_uid: 6vloa2w3 file: cache/cord-002006-pwlybr2h.json key: cord-002006-pwlybr2h authors: Liu, Yuan-yuan; Chen, Liang-jun; Zhong, Yan; Shen, Meng-xin; Ma, Nian; Liu, Bing-yu; Luo, Fan; Hou, Wei; Yang, Zhan-qiu; Xiong, Hai-rong title: Specific interference shRNA-expressing plasmids inhibit Hantaan virus infection in vitro and in vivo date: 2016-03-14 journal: Acta Pharmacol Sin DOI: 10.1038/aps.2015.165 sha: doc_id: 2006 cord_uid: pwlybr2h file: cache/cord-002180-gsdk5x3e.json key: cord-002180-gsdk5x3e authors: Davies, Colin; Ward, Vernon K. title: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date: 2016-08-24 journal: PLoS One DOI: 10.1371/journal.pone.0161582 sha: doc_id: 2180 cord_uid: gsdk5x3e file: cache/cord-000736-6f8vyziv.json key: cord-000736-6f8vyziv authors: Pripuzova, Natalia; Wang, Richard; Tsai, Shien; Li, Bingjie; Hung, Guo-Chiuan; Ptak, Roger G.; Lo, Shyh-Ching title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 journal: PLoS One DOI: 10.1371/journal.pone.0043246 sha: doc_id: 736 cord_uid: 6f8vyziv file: cache/cord-000547-adfigzc1.json key: cord-000547-adfigzc1 authors: Beniac, Daniel R.; Melito, Pasquale L.; deVarennes, Shauna L.; Hiebert, Shannon L.; Rabb, Melissa J.; Lamboo, Lindsey L.; Jones, Steven M.; Booth, Timothy F. title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date: 2012-01-11 journal: PLoS One DOI: 10.1371/journal.pone.0029608 sha: doc_id: 547 cord_uid: adfigzc1 file: cache/cord-000640-t0y0b0gb.json key: cord-000640-t0y0b0gb authors: Sumibcay, Laarni; Kadjo, Blaise; Gu, Se Hun; Kang, Hae Ji; Lim, Burton K; Cook, Joseph A; Song, Jin-Won; Yanagihara, Richard title: Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Côte d'Ivoire date: 2012-01-26 journal: Virol J DOI: 10.1186/1743-422x-9-34 sha: doc_id: 640 cord_uid: t0y0b0gb file: cache/cord-001152-v6uc0ijw.json key: cord-001152-v6uc0ijw authors: Girardi, Erika; Chane-Woon-Ming, Béatrice; Messmer, Mélanie; Kaukinen, Pasi; Pfeffer, Sébastien title: Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells date: 2013-11-19 journal: mBio DOI: 10.1128/mbio.00698-13 sha: doc_id: 1152 cord_uid: v6uc0ijw file: cache/cord-002312-jyk7f8hz.json key: cord-002312-jyk7f8hz authors: Branton, W. G.; Lu, J. Q.; Surette, M. G.; Holt, R. A.; Lind, J.; Laman, J. D.; Power, C. title: Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis date: 2016-11-28 journal: Sci Rep DOI: 10.1038/srep37344 sha: doc_id: 2312 cord_uid: jyk7f8hz file: cache/cord-002608-zn7tm1ww.json key: cord-002608-zn7tm1ww authors: Sokoloski, Kevin J.; Nease, Lauren M.; May, Nicholas A.; Gebhart, Natasha N.; Jones, Claire E.; Morrison, Thomas E.; Hardy, Richard W. title: Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants date: 2017-06-29 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1006473 sha: doc_id: 2608 cord_uid: zn7tm1ww file: cache/cord-001963-4wjvykx7.json key: cord-001963-4wjvykx7 authors: Liu, Chia-Lin; Hung, Hui-Chen; Lo, Shou-Chen; Chiang, Ching-Hui; Chen, I-Jung; Hsu, John T.-A.; Hou, Ming-Hon title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development date: 2016-02-26 journal: Sci Rep DOI: 10.1038/srep21662 sha: doc_id: 1963 cord_uid: 4wjvykx7 file: cache/cord-001829-rwnbxmt4.json key: cord-001829-rwnbxmt4 authors: Lu, Yi-Fan; Mauger, David M.; Goldstein, David B.; Urban, Thomas J.; Weeks, Kevin M.; Bradrick, Shelton S. title: IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance date: 2015-11-04 journal: Sci Rep DOI: 10.1038/srep16037 sha: doc_id: 1829 cord_uid: rwnbxmt4 file: cache/cord-002398-0a3okta0.json key: cord-002398-0a3okta0 authors: Myllykoski, Matti; Kursula, Petri title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase date: 2017-01-31 journal: PLoS One DOI: 10.1371/journal.pone.0170355 sha: doc_id: 2398 cord_uid: 0a3okta0 file: cache/cord-002179-v8lpw4r7.json key: cord-002179-v8lpw4r7 authors: Viktorovskaya, Olga V.; Greco, Todd M.; Cristea, Ileana M.; Thompson, Sunnie R. title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements date: 2016-08-24 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0004921 sha: doc_id: 2179 cord_uid: v8lpw4r7 file: cache/cord-002763-n952re94.json key: cord-002763-n952re94 authors: Niu, Xiaosai; Wang, Yuyang; Li, Min; Zhang, Xiaorong; Wu, Yantao title: Transcriptome analysis of avian reovirus-mediated changes in gene expression of normal chicken fibroblast DF-1 cells date: 2017-11-25 journal: BMC Genomics DOI: 10.1186/s12864-017-4310-5 sha: doc_id: 2763 cord_uid: n952re94 file: cache/cord-002937-7xauocti.json key: cord-002937-7xauocti authors: Huang, Chung-Guei; Lee, Li-Ang; Wu, Yi-Cheng; Hsiao, Mei-Jen; Horng, Jim-Tong; Kuo, Rei-Lin; Huang, Chih-Heng; Lin, Ya-Chu; Tsao, Kuo-Chien; Chen, Min-Chi; Chen, Tse-Ching; Shih, Shin-Ru title: A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date: 2018-02-20 journal: Oncotarget DOI: 10.18632/oncotarget.24537 sha: doc_id: 2937 cord_uid: 7xauocti file: cache/cord-001541-5d64esp4.json key: cord-001541-5d64esp4 authors: Walker, Peter J.; Firth, Cadhla; Widen, Steven G.; Blasdell, Kim R.; Guzman, Hilda; Wood, Thomas G.; Paradkar, Prasad N.; Holmes, Edward C.; Tesh, Robert B.; Vasilakis, Nikos title: Evolution of Genome Size and Complexity in the Rhabdoviridae date: 2015-02-13 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004664 sha: doc_id: 1541 cord_uid: 5d64esp4 file: cache/cord-002482-2t09zqqi.json key: cord-002482-2t09zqqi authors: Miras, Manuel; Miller, W. Allen; Truniger, Verónica; Aranda, Miguel A. title: Non-canonical Translation in Plant RNA Viruses date: 2017-04-06 journal: Front Plant Sci DOI: 10.3389/fpls.2017.00494 sha: doc_id: 2482 cord_uid: 2t09zqqi file: cache/cord-002994-1zjrunzc.json key: cord-002994-1zjrunzc authors: Faye, Martin; Faye, Oumar; Diagne, Moussa Moise; Fall, Gamou; Weidmann, Manfred; Sembene, Mbacke; Sall, Amadou Alpha; Faye, Ousmane title: Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus date: 2018-04-13 journal: Viruses DOI: 10.3390/v10040193 sha: doc_id: 2994 cord_uid: 1zjrunzc file: cache/cord-003006-lk2ny1wd.json key: cord-003006-lk2ny1wd authors: Cantoni, Diego; Rossman, Jeremy S. title: Ebolaviruses: New roles for old proteins date: 2018-05-03 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0006349 sha: doc_id: 3006 cord_uid: lk2ny1wd file: cache/cord-000866-dr2uow4m.json key: cord-000866-dr2uow4m authors: Picard-Jean, Frédéric; Bougie, Isabelle; Shuto, Satoshi; Bisaillon, Martin title: The Immunosuppressive Agent Mizoribine Monophosphate Is an Inhibitor of the Human RNA Capping Enzyme date: 2013-01-17 journal: PLoS One DOI: 10.1371/journal.pone.0054621 sha: doc_id: 866 cord_uid: dr2uow4m file: cache/cord-001453-l1r416w7.json key: cord-001453-l1r416w7 authors: Hou, Linlin; Klug, Gabriele; Evguenieva-Hackenberg, Elena title: Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome date: 2014-11-10 journal: Nucleic Acids Res DOI: 10.1093/nar/gku969 sha: doc_id: 1453 cord_uid: l1r416w7 file: cache/cord-003158-mhlqnj52.json key: cord-003158-mhlqnj52 authors: Wang, Qi; Hagedorn, Curt; Liu, Shuanghu title: Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date: 2018-07-13 journal: Int J Biol Sci DOI: 10.7150/ijbs.27411 sha: doc_id: 3158 cord_uid: mhlqnj52 file: cache/cord-001964-iy6qzq58.json key: cord-001964-iy6qzq58 authors: Muñoz-González, Sara; Pérez-Simó, Marta; Colom-Cadena, Andreu; Cabezón, Oscar; Bohórquez, José Alejandro; Rosell, Rosa; Pérez, Lester Josué; Marco, Ignasi; Lavín, Santiago; Domingo, Mariano; Ganges, Llilianne title: Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar date: 2016-02-26 journal: PLoS One DOI: 10.1371/journal.pone.0149469 sha: doc_id: 1964 cord_uid: iy6qzq58 file: cache/cord-002439-wesyiymn.json key: cord-002439-wesyiymn authors: Le, My-Tra; Kasprzak, Wojciech K; Kim, Taejin; Gao, Feng; Young, Megan YL; Yuan, Xuefeng; Shapiro, Bruce A; Seog, Joonil; Simon, Anne E title: Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch date: 2017-02-13 journal: nan DOI: 10.7554/elife.22883 sha: doc_id: 2439 cord_uid: wesyiymn file: cache/cord-003187-qdbcdn2j.json key: cord-003187-qdbcdn2j authors: Bassi, Maria Rosaria; Sempere, Raquel Navarro; Meyn, Prashansa; Polacek, Charlotta; Arias, Armando title: Extinction of Zika Virus and Usutu Virus by Lethal Mutagenesis Reveals Different Patterns of Sensitivity to Three Mutagenic Drugs date: 2018-08-27 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.00380-18 sha: doc_id: 3187 cord_uid: qdbcdn2j file: cache/cord-002676-zwkl1ywk.json key: cord-002676-zwkl1ywk authors: Yu, Dong-Shan; Weng, Tian-Hao; Wu, Xiao-Xin; Wang, Frederick X.C.; Lu, Xiang-Yun; Wu, Hai-Bo; Wu, Nan-Ping; Li, Lan-Juan; Yao, Hang-Ping title: The lifecycle of the Ebola virus in host cells date: 2017-06-15 journal: Oncotarget DOI: 10.18632/oncotarget.18498 sha: doc_id: 2676 cord_uid: zwkl1ywk file: cache/cord-003070-6oca1mrm.json key: cord-003070-6oca1mrm authors: Shen, Wen-Jun; Cui, Wenjuan; Chen, Danze; Zhang, Jieming; Xu, Jianzhen title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date: 2018-02-28 journal: Molecules DOI: 10.3390/molecules23030540 sha: doc_id: 3070 cord_uid: 6oca1mrm file: cache/cord-000794-l565gha4.json key: cord-000794-l565gha4 authors: Yan, Huan; Zhong, Guocai; Xu, Guangwei; He, Wenhui; Jing, Zhiyi; Gao, Zhenchao; Huang, Yi; Qi, Yonghe; Peng, Bo; Wang, Haimin; Fu, Liran; Song, Mei; Chen, Pan; Gao, Wenqing; Ren, Bijie; Sun, Yinyan; Cai, Tao; Feng, Xiaofeng; Sui, Jianhua; Li, Wenhui title: Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus date: 2012-11-13 journal: eLife DOI: 10.7554/elife.00049 sha: doc_id: 794 cord_uid: l565gha4 file: cache/cord-003044-9uqa39j9.json key: cord-003044-9uqa39j9 authors: Cervera, Héctor; Ambrós, Silvia; Bernet, Guillermo P; Rodrigo, Guillermo; Elena, Santiago F title: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date: 2018-03-19 journal: Mol Biol Evol DOI: 10.1093/molbev/msy038 sha: doc_id: 3044 cord_uid: 9uqa39j9 file: cache/cord-002687-ql6zo8ka.json key: cord-002687-ql6zo8ka authors: Li, Dan; He, Wenhui; Liu, Ximing; Zheng, Sanduo; Qi, Yonghe; Li, Huiyu; Mao, Fengfeng; Liu, Juan; Sun, Yinyan; Pan, Lijing; Du, Kaixin; Ye, Keqiong; Li, Wenhui; Sui, Jianhua title: A potent human neutralizing antibody Fc-dependently reduces established HBV infections date: 2017-09-26 journal: nan DOI: 10.7554/elife.26738 sha: doc_id: 2687 cord_uid: ql6zo8ka file: cache/cord-002673-5a1rfi6k.json key: cord-002673-5a1rfi6k authors: Knibb, Wayne; Luu, Giang; Premachandra, H. K. A.; Lu, Ming-Wei; Nguyen, Nguyen Hong title: Regional genetic diversity for NNV grouper viruses across the Indo-Asian region – implications for selecting virus resistance in farmed groupers date: 2017-09-06 journal: Sci Rep DOI: 10.1038/s41598-017-11263-4 sha: doc_id: 2673 cord_uid: 5a1rfi6k file: cache/cord-002764-px0cz6qn.json key: cord-002764-px0cz6qn authors: Lin, Yuan; Currie, Simon L.; Rosen, Michael K. title: Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs date: 2017-11-17 journal: J Biol Chem DOI: 10.1074/jbc.m117.800466 sha: doc_id: 2764 cord_uid: px0cz6qn file: cache/cord-003104-9cx1gdze.json key: cord-003104-9cx1gdze authors: Fitzsimmons, William J.; Woods, Robert J.; McCrone, John T.; Woodman, Andrew; Arnold, Jamie J.; Yennawar, Madhumita; Evans, Richard; Cameron, Craig E.; Lauring, Adam S. title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus date: 2018-06-28 journal: PLoS Biol DOI: 10.1371/journal.pbio.2006459 sha: doc_id: 3104 cord_uid: 9cx1gdze file: cache/cord-003130-p2h8p5bm.json key: cord-003130-p2h8p5bm authors: Lindqvist, Richard; Upadhyay, Arunkumar; Överby, Anna K. title: Tick-Borne Flaviviruses and the Type I Interferon Response date: 2018-06-21 journal: Viruses DOI: 10.3390/v10070340 sha: doc_id: 3130 cord_uid: p2h8p5bm file: cache/cord-003045-r707jl16.json key: cord-003045-r707jl16 authors: Bhuvaneshwar, Krithika; Song, Lei; Madhavan, Subha; Gusev, Yuriy title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date: 2018-06-05 journal: Front Microbiol DOI: 10.3389/fmicb.2018.01172 sha: doc_id: 3045 cord_uid: r707jl16 file: cache/cord-003122-a3f4l6iu.json key: cord-003122-a3f4l6iu authors: Dou, Dan; Revol, Rebecca; Östbye, Henrik; Wang, Hao; Daniels, Robert title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 journal: Front Immunol DOI: 10.3389/fimmu.2018.01581 sha: doc_id: 3122 cord_uid: a3f4l6iu file: cache/cord-003050-n25wnmq5.json key: cord-003050-n25wnmq5 authors: Nibert, Max L.; Manny, Austin R.; Debat, Humberto J.; Firth, Andrew E.; Bertini, Laura; Caruso, Carla title: A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date: 2018-03-07 journal: Arch Virol DOI: 10.1007/s00705-018-3794-x sha: doc_id: 3050 cord_uid: n25wnmq5 file: cache/cord-003284-hjx2d5rq.json key: cord-003284-hjx2d5rq authors: Márquez-Jurado, Silvia; Nogales, Aitor; Ávila-Pérez, Ginés; Iborra, Francisco J.; Martínez-Sobrido, Luis; Almazán, Fernando title: An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo date: 2018-10-07 journal: Viruses DOI: 10.3390/v10100547 sha: doc_id: 3284 cord_uid: hjx2d5rq file: cache/cord-003305-ya0siivm.json key: cord-003305-ya0siivm authors: Liu, Weichi; Shi, Xiaoling; Gong, Peng title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase date: 2018-11-16 journal: Nucleic Acids Res DOI: 10.1093/nar/gky848 sha: doc_id: 3305 cord_uid: ya0siivm file: cache/cord-001835-0s7ok4uw.json key: cord-001835-0s7ok4uw authors: nan title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 journal: Protein Science DOI: 10.1002/pro.2823 sha: doc_id: 1835 cord_uid: 0s7ok4uw file: cache/cord-003505-qr6ukfti.json key: cord-003505-qr6ukfti authors: Tabraue-Chávez, Mavys; Luque-González, María Angélica; Marín-Romero, Antonio; Sánchez-Martín, Rosario María; Escobedo-Araque, Pablo; Pernagallo, Salvatore; Díaz-Mochón, Juan José title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date: 2019-03-06 journal: Sci Rep DOI: 10.1038/s41598-019-39946-0 sha: doc_id: 3505 cord_uid: qr6ukfti file: cache/cord-003482-f1uvohf0.json key: cord-003482-f1uvohf0 authors: Malmlov, Ashley; Bantle, Collin; Aboellail, Tawfik; Wagner, Kaitlyn; Campbell, Corey L.; Eckley, Miles; Chotiwan, Nunya; Gullberg, Rebekah C.; Perera, Rushika; Tjalkens, Ronald; Schountz, Tony title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0007071 sha: doc_id: 3482 cord_uid: f1uvohf0 file: cache/cord-003711-l3brhmzq.json key: cord-003711-l3brhmzq authors: Munnur, Deeksha; Bartlett, Edward; Mikolčević, Petra; Kirby, Ilsa T; Matthias Rack, Johannes Gregor; Mikoč, Andreja; Cohen, Michael S; Ahel, Ivan title: Reversible ADP-ribosylation of RNA date: 2019-06-20 journal: Nucleic Acids Res DOI: 10.1093/nar/gkz305 sha: doc_id: 3711 cord_uid: l3brhmzq file: cache/cord-004827-bnf3mvaf.json key: cord-004827-bnf3mvaf authors: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 journal: Arch Virol DOI: 10.1007/s00705-004-0466-9 sha: doc_id: 4827 cord_uid: bnf3mvaf file: cache/cord-003792-v48xeqdz.json key: cord-003792-v48xeqdz authors: Izquierdo-Suzán, Mónica; Zárate, Selene; Torres-Flores, Jesús; Correa-Morales, Fabián; González-Acosta, Cassandra; Sevilla-Reyes, Edgar E.; Lira, Rosalia; Alcaraz-Estrada, Sofía L.; Yocupicio-Monroy, Martha title: Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date: 2019-08-17 journal: Emerg Infect Dis DOI: 10.3201/eid2508.181533 sha: doc_id: 3792 cord_uid: v48xeqdz file: cache/cord-004280-c470nlie.json key: cord-004280-c470nlie authors: Coleman, Kristen K.; Sigler, William V. title: Airborne Influenza A Virus Exposure in an Elementary School date: 2020-02-05 journal: Sci Rep DOI: 10.1038/s41598-020-58588-1 sha: doc_id: 4280 cord_uid: c470nlie file: cache/cord-004848-2cfphi88.json key: cord-004848-2cfphi88 authors: Carter, M. J. title: Transcription of feline calicivirus RNA date: 1990 journal: Arch Virol DOI: 10.1007/bf01310744 sha: doc_id: 4848 cord_uid: 2cfphi88 file: cache/cord-003382-v3w1wi5c.json key: cord-003382-v3w1wi5c authors: Rahmatpanah, Farah; Agrawal, Sudhanshu; Jaiswal, Natasha; Nguyen, Hannah M.; McClelland, Michael; Agrawal, Anshu title: Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors date: 2018-10-02 journal: Mucosal Immunol DOI: 10.1038/s41385-018-0097-1 sha: doc_id: 3382 cord_uid: v3w1wi5c file: cache/cord-003596-6dg7i06i.json key: cord-003596-6dg7i06i authors: Xiong, Qingqing; Lee, Gha Young; Ding, Jianxun; Li, Wenliang; Shi, Jinjun title: Biomedical applications of mRNA nanomedicine date: 2018-07-27 journal: Nano Res DOI: 10.1007/s12274-018-2146-1 sha: doc_id: 3596 cord_uid: 6dg7i06i file: cache/cord-003707-fbe47bgi.json key: cord-003707-fbe47bgi authors: Russo, Alice G; Kelly, Andrew G; Enosi Tuipulotu, Daniel; Tanaka, Mark M; White, Peter A title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date: 2019-06-18 journal: Virus Evol DOI: 10.1093/ve/vez010 sha: doc_id: 3707 cord_uid: fbe47bgi file: cache/cord-005281-wy0zk9p8.json key: cord-005281-wy0zk9p8 authors: Blinov, V. M.; Zverev, V. V.; Krasnov, G. S.; Filatov, F. P.; Shargunov, A. V. title: Viral component of the human genome date: 2017-05-09 journal: Mol Biol DOI: 10.1134/s0026893317020066 sha: doc_id: 5281 cord_uid: wy0zk9p8 file: cache/cord-005010-xg2bv9gy.json key: cord-005010-xg2bv9gy authors: Dayer, Mohammad Reza; Dayer, Mohammad Saaid; Rezatofighi, Seyedeh Elham title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date: 2015-01-30 journal: Protein J DOI: 10.1007/s10930-015-9601-6 sha: doc_id: 5010 cord_uid: xg2bv9gy file: cache/cord-001521-l36f1gp7.json key: cord-001521-l36f1gp7 authors: nan title: Oral and Poster Manuscripts date: 2011-04-08 journal: Influenza Other Respir Viruses DOI: 10.1111/j.1750-2659.2011.00209.x sha: doc_id: 1521 cord_uid: l36f1gp7 file: cache/cord-004656-n4h295e5.json key: cord-004656-n4h295e5 authors: Olson, Ann Louise; Perlman, Stanley; Robillard, Jean E title: Developmental Regulation of Angiotensinogen Gene Expression in Sheep date: 1990 journal: Pediatr Res DOI: 10.1203/00006450-199009000-00001 sha: doc_id: 4656 cord_uid: n4h295e5 file: cache/cord-006331-s2qf98lj.json key: cord-006331-s2qf98lj authors: Spiridonova, V. A. title: Molecular recognition elements: DNA/RNA-aptamers to proteins date: 2010-05-23 journal: Biochem Mosc Suppl B Biomed Chem DOI: 10.1134/s1990750810020046 sha: doc_id: 6331 cord_uid: s2qf98lj file: cache/cord-006049-sw1hki4r.json key: cord-006049-sw1hki4r authors: Keefe, Anthony D.; Pai, Supriya; Ellington, Andrew title: Aptamers as therapeutics date: 2010 journal: Nat Rev Drug Discov DOI: 10.1038/nrd3141 sha: doc_id: 6049 cord_uid: sw1hki4r file: cache/cord-006452-mmdk2xom.json key: cord-006452-mmdk2xom authors: Chen, Jing; Tang, Yue; Liu, Yun; Dou, Yushun title: Nucleic Acid-Based Therapeutics for Pulmonary Diseases date: 2018-10-18 journal: AAPS PharmSciTech DOI: 10.1208/s12249-018-1183-0 sha: doc_id: 6452 cord_uid: mmdk2xom file: cache/cord-003898-y6zpvw84.json key: cord-003898-y6zpvw84 authors: Tan, Kai Sen; Andiappan, Anand Kumar; Lee, Bernett; Yan, Yan; Liu, Jing; Tang, See Aik; Lum, Josephine; He, Ting Ting; Ong, Yew Kwang; Thong, Mark; Lim, Hui Fang; Choi, Hyung Won; Rotzschke, Olaf; Chow, Vincent T; Wang, De Yun title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date: 2019-08-27 journal: Cells DOI: 10.3390/cells8090986 sha: doc_id: 3898 cord_uid: y6zpvw84 file: cache/cord-004851-h9ppa064.json key: cord-004851-h9ppa064 authors: Plagemann, P. G. W. title: Hepatitis C virus date: 1991 journal: Arch Virol DOI: 10.1007/bf01310473 sha: doc_id: 4851 cord_uid: h9ppa064 file: cache/cord-007819-51h2jrsy.json key: cord-007819-51h2jrsy authors: Schommer, Susan K.; Kleiboeker, Steven B. title: Use of a PRRSV Infectious Clone to Evaluate in Vitro Quasispecies Evolution date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_78 sha: doc_id: 7819 cord_uid: 51h2jrsy file: cache/cord-003435-ke0az7nf.json key: cord-003435-ke0az7nf authors: Schlake, Thomas; Thess, Andreas; Thran, Moritz; Jordan, Ingo title: mRNA as novel technology for passive immunotherapy date: 2018-10-17 journal: Cell Mol Life Sci DOI: 10.1007/s00018-018-2935-4 sha: doc_id: 3435 cord_uid: ke0az7nf file: cache/cord-003676-kr4o8hoc.json key: cord-003676-kr4o8hoc authors: Tan, Chee Wah; Wittwer, Kevin; Lim, Xiao Fang; Uehara, Anna; Mani, Shailendra; Wang, Lin-Fa; Anderson, Danielle E. title: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans date: 2019-05-28 journal: Emerg Microbes Infect DOI: 10.1080/22221751.2019.1621668 sha: doc_id: 3676 cord_uid: kr4o8hoc file: cache/cord-007714-n3omlvfl.json key: cord-007714-n3omlvfl authors: Brown, J. W. S.; Shaw, P. J. title: The Role of the Plant Nucleolus in Pre-mRNA Processing date: 2008 journal: Nuclear pre-mRNA Processing in Plants DOI: 10.1007/978-3-540-76776-3_16 sha: doc_id: 7714 cord_uid: n3omlvfl file: cache/cord-004507-ezuyjcxs.json key: cord-004507-ezuyjcxs authors: Tomazatos, Alexandru; Marschang, Rachel E.; Maranda, Iulia; Baum, Heike; Bialonski, Alexandra; Spînu, Marina; Lühken, Renke; Schmidt-Chanasit, Jonas; Cadar, Daniel title: Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix) date: 2020-02-21 journal: Viruses DOI: 10.3390/v12020243 sha: doc_id: 4507 cord_uid: ezuyjcxs file: cache/cord-005654-n9u2em10.json key: cord-005654-n9u2em10 authors: Campbell, David A.; Thornton, Deborah A.; Boothroyd, John C. title: Apparent discontinuous transcription of Trypanosoma brucei variant surface antigen genes date: 1984 journal: Nature DOI: 10.1038/311350a0 sha: doc_id: 5654 cord_uid: n9u2em10 file: cache/cord-000083-3p81yr4n.json key: cord-000083-3p81yr4n authors: nan title: Poster Exhibition date: 2009-01-31 journal: Hepatol Int DOI: 10.1007/s12072-009-9123-4 sha: doc_id: 83 cord_uid: 3p81yr4n file: cache/cord-007009-4wbvdg1r.json key: cord-007009-4wbvdg1r authors: Takahashi, Toru; Maeda, Ken; Suzuki, Tadaki; Ishido, Aki; Shigeoka, Toru; Tominaga, Takayuki; Kamei, Toshiaki; Honda, Masahiro; Ninomiya, Daisuke; Sakai, Takenori; Senba, Takanori; Kaneyuki, Shozo; Sakaguchi, Shota; Satoh, Akira; Hosokawa, Takanori; Kawabe, Yojiro; Kurihara, Shintaro; Izumikawa, Koichi; Kohno, Shigeru; Azuma, Taichi; Suemori, Koichiro; Yasukawa, Masaki; Mizutani, Tetsuya; Omatsu, Tsutomu; Katayama, Yukie; Miyahara, Masaharu; Ijuin, Masahito; Doi, Kazuko; Okuda, Masaru; Umeki, Kazunori; Saito, Tomoya; Fukushima, Kazuko; Nakajima, Kensuke; Yoshikawa, Tomoki; Tani, Hideki; Fukushi, Shuetsu; Fukuma, Aiko; Ogata, Momoko; Shimojima, Masayuki; Nakajima, Noriko; Nagata, Noriyo; Katano, Harutaka; Fukumoto, Hitomi; Sato, Yuko; Hasegawa, Hideki; Yamagishi, Takuya; Oishi, Kazunori; Kurane, Ichiro; Morikawa, Shigeru; Saijo, Masayuki title: The First Identification and Retrospective Study of Severe Fever With Thrombocytopenia Syndrome in Japan date: 2014-03-15 journal: J Infect Dis DOI: 10.1093/infdis/jit603 sha: doc_id: 7009 cord_uid: 4wbvdg1r file: cache/cord-007236-8hiymqyb.json key: cord-007236-8hiymqyb authors: Sun, Ji-Min; Kim, Seong-Jun; Kim, Geon-Woo; Rhee, Jin-Kyu; Kim, Nam Doo; Jung, Heeyong; Jeun, Jungae; Lee, Seung-Hoon; Han, Seung Hyun; Shin, Chul Soo; Oh, Jong-Won title: Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway date: 2011-11-09 journal: J Antimicrob Chemother DOI: 10.1093/jac/dkr432 sha: doc_id: 7236 cord_uid: 8hiymqyb file: cache/cord-004274-cot05vx7.json key: cord-004274-cot05vx7 authors: Jackson, Nicholas A. C.; Kester, Kent E.; Casimiro, Danilo; Gurunathan, Sanjay; DeRosa, Frank title: The promise of mRNA vaccines: a biotech and industrial perspective date: 2020-02-04 journal: NPJ Vaccines DOI: 10.1038/s41541-020-0159-8 sha: doc_id: 4274 cord_uid: cot05vx7 file: cache/cord-003597-zj3w9ptj.json key: cord-003597-zj3w9ptj authors: Altman, Matthew C.; Gill, Michelle A.; Whalen, Elizabeth; Babineau, Denise C.; Shao, Baomei; Liu, Andrew H.; Jepson, Brett; Gruchalla, Rebecca S.; O’Connor, George T.; Pongracic, Jacqueline A.; Kercsmar, Carolyn M.; Khurana Hershey, Gurjit K.; Zoratti, Edward M.; Johnson, Christine C.; Teach, Stephen J.; Kattan, Meyer; Bacharier, Leonard B.; Beigelman, Avraham; Sigelman, Steve M.; Presnell, Scott; Gern, James E.; Gergen, Peter J.; Wheatley, Lisa M.; Togias, Alkis; Busse, William W.; Jackson, Daniel J. title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children date: 2019-04-08 journal: Nat Immunol DOI: 10.1038/s41590-019-0347-8 sha: doc_id: 3597 cord_uid: zj3w9ptj file: cache/cord-006129-5rog0s98.json key: cord-006129-5rog0s98 authors: Hemida, Maged Gomaa; Ye, Xin; Thair, Simone; Yang, Decheng title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date: 2012-08-16 journal: Mol Diagn Ther DOI: 10.1007/bf03256383 sha: doc_id: 6129 cord_uid: 5rog0s98 file: cache/cord-007041-rloey02j.json key: cord-007041-rloey02j authors: Harel, Noam; Meir, Moran; Gophna, Uri; Stern, Adi title: Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations date: 2019-12-16 journal: Nucleic Acids Res DOI: 10.1093/nar/gkz907 sha: doc_id: 7041 cord_uid: rloey02j file: cache/cord-004719-3stcx0dd.json key: cord-004719-3stcx0dd authors: Mushegian, A. R.; Koonin, E. V. title: Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date: 1993 journal: Arch Virol DOI: 10.1007/bf01313766 sha: doc_id: 4719 cord_uid: 3stcx0dd file: cache/cord-004509-jkzqmkz6.json key: cord-004509-jkzqmkz6 authors: Thirion, Laurence; Dubot-Peres, Audrey; Pezzi, Laura; Corcostegui, Iban; Touinssi, Mhammed; de Lamballerie, Xavier; Charrel, Remi N. title: Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology date: 2020-01-30 journal: Viruses DOI: 10.3390/v12020159 sha: doc_id: 4509 cord_uid: jkzqmkz6 file: cache/cord-007463-8g0zklzy.json key: cord-007463-8g0zklzy authors: Pocock, D.H. title: Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis date: 2002-11-13 journal: Vet Microbiol DOI: 10.1016/0378-1135(87)90095-2 sha: doc_id: 7463 cord_uid: 8g0zklzy file: cache/cord-009662-ntjngiem.json key: cord-009662-ntjngiem authors: Moulton, Jon D. title: Using Morpholinos to Control Gene Expression date: 2007-01-15 journal: Curr Protoc Nucleic Acid Chem DOI: 10.1002/0471142700.nc0430s27 sha: doc_id: 9662 cord_uid: ntjngiem file: cache/cord-009376-a35a92gh.json key: cord-009376-a35a92gh authors: Lovatt, Archie title: Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date: 2002-01-07 journal: nan DOI: 10.1016/s1389-0352(01)00043-5 sha: doc_id: 9376 cord_uid: a35a92gh file: cache/cord-007382-5kb16qb7.json key: cord-007382-5kb16qb7 authors: Hartmann, G. title: Nucleic Acid Immunity date: 2016-12-15 journal: Adv Immunol DOI: 10.1016/bs.ai.2016.11.001 sha: doc_id: 7382 cord_uid: 5kb16qb7 file: cache/cord-005865-7lohh5ty.json key: cord-005865-7lohh5ty authors: Pipper, Juergen; Inoue, Masafumi; Ng, Lisa F-P; Neuzil, Pavel; Zhang, Yi; Novak, Lukas title: Catching bird flu in a droplet date: 2007-09-23 journal: Nat Med DOI: 10.1038/nm1634 sha: doc_id: 5865 cord_uid: 7lohh5ty file: cache/cord-005378-u2bbgn8k.json key: cord-005378-u2bbgn8k authors: Yun, Sang-Im; Lee, Young-Min title: Overview: Replication of porcine reproductive and respiratory syndrome virus date: 2013-12-19 journal: J Microbiol DOI: 10.1007/s12275-013-3431-z sha: doc_id: 5378 cord_uid: u2bbgn8k file: cache/cord-005392-0pgcfk6b.json key: cord-005392-0pgcfk6b authors: Sidoti, Francesca; Bergallo, Massimiliano; Terlizzi, Maria Elena; Piasentin Alessio, Elsa; Astegiano, Sara; Gasparini, Giorgio; Cavallo, Rossana title: Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes date: 2011-07-05 journal: Mol Biotechnol DOI: 10.1007/s12033-011-9432-4 sha: doc_id: 5392 cord_uid: 0pgcfk6b file: cache/cord-006951-tj22dh5o.json key: cord-006951-tj22dh5o authors: Li, Siyu; Erdemci-Tandogan, Gonca; van der Schoot, Paul; Zandi, Roya title: The effect of RNA stiffness on the self-assembly of virus particles date: 2018-01-31 journal: J Phys Condens Matter DOI: 10.1088/1361-648x/aaa159 sha: doc_id: 6951 cord_uid: tj22dh5o file: cache/cord-007474-ckqghr3b.json key: cord-007474-ckqghr3b authors: Johnson, Michael E.; Paul, Prem S.; Gorziglia, Mario; Rosenbusch, Ricardo title: Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes date: 2002-11-13 journal: Vet Microbiol DOI: 10.1016/0378-1135(90)90180-4 sha: doc_id: 7474 cord_uid: ckqghr3b file: cache/cord-007621-rapinodd.json key: cord-007621-rapinodd authors: Vidovic, Maria; Sparacio, Shaun M.; Elovitz, Michal; Benveniste, Etty N. title: Induction and regulation of class II major histocompatibility complex mRNA expression in astrocytes by interferon-γ and tumor necrosis factor-α date: 2002-11-13 journal: J Neuroimmunol DOI: 10.1016/0165-5728(90)90103-t sha: doc_id: 7621 cord_uid: rapinodd file: cache/cord-008556-oetrdm8g.json key: cord-008556-oetrdm8g authors: Kozak, Marilyn title: Regulation of Protein Synthesis in Virus-Infected Animal Cells date: 2008-03-01 journal: Adv Virus Res DOI: 10.1016/s0065-3527(08)60265-1 sha: doc_id: 8556 cord_uid: oetrdm8g file: cache/cord-007066-zn10rnrm.json key: cord-007066-zn10rnrm authors: Park, Noh Jin; Li, Yang; Yu, Tianwei; Brinkman, Brigitta MN; Wong, David T title: Characterization of RNA in Saliva date: 2006-06-01 journal: Clin Chem DOI: 10.1373/clinchem.2005.063206 sha: doc_id: 7066 cord_uid: zn10rnrm file: cache/cord-006960-9pho3hk6.json key: cord-006960-9pho3hk6 authors: Prakash, R.; Pabbaraju, K.; Wong, S.; Wong, A.; Tellier, R.; Kaler, K. V. I. S. title: Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date: 2013-12-27 journal: J Electrochem Soc DOI: 10.1149/2.013402jes sha: doc_id: 6960 cord_uid: 9pho3hk6 file: cache/cord-005147-mvoq9vln.json key: cord-005147-mvoq9vln authors: nan title: Autorenregister date: 2017-02-23 journal: Med Genet DOI: 10.1007/s11825-017-0126-6 sha: doc_id: 5147 cord_uid: mvoq9vln file: cache/cord-005377-36io7zsm.json key: cord-005377-36io7zsm authors: Sidoti, Francesca; Bergallo, Massimiliano; Costa, Cristina; Cavallo, Rossana title: Alternative Molecular Tests for Virological Diagnosis date: 2012-04-09 journal: Mol Biotechnol DOI: 10.1007/s12033-012-9533-8 sha: doc_id: 5377 cord_uid: 36io7zsm file: cache/cord-007689-0vpp3xdl.json key: cord-007689-0vpp3xdl authors: Schlee, M.; Barchet, W.; Hornung, V.; Hartmann, G. title: Beyond Double-Stranded RNA-Type I IFN Induction by 3pRNA and Other Viral Nucleic Acids date: 2007 journal: Interferon: The 50th Anniversary DOI: 10.1007/978-3-540-71329-6_11 sha: doc_id: 7689 cord_uid: 0vpp3xdl file: cache/cord-008541-0u2fatbg.json key: cord-008541-0u2fatbg authors: Bujarski, Jozef J.; Nagy, Peter D.; Flasinski, Stanislaw title: Molecular Studies of Genetic RNA–RNA Recombination in Brome Mosaic Virus date: 2008-02-28 journal: Adv Virus Res DOI: 10.1016/s0065-3527(08)60051-2 sha: doc_id: 8541 cord_uid: 0u2fatbg file: cache/cord-006826-vnmg0zid.json key: cord-006826-vnmg0zid authors: Rayaprolu, Vamseedhar; Moore, Alan; Wang, Joseph Che-Yen; Goh, Boon Chong; Perilla, Juan R; Zlotnick, Adam; Mukhopadhyay, Suchetana title: Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles date: 2017-12-06 journal: J Phys Condens Matter DOI: 10.1088/1361-648x/aa90d0 sha: doc_id: 6826 cord_uid: vnmg0zid file: cache/cord-005060-n901y2d4.json key: cord-005060-n901y2d4 authors: ZHANG, Feiyun; TORIYAMA, Shigemitsu; TAKAHASHI, Mami title: Complete Nucleotide Sequence of Ryegrass Mottle Virus : A New Species of the Genus Sobemovirus date: 2001 journal: J DOI: 10.1007/pl00012989 sha: doc_id: 5060 cord_uid: n901y2d4 file: cache/cord-007181-qpahuqld.json key: cord-007181-qpahuqld authors: YOGO, Yoshiaki; HIRANO, Norio; HINO, Shigeo; SHIBUTA, Hiroshi; MATUMOTO, Minoru title: Polyadenylate in the Virion RNA of Mouse Hepatitis Virus date: 1977-10-17 journal: J Biochem DOI: 10.1093/oxfordjournals.jbchem.a131782 sha: doc_id: 7181 cord_uid: qpahuqld file: cache/cord-010161-bcuec2fz.json key: cord-010161-bcuec2fz authors: Matson, David O. title: IV, 6. Calicivirus RNA recombination date: 2004-09-14 journal: Perspect Med Virol DOI: 10.1016/s0168-7069(03)09032-3 sha: doc_id: 10161 cord_uid: bcuec2fz file: cache/cord-006935-wzz5t3sv.json key: cord-006935-wzz5t3sv authors: Gorbalenya, Alexander E.; Snijder, Eric J. title: Viral cysteine proteinases date: 1996 journal: Perspect Drug Discov Des DOI: 10.1007/bf02174046 sha: doc_id: 6935 cord_uid: wzz5t3sv file: cache/cord-009943-fzynh14x.json key: cord-009943-fzynh14x authors: Ai‐Nakib, W.; Stanway, G.; Forsyth, M.; Hughes, P. J.; Almond, J. W.; Tyrrell, D. A. J. title: Detection of Human Rhinoviruses and Their Molecular Relationship Using cDNA Probes date: 2005-12-11 journal: J Med Virol DOI: 10.1002/jmv.1890200311 sha: doc_id: 9943 cord_uid: fzynh14x file: cache/cord-011794-ejoufvvj.json key: cord-011794-ejoufvvj authors: Binder, Florian; Reiche, Sven; Roman-Sosa, Gleyder; Saathoff, Marion; Ryll, René; Trimpert, Jakob; Kunec, Dusan; Höper, Dirk; Ulrich, Rainer G. title: Isolation and characterization of new Puumala orthohantavirus strains from Germany date: 2020-04-23 journal: Virus Genes DOI: 10.1007/s11262-020-01755-3 sha: doc_id: 11794 cord_uid: ejoufvvj file: cache/cord-008575-bbpmlo3c.json key: cord-008575-bbpmlo3c authors: Lawton, Jeffrey A; Estes, Mary K; Venkataram Prasad, B.V title: Mechanism of genome transcription in segmented dsRNA viruses date: 2004-01-07 journal: Adv Virus Res DOI: 10.1016/s0065-3527(00)55004-0 sha: doc_id: 8575 cord_uid: bbpmlo3c file: cache/cord-010120-mqvm9zn4.json key: cord-010120-mqvm9zn4 authors: Dinman, Jonathan D. title: Ribosomal frameshifting in yeast viruses date: 2004-01-29 journal: Yeast DOI: 10.1002/yea.320111202 sha: doc_id: 10120 cord_uid: mqvm9zn4 file: cache/cord-010273-0c56x9f5.json key: cord-010273-0c56x9f5 authors: Simmonds, Peter title: Virology of hepatitis C virus date: 2001-10-10 journal: Clin Ther DOI: 10.1016/s0149-2918(96)80193-7 sha: doc_id: 10273 cord_uid: 0c56x9f5 file: cache/cord-008407-jbp8bxjz.json key: cord-008407-jbp8bxjz authors: Derdeyn, Cynthia A.; Frey, Teryl K. title: Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date: 1995-01-10 journal: Virology DOI: 10.1016/s0042-6822(95)80036-0 sha: doc_id: 8407 cord_uid: jbp8bxjz file: cache/cord-011803-9122f1zc.json key: cord-011803-9122f1zc authors: Zhao, Yang; Ye, Xiang; Shehata, Myriam; Dunker, William; Xie, Zhihang; Karijolich, John title: The RNA quality control pathway nonsense-mediated mRNA decay targets cellular and viral RNAs to restrict KSHV date: 2020-07-03 journal: Nat Commun DOI: 10.1038/s41467-020-17151-2 sha: doc_id: 11803 cord_uid: 9122f1zc file: cache/cord-008613-tysyq6o4.json key: cord-008613-tysyq6o4 authors: Thomas, Sheila M.; Lamb, Robert A.; Paterson, Reay G. title: Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5 date: 1988-09-09 journal: Cell DOI: 10.1016/s0092-8674(88)91285-8 sha: doc_id: 8613 cord_uid: tysyq6o4 file: cache/cord-006068-w3if1hns.json key: cord-006068-w3if1hns authors: Marshak-Rothstein, Ann title: Toll-like receptors in systemic autoimmune disease date: 2006 journal: Nat Rev Immunol DOI: 10.1038/nri1957 sha: doc_id: 6068 cord_uid: w3if1hns file: cache/cord-012784-c74jr4ga.json key: cord-012784-c74jr4ga authors: Zhang, Le-le; Guo, Jing; Jiang, Xiao-ming; Chen, Xiu-ping; Wang, Yi-tao; Li, Ao; Lin, Li-gen; Li, Hua; Lu, Jin-jian title: Identification of nagilactone E as a protein synthesis inhibitor with anticancer activity date: 2020-02-11 journal: Acta Pharmacol Sin DOI: 10.1038/s41401-019-0332-7 sha: doc_id: 12784 cord_uid: c74jr4ga file: cache/cord-004584-bcw90f5b.json key: cord-004584-bcw90f5b authors: nan title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date: 2011-08-06 journal: Eur Biophys J DOI: 10.1007/s00249-011-0734-z sha: doc_id: 4584 cord_uid: bcw90f5b file: cache/cord-004879-pgyzluwp.json key: cord-004879-pgyzluwp authors: nan title: Programmed cell death date: 1994 journal: Experientia DOI: 10.1007/bf02033112 sha: doc_id: 4879 cord_uid: pgyzluwp file: cache/cord-010374-z9ygudv6.json key: cord-010374-z9ygudv6 authors: Siddell, S.G.; Anderson, R.; Cavanagh, D.; Fujiwara, K.; Klenk, H.D.; Macnaughton, M.R.; Pensaert, M.; Stohlman, S.A.; Sturman, L.; van der Zeijst, B.A.M. title: Coronaviridae1 date: 2008-07-24 journal: Intervirology DOI: 10.1159/000149390 sha: doc_id: 10374 cord_uid: z9ygudv6 file: cache/cord-010045-eqzs01au.json key: cord-010045-eqzs01au authors: Britton, P.; Cármenes, R. S.; Page, K. W.; Garwes, D. J.; Parral, F. title: Sequence of the nucleoprotein gene from a virulent British field isolate of transmissible gastroenteritis virus and its expression in Saccharomyces cerevisiae date: 2006-10-27 journal: Mol Microbiol DOI: 10.1111/j.1365-2958.1988.tb00010.x sha: doc_id: 10045 cord_uid: eqzs01au file: cache/cord-008588-4eu9v5d3.json key: cord-008588-4eu9v5d3 authors: Chastain, Michael; Tinoco, Ignacio title: Structural Elements in RNA date: 2008-02-29 journal: Prog Nucleic Acid Res Mol Biol DOI: 10.1016/s0079-6603(08)60008-2 sha: doc_id: 8588 cord_uid: 4eu9v5d3 file: cache/cord-012032-zolowuhj.json key: cord-012032-zolowuhj authors: Yu, Peifa; Wang, Yining; Li, Yunlong; Li, Yang; Miao, Zhijiang; Peppelenbosch, Maikel P.; Pan, Qiuwei title: 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705 date: 2020-08-08 journal: Arch Virol DOI: 10.1007/s00705-020-04759-4 sha: doc_id: 12032 cord_uid: zolowuhj file: cache/cord-007208-wnkjdg6y.json key: cord-007208-wnkjdg6y authors: Li, Sheng-Hsiang; Lee, Robert Kuo-Kuang; Hsiao, Ya-Ling; Chen, Yee-Hsiung title: Demonstration of a Glycoprotein Derived From the Ceacam10 Gene in Mouse Seminal Vesicle Secretions(1) date: 2005-09-01 journal: Biol Reprod DOI: 10.1095/biolreprod.105.039651 sha: doc_id: 7208 cord_uid: wnkjdg6y file: cache/cord-008426-ktn8c0zx.json key: cord-008426-ktn8c0zx authors: Othman, Yasmin; Hull, Roger title: Nucleotide sequence of the bean strain of southern bean mosaic virus() date: 1995-01-10 journal: Virology DOI: 10.1016/s0042-6822(95)80044-1 sha: doc_id: 8426 cord_uid: ktn8c0zx file: cache/cord-007920-mh3tesdc.json key: cord-007920-mh3tesdc authors: Dhar, Arun K.; Cowley, Jeff A.; Hasson, Kenneth W.; Walker, Peter J. title: Genomic Organization, Biology, and Diagnosis of Taura Syndrome Virus and Yellowhead Virus of Penaeid Shrimp date: 2004-11-11 journal: Adv Virus Res DOI: 10.1016/s0065-3527(04)63006-5 sha: doc_id: 7920 cord_uid: mh3tesdc file: cache/cord-010762-c01wgg4v.json key: cord-010762-c01wgg4v authors: Wu, Jiqin; Ye, Han-Qing; Zhang, Qiu-Yan; Lu, Guoliang; Zhang, Bo; Gong, Peng title: A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase date: 2020-05-01 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008484 sha: doc_id: 10762 cord_uid: c01wgg4v file: cache/cord-014397-7b88ycv8.json key: cord-014397-7b88ycv8 authors: Gavora, JS title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date: 1996-12-15 journal: Genet Sel Evol DOI: 10.1186/1297-9686-28-5-385 sha: doc_id: 14397 cord_uid: 7b88ycv8 file: cache/cord-010977-fwz7chzf.json key: cord-010977-fwz7chzf authors: Myserlis, Pavlos; Radmanesh, Farid; Anderson, Christopher D. title: Translational Genomics in Neurocritical Care: a Review date: 2020-02-20 journal: Neurotherapeutics DOI: 10.1007/s13311-020-00838-1 sha: doc_id: 10977 cord_uid: fwz7chzf file: cache/cord-012484-c9ajmbw2.json key: cord-012484-c9ajmbw2 authors: Wahlund, Martina; Sinha, Indranil; Broliden, Kristina; Saghafian-Hedengren, Shanie; Nilsson, Anna; Berggren, Anna title: The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia date: 2020-07-26 journal: Int J Mol Sci DOI: 10.3390/ijms21155305 sha: doc_id: 12484 cord_uid: c9ajmbw2 file: cache/cord-010680-lc1onm53.json key: cord-010680-lc1onm53 authors: Patel, Ami; Bah, Mamadou A.; Weiner, David B. title: In Vivo Delivery of Nucleic Acid-Encoded Monoclonal Antibodies date: 2020-03-10 journal: BioDrugs DOI: 10.1007/s40259-020-00412-3 sha: doc_id: 10680 cord_uid: lc1onm53 file: cache/cord-010188-884d196k.json key: cord-010188-884d196k authors: Schlesinger, Sondra title: Alphaviruses — vectors for the expression of heterologous genes date: 2004-08-26 journal: Trends Biotechnol DOI: 10.1016/0167-7799(93)90070-p sha: doc_id: 10188 cord_uid: 884d196k file: cache/cord-013243-1hj5clsw.json key: cord-013243-1hj5clsw authors: Brewer, Gary; Li, Mei-Ling; Tolbert, Blanton S. title: Editorial for “Methods to characterize virus small RNAs and RNA structures” date: 2020-10-16 journal: Methods DOI: 10.1016/j.ymeth.2020.10.007 sha: doc_id: 13243 cord_uid: 1hj5clsw file: cache/cord-012420-llh22iq2.json key: cord-012420-llh22iq2 authors: Stott, Robert J.; Strecker, Thomas; Foster, Toshana L. title: Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins date: 2020-07-21 journal: Viruses DOI: 10.3390/v12070784 sha: doc_id: 12420 cord_uid: llh22iq2 file: cache/cord-012909-o6t2srim.json key: cord-012909-o6t2srim authors: Chaudhari, Jayeshbhai; Liew, Chia-Sin; Workman, Aspen M.; Riethoven, Jean-Jack M.; Steffen, David; Sillman, Sarah; Vu, Hiep L. X. title: Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain date: 2020-07-28 journal: Viruses DOI: 10.3390/v12080817 sha: doc_id: 12909 cord_uid: o6t2srim file: cache/cord-013176-6ckuya1w.json key: cord-013176-6ckuya1w authors: Ninfali, Paolino; Antonelli, Antonella; Magnani, Mauro; Scarpa, Emanuele Salvatore title: Antiviral Properties of Flavonoids and Delivery Strategies date: 2020-08-21 journal: Nutrients DOI: 10.3390/nu12092534 sha: doc_id: 13176 cord_uid: 6ckuya1w file: cache/cord-013280-kczj24se.json key: cord-013280-kczj24se authors: Yang, Bo; Zhang, Xiaohui; Zhang, Dajun; Hou, Jing; Xu, GuoWei; Sheng, Chaochao; Choudhury, Sk Mohiuddin; Zhu, Zixiang; Li, Dan; Zhang, Keshan; Zheng, Haixue; Liu, Xiangtao title: Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus date: 2020-09-04 journal: Pathogens DOI: 10.3390/pathogens9090729 sha: doc_id: 13280 cord_uid: kczj24se file: cache/cord-013412-gj443yei.json key: cord-013412-gj443yei authors: Lebedeva, Natalya Sh.; Gubarev, Yury A.; Koifman, Mikhail O.; Koifman, Oskar I. title: The Application of Porphyrins and Their Analogues for Inactivation of Viruses date: 2020-09-23 journal: Molecules DOI: 10.3390/molecules25194368 sha: doc_id: 13412 cord_uid: gj443yei file: cache/cord-013177-whd0znan.json key: cord-013177-whd0znan authors: Han, Zhenzhi; Xiao, Jinbo; Song, Yang; Hong, Mei; Dai, Guolong; Lu, Huanhuan; Zhang, Man; Liang, Yueling; Yan, Dongmei; Zhu, Shuangli; Xu, Wenbo; Zhang, Yong title: The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales date: 2020-09-07 journal: Viruses DOI: 10.3390/v12090995 sha: doc_id: 13177 cord_uid: whd0znan file: cache/cord-013171-wgn529rc.json key: cord-013171-wgn529rc authors: Zhong, Yi; Hu, Zhengchao; Wu, Jingcui; Dai, Fan; Lee, Feng; Xu, Yangping title: STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway date: 2020-09-16 journal: Oncol Rep DOI: 10.3892/or.2020.7769 sha: doc_id: 13171 cord_uid: wgn529rc file: cache/cord-014685-ihh30q6f.json key: cord-014685-ihh30q6f authors: nan title: Posters P788 - P999 date: 2005-09-21 journal: Eur Biophys J DOI: 10.1007/s00249-005-0504-x sha: doc_id: 14685 cord_uid: ihh30q6f file: cache/cord-013854-wadpugbj.json key: cord-013854-wadpugbj authors: Fratter, Carl; Dalgleish, Raymond; Allen, Stephanie K.; Santos, Rosário; Abbs, Stephen; Tuffery-Giraud, Sylvie; Ferlini, Alessandra title: EMQN best practice guidelines for genetic testing in dystrophinopathies date: 2020-05-18 journal: Eur J Hum Genet DOI: 10.1038/s41431-020-0643-7 sha: doc_id: 13854 cord_uid: wadpugbj file: cache/cord-015642-p46abodr.json key: cord-015642-p46abodr authors: Backofen, Rolf; Fricke, Markus; Marz, Manja; Qin, Jing; Stadler, Peter F. title: Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures date: 2013 journal: Algorithms in Bioinformatics DOI: 10.1007/978-3-642-40453-5_10 sha: doc_id: 15642 cord_uid: p46abodr file: cache/cord-012552-porty653.json key: cord-012552-porty653 authors: Tan, Kun; Jones, Samantha H; Lake, Blue B; Dumdie, Jennifer N; Shum, Eleen Y; Zhang, Lingjuan; Chen, Song; Sohni, Abhishek; Pandya, Shivam; Gallo, Richard L; Zhang, Kun; Cook-Andersen, Heidi; Wilkinson, Miles F title: The role of the NMD factor UPF3B in olfactory sensory neurons date: 2020-08-10 journal: nan DOI: 10.7554/elife.57525 sha: doc_id: 12552 cord_uid: porty653 file: cache/cord-015376-z739ifu5.json key: cord-015376-z739ifu5 authors: Savarino, Andrea; Buonavoglia, Canio; Norelli, Sandro; Trani, Livia Di; Cassone, Antonio title: Potential therapies for coronaviruses date: 2006-08-31 journal: Expert Opin Ther Pat DOI: 10.1517/13543776.16.9.1269 sha: doc_id: 15376 cord_uid: z739ifu5 file: cache/cord-015527-ph576eji.json key: cord-015527-ph576eji authors: Mostajo, Nelly F; Lataretu, Marie; Krautwurst, Sebastian; Mock, Florian; Desirò, Daniel; Lamkiewicz, Kevin; Collatz, Maximilian; Schoen, Andreas; Weber, Friedemann; Marz, Manja; Hölzer, Martin title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date: 2019-09-30 journal: NAR Genom Bioinform DOI: 10.1093/nargab/lqz006 sha: doc_id: 15527 cord_uid: ph576eji file: cache/cord-004534-jqm1hxps.json key: cord-004534-jqm1hxps authors: nan title: Abstract date: 2009-06-09 journal: Eur Biophys J DOI: 10.1007/s00249-009-0478-1 sha: doc_id: 4534 cord_uid: jqm1hxps file: cache/cord-013784-zhgjmt2j.json key: cord-013784-zhgjmt2j authors: Tang, Min; Xie, Qi; Gimple, Ryan C.; Zhong, Zheng; Tam, Trevor; Tian, Jing; Kidwell, Reilly L.; Wu, Qiulian; Prager, Briana C.; Qiu, Zhixin; Yu, Aaron; Zhu, Zhe; Mesci, Pinar; Jing, Hui; Schimelman, Jacob; Wang, Pengrui; Lee, Derrick; Lorenzini, Michael H.; Dixit, Deobrat; Zhao, Linjie; Bhargava, Shruti; Miller, Tyler E.; Wan, Xueyi; Tang, Jing; Sun, Bingjie; Cravatt, Benjamin F.; Muotri, Alysson R.; Chen, Shaochen; Rich, Jeremy N. title: Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions date: 2020-06-04 journal: Cell Res DOI: 10.1038/s41422-020-0338-1 sha: doc_id: 13784 cord_uid: zhgjmt2j file: cache/cord-014908-jys1y0k9.json key: cord-014908-jys1y0k9 authors: Yadav, Rakesh; Dwivedi, Sadhana; Kumar, Sandeep; Chaudhury, Ashok title: Trends and Perspectives of Biosensors for Food and Environmental Virology date: 2010-05-19 journal: Food Environ Virol DOI: 10.1007/s12560-010-9034-5 sha: doc_id: 14908 cord_uid: jys1y0k9 file: cache/cord-015673-rz74sh32.json key: cord-015673-rz74sh32 authors: Lamers, Anne E.; de Kleijn, Dominique P. V. title: RNA Interference Mechanisms and Therapeutic Applications date: 2006 journal: Cardiovascular Research DOI: 10.1007/0-387-23329-6_7 sha: doc_id: 15673 cord_uid: rz74sh32 file: cache/cord-016144-280kwlev.json key: cord-016144-280kwlev authors: Maan, Sushila; Dalal, Sangeeta; Kumar, Aman; Dalal, Anita; Bansal, Nitish; Chaudhary, Deepika; Gupta, Akhil; Maan, Narender Singh title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date: 2018-04-26 journal: Advances in Animal Biotechnology and its Applications DOI: 10.1007/978-981-10-4702-2_14 sha: doc_id: 16144 cord_uid: 280kwlev file: cache/cord-016108-jlono0x7.json key: cord-016108-jlono0x7 authors: Marthaler, Douglas; Bohac, Ann; Becker, Aaron; Peterson, Nichole title: Next-Generation Sequencing for Porcine Coronaviruses date: 2015-09-10 journal: Animal Coronaviruses DOI: 10.1007/978-1-4939-3414-0_19 sha: doc_id: 16108 cord_uid: jlono0x7 file: cache/cord-016209-6p9btua0.json key: cord-016209-6p9btua0 authors: Merl, S.; Wessely, R. title: Targeting Viral Heart Disease by RNA Interference date: 2008 journal: RNA Technologies in Cardiovascular Medicine and Research DOI: 10.1007/978-3-540-78709-9_6 sha: doc_id: 16209 cord_uid: 6p9btua0 file: cache/cord-016095-jop2rx61.json key: cord-016095-jop2rx61 authors: Vignais, Pierre V.; Vignais, Paulette M. title: Challenges for Experimentation on Living Beings at the Dawn of the 21(st) Century date: 2010-06-08 journal: Discovering Life, Manufacturing Life DOI: 10.1007/978-90-481-3767-1_5 sha: doc_id: 16095 cord_uid: jop2rx61 file: cache/cord-014462-11ggaqf1.json key: cord-014462-11ggaqf1 authors: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 journal: Indian J Virol DOI: 10.1007/s13337-011-0027-2 sha: doc_id: 14462 cord_uid: 11ggaqf1 file: cache/cord-016808-gy8d8285.json key: cord-016808-gy8d8285 authors: Agol, Vadim I. title: The Origin and Evolution of Viruses date: 2008 journal: Evolution from Cellular to Social Scales DOI: 10.1007/978-1-4020-8761-5_7 sha: doc_id: 16808 cord_uid: gy8d8285 file: cache/cord-016343-wc3i54fc.json key: cord-016343-wc3i54fc authors: Frese, Michael; Dazert, Eva title: Interferon-Induced Effector Proteins and Hepatitis C Virus Replication date: 2008 journal: Hepatitis C Virus Disease DOI: 10.1007/978-0-387-71376-2_6 sha: doc_id: 16343 cord_uid: wc3i54fc file: cache/cord-016261-jms7hrmp.json key: cord-016261-jms7hrmp authors: Liu, Chunmei; Song, Yinglei; Malmberg, Russell L.; Cai, Liming title: Profiling and Searching for RNA Pseudoknot Structures in Genomes date: 2005 journal: Transactions on Computational Systems Biology II DOI: 10.1007/11567752_2 sha: doc_id: 16261 cord_uid: jms7hrmp file: cache/cord-015237-8cxfa8wf.json key: cord-015237-8cxfa8wf authors: nan title: Structure Watch date: 2005 journal: Nat Rev Mol Cell Biol DOI: 10.1038/nrm1780 sha: doc_id: 15237 cord_uid: 8cxfa8wf file: cache/cord-015606-h9bbvpzd.json key: cord-015606-h9bbvpzd authors: Highfield, P.E.; Morser, J.; Lomniczi, B.; Stephenson, J.R. title: Translation of infectious bronchitis virus RNA date: 2006-03-27 journal: FEMS Microbiol Lett DOI: 10.1111/j.1574-6968.1978.tb01922.x sha: doc_id: 15606 cord_uid: h9bbvpzd file: cache/cord-016179-4i1n9j4x.json key: cord-016179-4i1n9j4x authors: Chen, Yi-Ning; Wu, Ching Ching; Lin, Tsang Long title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues date: 2015-09-10 journal: Animal Coronaviruses DOI: 10.1007/978-1-4939-3414-0_13 sha: doc_id: 16179 cord_uid: 4i1n9j4x file: cache/cord-016309-6mw8okmt.json key: cord-016309-6mw8okmt authors: Bule, Mohammed; Khan, Fazlullah; Niaz, Kamal title: Antivirals: Past, Present and Future date: 2019-06-06 journal: Recent Advances in Animal Virology DOI: 10.1007/978-981-13-9073-9_22 sha: doc_id: 16309 cord_uid: 6mw8okmt file: cache/cord-015871-1tuf4zxi.json key: cord-015871-1tuf4zxi authors: Ergonul, Onder; Mirazimi, Ali; Dimitrov, Dimiter S. title: Treatment of Crimean-Congo Hemorrhagic Fever date: 2007 journal: Crimean-Congo Hemorrhagic Fever DOI: 10.1007/978-1-4020-6106-6_19 sha: doc_id: 15871 cord_uid: 1tuf4zxi file: cache/cord-017181-ywz6w2po.json key: cord-017181-ywz6w2po authors: Maus, Carsten title: Component-Based Modelling of RNA Structure Folding date: 2008 journal: Computational Methods in Systems Biology DOI: 10.1007/978-3-540-88562-7_8 sha: doc_id: 17181 cord_uid: ywz6w2po file: cache/cord-017968-17d37a2z.json key: cord-017968-17d37a2z authors: Lewinski, Martin; Köster, Tino title: Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana date: 2018-08-30 journal: Systems Biology DOI: 10.1007/978-3-319-92967-5_5 sha: doc_id: 17968 cord_uid: 17d37a2z file: cache/cord-015933-x5cq4k4x.json key: cord-015933-x5cq4k4x authors: Verbrugh, H.A.; Kroes, A.C.M.; Sauerwein, R.W. title: 1 Micro-organismen, de mens en het ontstaan van infectieziekten: algemene principes date: 2011 journal: Microbiologie en infectieziekten DOI: 10.1007/978-90-313-7944-6_1 sha: doc_id: 15933 cord_uid: x5cq4k4x file: cache/cord-016293-pyb00pt5.json key: cord-016293-pyb00pt5 authors: Newell-McGloughlin, Martina; Re, Edward title: The flowering of the age of Biotechnology 1990–2000 date: 2006 journal: The Evolution of Biotechnology DOI: 10.1007/1-4020-5149-2_4 sha: doc_id: 16293 cord_uid: pyb00pt5 file: cache/cord-016499-5iqpl23p.json key: cord-016499-5iqpl23p authors: Mackay, Ian M.; Arden, Katherine E. title: Rhinoviruses date: 2014-02-27 journal: Viral Infections of Humans DOI: 10.1007/978-1-4899-7448-8_29 sha: doc_id: 16499 cord_uid: 5iqpl23p file: cache/cord-015850-ef6svn8f.json key: cord-015850-ef6svn8f authors: Saitou, Naruya title: Eukaryote Genomes date: 2013-08-22 journal: Introduction to Evolutionary Genomics DOI: 10.1007/978-1-4471-5304-7_8 sha: doc_id: 15850 cord_uid: ef6svn8f file: cache/cord-017297-q3qtgrfc.json key: cord-017297-q3qtgrfc authors: Rajagopal, Vaishnavi; Patel, Smita S. title: Viral Helicases date: 2008-11-01 journal: Viral Genome Replication DOI: 10.1007/b135974_20 sha: doc_id: 17297 cord_uid: q3qtgrfc file: cache/cord-016313-n4ewq0pt.json key: cord-016313-n4ewq0pt authors: Baranyi, Lajos; Dropulic, Boro title: Advances in Lentiviral Vector-based Cell Therapy with Mesenchymal Stem Cells date: 2012-09-27 journal: Mesenchymal Stem Cell Therapy DOI: 10.1007/978-1-62703-200-1_14 sha: doc_id: 16313 cord_uid: n4ewq0pt file: cache/cord-018164-h5k1zsyg.json key: cord-018164-h5k1zsyg authors: Taylor, Milton W. title: What Is a Virus? date: 2014-07-22 journal: Viruses and Man: A History of Interactions DOI: 10.1007/978-3-319-07758-1_2 sha: doc_id: 18164 cord_uid: h5k1zsyg file: cache/cord-018804-wj35q88f.json key: cord-018804-wj35q88f authors: Lázaro, Ester title: Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date: 2007 journal: Structural Approaches to Sequence Evolution DOI: 10.1007/978-3-540-35306-5_15 sha: doc_id: 18804 cord_uid: wj35q88f file: cache/cord-018944-du42ho11.json key: cord-018944-du42ho11 authors: Shin, Jeong Hwan title: Nucleic Acid Extraction and Enrichment date: 2018-11-10 journal: Advanced Techniques in Diagnostic Microbiology DOI: 10.1007/978-3-319-33900-9_13 sha: doc_id: 18944 cord_uid: du42ho11 file: cache/cord-016419-v1f6dx3e.json key: cord-016419-v1f6dx3e authors: Gupta, Varsha; Sengupta, Manjistha; Prakash, Jaya; Tripathy, Baishnab Charan title: Production of Recombinant Pharmaceutical Proteins date: 2016-10-23 journal: Basic and Applied Aspects of Biotechnology DOI: 10.1007/978-981-10-0875-7_4 sha: doc_id: 16419 cord_uid: v1f6dx3e file: cache/cord-017167-8cdbcrh7.json key: cord-017167-8cdbcrh7 authors: Ahola, Tero; Merits, Andres title: Functions of Chikungunya Virus Nonstructural Proteins date: 2016-12-03 journal: Chikungunya Virus DOI: 10.1007/978-3-319-42958-8_6 sha: doc_id: 17167 cord_uid: 8cdbcrh7 file: cache/cord-020969-lh2ergpm.json key: cord-020969-lh2ergpm authors: STRAUSS, JAMES H.; STRAUSS, ELLEN G. title: Gene Therapy date: 2012-07-27 journal: Viruses and Human Disease DOI: 10.1016/b978-0-12-373741-0.50014-3 sha: doc_id: 20969 cord_uid: lh2ergpm file: cache/cord-021115-2fkghukw.json key: cord-021115-2fkghukw authors: Guo, Yun; Zhang, Wenbing title: Molecular dynamics simulation of RNA pseudoknot unfolding pathway date: 2013-03-12 journal: nan DOI: 10.1007/s11859-013-0905-0 sha: doc_id: 21115 cord_uid: 2fkghukw file: cache/cord-018437-yjvwa1ot.json key: cord-018437-yjvwa1ot authors: Mitchell, Michael title: Taxonomy date: 2013-08-26 journal: Viruses and the Lung DOI: 10.1007/978-3-642-40605-8_3 sha: doc_id: 18437 cord_uid: yjvwa1ot file: cache/cord-019076-4qu9j953.json key: cord-019076-4qu9j953 authors: Ulferts, Rachel; Imbert, Isabelle; Canard, Bruno; Ziebuhr, John title: Expression and Functions of SARS Coronavirus Replicative Proteins date: 2009-07-22 journal: Molecular Biology of the SARS-Coronavirus DOI: 10.1007/978-3-642-03683-5_6 sha: doc_id: 19076 cord_uid: 4qu9j953 file: cache/cord-016755-ye37z5h9.json key: cord-016755-ye37z5h9 authors: Li, Jiandong; Li, Dexin title: The Discovery Process of SFTS in China date: 2019-10-12 journal: Severe Fever with Thrombocytopenia Syndrome DOI: 10.1007/978-981-13-9562-8_2 sha: doc_id: 16755 cord_uid: ye37z5h9 file: cache/cord-017732-1pwa6zsk.json key: cord-017732-1pwa6zsk authors: Miller, W. Allen; Giedroc, David P. title: Ribosomal Frameshifting in Decoding Plant Viral RNAs date: 2009-07-21 journal: Recoding: Expansion of Decoding Rules Enriches Gene Expression DOI: 10.1007/978-0-387-89382-2_9 sha: doc_id: 17732 cord_uid: 1pwa6zsk file: cache/cord-022084-hap7flng.json key: cord-022084-hap7flng authors: ARRUDA, EURICO; CINTRA, OTAVIO A.L.; HAYDEN, FREDERICK G. title: Respiratory Tract Viral Infections date: 2009-05-15 journal: Tropical Infectious Diseases DOI: 10.1016/b978-0-443-06668-9.50064-8 sha: doc_id: 22084 cord_uid: hap7flng file: cache/cord-016652-x8t3lf1x.json key: cord-016652-x8t3lf1x authors: Matthews, David; Emmott, Edward; Hiscox, Julian title: Viruses and the Nucleolus date: 2011-05-23 journal: The Nucleolus DOI: 10.1007/978-1-4614-0514-6_14 sha: doc_id: 16652 cord_uid: x8t3lf1x file: cache/cord-021481-tvs1pnib.json key: cord-021481-tvs1pnib authors: Singh, Gatikrushna; Heng, Xiao; Boris-Lawrie, Kathleen title: Cellular RNA Helicases Support Early and Late Events in Retroviral Replication date: 2018-08-17 journal: Retrovirus-Cell Interactions DOI: 10.1016/b978-0-12-811185-7.00007-8 sha: doc_id: 21481 cord_uid: tvs1pnib file: cache/cord-022348-w7z97wir.json key: cord-022348-w7z97wir authors: Sola, Monica; Wain-Hobson, Simon title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-012220360-2/50007-6 sha: doc_id: 22348 cord_uid: w7z97wir file: cache/cord-018724-ss8x2g3b.json key: cord-018724-ss8x2g3b authors: Stobbe, Anthony; Roossinck, Marilyn J. title: Plant Virus Diversity and Evolution date: 2016-06-22 journal: Current Research Topics in Plant Virology DOI: 10.1007/978-3-319-32919-2_8 sha: doc_id: 18724 cord_uid: ss8x2g3b file: cache/cord-016538-4og05fuo.json key: cord-016538-4og05fuo authors: Dolja, V. V.; Meng, B. title: Biotechnology Applications of Grapevine Viruses date: 2017-03-30 journal: Grapevine Viruses: Molecular Biology, Diagnostics and Management DOI: 10.1007/978-3-319-57706-7_31 sha: doc_id: 16538 cord_uid: 4og05fuo file: cache/cord-018798-yzxy9ogf.json key: cord-018798-yzxy9ogf authors: Jain, Pradeep Kumar; Bhattacharya, Ramcharan; Kohli, Deshika; Aminedi, Raghavendra; Agrawal, Pawan Kumar title: RNAi for Resistance Against Biotic Stresses in Crop Plants date: 2018-07-10 journal: Biotechnologies of Crop Improvement, Volume 2 DOI: 10.1007/978-3-319-90650-8_4 sha: doc_id: 18798 cord_uid: yzxy9ogf file: cache/cord-023865-6rafp3x3.json key: cord-023865-6rafp3x3 authors: Surjit, Milan; Lal, Sunil K. title: The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date: 2009-07-22 journal: Molecular Biology of the SARS-Coronavirus DOI: 10.1007/978-3-642-03683-5_9 sha: doc_id: 23865 cord_uid: 6rafp3x3 file: cache/cord-019051-gtruu1op.json key: cord-019051-gtruu1op authors: Weber, Olaf title: The role of viruses in the etiology and pathogenesis of common cold date: 2009-11-10 journal: Common Cold DOI: 10.1007/978-3-7643-9912-2_5 sha: doc_id: 19051 cord_uid: gtruu1op file: cache/cord-023724-5at0rhqk.json key: cord-023724-5at0rhqk authors: Cann, Alan J. title: Infection date: 2015-07-24 journal: Principles of Molecular Virology DOI: 10.1016/b978-0-12-801946-7.00006-7 sha: doc_id: 23724 cord_uid: 5at0rhqk file: cache/cord-016796-g4kqqpy1.json key: cord-016796-g4kqqpy1 authors: Bramhachari, Pallaval Veera; Mohana Sheela, Ganugula; Prathyusha, A. M. V. N.; Madhavi, M.; Satish Kumar, K.; Reddy, Neelapu Nageswara Rao; Berde, Chanda Parulekar title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 journal: Dynamics of Immune Activation in Viral Diseases DOI: 10.1007/978-981-15-1045-8_17 sha: doc_id: 16796 cord_uid: g4kqqpy1 file: cache/cord-022262-ck2lhojz.json key: cord-022262-ck2lhojz authors: Gromeier, Matthias; Wimmer, Eckard; Gorbalenya, Alexander E. title: Genetics, Pathogenesis and Evolution of Picornaviruses date: 2007-09-02 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-012220360-2/50013-1 sha: doc_id: 22262 cord_uid: ck2lhojz file: cache/cord-018017-c8myq6bi.json key: cord-018017-c8myq6bi authors: Iversen, Patrick L. title: The Threat from Viruses date: 2018-09-30 journal: Molecular Basis of Resilience DOI: 10.1007/978-3-319-98164-2_3 sha: doc_id: 18017 cord_uid: c8myq6bi file: cache/cord-023208-w99gc5nx.json key: cord-023208-w99gc5nx authors: nan title: Poster Presentation Abstracts date: 2006-09-01 journal: J Pept Sci DOI: 10.1002/psc.797 sha: doc_id: 23208 cord_uid: w99gc5nx file: cache/cord-020235-stcrozdw.json key: cord-020235-stcrozdw authors: nan title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 journal: Zentralbl Bakteriol Mikrobiol Hyg A DOI: 10.1016/s0174-3031(82)80128-5 sha: doc_id: 20235 cord_uid: stcrozdw file: cache/cord-023017-k6edtg58.json key: cord-023017-k6edtg58 authors: nan title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 journal: Hepatology DOI: 10.1002/hep.1840380505 sha: doc_id: 23017 cord_uid: k6edtg58 file: cache/cord-025181-eg108wcd.json key: cord-025181-eg108wcd authors: Zheng, Zhihang; Li, Min; Liu, Zhihua; Jin, Xia; Sun, Jin title: Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date: 2020-05-25 journal: Virol Sin DOI: 10.1007/s12250-020-00229-y sha: doc_id: 25181 cord_uid: eg108wcd file: cache/cord-021568-tdfn6up8.json key: cord-021568-tdfn6up8 authors: STRAUSS, JAMES H.; STRAUSS, ELLEN G. title: Subviral Agents date: 2012-07-27 journal: Viruses and Human Disease DOI: 10.1016/b978-0-12-373741-0.50012-x sha: doc_id: 21568 cord_uid: tdfn6up8 file: cache/cord-022336-zqnczjpp.json key: cord-022336-zqnczjpp authors: Robertson, Hugh D.; Neel, Olivia D. title: Virus Origins: Conjoined RNA Genomes as Precursors to DNA Genomes date: 2007-09-02 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-012220360-2/50003-9 sha: doc_id: 22336 cord_uid: zqnczjpp file: cache/cord-023120-jcgf2401.json key: cord-023120-jcgf2401 authors: nan title: Animal virus genetics date: 2004-06-18 journal: J Supramol Struct DOI: 10.1002/jss.400140505 sha: doc_id: 23120 cord_uid: jcgf2401 file: cache/cord-023726-2fduzqyb.json key: cord-023726-2fduzqyb authors: STRAUSS, JAMES H.; STRAUSS, ELLEN G. title: The Structure of Viruses date: 2012-07-27 journal: Viruses and Human Disease DOI: 10.1016/b978-0-12-373741-0.50005-2 sha: doc_id: 23726 cord_uid: 2fduzqyb file: cache/cord-023770-ymxapsv6.json key: cord-023770-ymxapsv6 authors: nan title: Closteroviridae date: 2011-11-23 journal: Virus Taxonomy DOI: 10.1016/b978-0-12-384684-6.00085-9 sha: doc_id: 23770 cord_uid: ymxapsv6 file: cache/cord-030028-s6sxi8uj.json key: cord-030028-s6sxi8uj authors: Rubio, Luis; Galipienso, Luis; Ferriol, Inmaculada title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 journal: Front Plant Sci DOI: 10.3389/fpls.2020.01092 sha: doc_id: 30028 cord_uid: s6sxi8uj file: cache/cord-017764-h1w9gbxk.json key: cord-017764-h1w9gbxk authors: Meanwell, Nicholas A.; Belema, Makonen title: The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date: 2018-06-08 journal: HCV: The Journey from Discovery to a Cure DOI: 10.1007/7355_2018_47 sha: doc_id: 17764 cord_uid: h1w9gbxk file: cache/cord-018564-3igg5s57.json key: cord-018564-3igg5s57 authors: Schomburg, Dietmar; Schomburg, Ida title: RNA helicase 3.6.4.13 date: 2013 journal: Class 3.4-6 Hydrolases, Lyases, Isomerases, Ligases DOI: 10.1007/978-3-642-36260-6_25 sha: doc_id: 18564 cord_uid: 3igg5s57 file: cache/cord-023705-3q9yr6np.json key: cord-023705-3q9yr6np authors: FENNER, FRANK; BACHMANN, PETER A.; GIBBS, E. PAUL J.; MURPHY, FREDERICK A.; STUDDERT, MICHAEL J.; WHITE, DAVID O. title: Viral Replication date: 2014-06-27 journal: Veterinary Virology DOI: 10.1016/b978-0-12-253055-5.50008-6 sha: doc_id: 23705 cord_uid: 3q9yr6np file: cache/cord-023766-qx0qdjmt.json key: cord-023766-qx0qdjmt authors: Nirwan, Sonam; Kakkar, Rita title: Rhinovirus RNA Polymerase: Structure, Function, and Inhibitors date: 2018-11-02 journal: Viral Polymerases DOI: 10.1016/b978-0-12-815422-9.00011-5 sha: doc_id: 23766 cord_uid: qx0qdjmt file: cache/cord-024282-t5wl0bih.json key: cord-024282-t5wl0bih authors: Mao, Shunfu; Jiang, Yihan; Mathew, Edwin Basil; Kannan, Sreeram title: BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance date: 2020-02-01 journal: Algorithms for Computational Biology DOI: 10.1007/978-3-030-42266-0_15 sha: doc_id: 24282 cord_uid: t5wl0bih file: cache/cord-027865-p1epjn51.json key: cord-027865-p1epjn51 authors: Sterchi, Diane L.; Astbury, Caroline title: Molecular pathology date: 2020-06-22 journal: Bancroft's Theory and Practice of Histological Techniques DOI: 10.1016/b978-0-7020-4226-3.00021-4 sha: doc_id: 27865 cord_uid: p1epjn51 file: cache/cord-027975-77544sed.json key: cord-027975-77544sed authors: Tars, Kaspars title: ssRNA Phages: Life Cycle, Structure and Applications date: 2020-06-30 journal: Biocommunication of Phages DOI: 10.1007/978-3-030-45885-0_13 sha: doc_id: 27975 cord_uid: 77544sed file: cache/cord-033692-txfuuu7d.json key: cord-033692-txfuuu7d authors: Lim, Byeonghwi; Kim, Sangwook; Lim, Kyu-Sang; Jeong, Chang-Gi; Kim, Seung-Chai; Lee, Sang-Myeong; Park, Choi-Kyu; te Pas, Marinus F. W.; Gho, Haesu; Kim, Tae-Hun; Lee, Kyung-Tai; Kim, Won-Il; Kim, Jun-Mo title: Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection date: 2020-10-13 journal: Vet Res DOI: 10.1186/s13567-020-00850-5 sha: doc_id: 33692 cord_uid: txfuuu7d file: cache/cord-035067-ic843wr9.json key: cord-035067-ic843wr9 authors: de Almeida, Joana Ferro Machado; Chehter, Ethel Zimberg title: COVID-19 and the gastrointestinal tract: what do we already know? date: 2020-11-05 journal: nan DOI: 10.31744/einstein_journal/2020rw5909 sha: doc_id: 35067 cord_uid: ic843wr9 file: cache/cord-007890-bie1veti.json key: cord-007890-bie1veti authors: nan title: ECC-4 Abstracts date: 2002-04-16 journal: Int J Antimicrob Agents DOI: 10.1016/s0924-8579(02)00033-x sha: doc_id: 7890 cord_uid: bie1veti file: cache/cord-022290-p0l1kv6n.json key: cord-022290-p0l1kv6n authors: Bergmann, Ernst M.; James, Michael N.G. title: Proteolytic Enzymes of the Viruses of the Family Picornaviridae date: 2007-05-09 journal: Proteases of Infectious Agents DOI: 10.1016/b978-012420510-9/50032-6 sha: doc_id: 22290 cord_uid: p0l1kv6n file: cache/cord-023608-w2g7v7g1.json key: cord-023608-w2g7v7g1 authors: nan title: ISAR News date: 2017-10-20 journal: Antiviral Res DOI: 10.1016/s0166-3542(17)30664-2 sha: doc_id: 23608 cord_uid: w2g7v7g1 file: cache/cord-034648-vfqth54o.json key: cord-034648-vfqth54o authors: nan title: WITHDRAWN date: 2020-10-12 journal: Fertil Steril DOI: 10.1016/j.fertnstert.2020.08.1019 sha: doc_id: 34648 cord_uid: vfqth54o file: cache/cord-020010-q58x6xb0.json key: cord-020010-q58x6xb0 authors: nan title: 19th ICAR Abstracts: date: 2006-03-13 journal: Antiviral Res DOI: 10.1016/j.antiviral.2006.02.001 sha: doc_id: 20010 cord_uid: q58x6xb0 file: cache/cord-022196-1tionxun.json key: cord-022196-1tionxun authors: FENNER, FRANK; McAUSLAN, B.R.; MIMS, C.A.; SAMBROOK, J.; WHITE, DAVID O. title: The Nature and Classification of Animal Viruses date: 2013-11-17 journal: The Biology of Animal Viruses DOI: 10.1016/b978-0-12-253040-1.50006-3 sha: doc_id: 22196 cord_uid: 1tionxun file: cache/cord-048204-6lvn10f4.json key: cord-048204-6lvn10f4 authors: Shi, Stephanie T.; Huang, Peiyong; Li, Hsin-Pai; Lai, Michael M.C. title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus date: 2000-09-01 journal: The EMBO Journal DOI: 10.1093/emboj/19.17.4701 sha: doc_id: 48204 cord_uid: 6lvn10f4 file: cache/cord-048327-xgwbl8em.json key: cord-048327-xgwbl8em authors: Henderson, Clark M.; Anderson, Christine B.; Howard, Michael T. title: Antisense-induced ribosomal frameshifting date: 2006-08-18 journal: Nucleic Acids Res DOI: 10.1093/nar/gkl531 sha: doc_id: 48327 cord_uid: xgwbl8em file: cache/cord-048471-7jszm1nd.json key: cord-048471-7jszm1nd authors: Salim, Omar; Clarke, Ian N.; Lambden, Paul R. title: Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus date: 2008-05-14 journal: PLoS One DOI: 10.1371/journal.pone.0002169 sha: doc_id: 48471 cord_uid: 7jszm1nd file: cache/cord-022128-r8el8nqm.json key: cord-022128-r8el8nqm authors: Domingo, Esteban title: Molecular basis of genetic variation of viruses: error-prone replication date: 2019-11-08 journal: Virus as Populations DOI: 10.1016/b978-0-12-816331-3.00002-7 sha: doc_id: 22128 cord_uid: r8el8nqm file: cache/cord-022889-lv6fy6e6.json key: cord-022889-lv6fy6e6 authors: Dávalos, Alberto; Henriques, Rossana; Latasa, María Jesús; Laparra, Moisés; Coca, María title: Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date: 2019-08-07 journal: nan DOI: 10.2903/sp.efsa.2019.en-1688 sha: doc_id: 22889 cord_uid: lv6fy6e6 file: cache/cord-048198-zjufx4fo.json key: cord-048198-zjufx4fo authors: Pasternak, Alexander O.; van den Born, Erwin; Spaan, Willy J.M.; Snijder, Eric J. title: Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis date: 2001-12-17 journal: The EMBO Journal DOI: 10.1093/emboj/20.24.7220 sha: doc_id: 48198 cord_uid: zjufx4fo file: cache/cord-102547-nxut8ov1.json key: cord-102547-nxut8ov1 authors: Grädel, C.; Terrazos Miani, M. A.; Baumann, C.; Barbani, M. T.; Neuenschwander, S.; Leib, S. L.; Suter-Riniker, F.; Ramette, A. title: Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing date: 2020-06-09 journal: nan DOI: 10.1101/2020.06.09.20126219 sha: doc_id: 102547 cord_uid: nxut8ov1 file: cache/cord-035110-5lkzhjfh.json key: cord-035110-5lkzhjfh authors: Zhu, Le; Sun, Hao-Ting; Wang, Shun; Huang, Sheng-Lin; Zheng, Yan; Wang, Chao-Qun; Hu, Bei-Yuan; Qin, Wei; Zou, Tian-Tian; Fu, Yan; Shen, Xiao-Tian; Zhu, Wen-Wei; Geng, Yan; Lu, Lu; Jia, Hu-liang; Qin, Lun-Xiu; Dong, Qiong-Zhu title: Isolation and characterization of exosomes for cancer research date: 2020-11-10 journal: J Hematol Oncol DOI: 10.1186/s13045-020-00987-y sha: doc_id: 35110 cord_uid: 5lkzhjfh file: cache/cord-048222-1pq6dkl5.json key: cord-048222-1pq6dkl5 authors: Imbeaud, Sandrine; Graudens, Esther; Boulanger, Virginie; Barlet, Xavier; Zaborski, Patrick; Eveno, Eric; Mueller, Odilo; Schroeder, Andreas; Auffray, Charles title: Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces date: 2005-03-30 journal: Nucleic Acids Res DOI: 10.1093/nar/gni054 sha: doc_id: 48222 cord_uid: 1pq6dkl5 file: cache/cord-102892-nt1zoktv.json key: cord-102892-nt1zoktv authors: Sweeney, Blake A.; Hoksza, David; Nawrocki, Eric P.; Ribas, Carlos Eduardo; Madeira, Fábio; Cannone, Jamie J.; Gutell, Robin; Maddala, Aparna; Meade, Caeden; Williams, Loren Dean; Petrov, Anton S.; Chan, Patricia P.; Lowe, Todd M.; Finn, Robert D.; Petrov, Anton I. title: R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types date: 2020-09-11 journal: bioRxiv DOI: 10.1101/2020.09.10.290924 sha: doc_id: 102892 cord_uid: nt1zoktv file: cache/cord-102967-dx0tg077.json key: cord-102967-dx0tg077 authors: Mahajan, Lakshmi S.; Kim, Grace Eunyoo; Kwak, Hojoong title: Mapping RNA dependent RNA polymerase activity and immune gene expression using PRO-seq date: 2020-06-16 journal: bioRxiv DOI: 10.1101/2020.06.15.151738 sha: doc_id: 102967 cord_uid: dx0tg077 file: cache/cord-030654-8yxa1r1c.json key: cord-030654-8yxa1r1c authors: Zhang, Changhui; Chen, Yiping; Li, Li; Yang, Yan; He, Jun; Chen, Cheng; Su, Dan title: Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date: 2020-08-20 journal: Mol Biomed DOI: 10.1186/s43556-020-00005-0 sha: doc_id: 30654 cord_uid: 8yxa1r1c file: cache/cord-048485-b8xb1f12.json key: cord-048485-b8xb1f12 authors: Hulst, Marcel; Kerstens, Hinri; de Wit, Agnes; Smits, Mari; van der Meulen, Jan; Niewold, Theo title: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date: 2008-06-04 journal: Arch Virol DOI: 10.1007/s00705-008-0118-6 sha: doc_id: 48485 cord_uid: b8xb1f12 file: cache/cord-048322-5eqdrd52.json key: cord-048322-5eqdrd52 authors: Aigner, Achim title: Delivery Systems for the Direct Application of siRNAs to Induce RNA Interference (RNAi) In Vivo date: 2006-05-18 journal: J Biomed Biotechnol DOI: 10.1155/jbb/2006/71659 sha: doc_id: 48322 cord_uid: 5eqdrd52 file: cache/cord-102336-ex3zlq38.json key: cord-102336-ex3zlq38 authors: De Wijngaert, Brent; Sultana, Shemaila; Dharia, Chhaya; Vanbuel, Hans; Shen, Jiayu; Vasilchuk, Daniel; Martinez, Sergio E.; Kandiah, Eaazhisai; Patel, Smita S.; Das, Kalyan title: Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase date: 2020-04-14 journal: bioRxiv DOI: 10.1101/2020.04.13.038620 sha: doc_id: 102336 cord_uid: ex3zlq38 file: cache/cord-102898-eyyd7ent.json key: cord-102898-eyyd7ent authors: Rizvi, Vaseef A.; Sarkar, Maharnob; Roy, Rahul title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date: 2020-07-17 journal: bioRxiv DOI: 10.1101/2020.07.16.206920 sha: doc_id: 102898 cord_uid: eyyd7ent file: cache/cord-102931-vxkbctiz.json key: cord-102931-vxkbctiz authors: Mao, Kai; Breen, Peter; Ruvkun, Gary title: Induction of RNA interference by C. elegans mitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme date: 2020-06-06 journal: bioRxiv DOI: 10.1101/2020.06.05.136978 sha: doc_id: 102931 cord_uid: vxkbctiz file: cache/cord-102934-7e2mqooe.json key: cord-102934-7e2mqooe authors: Dogra, N.; Ahsen, M. E.; Kozlova, E. G.; Chen, T.-y.; allette, k.; Olsen, R.; Han, D.; Kim, S.; Gifford, S. M.; Smith, J. T.; Wunsch, B. H.; Weil, R.; Bhatt, K.; Yadav, k. K.; vlachos, k.; Nair, S.; Gordon, R. E.; Smith, M.; Sebra, R.; Margolin, A.; Sahoo, S.; Tewari, A.; Cordon-Cardo, C.; Losic, B.; Stolovitzky, G. A. title: exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer date: 2020-09-30 journal: nan DOI: 10.1101/2020.09.28.20190009 sha: doc_id: 102934 cord_uid: 7e2mqooe file: cache/cord-029779-9b6zs1sb.json key: cord-029779-9b6zs1sb authors: Casey, Sophie; Goasdoue, Kate; Miller, Stephanie M.; Brennan, Gary P.; Cowin, Gary; O’Mahony, Adam G.; Burke, Christopher; Hallberg, Boubou; Boylan, Geraldine B.; Sullivan, Aideen M.; Henshall, David C.; O’Keeffe, Gerard W.; Mooney, Catherine; Bjorkman, Tracey; Murray, Deirdre M. title: Temporally Altered miRNA Expression in a Piglet Model of Hypoxic Ischemic Brain Injury date: 2020-07-27 journal: Mol Neurobiol DOI: 10.1007/s12035-020-02018-w sha: doc_id: 29779 cord_uid: 9b6zs1sb file: cache/cord-048478-ftlb5b95.json key: cord-048478-ftlb5b95 authors: Mroczek, Seweryn; Kufel, Joanna title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast date: 2008-04-01 journal: Nucleic Acids Res DOI: 10.1093/nar/gkm1100 sha: doc_id: 48478 cord_uid: ftlb5b95 file: cache/cord-102766-n6mpdhyu.json key: cord-102766-n6mpdhyu authors: Alam, Md. Nafis Ul; Chowdhury, Umar Faruq title: Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses date: 2020-06-25 journal: bioRxiv DOI: 10.1101/2020.06.25.170779 sha: doc_id: 102766 cord_uid: n6mpdhyu file: cache/cord-103015-3dxwbmd2.json key: cord-103015-3dxwbmd2 authors: Shengjuler, Djoshkun; Chan, Yan Mei; Sun, Simou; Moustafa, Ibrahim M.; Li, Zhen-Lu; Gohara, David W.; Buck, Matthias; Cremer, Paul S.; Boehr, David D.; Cameron, Craig E. title: The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain date: 2017-08-04 journal: bioRxiv DOI: 10.1101/172742 sha: doc_id: 103015 cord_uid: 3dxwbmd2 file: cache/cord-103511-31njndob.json key: cord-103511-31njndob authors: Broggi, Achille; Ghosh, Sreya; Sposito, Benedetta; Spreafico, Roberto; Balzarini, Fabio; Lo Cascio, Antonino; Clementi, Nicola; De Santis, Maria; Mancini, Nicasio; Granucci, Francesca; Zanoni, Ivan title: Type III interferons disrupt the lung epithelial barrier upon viral recognition date: 2020-05-05 journal: bioRxiv DOI: 10.1101/2020.05.05.077867 sha: doc_id: 103511 cord_uid: 31njndob file: cache/cord-104162-fe51v2pt.json key: cord-104162-fe51v2pt authors: Zhang, Chiyu; Forsdyke, Donald R. title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.10.22.343673 sha: doc_id: 104162 cord_uid: fe51v2pt file: cache/cord-025948-6dsx7pey.json key: cord-025948-6dsx7pey authors: Maitra, Arindam; Sarkar, Mamta Chawla; Raheja, Harsha; Biswas, Nidhan K; Chakraborti, Sohini; Singh, Animesh Kumar; Ghosh, Shekhar; Sarkar, Sumanta; Patra, Subrata; Mondal, Rajiv Kumar; Ghosh, Trinath; Chatterjee, Ananya; Banu, Hasina; Majumdar, Agniva; Chinnaswamy, Sreedhar; Srinivasan, Narayanaswamy; Dutta, Shanta; Das, Saumitra title: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date: 2020-06-04 journal: J Biosci DOI: 10.1007/s12038-020-00046-1 sha: doc_id: 25948 cord_uid: 6dsx7pey file: cache/cord-103914-ppgx7mci.json key: cord-103914-ppgx7mci authors: Maughan, Elizabeth F.; Nigro, Ersilia; Pennycuick, Adam; Gowers, Kate H.C.; Denais, Celine; Gómez-López, Sandra; Lazarus, Kyren A.; Butler, Colin R.; Lee, Dani Do Hyang; Orr, Jessica C.; Teixeira, Vitor H.; Hartley, Benjamin E.; Hewitt, Richard J.; Yaghchi, Chadwan Al; Sandhu, Gurpreet S.; Birchall, Martin A.; O’Callaghan, Christopher; Smith, Claire M.; De Coppi, Paolo; Hynds, Robert E.; Janes, Sam M. title: Cell-intrinsic differences between human airway epithelial cells from children and adults date: 2020-04-20 journal: bioRxiv DOI: 10.1101/2020.04.20.027144 sha: doc_id: 103914 cord_uid: ppgx7mci file: cache/cord-252268-o63ep08b.json key: cord-252268-o63ep08b authors: Carolan, Louise A.; Butler, Jeff; Rockman, Steve; Guarnaccia, Teagan; Hurt, Aeron C.; Reading, Patrick; Kelso, Anne; Barr, Ian; Laurie, Karen L. title: TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date: 2014-09-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2014.04.014 sha: doc_id: 252268 cord_uid: o63ep08b file: cache/cord-102412-cnlvyey4.json key: cord-102412-cnlvyey4 authors: Tekman, Mehmet; Batut, Bérénice; Ostrovsky, Alexander; Antoniewski, Christophe; Clements, Dave; Ramirez, Fidel; Etherington, Graham J; Hotz, Hans-Rudolf; Scholtalbers, Jelle; Manning, Jonathan R; Bellenger, Lea; Doyle, Maria A; Heydarian, Mohammad; Huang, Ni; Soranzo, Nicola; Moreno, Pablo; Mautner, Stefan; Papatheodorou, Irene; Nekrutenko, Anton; Taylor, James; Blankenberg, Daniel; Backofen, Rolf; Grüning, Björn title: A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework date: 2020-08-28 journal: bioRxiv DOI: 10.1101/2020.06.06.137570 sha: doc_id: 102412 cord_uid: cnlvyey4 file: cache/cord-026641-eemp6b5j.json key: cord-026641-eemp6b5j authors: Kabiljo, Julijan; Laengle, Johannes; Bergmann, Michael title: From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date: 2020-06-11 journal: Cell Death Discov DOI: 10.1038/s41420-020-0284-1 sha: doc_id: 26641 cord_uid: eemp6b5j file: cache/cord-103807-x4hrwhkz.json key: cord-103807-x4hrwhkz authors: Prokop, J. W. title: Viral Induced Genetics Revealed by Multi-Dimensional Precision Medicine Transcriptional Workflow date: 2020-04-06 journal: nan DOI: 10.1101/2020.04.01.20050054 sha: doc_id: 103807 cord_uid: x4hrwhkz file: cache/cord-146406-85usg3uh.json key: cord-146406-85usg3uh authors: Morelli, Marco J.; Wright, Caroline F.; Th'ebaud, Gael; Knowles, Nick J.; Herzyk, Pawel; Paton, David J.; Haydon, Daniel T.; King, Donald P. title: Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing date: 2011-01-27 journal: nan DOI: nan sha: doc_id: 146406 cord_uid: 85usg3uh file: cache/cord-243806-26n22jbx.json key: cord-243806-26n22jbx authors: Vandelli, Andrea; Monti, Michele; Milanetti, Edoardo; Ponti, Riccardo Delli; Tartaglia, Gian Gaetano title: Structural analysis of SARS-CoV-2 and prediction of the human interactome date: 2020-03-30 journal: nan DOI: nan sha: doc_id: 243806 cord_uid: 26n22jbx file: cache/cord-102866-40s64455.json key: cord-102866-40s64455 authors: Bhadra, Sanchita; Maranhao, Andre C.; Ellington, Andrew D. title: One enzyme reverse transcription qPCR using Taq DNA polymerase date: 2020-05-30 journal: bioRxiv DOI: 10.1101/2020.05.27.120238 sha: doc_id: 102866 cord_uid: 40s64455 file: cache/cord-254192-86ksgl5t.json key: cord-254192-86ksgl5t authors: Li, Liang; Xue, Mei; Fu, Fang; Yin, Lingdan; Feng, Li; Liu, Pinghuang title: IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia date: 2019-10-17 journal: Front Immunol DOI: 10.3389/fimmu.2019.02394 sha: doc_id: 254192 cord_uid: 86ksgl5t file: cache/cord-103853-ar09nzmw.json key: cord-103853-ar09nzmw authors: Wayment-Steele, Hannah K.; Kladwang, Wipapat; Das, Rhiju title: RNA secondary structure packages ranked and improved by high-throughput experiments date: 2020-05-31 journal: bioRxiv DOI: 10.1101/2020.05.29.124511 sha: doc_id: 103853 cord_uid: ar09nzmw file: cache/cord-253024-b393ea2u.json key: cord-253024-b393ea2u authors: Fu, Kaisong; Baric, Ralph S. title: Evidence for variable rates of recombination in the MHV genome date: 1992-07-31 journal: Virology DOI: 10.1016/0042-6822(92)90684-h sha: doc_id: 253024 cord_uid: b393ea2u file: cache/cord-253115-ekgdsv4f.json key: cord-253115-ekgdsv4f authors: Mehta, Meenu; Deeksha,; Tewari, Devesh; Gupta, Gaurav; Awasthi, Rajendra; Singh, Harjeet; Pandey, Parijat; Chellappan, Dinesh Kumar; Wadhwa, Ridhima; Collet, Trudi; Hansbro, Philip M.; Kumar, S Rajesh; Thangavelu, Lakshmi; Negi, Poonam; Dua, Kamal; Satija, Saurabh title: Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases date: 2019-08-01 journal: Chemico-Biological Interactions DOI: 10.1016/j.cbi.2019.05.028 sha: doc_id: 253115 cord_uid: ekgdsv4f file: cache/cord-253282-zwl0safn.json key: cord-253282-zwl0safn authors: Plant, Ewan P.; Sims, Amy C.; Baric, Ralph S.; Dinman, Jonathan D.; Taylor, Deborah R. title: Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date: 2013-01-18 journal: Viruses DOI: 10.3390/v5010279 sha: doc_id: 253282 cord_uid: zwl0safn file: cache/cord-254250-l0v602x9.json key: cord-254250-l0v602x9 authors: Hooper, Chantelle; Debnath, Partho P.; Biswas, Sukumar; van Aerle, Ronny; Bateman, Kelly S.; Basak, Siddhawartha K.; Rahman, Muhammad M.; Mohan, Chadag V.; Islam, H. M. Rakibul; Ross, Stuart; Stentiford, Grant D.; Currie, David; Bass, David title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date: 2020-10-02 journal: Viruses DOI: 10.3390/v12101120 sha: doc_id: 254250 cord_uid: l0v602x9 file: cache/cord-103377-j1mmx7k7.json key: cord-103377-j1mmx7k7 authors: Karasik, Agnes; Jones, Grant D.; DePass, Andrew V.; Guydosh, Nicholas R. title: Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences date: 2020-09-11 journal: bioRxiv DOI: 10.1101/2020.09.10.291690 sha: doc_id: 103377 cord_uid: j1mmx7k7 file: cache/cord-103638-n5kpvsvg.json key: cord-103638-n5kpvsvg authors: Nguyen, Long T.; Smith, Brianna M.; Jain, Piyush K. title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date: 2020-04-14 journal: bioRxiv DOI: 10.1101/2020.04.13.036079 sha: doc_id: 103638 cord_uid: n5kpvsvg file: cache/cord-103735-nil1vv6h.json key: cord-103735-nil1vv6h authors: Alfano, Niccolo; Dayaram, Anisha; Axtner, Jan; Tsangaras, Kyriakos; Kampmann, Marie-Louise; Mohamed, Azlan; Wong, Seth T.; Gilbert, M. Thomas P.; Wilting, Andreas; Greenwood, Alex D. title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 journal: bioRxiv DOI: 10.1101/2020.03.26.009993 sha: doc_id: 103735 cord_uid: nil1vv6h file: cache/cord-103899-6tqm99g1.json key: cord-103899-6tqm99g1 authors: Mirzaei, Rasoul; Mahdavi, Farzad; Badrzadeh, Fariba; Reza Hosseini-Fard, Seyed; Heidary, Maryam; Salimi Jeda, Ali; Mohammadi, Tayeb; Roshani, Mahdane; Yousefimashouf, Rasoul; Keyvani, Hossein; Darvishmotevalli, Mohammad; Zarei Sani, Melika; Karampoor, Sajad title: The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date: 2020-11-13 journal: nan DOI: 10.1016/j.intimp.2020.107204 sha: doc_id: 103899 cord_uid: 6tqm99g1 file: cache/cord-253616-7jyui5ca.json key: cord-253616-7jyui5ca authors: Lai, Zheng-Zong; Ho, Yi-Jung; Lu, Jeng-Wei title: Harringtonine Inhibits Zika Virus Infection through Multiple Mechanisms date: 2020-09-07 journal: Molecules DOI: 10.3390/molecules25184082 sha: doc_id: 253616 cord_uid: 7jyui5ca file: cache/cord-102968-mhawyect.json key: cord-102968-mhawyect authors: Desirò, Daniel; Hölzer, Martin; Ibrahim, Bashar; Marz, Manja title: SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs date: 2018-09-23 journal: bioRxiv DOI: 10.1101/424002 sha: doc_id: 102968 cord_uid: mhawyect file: cache/cord-103823-3rchp9yy.json key: cord-103823-3rchp9yy authors: Taufer, Michela; Leung, Ming-Ying; Solorio, Thamar; Licon, Abel; Mireles, David; Araiza, Roberto; Johnson, Kyle L. title: RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology date: 2008-11-30 journal: Parallel Computing DOI: 10.1016/j.parco.2008.08.002 sha: doc_id: 103823 cord_uid: 3rchp9yy file: cache/cord-122092-gdyt02er.json key: cord-122092-gdyt02er authors: Fatehi, Farzad; Bingham, Richard J; Dykeman, Eric C; Stockley, Peter G; Twarock, Reidun title: Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date: 2020-10-18 journal: nan DOI: nan sha: doc_id: 122092 cord_uid: gdyt02er file: cache/cord-253539-0kcujnfa.json key: cord-253539-0kcujnfa authors: Agranovsky, A. A. title: Principles of Molecular Organization, Expression, and Evolution of Closteroviruses: Over The Barriers date: 1996-12-31 journal: Advances in Virus Research DOI: 10.1016/s0065-3527(08)60735-6 sha: doc_id: 253539 cord_uid: 0kcujnfa file: cache/cord-253862-jl1zhg13.json key: cord-253862-jl1zhg13 authors: Khalaf, Khalil; Papp, Natalia; Chou, Jadzia Tin-Tsen; Hana, Doris; Mackiewicz, Andrzej; Kaczmarek, Mariusz title: SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date: 2020-10-06 journal: Front Immunol DOI: 10.3389/fimmu.2020.570927 sha: doc_id: 253862 cord_uid: jl1zhg13 file: cache/cord-023354-f2ciho6o.json key: cord-023354-f2ciho6o authors: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 journal: Vox Sang DOI: 10.1111/j.1423-0410.2005.00654.x sha: doc_id: 23354 cord_uid: f2ciho6o file: cache/cord-103163-0rreoh4o.json key: cord-103163-0rreoh4o authors: Smith, Sydni Caet; Gribble, Jennifer; Diller, Julia R.; Wiebe, Michelle A.; Thoner, Timothy W.; Denison, Mark R.; Ogden, Kristen M. title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date: 2020-10-22 journal: bioRxiv DOI: 10.1101/2020.10.19.346031 sha: doc_id: 103163 cord_uid: 0rreoh4o file: cache/cord-103430-x6zzuu7v.json key: cord-103430-x6zzuu7v authors: Contu, Lara; Balistreri, Giuseppe; Domanski, Michal; Uldry, Anne-Christine; Mühlemann, Oliver title: Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date: 2020-10-12 journal: bioRxiv DOI: 10.1101/2020.10.12.335497 sha: doc_id: 103430 cord_uid: x6zzuu7v file: cache/cord-103787-qhftb6d7.json key: cord-103787-qhftb6d7 authors: Garcia, Elizabeth P.; Dowding, Lori A.; Stanton, Lawrence W.; Slepnev, Vladimir I. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 journal: The Journal of Molecular Diagnostics DOI: 10.1016/s1525-1578(10)60575-2 sha: doc_id: 103787 cord_uid: qhftb6d7 file: cache/cord-103925-i73ymrov.json key: cord-103925-i73ymrov authors: Hill, Chris H.; Cook, Georgia; Napthine, Sawsan; Kibe, Anuja; Brown, Katherine; Caliskan, Neva; Firth, Andrew E.; Graham, Stephen C.; Brierley, Ian title: Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus date: 2020-08-11 journal: bioRxiv DOI: 10.1101/2020.08.11.245068 sha: doc_id: 103925 cord_uid: i73ymrov file: cache/cord-184744-oyc2djxk.json key: cord-184744-oyc2djxk authors: Parvez, Md Sorwer Alam; Azim, Kazi Faizul; Imran, Abdus Shukur; Raihan, Topu; Begum, Aklima; Shammi, Tasfia Saiyara; Howlader, Sabbir; Bhuiyan, Farhana Rumzum; Hasan, Mahmudul title: Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date: 2020-05-22 journal: nan DOI: nan sha: doc_id: 184744 cord_uid: oyc2djxk file: cache/cord-252485-cxi3cr15.json key: cord-252485-cxi3cr15 authors: Yoshida, Asuka; Kawabata, Ryoko; Honda, Tomoyuki; Tomonaga, Keizo; Sakaguchi, Takemasa; Irie, Takashi title: IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date: 2015-08-04 journal: Front Microbiol DOI: 10.3389/fmicb.2015.00804 sha: doc_id: 252485 cord_uid: cxi3cr15 file: cache/cord-254210-3mi2aop5.json key: cord-254210-3mi2aop5 authors: Haddad, Rodrigo; Kashima, Simone; Rodrigues, Evandra Strazza; Azevedo, Rochele; Palma, Patrícia Vianna Bonini; de Magalhães, Danielle Aparecida Rosa; Zago, Marco Antonio; Covas, Dimas Tadeu title: Silencing of HTLV-1 gag and env genes by small interfering RNAs in HEK 293 cells date: 2011-01-26 journal: J Virol Methods DOI: 10.1016/j.jviromet.2011.01.012 sha: doc_id: 254210 cord_uid: 3mi2aop5 file: cache/cord-103739-mmkrwj8t.json key: cord-103739-mmkrwj8t authors: Snijder, Eric J.; Limpens, Ronald W.A.L.; de Wilde, Adriaan H.; de Jong, Anja W. M.; Zevenhoven-Dobbe, Jessika C.; Maier, Helena J.; Faas, Frank F.G.A.; Koster, Abraham J.; Bárcena, Montserrat title: A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date: 2020-03-24 journal: bioRxiv DOI: 10.1101/2020.03.24.005298 sha: doc_id: 103739 cord_uid: mmkrwj8t file: cache/cord-104186-fyw1xfgi.json key: cord-104186-fyw1xfgi authors: Cui, Y; Dinman, J D; Peltz, S W title: Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. date: 1996-10-15 journal: EMBO J DOI: nan sha: doc_id: 104186 cord_uid: fyw1xfgi file: cache/cord-252871-qfrpuy3t.json key: cord-252871-qfrpuy3t authors: Nasir, Arshan; Romero-Severson, Ethan; Claverie, Jean-Michel title: Investigating the Concept and Origin of Viruses date: 2020-11-03 journal: Trends Microbiol DOI: 10.1016/j.tim.2020.08.003 sha: doc_id: 252871 cord_uid: qfrpuy3t file: cache/cord-253466-7gpije5d.json key: cord-253466-7gpije5d authors: Netherton, Christopher; Moffat, Katy; Brooks, Elizabeth; Wileman, Thomas title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date: 2007-08-31 journal: Adv Virus Res DOI: 10.1016/s0065-3527(07)70004-0 sha: doc_id: 253466 cord_uid: 7gpije5d file: cache/cord-252433-0e9lonq4.json key: cord-252433-0e9lonq4 authors: Cullen, Bryan R. title: Viral RNAs: Lessons from the Enemy date: 2009-02-20 journal: Cell DOI: 10.1016/j.cell.2009.01.048 sha: doc_id: 252433 cord_uid: 0e9lonq4 file: cache/cord-252466-usrpodjx.json key: cord-252466-usrpodjx authors: Yun, Nadezhda E.; Walker, David H. title: Pathogenesis of Lassa Fever date: 2012-10-09 journal: Viruses DOI: 10.3390/v4102031 sha: doc_id: 252466 cord_uid: usrpodjx file: cache/cord-253480-qchrw337.json key: cord-253480-qchrw337 authors: Pu, Jieying; He, Li; Xie, Heping; Wu, Siyu; Li, Yuye; Zhang, Ping; Yang, Zhicong; Huang, Xi title: Antiviral activity of Carbenoxolone disodium against dengue virus infection date: 2016-12-23 journal: J Med Virol DOI: 10.1002/jmv.24571 sha: doc_id: 253480 cord_uid: qchrw337 file: cache/cord-254747-vox5xsgd.json key: cord-254747-vox5xsgd authors: Deng, Xufang; Baker, Susan C title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 journal: Virology DOI: 10.1016/j.virol.2017.12.024 sha: doc_id: 254747 cord_uid: vox5xsgd file: cache/cord-253307-4bpdfgau.json key: cord-253307-4bpdfgau authors: Sanz, Miguel A.; García‐Moreno, Manuel; Carrasco, Luis title: Inhibition of host protein synthesis by Sindbis virus: correlation with viral RNA replication and release of nuclear proteins to the cytoplasm date: 2014-11-19 journal: Cell Microbiol DOI: 10.1111/cmi.12381 sha: doc_id: 253307 cord_uid: 4bpdfgau file: cache/cord-254592-wa5il5go.json key: cord-254592-wa5il5go authors: Brierley, Liam; Pedersen, Amy B.; Woolhouse, Mark E. J. title: Tissue tropism and transmission ecology predict virulence of human RNA viruses date: 2019-11-26 journal: PLoS Biol DOI: 10.1371/journal.pbio.3000206 sha: doc_id: 254592 cord_uid: wa5il5go file: cache/cord-253501-hkxlq3os.json key: cord-253501-hkxlq3os authors: Anang, Saumya; Kaushik, Nidhi; Surjit, Milan title: Recent Advances Towards the Development of a Potent Antiviral Against the Hepatitis E Virus date: 2018-06-28 journal: J Clin Transl Hepatol DOI: 10.14218/jcth.2018.00005 sha: doc_id: 253501 cord_uid: hkxlq3os file: cache/cord-254100-u6x5zd4i.json key: cord-254100-u6x5zd4i authors: Taliansky, M.E.; Brown, J.W.S.; Rajamäki, M.L.; Valkonen, J.P.T.; Kalinina, N.O. title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date: 2010-10-15 journal: Adv Virus Res DOI: 10.1016/b978-0-12-385034-8.00005-3 sha: doc_id: 254100 cord_uid: u6x5zd4i file: cache/cord-254916-y1rw9q11.json key: cord-254916-y1rw9q11 authors: Ogando, Natacha S.; Dalebout, Tim J.; Zevenhoven-Dobbe, Jessika C.; Limpens, Ronald W.A.L.; van der Meer, Yvonne; Caly, Leon; Druce, Julian; de Vries, Jutte J. C.; Kikkert, Marjolein; Bárcena, Montserrat; Sidorov, Igor; Snijder, Eric J. title: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date: 2020-06-22 journal: J Gen Virol DOI: 10.1099/jgv.0.001453 sha: doc_id: 254916 cord_uid: y1rw9q11 file: cache/cord-023346-8sqbqjm1.json key: cord-023346-8sqbqjm1 authors: nan title: MONDAY: POSTERS date: 2005-06-08 journal: Vox Sang DOI: 10.1111/j.1423-0410.2005.00652.x sha: doc_id: 23346 cord_uid: 8sqbqjm1 file: cache/cord-254070-v9gabn1a.json key: cord-254070-v9gabn1a authors: Bordería, Antonio V.; Rozen-Gagnon, Kathryn; Vignuzzi, Marco title: Fidelity Variants and RNA Quasispecies date: 2015-10-25 journal: Quasispecies: From Theory to Experimental Systems DOI: 10.1007/82_2015_483 sha: doc_id: 254070 cord_uid: v9gabn1a file: cache/cord-254713-ghcwfcx2.json key: cord-254713-ghcwfcx2 authors: Razanajatovo, Norosoa H; Nomenjanahary, Lalaina A; Wilkinson, David A; Razafimanahaka, Julie H; Goodman, Steven M; Jenkins, Richard K; Jones, Julia PG; Heraud, Jean-Michel title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date: 2015-03-12 journal: Virol J DOI: 10.1186/s12985-015-0271-y sha: doc_id: 254713 cord_uid: ghcwfcx2 file: cache/cord-254903-g9ropt9c.json key: cord-254903-g9ropt9c authors: Xu, Xiaofeng; Bei, Jinlong; Xuan, Yibo; Chen, Jiayuan; Chen, Defu; Barker, Stephen C.; Kelava, Samuel; Zhang, Xiaoai; Gao, Shan; Chen, Ze title: Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data date: 2020-09-16 journal: BMC Genomics DOI: 10.1186/s12864-020-07060-5 sha: doc_id: 254903 cord_uid: g9ropt9c file: cache/cord-254596-wsmnlnlk.json key: cord-254596-wsmnlnlk authors: Grädel, Carole; Terrazos Miani, Miguel A.; Baumann, Christian; Barbani, Maria Teresa; Neuenschwander, Stefan; Leib, Stephen L.; Suter-Riniker, Franziska; Ramette, Alban title: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing date: 2020-07-31 journal: Viruses DOI: 10.3390/v12080841 sha: doc_id: 254596 cord_uid: wsmnlnlk file: cache/cord-023364-ut56gczm.json key: cord-023364-ut56gczm authors: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 journal: Vox Sang DOI: 10.1111/j.1423-0410.2005.00651.x sha: doc_id: 23364 cord_uid: ut56gczm file: cache/cord-254963-cnvxlv6h.json key: cord-254963-cnvxlv6h authors: Paskey, Adrian C.; Frey, Kenneth G.; Schroth, Gary; Gross, Stephen; Hamilton, Theron; Bishop-Lilly, Kimberly A. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 journal: BMC Genomics DOI: 10.1186/s12864-019-5543-2 sha: doc_id: 254963 cord_uid: cnvxlv6h file: cache/cord-255576-738khdwv.json key: cord-255576-738khdwv authors: Van Duyne, Rachel; Guendel, Irene; Klase, Zachary; Narayanan, Aarthi; Coley, William; Jaworski, Elizabeth; Roman, Jessica; Popratiloff, Anastas; Mahieux, Renaud; Kehn-Hall, Kylene; Kashanchi, Fatah title: Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery date: 2012-07-10 journal: PLoS One DOI: 10.1371/journal.pone.0040662 sha: doc_id: 255576 cord_uid: 738khdwv file: cache/cord-254895-ym0jsir5.json key: cord-254895-ym0jsir5 authors: Eisenächer, Katharina; Steinberg, Christian; Reindl, Wolfgang; Krug, Anne title: The role of viral nucleic acid recognition in dendritic cells for innate and adaptive antiviral immunity date: 2008-01-18 journal: Immunobiology DOI: 10.1016/j.imbio.2007.09.007 sha: doc_id: 254895 cord_uid: ym0jsir5 file: cache/cord-255252-md0avnqg.json key: cord-255252-md0avnqg authors: Tang, Julian W.; To, Ka‐Fai; Lo, Anthony W.I.; Sung, Joseph J.Y.; Ng, H.K.; Chan, Paul K.S. title: Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date: 2007-07-02 journal: J Med Virol DOI: 10.1002/jmv.20873 sha: doc_id: 255252 cord_uid: md0avnqg file: cache/cord-255607-dbexsugq.json key: cord-255607-dbexsugq authors: Wu, Yang; Zhang, Hongling; Shi, Zhaorong; Chen, Jianfei; Li, Mingwei; Shi, Hongyan; Shi, Da; Guo, Longjun; Feng, Li title: Porcine Epidemic Diarrhea Virus nsp15 Antagonizes Interferon Signaling by RNA Degradation of TBK1 and IRF3 date: 2020-05-31 journal: Viruses DOI: 10.3390/v12060599 sha: doc_id: 255607 cord_uid: dbexsugq file: cache/cord-255090-2gpsu1y4.json key: cord-255090-2gpsu1y4 authors: Lv, Ke; Guo, Yingjun; Zhang, Yiliang; Wang, Kaiyu; Li, Ka; Zhu, Yan; Sun, Shuhan title: Transient inhibition of foot-and-mouth disease virus replication by siRNAs silencing VP1 protein coding region date: 2009-06-30 journal: Research in Veterinary Science DOI: 10.1016/j.rvsc.2008.10.011 sha: doc_id: 255090 cord_uid: 2gpsu1y4 file: cache/cord-255619-5h3l6nh6.json key: cord-255619-5h3l6nh6 authors: Kuo, Shu-Ming; Kao, Hsiao-Wei; Hou, Ming-Hon; Wang, Ching-Ho; Lin, Siou-Hong; Su, Hong-Lin title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date: 2013-03-23 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2012.10.020 sha: doc_id: 255619 cord_uid: 5h3l6nh6 file: cache/cord-255499-31xmue1g.json key: cord-255499-31xmue1g authors: Bujarski, J.J. title: Recombination date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00545-8 sha: doc_id: 255499 cord_uid: 31xmue1g file: cache/cord-256036-gd53s4dv.json key: cord-256036-gd53s4dv authors: Sandmann, Lisa; Ploss, Alexander title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 journal: Virology DOI: 10.1016/j.virol.2012.09.044 sha: doc_id: 256036 cord_uid: gd53s4dv file: cache/cord-255495-xnoppq3y.json key: cord-255495-xnoppq3y authors: Elrashdy, Fatma; Aljaddawi, Abdullah A.; Redwan, Elrashdy M.; Uversky, Vladimir N. title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date: 2020-07-09 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1790426 sha: doc_id: 255495 cord_uid: xnoppq3y file: cache/cord-255545-nycdhdsd.json key: cord-255545-nycdhdsd authors: Schoenike, Barry; Franta, Amy K.; Fleming, John O. title: Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date: 1999-03-10 journal: J Virol Methods DOI: 10.1016/s0166-0934(98)00167-0 sha: doc_id: 255545 cord_uid: nycdhdsd file: cache/cord-255738-r8zfdsix.json key: cord-255738-r8zfdsix authors: Ge, Feng; Luo, Yonghu; Liew, Pei Xiong; Hung, Eugene title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 journal: Virology DOI: 10.1016/j.virol.2006.10.016 sha: doc_id: 255738 cord_uid: r8zfdsix file: cache/cord-255795-su7f5ges.json key: cord-255795-su7f5ges authors: Yelin, Idan; Aharony, Noga; Shaer-Tamar, Einat; Argoetti, Amir; Messer, Esther; Berenbaum, Dina; Shafran, Einat; Kuzli, Areen; Gandali, Nagam; Hashimshony, Tamar; Mandel-Gutfreund, Yael; Halberthal, Michael; Geffen, Yuval; Szwarcwort-Cohen, Moran; Kishony, Roy title: Evaluation of COVID-19 RT-qPCR test in multi-sample pools date: 2020-03-27 journal: nan DOI: 10.1101/2020.03.26.20039438 sha: doc_id: 255795 cord_uid: su7f5ges file: cache/cord-256325-q70rky3r.json key: cord-256325-q70rky3r authors: Stewart, Cameron R.; Deffrasnes, Celine; Foo, Chwan Hong; Bean, Andrew G. D.; Wang, Lin-Fa title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date: 2017-07-04 journal: Roles of Host Gene and Non-coding RNA Expression in Virus Infection DOI: 10.1007/82_2017_28 sha: doc_id: 256325 cord_uid: q70rky3r file: cache/cord-255883-mz6nyisw.json key: cord-255883-mz6nyisw authors: Asif, Muhammad; Saleem, Mohammad; Saadullah, Malik; Yaseen, Hafiza Sidra; Al Zarzour, Raghdaa title: COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date: 2020-08-14 journal: Inflammopharmacology DOI: 10.1007/s10787-020-00744-0 sha: doc_id: 255883 cord_uid: mz6nyisw file: cache/cord-256370-cz88t29n.json key: cord-256370-cz88t29n authors: Jansen van Vuren, Petrus; Wiley, Michael; Palacios, Gustavo; Storm, Nadia; McCulloch, Stewart; Markotter, Wanda; Birkhead, Monica; Kemp, Alan; Paweska, Janusz T. title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date: 2016-02-29 journal: Viruses DOI: 10.3390/v8030065 sha: doc_id: 256370 cord_uid: cz88t29n file: cache/cord-022888-dnsdg04n.json key: cord-022888-dnsdg04n authors: nan title: Poster Sessions date: 2009-08-19 journal: Eur J Immunol DOI: 10.1002/eji.200990224 sha: doc_id: 22888 cord_uid: dnsdg04n file: cache/cord-256444-grw5s2pf.json key: cord-256444-grw5s2pf authors: Lai, Michael M.C.; Cavanagh, David title: The Molecular Biology of Coronaviruses date: 1997-12-31 journal: Advances in Virus Research DOI: 10.1016/s0065-3527(08)60286-9 sha: doc_id: 256444 cord_uid: grw5s2pf file: cache/cord-256508-ce59ovan.json key: cord-256508-ce59ovan authors: Asselah, Tarik; Durantel, David; Pasmant, Eric; Lau, George; Schinazi, Raymond F. title: COVID-19: discovery, diagnostics and drug development date: 2020-10-08 journal: J Hepatol DOI: 10.1016/j.jhep.2020.09.031 sha: doc_id: 256508 cord_uid: ce59ovan file: cache/cord-256510-orr2roxz.json key: cord-256510-orr2roxz authors: de Castro, Isabel Fernández; Volonté, Luca; Risco, Cristina title: Virus factories: biogenesis and structural design date: 2012-10-04 journal: Cell Microbiol DOI: 10.1111/cmi.12029 sha: doc_id: 256510 cord_uid: orr2roxz file: cache/cord-256561-fnh2do4z.json key: cord-256561-fnh2do4z authors: Barik, Sailen; Lu, Patrick title: Therapy of Respiratory Viral Infections with Intranasal siRNAs date: 2014-09-23 journal: RNA Interference DOI: 10.1007/978-1-4939-1538-5_14 sha: doc_id: 256561 cord_uid: fnh2do4z file: cache/cord-256918-mauzesor.json key: cord-256918-mauzesor authors: Domingo, Esteban title: Quasispecies and the implications for virus persistence and escape date: 1998-07-15 journal: Clinical and Diagnostic Virology DOI: 10.1016/s0928-0197(98)00032-4 sha: doc_id: 256918 cord_uid: mauzesor file: cache/cord-256940-yuja99jg.json key: cord-256940-yuja99jg authors: Wei, Bo; Hang, Xiaofeng; Xie, Ying; Zhang, Yuanjing; Wang, Jianrong; Cao, Xinghao; Wu, Jinzi J.; Wang, Junxue title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date: 2020-07-20 journal: Revista da Sociedade Brasileira de Medicina Tropical DOI: 10.1590/0037-8682-0372-2020 sha: doc_id: 256940 cord_uid: yuja99jg file: cache/cord-257456-15bm9psj.json key: cord-257456-15bm9psj authors: Arumugam, Arunkumar; Faron, Matthew L.; Yu, Peter; Markham, Cole; Wu, Michelle; Wong, Season title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 journal: Diagnostics (Basel) DOI: 10.3390/diagnostics10100739 sha: doc_id: 257456 cord_uid: 15bm9psj file: cache/cord-256615-gvq8uyfk.json key: cord-256615-gvq8uyfk authors: Rosenberg, Ronald title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans date: 2014-11-22 journal: Cell Mol Life Sci DOI: 10.1007/s00018-014-1785-y sha: doc_id: 256615 cord_uid: gvq8uyfk file: cache/cord-257652-ndt8f812.json key: cord-257652-ndt8f812 authors: Zhang, Yong-Zhen; Wu, Wei-Chen; Shi, Mang; Holmes, Edward C title: The diversity, evolution and origins of vertebrate RNA viruses date: 2018-08-13 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2018.07.017 sha: doc_id: 257652 cord_uid: ndt8f812 file: cache/cord-257693-rnchfjbe.json key: cord-257693-rnchfjbe authors: Wang, Yeming; Guo, Qiang; Yan, Zheng; Zhou, Daming; Zhang, Wei; Zhou, Shujun; Li, Yu-Ping; Yuan, Jing; Uyeki, Timothy M.; Shen, Xinghua; Wu, Wenjuan; Zhao, Hui; Wu, Yun-Fu; Shang, Jia; He, Zhengguang; Yang, Yi; Zhao, Hongsheng; Hong, Yongqing; Zhang, Zehua; Wu, Min; Wei, Tiemin; Deng, Xilong; Deng, Yijun; Cai, Li-hua; Lu, Weihua; Shu, Hongmei; Zhang, Lin; Luo, Hong; Zhou, Ying; Weng, Heng; Song, Keyi; Yao, Li; Jiang, Mingguang; Zhao, Boliang; Chi, Ruibin; Guo, Boqi; Fu, Lin; Yu, Long; Min, Haiyan; Chen, Pu; Chen, Shuifang; Hong, Liang; Mao, Wei; Huang, Xiaoping; Gu, Lijun; Li, Hui; Wang, Chen; Cao, Bin title: Factors Associated With Prolonged Viral Shedding in Patients With Avian Influenza A(H7N9) Virus Infection date: 2018-04-10 journal: The Journal of Infectious Diseases DOI: 10.1093/infdis/jiy115 sha: doc_id: 257693 cord_uid: rnchfjbe file: cache/cord-257569-36qx1sy9.json key: cord-257569-36qx1sy9 authors: Hanada, Kousuke; Suzuki, Yoshiyuki; Gojobori, Takashi title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date: 2004-06-17 journal: Mol Biol Evol DOI: 10.1093/molbev/msh109 sha: doc_id: 257569 cord_uid: 36qx1sy9 file: cache/cord-258035-2tk7maqk.json key: cord-258035-2tk7maqk authors: DeFilippis, Victor; Raggo, Camilo; Moses, Ashlee; Früh, Klaus title: Functional genomics in virology and antiviral drug discovery date: 2003-10-31 journal: Trends in Biotechnology DOI: 10.1016/s0167-7799(03)00207-5 sha: doc_id: 258035 cord_uid: 2tk7maqk file: cache/cord-258547-47cyyetb.json key: cord-258547-47cyyetb authors: Asasi, Keramat; Mohammadi, Ali; Boroomand, Zahra; Hosseinian, Seyedeh Alemeh; Nazifi, Saeed title: Changes of several acute phase factors in broiler chickens in response to infectious bronchitis virus infection date: 2013-08-01 journal: Poult Sci DOI: 10.3382/ps.2012-02902 sha: doc_id: 258547 cord_uid: 47cyyetb file: cache/cord-259152-pwvcwlh8.json key: cord-259152-pwvcwlh8 authors: Ji, Wei; Wang, Wei; Zhao, Xiaofang; Zai, Junjie; Li, Xingguang title: Cross‐species transmission of the newly identified coronavirus 2019‐nCoV date: 2020-02-19 journal: J Med Virol DOI: 10.1002/jmv.25682 sha: doc_id: 259152 cord_uid: pwvcwlh8 file: cache/cord-258286-lodjcj8c.json key: cord-258286-lodjcj8c authors: Zhang, Xuming; Hinton, David R.; Cua, Daniel J.; Stohlman, Stephen A.; Lai, Michael M.C. title: Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date: 1997-07-07 journal: Virology DOI: 10.1006/viro.1997.8598 sha: doc_id: 258286 cord_uid: lodjcj8c file: cache/cord-258696-01wj76es.json key: cord-258696-01wj76es authors: Decaro, Nicola; Campolo, Marco; Lorusso, Alessio; Desario, Costantina; Mari, Viviana; Colaianni, Maria Loredana; Elia, Gabriella; Martella, Vito; Buonavoglia, Canio title: Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia date: 2008-04-30 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2007.10.008 sha: doc_id: 258696 cord_uid: 01wj76es file: cache/cord-258172-p54j4zzo.json key: cord-258172-p54j4zzo authors: Barker, Harlan; Parkkila, Seppo title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 journal: PLoS One DOI: 10.1371/journal.pone.0240647 sha: doc_id: 258172 cord_uid: p54j4zzo file: cache/cord-259500-ndjbrtrv.json key: cord-259500-ndjbrtrv authors: Satyanarayana, Tatineni; Gowda, Siddarame; Ayllón, María A; Dawson, William O title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date: 2003-09-01 journal: Virology DOI: 10.1016/s0042-6822(03)00387-8 sha: doc_id: 259500 cord_uid: ndjbrtrv file: cache/cord-259916-gr6v098c.json key: cord-259916-gr6v098c authors: Wang, Hongliang; Tai, Andrew W. title: Mechanisms of Cellular Membrane Reorganization to Support Hepatitis C Virus Replication date: 2016-05-20 journal: Viruses DOI: 10.3390/v8050142 sha: doc_id: 259916 cord_uid: gr6v098c file: cache/cord-258678-0atfsivf.json key: cord-258678-0atfsivf authors: Liu, Hong Yan; Gao, Xiaohu title: A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date: 2013-11-07 journal: Sci Rep DOI: 10.1038/srep03129 sha: doc_id: 258678 cord_uid: 0atfsivf file: cache/cord-259710-qrht9tq3.json key: cord-259710-qrht9tq3 authors: Burimuah, Vitus; Sylverken, Augustina; Owusu, Michael; El-Duah, Philip; Yeboah, Richmond; Lamptey, Jones; Frimpong, Yaw Oppong; Agbenyega, Olivia; Folitse, Raphael; Emikpe, Ben; Tasiame, William; Owiredu, Eddie-Williams; Oppong, Samuel; Antwi, Christopher; Adu-Sarkodie, Yaw; Drosten, Christian title: Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana date: 2020-10-27 journal: BMC Vet Res DOI: 10.1186/s12917-020-02606-x sha: doc_id: 259710 cord_uid: qrht9tq3 file: cache/cord-258595-bk35vxlr.json key: cord-258595-bk35vxlr authors: Westhaus, Sandra; Weber, Frank-Andreas; Schiwy, Sabrina; Linnemann, Volker; Brinkmann, Markus; Widera, Marek; Greve, Carola; Janke, Axel; Hollert, Henner; Wintgens, Thomas; Ciesek, Sandra title: Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date: 2020-08-18 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.141750 sha: doc_id: 258595 cord_uid: bk35vxlr file: cache/cord-259246-azt5sr9w.json key: cord-259246-azt5sr9w authors: Peng, Qi; Peng, Ruchao; Yuan, Bin; Wang, Min; Zhao, Jingru; Fu, Lifeng; Qi, Jianxun; Shi, Yi title: Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir date: 2020-10-19 journal: bioRxiv DOI: 10.1101/2020.10.19.345470 sha: doc_id: 259246 cord_uid: azt5sr9w file: cache/cord-259593-shrd1s7r.json key: cord-259593-shrd1s7r authors: Qin, Zhao-ling; Zhao, Ping; Cao, Ming-mei; Qi, Zhong-tian title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date: 2007-06-27 journal: J Virol Methods DOI: 10.1016/j.jviromet.2007.05.017 sha: doc_id: 259593 cord_uid: shrd1s7r file: cache/cord-031907-ilhr3iu5.json key: cord-031907-ilhr3iu5 authors: nan title: ISEV2020 Abstract Book date: 2020-07-15 journal: nan DOI: 10.1080/20013078.2020.1784511 sha: doc_id: 31907 cord_uid: ilhr3iu5 file: cache/cord-259603-bh198xgl.json key: cord-259603-bh198xgl authors: Snijder, E.J.; Decroly, E.; Ziebuhr, J. title: The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date: 2016-09-14 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2016.08.008 sha: doc_id: 259603 cord_uid: bh198xgl file: cache/cord-261735-03hvi4el.json key: cord-261735-03hvi4el authors: Rodrigues, R.; Telles, J.-N.; Essere, K.; Ducournau, C.; Roqueplo, C.; Levieuge, A.; Davoust, B.; Parola, P.; Paranhos-Baccalà, G.; Peyrefitte, C.N. title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date: 2011-06-14 journal: J Virol Methods DOI: 10.1016/j.jviromet.2011.06.003 sha: doc_id: 261735 cord_uid: 03hvi4el file: cache/cord-259927-xh9cw9ao.json key: cord-259927-xh9cw9ao authors: Papadopoulos, Nikolaos G.; Megremis, Spyridon; Kitsioulis, Nikolaos A.; Vangelatou, Olympia; West, Peter; Xepapadaki, Paraskevi title: Promising approaches for the treatment and prevention of viral respiratory illnesses date: 2017-07-21 journal: J Allergy Clin Immunol DOI: 10.1016/j.jaci.2017.07.001 sha: doc_id: 259927 cord_uid: xh9cw9ao file: cache/cord-259311-ccx61owl.json key: cord-259311-ccx61owl authors: Kapitula, D. S.; Jiang, Z.; Jiang, J.; Zhu, J.; Chen, X.; Lin, C. Q. title: Performance & Quality Evaluation of Marketed COVID-19 RNA Detection Kits date: 2020-05-01 journal: nan DOI: 10.1101/2020.04.25.20080002 sha: doc_id: 259311 cord_uid: ccx61owl file: cache/cord-261417-4pf5nsw2.json key: cord-261417-4pf5nsw2 authors: Harwig, Alex; Landick, Robert; Berkhout, Ben title: The Battle of RNA Synthesis: Virus versus Host date: 2017-10-21 journal: Viruses DOI: 10.3390/v9100309 sha: doc_id: 261417 cord_uid: 4pf5nsw2 file: cache/cord-261532-q923xxn2.json key: cord-261532-q923xxn2 authors: Chen, Huihui; Jiang, Zhengfan title: The essential adaptors of innate immune signaling date: 2012-09-21 journal: Protein & Cell DOI: 10.1007/s13238-012-2063-0 sha: doc_id: 261532 cord_uid: q923xxn2 file: cache/cord-262592-0rdiosxd.json key: cord-262592-0rdiosxd authors: Cuevas, José M.; Combe, Marine; Torres-Puente, Manoli; Garijo, Raquel; Guix, Susana; Buesa, Javier; Rodríguez-Díaz, Jesús; Sanjuán, Rafael title: Human norovirus hyper-mutation revealed by ultra-deep sequencing date: 2016-04-17 journal: Infect Genet Evol DOI: 10.1016/j.meegid.2016.04.017 sha: doc_id: 262592 cord_uid: 0rdiosxd file: cache/cord-259233-smmhhroe.json key: cord-259233-smmhhroe authors: de Armas‐Rillo, Laura; Valera, María‐Soledad; Marrero‐Hernández, Sara; Valenzuela‐Fernández, Agustín title: Membrane dynamics associated with viral infection date: 2016-01-28 journal: Rev Med Virol DOI: 10.1002/rmv.1872 sha: doc_id: 259233 cord_uid: smmhhroe file: cache/cord-261160-g92zhv19.json key: cord-261160-g92zhv19 authors: Rowland, Raymond R.R; Lawson, Steven; Rossow, Kurt; Benfield, David A title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2003.07.006 sha: doc_id: 261160 cord_uid: g92zhv19 file: cache/cord-260225-bc1hr0fr.json key: cord-260225-bc1hr0fr authors: Sirpilla, Olivia; Bauss, Jacob; Gupta, Ruchir; Underwood, Adam; Qutob, Dinah; Freeland, Tom; Bupp, Caleb; Carcillo, Joseph; Hartog, Nicholas; Rajasekaran, Surender; Prokop, Jeremy W. title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00421 sha: doc_id: 260225 cord_uid: bc1hr0fr file: cache/cord-260042-cs0wp99n.json key: cord-260042-cs0wp99n authors: Khan, Samiullah; Roberts, Juliet; Wu, Shu-Biao title: Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date: 2019-04-01 journal: BMC Mol Cell Biol DOI: 10.1186/s12860-019-0190-7 sha: doc_id: 260042 cord_uid: cs0wp99n file: cache/cord-260168-rb7j94dh.json key: cord-260168-rb7j94dh authors: Gu, Jiang; Xie, Zhigang; Gao, Zhancheng; Liu, Jinhua; Korteweg, Christine; Ye, Juxiang; Lau, Lok Ting; Lu, Jie; Gao, Zifen; Zhang, Bo; McNutt, Michael A; Lu, Min; Anderson, Virginia M; Gong, Encong; Yu, Albert Cheung Hoi; Lipkin, W Ian title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 journal: Lancet DOI: 10.1016/s0140-6736(07)61515-3 sha: doc_id: 260168 cord_uid: rb7j94dh file: cache/cord-260782-1lm8tzbc.json key: cord-260782-1lm8tzbc authors: Giles, Julia; Perrott, Matthew; Roe, Wendi; Shrestha, Kshitiz; Aberdein, Danielle; Morel, Patrick; Dunowska, Magdalena title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date: 2018-07-14 journal: Virology DOI: 10.1016/j.virol.2018.07.003 sha: doc_id: 260782 cord_uid: 1lm8tzbc file: cache/cord-262318-qpztmdnw.json key: cord-262318-qpztmdnw authors: Guo, Jingxu; Douangamath, Alice; Song, Weixiao; Coker, Alun R.; Edith Chan, A.W.; Wood, Steve P.; Cooper, Jonathan B.; Resnick, Efrat; London, Nir; von Delft., Frank title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors date: 2020-07-16 journal: J Struct Biol X DOI: 10.1016/j.yjsbx.2020.100031 sha: doc_id: 262318 cord_uid: qpztmdnw file: cache/cord-260250-t48y27wg.json key: cord-260250-t48y27wg authors: Decaro, Nicola; Pratelli, Annamaria; Campolo, Marco; Elia, Gabriella; Martella, Vito; Tempesta, Maria; Buonavoglia, Canio title: Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date: 2004-05-07 journal: J Virol Methods DOI: 10.1016/j.jviromet.2004.03.012 sha: doc_id: 260250 cord_uid: t48y27wg file: cache/cord-259671-7de21oaq.json key: cord-259671-7de21oaq authors: Madhugiri, Ramakanth; Fricke, Markus; Marz, Manja; Ziebuhr, John title: RNA structure analysis of alphacoronavirus terminal genome regions date: 2014-12-19 journal: Virus Res DOI: 10.1016/j.virusres.2014.10.001 sha: doc_id: 259671 cord_uid: 7de21oaq file: cache/cord-260452-js4nr4d8.json key: cord-260452-js4nr4d8 authors: Yu, Junyang; Wu, Yuzhang; Wang, Jingxue title: Activation and Role of NACHT, LRR, and PYD Domains-Containing Protein 3 Inflammasome in RNA Viral Infection date: 2017-10-31 journal: Front Immunol DOI: 10.3389/fimmu.2017.01420 sha: doc_id: 260452 cord_uid: js4nr4d8 file: cache/cord-261110-cnj0e0s9.json key: cord-261110-cnj0e0s9 authors: Debarnot, Claire; Imbert, Isabelle; Ferron, François; Gluais, Laure; Varlet, Isabelle; Papageorgiou, Nicolas; Bouvet, Mickaël; Lescar, Julien; Decroly, Etienne; Canard, Bruno title: Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date: 2011-02-25 journal: Acta Crystallographica Section F Structural Biology and Crystallization Communications DOI: 10.1107/s1744309111002867 sha: doc_id: 261110 cord_uid: cnj0e0s9 file: cache/cord-262923-kgzbd6w3.json key: cord-262923-kgzbd6w3 authors: Koo, Bonhan; Kim, Da-eun; Kweon, Jiyeon; Jin, Choong Eun; Kim, Sung-Han; Kim, Yongsub; Shin, Yong title: CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases date: 2018-11-10 journal: Sens Actuators B Chem DOI: 10.1016/j.snb.2018.06.069 sha: doc_id: 262923 cord_uid: kgzbd6w3 file: cache/cord-262841-nr42rs8f.json key: cord-262841-nr42rs8f authors: Li, Lanjuan; Wo, Jianer; Shao, Junbing; Zhu, Haihong; Wu, Nanping; Li, Minwei; Yao, Hangpin; Hu, Minjun; Dennin, Reinhard H. title: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date: 2003-12-31 journal: Journal of Clinical Virology DOI: 10.1016/s1386-6532(03)00195-1 sha: doc_id: 262841 cord_uid: nr42rs8f file: cache/cord-260695-qwepi0we.json key: cord-260695-qwepi0we authors: Postler, Thomas S.; Pantry, Shara N.; Desrosiers, Ronald C.; Ghosh, Sankar title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date: 2017-11-01 journal: Virology DOI: 10.1016/j.virol.2017.08.006 sha: doc_id: 260695 cord_uid: qwepi0we file: cache/cord-262753-jld1ygxt.json key: cord-262753-jld1ygxt authors: Neidermyer, William J.; Whelan, Sean P. J. title: Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date: 2019-06-21 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1007875 sha: doc_id: 262753 cord_uid: jld1ygxt file: cache/cord-263699-gosqpg3k.json key: cord-263699-gosqpg3k authors: Martínez, José L.; Arias, Carlos F. title: Role of the Guanine Nucleotide Exchange Factor GBF1 in the Replication of RNA Viruses date: 2020-06-24 journal: Viruses DOI: 10.3390/v12060682 sha: doc_id: 263699 cord_uid: gosqpg3k file: cache/cord-260345-ugd8kkor.json key: cord-260345-ugd8kkor authors: Giles, Ian G. title: A compendium of reviews in biochemistry and molecular biology published in the first half of 1992 date: 1992-12-31 journal: International Journal of Biochemistry DOI: 10.1016/0020-711x(92)90283-7 sha: doc_id: 260345 cord_uid: ugd8kkor file: cache/cord-263033-4790dhc5.json key: cord-263033-4790dhc5 authors: Laptev, I. G.; Golovina, A. Ya.; Sergiev, P. V.; Dontsova, O. A. title: Posttranscriptional modification of messenger RNAs in eukaryotes date: 2015-12-11 journal: Mol Biol DOI: 10.1134/s002689331506014x sha: doc_id: 263033 cord_uid: 4790dhc5 file: cache/cord-263433-oldy0gta.json key: cord-263433-oldy0gta authors: Barriocanal, Marina; Carnero, Elena; Segura, Victor; Fortes, Puri title: Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin date: 2015-01-09 journal: Front Immunol DOI: 10.3389/fimmu.2014.00655 sha: doc_id: 263433 cord_uid: oldy0gta file: cache/cord-261279-6mef38eo.json key: cord-261279-6mef38eo authors: Chu, Daniel K W; Pan, Yang; Cheng, Samuel M S; Hui, Kenrie P Y; Krishnan, Pavithra; Liu, Yingzhi; Ng, Daisy Y M; Wan, Carrie K C; Yang, Peng; Wang, Quanyi; Peiris, Malik; Poon, Leo L M title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 journal: Clin Chem DOI: 10.1093/clinchem/hvaa029 sha: doc_id: 261279 cord_uid: 6mef38eo file: cache/cord-262776-6k7tcgfs.json key: cord-262776-6k7tcgfs authors: Burnouf, Thierry; Griffiths, Elwyn; Padilla, Ana; Seddik, Salwa; Stephano, Marco Antonio; Gutiérrez, José-María title: Assessment of the viral safety of antivenoms fractionated from equine plasma date: 2004-09-30 journal: Biologicals DOI: 10.1016/j.biologicals.2004.07.001 sha: doc_id: 262776 cord_uid: 6k7tcgfs file: cache/cord-262844-qeheeqe3.json key: cord-262844-qeheeqe3 authors: Xia, Xuhua title: Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date: 2020-04-14 journal: Mol Biol Evol DOI: 10.1093/molbev/msaa094 sha: doc_id: 262844 cord_uid: qeheeqe3 file: cache/cord-263239-andje0wu.json key: cord-263239-andje0wu authors: Dorobantu, Cristina M.; Albulescu, Lucian; Harak, Christian; Feng, Qian; van Kampen, Mirjam; Strating, Jeroen R. P. M.; Gorbalenya, Alexander E.; Lohmann, Volker; van der Schaar, Hilde M.; van Kuppeveld, Frank J. M. title: Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus date: 2015-09-25 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1005185 sha: doc_id: 263239 cord_uid: andje0wu file: cache/cord-263468-996kl9jz.json key: cord-263468-996kl9jz authors: Cattaneo, Roberto; Schmid, Anita; Eschle, Daniel; Baczko, Knut; ter Meulen, Volker; Billeter, Martin A. title: Biased hypermutation and other genetic changes in defective measles viruses in human brain infections date: 1988-10-21 journal: Cell DOI: 10.1016/0092-8674(88)90048-7 sha: doc_id: 263468 cord_uid: 996kl9jz file: cache/cord-260647-7bjhobg7.json key: cord-260647-7bjhobg7 authors: Coudray-Meunier, Coralie; Fraisse, Audrey; Martin-Latil, Sandra; Delannoy, Sabine; Fach, Patrick; Perelle, Sylvie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 journal: PLoS One DOI: 10.1371/journal.pone.0147832 sha: doc_id: 260647 cord_uid: 7bjhobg7 file: cache/cord-262282-9xh51cd1.json key: cord-262282-9xh51cd1 authors: Serwer, Philip title: Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date: 2020-05-15 journal: Antibiotics (Basel) DOI: 10.3390/antibiotics9050255 sha: doc_id: 262282 cord_uid: 9xh51cd1 file: cache/cord-263315-g7os15m1.json key: cord-263315-g7os15m1 authors: Martins-da-Silva, Andrea; Telleria, Erich Loza; Batista, Michel; Marchini, Fabricio Klerynton; Traub-Csekö, Yara Maria; Tempone, Antonio Jorge title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 journal: Viruses DOI: 10.3390/v10010043 sha: doc_id: 263315 cord_uid: g7os15m1 file: cache/cord-260705-huyyw5z6.json key: cord-260705-huyyw5z6 authors: Moshe, Adi; Gorovits, Rena title: Virus-Induced Aggregates in Infected Cells date: 2012-10-17 journal: Viruses DOI: 10.3390/v4102218 sha: doc_id: 260705 cord_uid: huyyw5z6 file: cache/cord-265095-lf5j4ic7.json key: cord-265095-lf5j4ic7 authors: Ten Dam, Edwin B.; Pleij, Cornelius W. A.; Bosch, Leendert title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs date: 1990 journal: Virus Genes DOI: 10.1007/bf00678404 sha: doc_id: 265095 cord_uid: lf5j4ic7 file: cache/cord-266585-jfjrk9gy.json key: cord-266585-jfjrk9gy authors: Fang, Shouguo; Chen, Bo; Tay, Felicia P.L.; Ng, Beng Sern; Liu, Ding Xing title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 journal: Virology DOI: 10.1016/j.virol.2006.08.020 sha: doc_id: 266585 cord_uid: jfjrk9gy file: cache/cord-264884-ydkigome.json key: cord-264884-ydkigome authors: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 journal: Origin and Evolution of Viruses DOI: 10.1016/b978-0-12-374153-0.00021-7 sha: doc_id: 264884 cord_uid: ydkigome file: cache/cord-260422-z22t57ju.json key: cord-260422-z22t57ju authors: Godet, Julien; Boudier, Christian; Humbert, Nicolas; Ivanyi-Nagy, Roland; Darlix, Jean-Luc; Mély, Yves title: Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1 date: 2012-06-26 journal: Virus Res DOI: 10.1016/j.virusres.2012.06.021 sha: doc_id: 260422 cord_uid: z22t57ju file: cache/cord-260708-l9w5jhsw.json key: cord-260708-l9w5jhsw authors: Lasecka, Lidia; Baron, Michael D. title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 journal: Arch Virol DOI: 10.1007/s00705-013-1940-z sha: doc_id: 260708 cord_uid: l9w5jhsw file: cache/cord-262347-ejhz9rra.json key: cord-262347-ejhz9rra authors: Kappes, Matthew A.; Faaberg, Kay S. title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity date: 2015-03-07 journal: Virology DOI: 10.1016/j.virol.2015.02.012 sha: doc_id: 262347 cord_uid: ejhz9rra file: cache/cord-263334-wwkdum94.json key: cord-263334-wwkdum94 authors: Li, Chen; Ge, Ling-ling; Li, Peng-peng; Wang, Yue; Dai, Juan-juan; Sun, Ming-xia; Huang, Li; Shen, Zhi-qiang; Hu, Xiao-chun; Ishag, Hassan; Mao, Xiang title: Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date: 2014-01-20 journal: Virology DOI: 10.1016/j.virol.2013.11.008 sha: doc_id: 263334 cord_uid: wwkdum94 file: cache/cord-264159-e9071tyv.json key: cord-264159-e9071tyv authors: Lin, Weikang Nicholas; Tay, Matthew Zirui; Lu, Ri; Liu, Yi; Chen, Chia-Hung; Cheow, Lih Feng title: The Role of Single-Cell Technology in the Study and Control of Infectious Diseases date: 2020-06-10 journal: Cells DOI: 10.3390/cells9061440 sha: doc_id: 264159 cord_uid: e9071tyv file: cache/cord-265855-zf52vl11.json key: cord-265855-zf52vl11 authors: Mayor-Ibarguren, Ander; Busca-Arenzana, Carmen; Robles-Marhuenda, Ángel title: A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date: 2020-07-10 journal: Front Immunol DOI: 10.3389/fimmu.2020.01736 sha: doc_id: 265855 cord_uid: zf52vl11 file: cache/cord-263157-8jin6oru.json key: cord-263157-8jin6oru authors: Martínez, Miguel Angel title: Progress in the Therapeutic Applications of siRNAs Against HIV-1 date: 2008-10-13 journal: siRNA and miRNA Gene Silencing DOI: 10.1007/978-1-60327-547-7_17 sha: doc_id: 263157 cord_uid: 8jin6oru file: cache/cord-264678-wt0lvhfl.json key: cord-264678-wt0lvhfl authors: Wu, Tzong-Yuan; Hsieh, Chi-Chun; Hong, Jun-Jie; Chen, Chung-Yung; Tsai, Yuh-Show title: IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico date: 2009-05-27 journal: BMC Bioinformatics DOI: 10.1186/1471-2105-10-160 sha: doc_id: 264678 cord_uid: wt0lvhfl file: cache/cord-264944-7xj27r98.json key: cord-264944-7xj27r98 authors: Koopmans, Marion; Monroe, Stephan S.; Coffield, Lisa M.; Zaki, Sherif R. title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date: 1993-07-31 journal: Journal of Virological Methods DOI: 10.1016/0166-0934(93)90076-4 sha: doc_id: 264944 cord_uid: 7xj27r98 file: cache/cord-265895-ck7eto16.json key: cord-265895-ck7eto16 authors: Baric, Ralph S.; Shieh, Chien-Kou; Stohlman, Stephen A.; Lai, Michael M.C. title: Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date: 1987-02-28 journal: Virology DOI: 10.1016/0042-6822(87)90414-4 sha: doc_id: 265895 cord_uid: ck7eto16 file: cache/cord-264051-ps0x2es1.json key: cord-264051-ps0x2es1 authors: Li, Wei; Yang, Shuai; Xu, Peng; Zhang, Dapeng; Tong, Ying; Chen, Lu; Jia, Ben; Li, Ang; Ru, Daoping; Zhang, Baolong; Liu, Mengxing; Lian, Cheng; Chen, Cancan; Fu, Weihui; Yuan, Songhua; Ren, Xiaoguang; Liang, Ying; Yang, Zhicong; Li, Wenxuan; Wang, Shaoxuan; Zhang, Xiaoyan; Lu, Hongzhou; Xu, Jianqing; Wang, Hailing; Yu, Wenqiang title: Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.04.361576 sha: doc_id: 264051 cord_uid: ps0x2es1 file: cache/cord-263987-ff6kor0c.json key: cord-263987-ff6kor0c authors: Holmes, Ian H. title: Solving the master equation for Indels date: 2017-05-12 journal: BMC Bioinformatics DOI: 10.1186/s12859-017-1665-1 sha: doc_id: 263987 cord_uid: ff6kor0c file: cache/cord-266921-x9q7dwc4.json key: cord-266921-x9q7dwc4 authors: Worrall, Jonathan AR; Luisi, Ben F title: Information available at cut rates: structure and mechanism of ribonucleases date: 2006-12-26 journal: Curr Opin Struct Biol DOI: 10.1016/j.sbi.2006.12.001 sha: doc_id: 266921 cord_uid: x9q7dwc4 file: cache/cord-266521-vovas81d.json key: cord-266521-vovas81d authors: Yokobayashi, Yohei title: Aptamer-based and aptazyme-based riboswitches in mammalian cells date: 2019-06-22 journal: Curr Opin Chem Biol DOI: 10.1016/j.cbpa.2019.05.018 sha: doc_id: 266521 cord_uid: vovas81d file: cache/cord-262076-b5u5hp2r.json key: cord-262076-b5u5hp2r authors: Liu, Ying Poi; Haasnoot, Joost; ter Brake, Olivier; Berkhout, Ben; Konstantinova, Pavlina title: Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron date: 2008-03-16 journal: Nucleic Acids Res DOI: 10.1093/nar/gkn109 sha: doc_id: 262076 cord_uid: b5u5hp2r file: cache/cord-262511-96xp1v0r.json key: cord-262511-96xp1v0r authors: Khabar, Khalid S. A. title: Rapid transit in the immune cells: the role of mRNA turnover regulation date: 2007-03-30 journal: J Leukoc Biol DOI: 10.1189/jlb.0207109 sha: doc_id: 262511 cord_uid: 96xp1v0r file: cache/cord-267115-6jqdi417.json key: cord-267115-6jqdi417 authors: Giobbe, Giovanni Giuseppe; Bonfante, Francesco; Zambaiti, Elisa; Gagliano, Onelia; Jones, Brendan C.; Luni, Camilla; Laterza, Cecilia; Perin, Silvia; Stuart, Hannah T.; Pagliari, Matteo; Bortolami, Alessio; Mazzetto, Eva; Manfredi, Anna; Colantuono, Chiara; Di Filippo, Lucio; Pellegata, Alessandro; Li, Vivian Sze Wing; Eaton, Simon; Thapar, Nikhil; Cacchiarelli, Davide; Elvassore, Nicola; De Coppi, Paolo title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date: 2020-06-24 journal: bioRxiv DOI: 10.1101/2020.06.24.167049 sha: doc_id: 267115 cord_uid: 6jqdi417 file: cache/cord-262609-cssgzvus.json key: cord-262609-cssgzvus authors: Sivakumaran, K; Kim, Chul-Hyun; Tayon, Robert; Kao, C.Cheng title: RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis date: 1999-12-03 journal: J Mol Biol DOI: 10.1006/jmbi.1999.3297 sha: doc_id: 262609 cord_uid: cssgzvus file: cache/cord-267588-ruuzr6l1.json key: cord-267588-ruuzr6l1 authors: Garnett, Lauren; Bello, Alexander; Tran, Kaylie N.; Audet, Jonathan; Leung, Anders; Schiffman, Zachary; Griffin, Bryan D.; Tailor, Nikesh; Kobasa, Darwyn; Strong, James E. title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date: 2020-08-08 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113947 sha: doc_id: 267588 cord_uid: ruuzr6l1 file: cache/cord-266520-n439dwcx.json key: cord-266520-n439dwcx authors: Levanova, Alesia A.; Kalke, Kiira M.; Lund, Liisa M.; Sipari, Nina; Sadeghi, Mohammadreza; Nyman, Marie C.; Paavilainen, Henrik; Hukkanen, Veijo; Poranen, Minna M. title: Enzymatically synthesized 2'-fluoro-modified Dicer-substrate siRNA swarms against herpes simplex virus demonstrate enhanced antiviral efficacy and low cytotoxicity date: 2020-08-13 journal: Antiviral Res DOI: 10.1016/j.antiviral.2020.104916 sha: doc_id: 266520 cord_uid: n439dwcx file: cache/cord-266960-kyx6xhvj.json key: cord-266960-kyx6xhvj authors: Temple, Mark D. title: Real-time audio and visual display of the Coronavirus genome date: 2020-10-02 journal: BMC Bioinformatics DOI: 10.1186/s12859-020-03760-7 sha: doc_id: 266960 cord_uid: kyx6xhvj file: cache/cord-266464-wuf3s8m0.json key: cord-266464-wuf3s8m0 authors: Kim, So Yeon; Park, Sun Jae; Cho, Sook Young; Cha, Ran-hui; Jee, Hyeon-Gun; Kim, Gayeon; Shin, Hyoung-Shik; Kim, Yeonjae; Jung, Yu Mi; Yang, Jeong-Sun; Kim, Sung Soon; Cho, Sung Im; Kim, Man Jin; Lee, Jee-Soo; Lee, Seung Jun; Seo, Soo Hyun; Park, Sung Sup; Seong, Moon-Woo title: Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection date: 2016-10-17 journal: Emerg Infect Dis DOI: 10.3201/eid2210.160218 sha: doc_id: 266464 cord_uid: wuf3s8m0 file: cache/cord-267027-diwm1940.json key: cord-267027-diwm1940 authors: Le, Shu-Yun; Chen, Jih-H.; Sonenberg, Nahum; Maizel, Jacob V. title: Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses date: 1992-12-31 journal: Virology DOI: 10.1016/0042-6822(92)90261-m sha: doc_id: 267027 cord_uid: diwm1940 file: cache/cord-263645-wupre5uj.json key: cord-263645-wupre5uj authors: Morgan, Brittany S; Forte, Jordan E; Hargrove, Amanda E title: Insights into the development of chemical probes for RNA date: 2018-09-19 journal: Nucleic Acids Res DOI: 10.1093/nar/gky718 sha: doc_id: 263645 cord_uid: wupre5uj file: cache/cord-265381-ppjohov8.json key: cord-265381-ppjohov8 authors: Pillai-Nair, Neeta; Kim, Kook-Hyung; Hemenway, Cynthia title: Cis-acting Regulatory Elements in the Potato Virus X 3′ Non-translated Region Differentially Affect Minus-strand and Plus-strand RNA Accumulation date: 2003-02-21 journal: J Mol Biol DOI: 10.1016/s0022-2836(02)01369-4 sha: doc_id: 265381 cord_uid: ppjohov8 file: cache/cord-267036-llngs3v5.json key: cord-267036-llngs3v5 authors: Lai, Ming‐Chih; Peng, Tsui‐Yi; Tarn, Woan‐Yuh title: Functional interplay between viral and cellular SR proteins in control of post‐transcriptional gene regulation date: 2009-02-10 journal: FEBS J DOI: 10.1111/j.1742-4658.2009.06894.x sha: doc_id: 267036 cord_uid: llngs3v5 file: cache/cord-267326-355q6k6k.json key: cord-267326-355q6k6k authors: Gu, Xiaoqiong; Tay, Qi Xiang Martin; Te, Shu Harn; Saeidi, Nazanin; Goh, Shin Giek; Kushmaro, Ariel; Thompson, Janelle R.; Gin, Karina Yew-Hoong title: Geospatial distribution of viromes in tropical freshwater ecosystems date: 2018-06-15 journal: Water Res DOI: 10.1016/j.watres.2018.03.017 sha: doc_id: 267326 cord_uid: 355q6k6k file: cache/cord-265173-70wyecwj.json key: cord-265173-70wyecwj authors: Trujillo-Uscanga, Adrian; Gutiérrez-Escolano, Ana Lorena title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date: 2020-08-27 journal: Virology DOI: 10.1016/j.virol.2020.08.008 sha: doc_id: 265173 cord_uid: 70wyecwj file: cache/cord-267377-wyhsxj6g.json key: cord-267377-wyhsxj6g authors: Edwards, Michael C.; Weiland, John J. title: Coat protein expression strategy of oat blue dwarf virus() date: 2014-01-14 journal: Virology DOI: 10.1016/j.virol.2013.12.018 sha: doc_id: 267377 cord_uid: wyhsxj6g file: cache/cord-267867-q52nvn0n.json key: cord-267867-q52nvn0n authors: Chevalier, Christophe; Saulnier, Aure; Benureau, Yann; Fléchet, Dorian; Delgrange, David; Colbère-Garapin, Florence; Wychowski, Czeslaw; Martin, Annette title: Inhibition of Hepatitis C Virus Infection in Cell Culture by Small Interfering RNAs date: 2016-12-14 journal: Mol Ther DOI: 10.1038/sj.mt.6300186 sha: doc_id: 267867 cord_uid: q52nvn0n file: cache/cord-265508-t1nfyzf5.json key: cord-265508-t1nfyzf5 authors: Boursnell, M.E.G.; Brown, T.D.K. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date: 1984-08-31 journal: Gene DOI: 10.1016/0378-1119(84)90169-0 sha: doc_id: 265508 cord_uid: t1nfyzf5 file: cache/cord-265139-x7g3jcjm.json key: cord-265139-x7g3jcjm authors: Zaiou, Mohamed title: The Emerging Role and Promise of Circular RNAs in Obesity and Related Metabolic Disorders date: 2020-06-16 journal: Cells DOI: 10.3390/cells9061473 sha: doc_id: 265139 cord_uid: x7g3jcjm file: cache/cord-263302-z5uhrta5.json key: cord-263302-z5uhrta5 authors: Zhang, Xuming; Liu, Runzhong title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 journal: Virology DOI: 10.1006/viro.2000.0637 sha: doc_id: 263302 cord_uid: z5uhrta5 file: cache/cord-263357-krvei97r.json key: cord-263357-krvei97r authors: Holmes, Kathryn V.; Dominguez, Samuel R. title: The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia date: 2013-01-08 journal: mBio DOI: 10.1128/mbio.00548-12 sha: doc_id: 263357 cord_uid: krvei97r file: cache/cord-264746-gfn312aa.json key: cord-264746-gfn312aa authors: Muse, Spencer title: GENOMICS AND BIOINFORMATICS date: 2012-03-29 journal: Introduction to Biomedical Engineering DOI: 10.1016/b978-0-12-238662-6.50015-x sha: doc_id: 264746 cord_uid: gfn312aa file: cache/cord-263580-zxnmylkw.json key: cord-263580-zxnmylkw authors: Pyle, Anna Marie title: RNA helicases and remodeling proteins date: 2011-08-20 journal: Curr Opin Chem Biol DOI: 10.1016/j.cbpa.2011.07.019 sha: doc_id: 263580 cord_uid: zxnmylkw file: cache/cord-266127-phv08xe2.json key: cord-266127-phv08xe2 authors: Mukhopadhyay, Urbi; Chanda, Shampa; Patra, Upayan; Mukherjee, Anupam; Komoto, Satoshi; Chawla‐Sarkar, Mamta title: Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date: 2019-08-26 journal: Cell Microbiol DOI: 10.1111/cmi.13101 sha: doc_id: 266127 cord_uid: phv08xe2 file: cache/cord-267533-nmgtan4e.json key: cord-267533-nmgtan4e authors: Hu, Zhigang; Li, Sijia; Yang, Ailan; Li, Wenxin; Xiong, Xiaoqi; Hu, Jianwu; Jiang, Jun; Song, Xinyu title: Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date: 2020-10-29 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04085-2 sha: doc_id: 267533 cord_uid: nmgtan4e file: cache/cord-268071-ow2aijmj.json key: cord-268071-ow2aijmj authors: Pachetti, Maria; Marini, Bruna; Benedetti, Francesca; Giudici, Fabiola; Mauro, Elisabetta; Storici, Paola; Masciovecchio, Claudio; Angeletti, Silvia; Ciccozzi, Massimo; Gallo, Robert C.; Zella, Davide; Ippodrino, Rudy title: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date: 2020-04-22 journal: J Transl Med DOI: 10.1186/s12967-020-02344-6 sha: doc_id: 268071 cord_uid: ow2aijmj file: cache/cord-266634-bww62vx8.json key: cord-266634-bww62vx8 authors: Gopinath, M.; Shaila, M. S. title: Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus date: 2015-10-07 journal: Virus Genes DOI: 10.1007/s11262-015-1252-3 sha: doc_id: 266634 cord_uid: bww62vx8 file: cache/cord-265461-hj2b1wc4.json key: cord-265461-hj2b1wc4 authors: Decroly, Etienne; Canard, Bruno title: Biochemical principles and inhibitors to interfere with viral capping pathways date: 2017-05-18 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2017.04.003 sha: doc_id: 265461 cord_uid: hj2b1wc4 file: cache/cord-267124-8efdzlc0.json key: cord-267124-8efdzlc0 authors: Wichmann, Dominic; Sperhake, Jan-Peter; Lütgehetmann, Marc; Steurer, Stefan; Edler, Carolin; Heinemann, Axel; Heinrich, Fabian; Mushumba, Herbert; Kniep, Inga; Schröder, Ann Sophie; Burdelski, Christoph; de Heer, Geraldine; Nierhaus, Axel; Frings, Daniel; Pfefferle, Susanne; Becker, Heinrich; Bredereke-Wiedling, Hanns; de Weerth, Andreas; Paschen, Hans-Richard; Sheikhzadeh-Eggers, Sara; Stang, Axel; Schmiedel, Stefan; Bokemeyer, Carsten; Addo, Marylyn M.; Aepfelbacher, Martin; Püschel, Klaus; Kluge, Stefan title: Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date: 2020-05-06 journal: Ann Intern Med DOI: 10.7326/m20-2003 sha: doc_id: 267124 cord_uid: 8efdzlc0 file: cache/cord-264488-989t9ld1.json key: cord-264488-989t9ld1 authors: Park, Il-Hyun; Kwon, Young-Chan; Ryu, Wang-Shick; Ahn, Byung-Yoon title: Inhibition of hepatitis B virus replication by ligand-mediated activation of RNase L date: 2014-02-06 journal: Antiviral Res DOI: 10.1016/j.antiviral.2014.01.021 sha: doc_id: 264488 cord_uid: 989t9ld1 file: cache/cord-268337-o6lo55o8.json key: cord-268337-o6lo55o8 authors: Lloyd, Richard E. title: Translational control by viral proteinases date: 2005-11-21 journal: Virus Res DOI: 10.1016/j.virusres.2005.10.016 sha: doc_id: 268337 cord_uid: o6lo55o8 file: cache/cord-265410-khwzdi79.json key: cord-265410-khwzdi79 authors: Bartlett, Stuart; Wong, Michael L. title: Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars date: 2020-04-16 journal: Life (Basel) DOI: 10.3390/life10040042 sha: doc_id: 265410 cord_uid: khwzdi79 file: cache/cord-266985-9qwttt2y.json key: cord-266985-9qwttt2y authors: Gale, P.; Hill, A.; Kelly, L.; Bassett, J.; McClure, P.; Le Marc, Y.; Soumpasis, I. title: Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date: 2014-11-04 journal: J Appl Microbiol DOI: 10.1111/jam.12656 sha: doc_id: 266985 cord_uid: 9qwttt2y file: cache/cord-267475-6f4h3cck.json key: cord-267475-6f4h3cck authors: Kozak, Marilyn title: Pushing the limits of the scanning mechanism for initiation of translation date: 2002-10-16 journal: Gene DOI: 10.1016/s0378-1119(02)01056-9 sha: doc_id: 267475 cord_uid: 6f4h3cck file: cache/cord-269496-tnw7sxlh.json key: cord-269496-tnw7sxlh authors: Sen Gupta, Parth Sarthi; Biswal, Satyaranjan; Panda, Saroj Kumar; Ray, Abhik Kumar; Rana, Malay Kumar title: Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date: 2020-10-28 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1839564 sha: doc_id: 269496 cord_uid: tnw7sxlh file: cache/cord-015394-uj7fe5y6.json key: cord-015394-uj7fe5y6 authors: nan title: Scientific Abstracts date: 2008-12-23 journal: Reprod Sci DOI: 10.1177/19337191080150020102 sha: doc_id: 15394 cord_uid: uj7fe5y6 file: cache/cord-268206-ino9srb6.json key: cord-268206-ino9srb6 authors: Hamed, Manal A. title: An overview on COVID-19: reality and expectation date: 2020-06-01 journal: Bull Natl Res Cent DOI: 10.1186/s42269-020-00341-9 sha: doc_id: 268206 cord_uid: ino9srb6 file: cache/cord-268122-74nj66vb.json key: cord-268122-74nj66vb authors: Xie, Na; Zhang, Lu; Gao, Wei; Huang, Canhua; Huber, Peter Ernst; Zhou, Xiaobo; Li, Changlong; Shen, Guobo; Zou, Bingwen title: NAD(+) metabolism: pathophysiologic mechanisms and therapeutic potential date: 2020-10-07 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00311-7 sha: doc_id: 268122 cord_uid: 74nj66vb file: cache/cord-267532-5rnqd9mb.json key: cord-267532-5rnqd9mb authors: Zhang, Xuming; Hinton, David R.; Park, Sungmin; Parra, Beatriz; Liao, Ching-Len; Lai, Michael M.C.; Stohlman, Stephen A. title: Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date: 1998-03-01 journal: Virology DOI: 10.1006/viro.1997.8993 sha: doc_id: 267532 cord_uid: 5rnqd9mb file: cache/cord-269193-a647hwu9.json key: cord-269193-a647hwu9 authors: Lin, Debby A.; Roychoudhury, Sonali; Palese, Peter; Clay, William C.; Fuller, Frederick J. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 journal: Virology DOI: 10.1016/0042-6822(91)90641-n sha: doc_id: 269193 cord_uid: a647hwu9 file: cache/cord-268763-s16n7f17.json key: cord-268763-s16n7f17 authors: Williams, J. G.; Joshi, R.; Jones, R.; Yunger, T.; Stoneman, E.; Varisco, B. M. title: Identification of Three Endotypes in Pediatric Acute Respiratory Distress Syndrome by Nasal Transcriptomic Profiling date: 2020-05-02 journal: nan DOI: 10.1101/2020.04.28.20083451 sha: doc_id: 268763 cord_uid: s16n7f17 file: cache/cord-268565-2sg1tlrg.json key: cord-268565-2sg1tlrg authors: Clarke, David K.; Cooper, David; Egan, Michael A.; Hendry, R. Michael; Parks, Christopher L.; Udem, Stephen A. title: Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector date: 2006-09-15 journal: Springer Semin Immunopathol DOI: 10.1007/s00281-006-0042-3 sha: doc_id: 268565 cord_uid: 2sg1tlrg file: cache/cord-269726-z0frgm7s.json key: cord-269726-z0frgm7s authors: Gidari, Anna; Nofri, Marco; Saccarelli, Luca; Bastianelli, Sabrina; Sabbatini, Samuele; Bozza, Silvia; Camilloni, Barbara; Fusco-Moffa, Igino; Monari, Claudia; De Robertis, Edoardo; Mencacci, Antonella; Francisci, Daniela title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-04057-6 sha: doc_id: 269726 cord_uid: z0frgm7s file: cache/cord-268718-tt07cwrf.json key: cord-268718-tt07cwrf authors: Tan, Heng Wee; Xu, Yan‐Ming; Lau, Andy T. Y. title: Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date: 2020-06-30 journal: Rev Med Virol DOI: 10.1002/rmv.2122 sha: doc_id: 268718 cord_uid: tt07cwrf file: cache/cord-268139-tgpsu4qz.json key: cord-268139-tgpsu4qz authors: Brockway, Sarah M.; Denison, Mark R. title: Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication date: 2005-09-30 journal: Virology DOI: 10.1016/j.virol.2005.06.035 sha: doc_id: 268139 cord_uid: tgpsu4qz file: cache/cord-269011-230p8rsf.json key: cord-269011-230p8rsf authors: de Haan, Cornelis A.M.; Rottier, Peter J.M. title: Molecular Interactions in the Assembly of Coronaviruses date: 2005-08-31 journal: Adv Virus Res DOI: 10.1016/s0065-3527(05)64006-7 sha: doc_id: 269011 cord_uid: 230p8rsf file: cache/cord-269771-hffxb7bm.json key: cord-269771-hffxb7bm authors: Cheung, Ka Shing; Hung, Ivan FN.; Chan, Pierre PY.; Lung, K. C.; Tso, Eugene; Liu, Raymond; Ng, Y. Y.; Chu, Man Y.; Chung, Tom WH.; Tam, Anthony Raymond; Yip, Cyril CY.; Leung, Kit-Hang; Yim-Fong Fung, Agnes; Zhang, Ricky R.; Lin, Yansheng; Cheng, Ho Ming; Zhang, Anna JX.; To, Kelvin KW.; Chan, Kwok-H.; Yuen, Kwok-Y.; Leung, Wai K. title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date: 2020-04-03 journal: Gastroenterology DOI: 10.1053/j.gastro.2020.03.065 sha: doc_id: 269771 cord_uid: hffxb7bm file: cache/cord-269194-b1wlr3t7.json key: cord-269194-b1wlr3t7 authors: Engstrom-Melnyk, Julia; Rodriguez, Pedro L.; Peraud, Olivier; Hein, Raymond C. title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 journal: Methods in Microbiology DOI: 10.1016/bs.mim.2015.04.005 sha: doc_id: 269194 cord_uid: b1wlr3t7 file: cache/cord-268970-uz7q6z2f.json key: cord-268970-uz7q6z2f authors: Ott, Isabel M.; Strine, Madison S.; Watkins, Anne E.; Boot, Maikel; Kalinich, Chaney C.; Harden, Christina A.; Vogels, Chantal B.F.; Casanovas-Massana, Arnau; Moore, Adam J.; Muenker, M. Catherine; Nakahata, Maura; Tokuyama, Maria; Nelson, Allison; Fournier, John; Bermejo, Santos; Campbell, Melissa; Datta, Rupak; Dela Cruz, Charles S.; Farhadian, Shelli F.; Ko, Albert I.; Iwasaki, Akiko; Grubaugh, Nathan D.; Wilen, Craig B.; Wyllie, Anne L. title: Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date: 2020-08-04 journal: medRxiv DOI: 10.1101/2020.08.03.20165233 sha: doc_id: 268970 cord_uid: uz7q6z2f file: cache/cord-268467-btfz6ye8.json key: cord-268467-btfz6ye8 authors: Schreiber, Steven S.; Kamahora, Toshio; Lai, Michael M.C. title: Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E date: 1989-03-31 journal: Virology DOI: 10.1016/0042-6822(89)90050-0 sha: doc_id: 268467 cord_uid: btfz6ye8 file: cache/cord-269150-d1sgnxc0.json key: cord-269150-d1sgnxc0 authors: Tan, Yong Wah; Hong, Wanjin; Liu, Ding Xiang title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 journal: Nucleic Acids Res DOI: 10.1093/nar/gks165 sha: doc_id: 269150 cord_uid: d1sgnxc0 file: cache/cord-269466-9hnal9ad.json key: cord-269466-9hnal9ad authors: Agbeci, Maxime; Grangeon, Romain; Nelson, Richard S.; Zheng, Huanquan; Laliberté, Jean-François title: Contribution of Host Intracellular Transport Machineries to Intercellular Movement of Turnip Mosaic Virus date: 2013-10-03 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003683 sha: doc_id: 269466 cord_uid: 9hnal9ad file: cache/cord-270550-if748w2n.json key: cord-270550-if748w2n authors: Bailey, Adam L.; Dmytrenko, Oleksandr; Greenberg, Lina; Bredemeyer, Andrea L.; Ma, Pan; Liu, Jing; Penna, Vinay; Lai, Lulu; Winkler, Emma S.; Sviben, Sanja; Brooks, Erin; Nair, Ajith P.; Heck, Kent A.; Rali, Aniket S.; Simpson, Leo; Saririan, Mehrdad; Hobohm, Dan; Stump, W. Tom; Fitzpatrick, James A.; Xie, Xuping; Shi, Pei-Yong; Hinson, J. Travis; Gi, Weng-Tein; Schmidt, Constanze; Leuschner, Florian; Lin, Chieh-Yu; Diamond, Michael S.; Greenberg, Michael J.; Lavine, Kory J. title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.04.364315 sha: doc_id: 270550 cord_uid: if748w2n file: cache/cord-269294-vx7xr80t.json key: cord-269294-vx7xr80t authors: Kwong, Ann D.; Rao, B. Govinda; Jeang, Kuan-Teh title: Viral and cellular RNA helicases as antiviral targets date: 2005-09-23 journal: Nat Rev Drug Discov DOI: 10.1038/nrd1853 sha: doc_id: 269294 cord_uid: vx7xr80t file: cache/cord-270143-muxrxvyo.json key: cord-270143-muxrxvyo authors: Markotter, Wanda; Geldenhuys, Marike; Jansen van Vuren, Petrus; Kemp, Alan; Mortlock, Marinda; Mudakikwa, Antoine; Nel, Louis; Nziza, Julius; Paweska, Janusz; Weyer, Jacqueline title: Paramyxo- and Coronaviruses in Rwandan Bats date: 2019-07-02 journal: Trop Med Infect Dis DOI: 10.3390/tropicalmed4030099 sha: doc_id: 270143 cord_uid: muxrxvyo file: cache/cord-270243-moxleyjg.json key: cord-270243-moxleyjg authors: Cholleti, Harindranath; Hayer, Juliette; Mulandane, Fernando Chanisso; Falk, Kerstin; Fafetine, Jose; Berg, Mikael; Blomström, Anne-Lie title: Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date: 2018-05-28 journal: Infect Ecol Epidemiol DOI: 10.1080/20008686.2018.1478585 sha: doc_id: 270243 cord_uid: moxleyjg file: cache/cord-269766-arjoemla.json key: cord-269766-arjoemla authors: Dutescu, R. Michael; Banasik, Peter; Schildgen, Oliver; Schrage, Norbert; Uthoff, Daniel title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date: 2020-09-08 journal: Cornea DOI: 10.1097/ico.0000000000002562 sha: doc_id: 269766 cord_uid: arjoemla file: cache/cord-271648-m2c5bvuj.json key: cord-271648-m2c5bvuj authors: Ashour, Hossam M.; Elkhatib, Walid F.; Rahman, Md. Masudur; Elshabrawy, Hatem A. title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date: 2020-03-04 journal: Pathogens DOI: 10.3390/pathogens9030186 sha: doc_id: 271648 cord_uid: m2c5bvuj file: cache/cord-270594-62xotol3.json key: cord-270594-62xotol3 authors: He, Lei; Hu, Xiaolong; Zhu, Min; Liang, Zi; Chen, Fei; Zhu, Liyuan; Kuang, Sulan; Cao, Guangli; Xue, Renyu; Gong, Chengliang title: Identification and characterization of vp7 gene in Bombyx mori cytoplasmic polyhedrosis virus date: 2017-09-05 journal: Gene DOI: 10.1016/j.gene.2017.06.048 sha: doc_id: 270594 cord_uid: 62xotol3 file: cache/cord-270940-acwkh6ed.json key: cord-270940-acwkh6ed authors: Kallio-Kokko, Hannimari; Uzcategui, Nathalie; Vapalahti, Olli; Vaheri, Antti title: Viral zoonoses in Europe date: 2005-06-29 journal: FEMS Microbiol Rev DOI: 10.1016/j.femsre.2005.04.012 sha: doc_id: 270940 cord_uid: acwkh6ed file: cache/cord-269720-o81j3d1j.json key: cord-269720-o81j3d1j authors: Page, Kevin W.; Britton, Paul; Boursnell, Michael E. G. title: Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus date: 1990 journal: Virus Genes DOI: 10.1007/bf00570024 sha: doc_id: 269720 cord_uid: o81j3d1j file: cache/cord-270604-u62437dh.json key: cord-270604-u62437dh authors: Cuthill, Jennifer Hoyal; Charleston, Michael A. title: A SIMPLE MODEL EXPLAINS THE DYNAMICS OF PREFERENTIAL HOST SWITCHING AMONG MAMMAL RNA VIRUSES date: 2013-02-19 journal: Evolution DOI: 10.1111/evo.12064 sha: doc_id: 270604 cord_uid: u62437dh file: cache/cord-270670-cubh9jxc.json key: cord-270670-cubh9jxc authors: Domingo, E.; Martín, V.; Perales, C.; Grande-Pérez, A.; García-Arriaza, J.; Arias, A. title: Viruses as Quasispecies: Biological Implications date: 2006 journal: Quasispecies: Concept and Implications for Virology DOI: 10.1007/3-540-26397-7_3 sha: doc_id: 270670 cord_uid: cubh9jxc file: cache/cord-269975-1ebmq7t8.json key: cord-269975-1ebmq7t8 authors: Duplantier, Allen J.; Shurtleff, Amy C.; Miller, Cheryl; Chiang, Chih-Yuan; Panchal, Rekha G.; Sunay, Melek title: Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date: 2020-05-27 journal: Drug Discovery Targeting Drug-Resistant Bacteria DOI: 10.1016/b978-0-12-818480-6.00007-2 sha: doc_id: 269975 cord_uid: 1ebmq7t8 file: cache/cord-270473-5tok4mqk.json key: cord-270473-5tok4mqk authors: Nanda, S. K.; Johnson, R. F.; Liu, Q.; Leibowitz, J. L. title: Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome date: 2003-09-19 journal: Arch Virol DOI: 10.1007/s00705-003-0196-4 sha: doc_id: 270473 cord_uid: 5tok4mqk file: cache/cord-271972-qhr6iir6.json key: cord-271972-qhr6iir6 authors: Gaglia, Marta Maria; Glaunsinger, Britt A. title: Viruses and the cellular RNA decay machinery date: 2010-05-06 journal: Wiley Interdiscip Rev RNA DOI: 10.1002/wrna.3 sha: doc_id: 271972 cord_uid: qhr6iir6 file: cache/cord-272378-umvi0veu.json key: cord-272378-umvi0veu authors: Subramanian, Subbaya; Steer, Clifford J. title: Special Issue: MicroRNA Regulation in Health and Disease date: 2019-06-15 journal: Genes (Basel) DOI: 10.3390/genes10060457 sha: doc_id: 272378 cord_uid: umvi0veu file: cache/cord-271091-ffn59sgf.json key: cord-271091-ffn59sgf authors: Galao, Rui P; Scheller, Nicoletta; Alves-Rodrigues, Isabel; Breinig, Tanja; Meyerhans, Andreas; Díez, Juana title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology date: 2007-10-10 journal: Microb Cell Fact DOI: 10.1186/1475-2859-6-32 sha: doc_id: 271091 cord_uid: ffn59sgf file: cache/cord-271127-l9bxqtqs.json key: cord-271127-l9bxqtqs authors: Renault, Sylvaine; Stasiak, Karine; Federici, Brian; Bigot, Yves title: Commensal and mutualistic relationships of reoviruses with their parasitoid wasp hosts date: 2005-02-28 journal: Journal of Insect Physiology DOI: 10.1016/j.jinsphys.2004.08.002 sha: doc_id: 271127 cord_uid: l9bxqtqs file: cache/cord-269866-3tpyj04y.json key: cord-269866-3tpyj04y authors: Liu, D. X.; Inglis, S. C. title: Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus date: 1992-01-31 journal: Virology DOI: 10.1016/0042-6822(92)90094-6 sha: doc_id: 269866 cord_uid: 3tpyj04y file: cache/cord-271504-t3y1w9ef.json key: cord-271504-t3y1w9ef authors: Luo, Zichao; Ang, Melgious Jin Yan; Chan, Siew Yin; Yi, Zhigao; Goh, Yi Yiing; Yan, Shuangqian; Tao, Jun; Liu, Kai; Li, Xiaosong; Zhang, Hongjie; Huang, Wei; Liu, Xiaogang title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 journal: Research (Wash D C) DOI: 10.34133/2020/6925296 sha: doc_id: 271504 cord_uid: t3y1w9ef file: cache/cord-271526-14nfqusv.json key: cord-271526-14nfqusv authors: Molenkamp, Richard; Spaan, Willy J.M. title: Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal date: 1997-12-08 journal: Virology DOI: 10.1006/viro.1997.8867 sha: doc_id: 271526 cord_uid: 14nfqusv file: cache/cord-272050-0u62j7nj.json key: cord-272050-0u62j7nj authors: Okamoto, Kimiyuki; Nagano, Hideaki; Iwakawa, Hirooki; Mizumoto, Hiroyuki; Takeda, Atsushi; Kaido, Masanori; Mise, Kazuyuki; Okuno, Tetsuro title: cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1 date: 2008-05-25 journal: Virology DOI: 10.1016/j.virol.2008.02.004 sha: doc_id: 272050 cord_uid: 0u62j7nj file: cache/cord-271130-6s79q1c1.json key: cord-271130-6s79q1c1 authors: Filoni, Claudia; Helfer-Hungerbuehler, A. Katrin; Catão-Dias, José Luiz; Marques, Mara Cristina; Torres, Luciana Neves; Reinacher, Manfred; Hofmann-Lehmann, Regina title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date: 2017-11-17 journal: Virol J DOI: 10.1186/s12985-017-0889-z sha: doc_id: 271130 cord_uid: 6s79q1c1 file: cache/cord-271701-tx0lqgff.json key: cord-271701-tx0lqgff authors: te Velthuis, Aartjan J.W.; van den Worm, Sjoerd H. E.; Snijder, Eric J. title: The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date: 2011-10-29 journal: Nucleic Acids Res DOI: 10.1093/nar/gkr893 sha: doc_id: 271701 cord_uid: tx0lqgff file: cache/cord-273487-nfgjz6f9.json key: cord-273487-nfgjz6f9 authors: Xu, Zaikun; Hobman, Tom C. title: The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles date: 2012-11-10 journal: Virology DOI: 10.1016/j.virol.2012.08.011 sha: doc_id: 273487 cord_uid: nfgjz6f9 file: cache/cord-274110-nyyunoha.json key: cord-274110-nyyunoha authors: Orlinger, Klaus K.; Holzer, Georg W.; Schwaiger, Julia; Mayrhofer, Josef; Schmid, Karl; Kistner, Otfried; Noel Barrett, P.; Falkner, Falko G. title: An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system date: 2010-04-26 journal: Vaccine DOI: 10.1016/j.vaccine.2010.02.092 sha: doc_id: 274110 cord_uid: nyyunoha file: cache/cord-271434-30nh2gc7.json key: cord-271434-30nh2gc7 authors: Tian, Fei; Liu, Chao; Deng, Jinqi; Han, Ziwei; Zhang, Lu; Chen, Qinghua; Sun, Jiashu title: A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing date: 2020-07-27 journal: Sci China Chem DOI: 10.1007/s11426-020-9800-6 sha: doc_id: 271434 cord_uid: 30nh2gc7 file: cache/cord-270892-ycc3csyh.json key: cord-270892-ycc3csyh authors: Rollinger, Judith M.; Schmidtke, Michaela title: The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date: 2010-12-13 journal: Med Res Rev DOI: 10.1002/med.20176 sha: doc_id: 270892 cord_uid: ycc3csyh file: cache/cord-271188-ewlxy5po.json key: cord-271188-ewlxy5po authors: Liu, Wei; Zhang, Shuping; Nekhai, Sergei; Liu, Sijin title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 journal: Curr Clin Microbiol Rep DOI: 10.1007/s40588-020-00140-w sha: doc_id: 271188 cord_uid: ewlxy5po file: cache/cord-271781-cfv0ta10.json key: cord-271781-cfv0ta10 authors: Patel, Kishan P.; Vunnam, Srinivas R.; Patel, Puja A.; Krill, Kaleigh L.; Korbitz, Parker M.; Gallagher, John P.; Suh, Jane E.; Vunnam, Rama R. title: Transmission of SARS-CoV-2: an update of current literature date: 2020-07-07 journal: Eur J Clin Microbiol Infect Dis DOI: 10.1007/s10096-020-03961-1 sha: doc_id: 271781 cord_uid: cfv0ta10 file: cache/cord-273326-gmw8gl2r.json key: cord-273326-gmw8gl2r authors: Saiz, Juan-Carlos; de Oya, Nereida Jiménez; Blázquez, Ana-Belén; Escribano-Romero, Estela; Martín-Acebes, Miguel A. title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 journal: Viruses DOI: 10.3390/v10090453 sha: doc_id: 273326 cord_uid: gmw8gl2r file: cache/cord-272871-gu9ptt9y.json key: cord-272871-gu9ptt9y authors: White, K.Andrew; Brancroft, J. B.; Mackie, George A. title: Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products date: 1991-08-31 journal: Virology DOI: 10.1016/0042-6822(91)90977-j sha: doc_id: 272871 cord_uid: gu9ptt9y file: cache/cord-274049-3gw65kpu.json key: cord-274049-3gw65kpu authors: Zhang, Han; McCarty, Nami title: CRISPR Editing in Biological and Biomedical Investigation date: 2017-05-31 journal: J Cell Biochem DOI: 10.1002/jcb.26111 sha: doc_id: 274049 cord_uid: 3gw65kpu file: cache/cord-271241-w1q46y63.json key: cord-271241-w1q46y63 authors: Ruggiero, Emanuela; Richter, Sara N. title: Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy date: 2020-05-18 journal: Annu Rep Med Chem DOI: 10.1016/bs.armc.2020.04.001 sha: doc_id: 271241 cord_uid: w1q46y63 file: cache/cord-274080-884x48on.json key: cord-274080-884x48on authors: Rumlová, Michaela; Ruml, Tomáš title: In vitro methods for testing antiviral drugs date: 2018-06-30 journal: Biotechnology Advances DOI: 10.1016/j.biotechadv.2017.12.016 sha: doc_id: 274080 cord_uid: 884x48on file: cache/cord-272268-8vrcwwll.json key: cord-272268-8vrcwwll authors: Kedersha, Nancy; Anderson, Paul title: Chapter 4 Regulation of Translation by Stress Granules and Processing Bodies date: 2009-10-27 journal: Prog Mol Biol Transl Sci DOI: 10.1016/s1877-1173(09)90004-7 sha: doc_id: 272268 cord_uid: 8vrcwwll file: cache/cord-274353-tzlcpx7q.json key: cord-274353-tzlcpx7q authors: McDermott, Amy title: Inner Workings: Molecular biologists offer “wartime service” in the effort to test for COVID-19 date: 2020-05-05 journal: Proc Natl Acad Sci U S A DOI: 10.1073/pnas.2006240117 sha: doc_id: 274353 cord_uid: tzlcpx7q file: cache/cord-272579-aenuyht0.json key: cord-272579-aenuyht0 authors: Emmett, Stevan R.; Dove, Brian; Mahoney, Laura; Wurm, Torsten; Hiscox, Julian A. title: The Cell Cycle and Virus Infection date: 2005 journal: Cell Cycle Control DOI: 10.1385/1-59259-857-9:197 sha: doc_id: 272579 cord_uid: aenuyht0 file: cache/cord-272573-wxqly479.json key: cord-272573-wxqly479 authors: Maia Chagas, Andre; Molloy, Jennifer C.; Prieto-Godino, Lucia L.; Baden, Tom title: Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date: 2020-04-24 journal: PLoS Biol DOI: 10.1371/journal.pbio.3000730 sha: doc_id: 272573 cord_uid: wxqly479 file: cache/cord-273609-whm2ce4u.json key: cord-273609-whm2ce4u authors: Li, Qingdi Quentin; Skinner, Jeff; Bennett, John E title: Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment date: 2012-06-29 journal: BMC Mol Biol DOI: 10.1186/1471-2199-13-22 sha: doc_id: 273609 cord_uid: whm2ce4u file: cache/cord-275720-kf9m4zho.json key: cord-275720-kf9m4zho authors: Cho, Won Kyong; Yu, Jisuk; Lee, Kyung-Mi; Son, Moonil; Min, Kyunghun; Lee, Yin-Won; Kim, Kook-Hyung title: Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date: 2012-05-06 journal: BMC Genomics DOI: 10.1186/1471-2164-13-173 sha: doc_id: 275720 cord_uid: kf9m4zho file: cache/cord-274536-fv7mltj7.json key: cord-274536-fv7mltj7 authors: Tong, Yongqing; Bao, Anyu; Chen, Hongbing; Huang, Jingtao; Lv, Zhihua; Feng, Lina; Cheng, Yun; Wang, Youna; Bai, Li; Rao, Wenlong; Zheng, Hongyun; Wu, Zegang; Qiao, Bin; Zhao, Zhijun; Wang, Huiming; Li, Yan title: Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date: 2020-11-02 journal: J Transl Med DOI: 10.1186/s12967-020-02580-w sha: doc_id: 274536 cord_uid: fv7mltj7 file: cache/cord-275225-fvq8hezk.json key: cord-275225-fvq8hezk authors: Hornyák, Ákos; Bálint, Ádám; Farsang, Attila; Balka, Gyula; Hakhverdyan, Mikhayil; Rasmussen, Thomas Bruun; Blomberg, Jonas; Belák, Sándor title: Detection of subgenomic mRNA of feline coronavirus by real-time polymerase chain reaction based on primer-probe energy transfer (P-sg-QPCR) date: 2012-02-18 journal: J Virol Methods DOI: 10.1016/j.jviromet.2012.01.022 sha: doc_id: 275225 cord_uid: fvq8hezk file: cache/cord-271419-v6dfel3l.json key: cord-271419-v6dfel3l authors: Adachi, Shun; Koma, Takaaki; Doi, Naoya; Nomaguchi, Masako; Adachi, Akio title: Commentary: Origin and evolution of pathogenic coronaviruses date: 2020-04-21 journal: Front Immunol DOI: 10.3389/fimmu.2020.00811 sha: doc_id: 271419 cord_uid: v6dfel3l file: cache/cord-273019-hbpfz8rt.json key: cord-273019-hbpfz8rt authors: Glingston, R. Sahaya; Deb, Rachayeeta; Kumar, Sachin; Nagotu, Shirisha title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 journal: Microbes Infect DOI: 10.1016/j.micinf.2018.06.002 sha: doc_id: 273019 cord_uid: hbpfz8rt file: cache/cord-276988-bvsz5q6d.json key: cord-276988-bvsz5q6d authors: Neu, Carolin T.; Gutschner, Tony; Haemmerle, Monika title: Post-Transcriptional Expression Control in Platelet Biogenesis and Function date: 2020-10-15 journal: Int J Mol Sci DOI: 10.3390/ijms21207614 sha: doc_id: 276988 cord_uid: bvsz5q6d file: cache/cord-274569-jh0dyyz7.json key: cord-274569-jh0dyyz7 authors: Alenquer, Marta; Amorim, Maria João title: Exosome Biogenesis, Regulation, and Function in Viral Infection date: 2015-09-17 journal: Viruses DOI: 10.3390/v7092862 sha: doc_id: 274569 cord_uid: jh0dyyz7 file: cache/cord-275602-cog4nma0.json key: cord-275602-cog4nma0 authors: Watkins, Kevin title: Emerging Infectious Diseases: a Review date: 2018-06-22 journal: Curr Emerg Hosp Med Rep DOI: 10.1007/s40138-018-0162-9 sha: doc_id: 275602 cord_uid: cog4nma0 file: cache/cord-275683-1qj9ri18.json key: cord-275683-1qj9ri18 authors: Roux, Simon; Matthijnssens, Jelle; Dutilh, Bas E. title: Metagenomics in Virology date: 2019-06-12 journal: Reference Module in Life Sciences DOI: 10.1016/b978-0-12-809633-8.20957-6 sha: doc_id: 275683 cord_uid: 1qj9ri18 file: cache/cord-274401-pjyvg53w.json key: cord-274401-pjyvg53w authors: Hrkach, Jeff; Langer, Robert title: From micro to nano: evolution and impact of drug delivery in treating disease date: 2020-05-08 journal: Drug Deliv Transl Res DOI: 10.1007/s13346-020-00769-6 sha: doc_id: 274401 cord_uid: pjyvg53w file: cache/cord-273379-w8vy5rl8.json key: cord-273379-w8vy5rl8 authors: Mizutani, Tetsuya; Repass, John F.; Makino, Shinji title: Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA date: 2000-09-30 journal: Virology DOI: 10.1006/viro.2000.0489 sha: doc_id: 273379 cord_uid: w8vy5rl8 file: cache/cord-275403-g4rohhtt.json key: cord-275403-g4rohhtt authors: Bautista, Elida M.; Faaberg, Kay S.; Mickelson, Dan; McGruder, Edward D. title: Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus date: 2002-07-05 journal: Virology DOI: 10.1006/viro.2002.1495 sha: doc_id: 275403 cord_uid: g4rohhtt file: cache/cord-010092-uftc8inx.json key: cord-010092-uftc8inx authors: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 journal: Vox Sang DOI: 10.1111/vox.12792 sha: doc_id: 10092 cord_uid: uftc8inx file: cache/cord-272576-ez731lif.json key: cord-272576-ez731lif authors: Wada, Yoshiko; Wada, Kennosuke; Iwasaki, Yuki; Kanaya, Shigehiko; Ikemura, Toshimichi title: Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count date: 2016-11-03 journal: Sci Rep DOI: 10.1038/srep36197 sha: doc_id: 272576 cord_uid: ez731lif file: cache/cord-272666-3uidpr79.json key: cord-272666-3uidpr79 authors: Doyle, Nicole; Neuman, Benjamin W.; Simpson, Jennifer; Hawes, Philippa C.; Mantell, Judith; Verkade, Paul; Alrashedi, Hasan; Maier, Helena J. title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date: 2018-09-06 journal: Viruses DOI: 10.3390/v10090477 sha: doc_id: 272666 cord_uid: 3uidpr79 file: cache/cord-272702-7uc4ozjy.json key: cord-272702-7uc4ozjy authors: Graham, T. G. W.; Dugast-Darzacq, C.; Dailey, G. M.; Nguyenla, X. H.; Van Dis, E.; Esbin, M. N.; Abidi, A.; Stanley, S. A.; Darzacq, X.; Tjian, R. title: Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date: 2020-09-18 journal: nan DOI: 10.1101/2020.09.16.20193466 sha: doc_id: 272702 cord_uid: 7uc4ozjy file: cache/cord-272729-nbgdmavr.json key: cord-272729-nbgdmavr authors: Kim, Youngnam; Lee, Changhee title: Ribavirin efficiently suppresses porcine nidovirus replication date: 2012-10-27 journal: Virus Res DOI: 10.1016/j.virusres.2012.10.018 sha: doc_id: 272729 cord_uid: nbgdmavr file: cache/cord-273711-bxijla09.json key: cord-273711-bxijla09 authors: Zhao, Zhixun; Wu, Guohua; Zhu, Xueliang; Yan, Xinmin; Dou, Yongxi; Li, Jian; Zhu, Haixia; Zhang, Qiang; Cai, Xuepeng title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells date: 2012-02-17 journal: Virol J DOI: 10.1186/1743-422x-9-48 sha: doc_id: 273711 cord_uid: bxijla09 file: cache/cord-273723-srfypn7j.json key: cord-273723-srfypn7j authors: Omar, Sarah; Bartz, Christoph; Becker, Sabine; Basenach, Silke; Pfeifer, Sandra; Trapp, Corinna; Hamm, Hildegard; Schlichting, Hans Christoph; Friederichs, Magdalena; Koch, Ulrich; Jestrabek, Christian; Hilger, Ernst; Vogt, Manfred; Jahn, Klaus; Chen, Simiao; Bärnighausen, Till; Zanger, Philipp title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date: 2020-07-30 journal: Euro Surveill DOI: 10.2807/1560-7917.es.2020.25.30.2001292 sha: doc_id: 273723 cord_uid: srfypn7j file: cache/cord-273910-fna7s9te.json key: cord-273910-fna7s9te authors: Bochud, Pierre-Yves; Bochud, Murielle; Telenti, Amalio; Calandra, Thierry title: Innate immunogenetics: a tool for exploring new frontiers of host defence date: 2007-07-20 journal: Lancet Infect Dis DOI: 10.1016/s1473-3099(07)70185-8 sha: doc_id: 273910 cord_uid: fna7s9te file: cache/cord-274773-3jhka8wl.json key: cord-274773-3jhka8wl authors: Zhang, Jialin; Chen, Jianfei; Liu, Ye; Da, Shi; Shi, Hongyan; Zhang, Xin; Liu, Jianbo; Cao, Liyan; Zhu, Xiangdong; Wang, Xiaobo; Ji, Zhaoyang; Feng, Li title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date: 2019-09-30 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13369 sha: doc_id: 274773 cord_uid: 3jhka8wl file: cache/cord-275252-4e3cn50u.json key: cord-275252-4e3cn50u authors: Rad SM, Ali Hosseini; McLellan, Alexander D. title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date: 2020-05-16 journal: bioRxiv DOI: 10.1101/2020.05.15.098947 sha: doc_id: 275252 cord_uid: 4e3cn50u file: cache/cord-275565-xerr4vki.json key: cord-275565-xerr4vki authors: Kumar, Manish; Kuroda, Keisuke; Patel, Arbind Kumar; Patel, Nidhi; Bhattacharya, Prosun; Joshi, Madhvi; Joshi, Chaitanya G. title: Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date: 2020-09-15 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142329 sha: doc_id: 275565 cord_uid: xerr4vki file: cache/cord-275859-ix8du1er.json key: cord-275859-ix8du1er authors: Mouzakis, Kathryn D.; 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M.; Burge, C. A.; Couch, C. S.; LaBarre, B. A.; Mouchka, M. E.; Naito, M.; Harvell, C. D. title: Description of viral assemblages associated with the Gorgonia ventalina holobiont date: 2011-12-29 journal: Coral Reefs DOI: 10.1007/s00338-011-0864-x sha: doc_id: 279070 cord_uid: cy049zbi file: cache/cord-276575-jfug80yu.json key: cord-276575-jfug80yu authors: Aigner, Achim title: Applications of RNA interference: current state and prospects for siRNA-based strategies in vivo date: 2007-04-25 journal: Appl Microbiol Biotechnol DOI: 10.1007/s00253-007-0984-y sha: doc_id: 276575 cord_uid: jfug80yu file: cache/cord-277566-j3ehiwn9.json key: cord-277566-j3ehiwn9 authors: Verheije, Monique H.; Raaben, Matthijs; Mari, Muriel; te Lintelo, Eddie G.; Reggiori, Fulvio; van Kuppeveld, Frank J. M.; Rottier, Peter J. M.; de Haan, Cornelis A. 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E.; Delatolla, R. title: SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date: 2020-09-03 journal: nan DOI: 10.1101/2020.09.01.20185280 sha: doc_id: 277874 cord_uid: cr53ycrm file: cache/cord-280001-y7pvj2l1.json key: cord-280001-y7pvj2l1 authors: Patel, Robin; Babady, Esther; Theel, Elitza S.; Storch, Gregory A.; Pinsky, Benjamin A.; St. George, Kirsten; Smith, Tara C.; Bertuzzi, Stefano title: Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date: 2020-03-26 journal: mBio DOI: 10.1128/mbio.00722-20 sha: doc_id: 280001 cord_uid: y7pvj2l1 file: cache/cord-022940-atbjwpo5.json key: cord-022940-atbjwpo5 authors: nan title: Poster Sessions date: 2016-09-07 journal: FEBS J DOI: 10.1111/febs.13808 sha: doc_id: 22940 cord_uid: atbjwpo5 file: cache/cord-280130-ewqe9edq.json key: cord-280130-ewqe9edq authors: Weber, Friedemann; Haller, Otto title: Viral suppression of the interferon system date: 2007-01-27 journal: Biochimie DOI: 10.1016/j.biochi.2007.01.005 sha: doc_id: 280130 cord_uid: ewqe9edq file: cache/cord-278635-vwdxr1bl.json key: cord-278635-vwdxr1bl authors: Świętoń, Edyta; Tarasiuk, Karolina; Śmietanka, Krzysztof title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 journal: Vet Res DOI: 10.1186/s13567-020-00833-6 sha: doc_id: 278635 cord_uid: vwdxr1bl file: cache/cord-281124-4nhy35xn.json key: cord-281124-4nhy35xn authors: Soowannayan, Chumporn; Cowley, Jeff A.; Michalski, Wojtek P.; Walker, Peter J. title: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date: 2011-08-03 journal: PLoS One DOI: 10.1371/journal.pone.0022156 sha: doc_id: 281124 cord_uid: 4nhy35xn file: cache/cord-280941-ds6x0yym.json key: cord-280941-ds6x0yym authors: Kim, Young-Seok; Son, Ahyun; Kim, Jihoon; Kwon, Soon Bin; Kim, Myung Hee; Kim, Paul; Kim, Jieun; Byun, Young Ho; Sung, Jemin; Lee, Jinhee; Yu, Ji Eun; Park, Chan; Kim, Yeon-Sook; Cho, Nam-Hyuk; Chang, Jun; Seong, Baik L. title: Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date: 2018-05-17 journal: Front Immunol DOI: 10.3389/fimmu.2018.01093 sha: doc_id: 280941 cord_uid: ds6x0yym file: cache/cord-279623-ezax8c1u.json key: cord-279623-ezax8c1u authors: Huang, Yong; Liu, Ning; Wang, Jian Ping; Wang, Yu Qin; Yu, Xue Li; Wang, Zhan Bin; Cheng, Xiang Chao; Zou, Quan title: Regulatory long non-coding RNA and its functions date: 2012-04-26 journal: J Physiol Biochem DOI: 10.1007/s13105-012-0166-y sha: doc_id: 279623 cord_uid: ezax8c1u file: cache/cord-281174-3c1vue0y.json key: cord-281174-3c1vue0y authors: Greene, Shermalyn R; Moe, Christine L; Jaykus, Lee-Ann; Cronin, Mike; Grosso, Lynell; Aarle, Pierre van title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 journal: J Virol Methods DOI: 10.1016/s0166-0934(02)00286-0 sha: doc_id: 281174 cord_uid: 3c1vue0y file: cache/cord-278186-t3izmz6n.json key: cord-278186-t3izmz6n authors: Le Naour, Julie; Galluzzi, Lorenzo; Zitvogel, Laurence; Kroemer, Guido; Vacchelli, Erika title: Trial watch: TLR3 agonists in cancer therapy date: 2020-06-02 journal: Oncoimmunology DOI: 10.1080/2162402x.2020.1771143 sha: doc_id: 278186 cord_uid: t3izmz6n file: cache/cord-277830-6fsz9iy7.json key: cord-277830-6fsz9iy7 authors: Saikatendu, Kumar Singh; Joseph, Jeremiah S.; Subramanian, Vanitha; Clayton, Tom; Griffith, Mark; Moy, Kin; Velasquez, Jeffrey; Neuman, Benjamin W.; Buchmeier, Michael J.; Stevens, Raymond C.; Kuhn, Peter title: Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date: 2005-11-08 journal: Structure DOI: 10.1016/j.str.2005.07.022 sha: doc_id: 277830 cord_uid: 6fsz9iy7 file: cache/cord-282372-nmii30mc.json key: cord-282372-nmii30mc authors: Youk, Jeonghwan; Kim, Taewoo; Evans, Kelly V.; Jeong, Young-Il; Hur, Yongsuk; Hong, Seon Pyo; Kim, Je Hyoung; Yi, Kijong; Kim, Su Yeon; Na, Kwon Joong; Bleazard, Thomas; Kim, Ho Min; Ivory, Natasha; Mahbubani, Krishnaa T.; Saeb-Parsy, Kourosh; Kim, Young Tae; Koh, Gou Young; Choi, Byeong-Sun; Ju, Young Seok; Lee, Joo-Hyeon title: Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date: 2020-07-10 journal: bioRxiv DOI: 10.1101/2020.07.10.194498 sha: doc_id: 282372 cord_uid: nmii30mc file: cache/cord-278081-tk7vn1v1.json key: cord-278081-tk7vn1v1 authors: Brooks, Wesley H. title: Viral Impact in Autoimmune Diseases: Expanding the “X Chromosome–Nucleolus Nexus” Hypothesis date: 2017-11-28 journal: Front Immunol DOI: 10.3389/fimmu.2017.01657 sha: doc_id: 278081 cord_uid: tk7vn1v1 file: cache/cord-279691-v5kpmk0b.json key: cord-279691-v5kpmk0b authors: Hagemeijer, Marne C.; Rottier, Peter J.M.; de Haan, Cornelis A.M. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 journal: Viruses DOI: 10.3390/v4113245 sha: doc_id: 279691 cord_uid: v5kpmk0b file: cache/cord-279346-7del8d2p.json key: cord-279346-7del8d2p authors: Callendret, Benoît; Lorin, Valérie; Charneau, Pierre; Marianneau, Philippe; Contamin, Hugues; Betton, Jean-Michel; van der Werf, Sylvie; Escriou, Nicolas title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date: 2007-07-05 journal: Virology DOI: 10.1016/j.virol.2007.01.012 sha: doc_id: 279346 cord_uid: 7del8d2p file: cache/cord-278250-dwok857k.json key: cord-278250-dwok857k authors: Li, Heng; Li, Hongzhe; Wang, Jingjing; Guo, Lei; Fan, Haitao; Zheng, Huiwen; Yang, Zening; Huang, Xing; Chu, Manman; Yang, Fengmei; He, Zhanlong; Li, Nan; Yang, Jinxi; Wu, Qiongwen; Shi, Haijing; Liu, Longding title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date: 2019-08-19 journal: Virol J DOI: 10.1186/s12985-019-1211-z sha: doc_id: 278250 cord_uid: dwok857k file: cache/cord-278647-krh63hqp.json key: cord-278647-krh63hqp authors: Carter, Robert W; Sanford, John C title: A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918 date: 2012-10-12 journal: Theor Biol Med Model DOI: 10.1186/1742-4682-9-42 sha: doc_id: 278647 cord_uid: krh63hqp file: cache/cord-280616-9mwr6a4x.json key: cord-280616-9mwr6a4x authors: Yang, Ying; Fang, Sijie title: Small non-coding RNAs-based bone regulation and targeting therapeutic strategies date: 2017-11-15 journal: Mol Cell Endocrinol DOI: 10.1016/j.mce.2016.11.018 sha: doc_id: 280616 cord_uid: 9mwr6a4x file: cache/cord-278055-v2ed3tei.json key: cord-278055-v2ed3tei authors: Sia, Sin Fun; Yan, Li-Meng; Chin, Alex WH; Fung, Kevin; Choy, Ka-Tim; Wong, Alvina YL; Kaewpreedee, Prathanporn; Perera, Ranawaka APM; Poon, Leo LM; Nicholls, John M; Peiris, Malik; Yen, Hui-Ling title: Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date: 2020-05-14 journal: Nature DOI: 10.1038/s41586-020-2342-5 sha: doc_id: 278055 cord_uid: v2ed3tei file: cache/cord-283132-rfw8njpo.json key: cord-283132-rfw8njpo authors: Olsen, Christopher W. title: A review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination date: 1993-07-31 journal: Veterinary Microbiology DOI: 10.1016/0378-1135(93)90126-r sha: doc_id: 283132 cord_uid: rfw8njpo file: cache/cord-280994-w8dtfjel.json key: cord-280994-w8dtfjel authors: Peng, Qi; Peng, Ruchao; Yuan, Bin; Zhao, Jingru; Wang, Min; Wang, Xixi; Wang, Qian; Sun, Yan; Fan, Zheng; Qi, Jianxun; Gao, George F.; Shi, Yi title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date: 2020-04-23 journal: bioRxiv DOI: 10.1101/2020.04.23.057265 sha: doc_id: 280994 cord_uid: w8dtfjel file: cache/cord-286332-cdg4im5h.json key: cord-286332-cdg4im5h authors: van Beurden, Steven J.; Berends, Alinda J.; Krämer-Kühl, Annika; Spekreijse, Dieuwertje; Chénard, Gilles; Philipp, Hans-Christian; Mundt, Egbert; Rottier, Peter J. M.; Verheije, M. Hélène title: A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination date: 2017-06-12 journal: Virol J DOI: 10.1186/s12985-017-0775-8 sha: doc_id: 286332 cord_uid: cdg4im5h file: cache/cord-281385-oxohdfpu.json key: cord-281385-oxohdfpu authors: Noble, Christian G.; Li, Shi-Hua; Dong, Hongping; Chew, Sock Hui; Shi, Pei-Yong title: Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine date: 2014-09-19 journal: Antiviral Res DOI: 10.1016/j.antiviral.2014.09.003 sha: doc_id: 281385 cord_uid: oxohdfpu file: cache/cord-281717-kzd9vvci.json key: cord-281717-kzd9vvci authors: Digard, Paul; Lee, Hui Min; Sharp, Colin; Grey, Finn; Gaunt, Eleanor title: Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date: 2020-05-08 journal: bioRxiv DOI: 10.1101/2020.05.08.083816 sha: doc_id: 281717 cord_uid: kzd9vvci file: cache/cord-282764-d9x1wii6.json key: cord-282764-d9x1wii6 authors: Chang, Chia-Yin; Hong, Willy W.L.; Chong, Pele; Wu, Suh-Chin title: Influence of intron and exon splicing enhancers on mammalian cell expression of a truncated spike protein of SARS-CoV and its implication for subunit vaccine development date: 2006-02-20 journal: Vaccine DOI: 10.1016/j.vaccine.2005.09.011 sha: doc_id: 282764 cord_uid: d9x1wii6 file: cache/cord-280427-smqc23vr.json key: cord-280427-smqc23vr authors: Singla, Rubal; Mishra, Abhishek; Joshi, Rupa; Jha, Sonali; Sharma, Amit Raj; Upadhyay, Sujata; Sarma, Phulen; Prakash, Ajay; Medhi, Bikash title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 journal: Vet Res Commun DOI: 10.1007/s11259-020-09781-0 sha: doc_id: 280427 cord_uid: smqc23vr file: cache/cord-285290-l7mnq4yb.json key: cord-285290-l7mnq4yb authors: Warner, Katherine Deigan; Hajdin, Christine E.; Weeks, Kevin M. title: Principles for targeting RNA with drug-like small molecules date: 2018-07-06 journal: Nature Reviews Drug Discovery DOI: 10.1038/nrd.2018.93 sha: doc_id: 285290 cord_uid: l7mnq4yb file: cache/cord-284549-edliu3it.json key: cord-284549-edliu3it authors: Zhou, Hui; Qian, Qi; Shu, Ting; Xu, Jiuyue; Kong, Jing; Mu, Jingfang; Qiu, Yang; Zhou, Xi title: Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells date: 2019-11-27 journal: Virol Sin DOI: 10.1007/s12250-019-00182-5 sha: doc_id: 284549 cord_uid: edliu3it file: cache/cord-286298-pn9nwl64.json key: cord-286298-pn9nwl64 authors: Helmy, Yosra A.; Fawzy, Mohamed; Elaswad, Ahmed; Sobieh, Ahmed; Kenney, Scott P.; Shehata, Awad A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 journal: J Clin Med DOI: 10.3390/jcm9041225 sha: doc_id: 286298 cord_uid: pn9nwl64 file: cache/cord-281254-x7ivjvti.json key: cord-281254-x7ivjvti authors: Chang, Zhijie; Babiuk, Lorne A.; Hu, Jim title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date: 2012-08-16 journal: BioDrugs DOI: 10.2165/00063030-200721010-00002 sha: doc_id: 281254 cord_uid: x7ivjvti file: cache/cord-281285-5g1rw202.json key: cord-281285-5g1rw202 authors: Simonis, Alexander; Theobald, Sebastian J; Fätkenheuer, Gerd; Rybniker, Jan; Malin, Jakob J title: A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date: 2020-11-03 journal: EMBO Mol Med DOI: 10.15252/emmm.202013105 sha: doc_id: 281285 cord_uid: 5g1rw202 file: cache/cord-284076-087oltss.json key: cord-284076-087oltss authors: Patel, Deendayal; Opriessnig, Tanja; Stein, David A.; Halbur, Patrick G.; Meng, Xiang-Jin; Iversen, Patrick L.; Zhang, Yan-Jin title: Peptide-conjugated morpholino oligomers inhibit porcine reproductive and respiratory syndrome virus replication date: 2007-10-04 journal: Antiviral Res DOI: 10.1016/j.antiviral.2007.09.002 sha: doc_id: 284076 cord_uid: 087oltss file: cache/cord-284941-wfn0pnev.json key: cord-284941-wfn0pnev authors: Samal, S.K. title: Paramyxoviruses of Animals date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00460-x sha: doc_id: 284941 cord_uid: wfn0pnev file: cache/cord-285935-5rsk6g7l.json key: cord-285935-5rsk6g7l authors: Kinast, Volker; Burkard, Thomas L; Todt, Daniel; Steinmann, Eike title: Hepatitis E Virus Drug Development date: 2019-05-28 journal: Viruses DOI: 10.3390/v11060485 sha: doc_id: 285935 cord_uid: 5rsk6g7l file: cache/cord-286149-awhnjwyc.json key: cord-286149-awhnjwyc authors: Hoon‐Hanks, L.L.; McGrath, S.; Tyler, K.L.; Owen, C.; Stenglein, M.D. title: Metagenomic Investigation of Idiopathic Meningoencephalomyelitis in Dogs date: 2017-12-02 journal: J Vet Intern Med DOI: 10.1111/jvim.14877 sha: doc_id: 286149 cord_uid: awhnjwyc file: cache/cord-286232-jo24ia4s.json key: cord-286232-jo24ia4s authors: Hasebe, Rie; Sasaki, Michihito; Sawa, Hirofumi; Wada, Ryuichi; Umemura, Takashi; Kimura, Takashi title: Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways date: 2009-10-25 journal: Virology DOI: 10.1016/j.virol.2009.07.032 sha: doc_id: 286232 cord_uid: jo24ia4s file: cache/cord-286352-uftl1mx5.json key: cord-286352-uftl1mx5 authors: Baril, Martin; Dulude, Dominic; Steinberg, Sergey V; Brakier-Gingras, Léa title: The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot date: 2003-08-15 journal: Journal of Molecular Biology DOI: 10.1016/s0022-2836(03)00784-8 sha: doc_id: 286352 cord_uid: uftl1mx5 file: cache/cord-285159-gytebbua.json key: cord-285159-gytebbua authors: Eydoux, Cecilia; Fattorini, Veronique; Shannon, Ashleigh; Le, Thi-Tuyet-Nhung; Didier, Bruno; Canard, Bruno; Guillemot, Jean-Claude title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date: 2020-07-07 journal: bioRxiv DOI: 10.1101/2020.07.07.192005 sha: doc_id: 285159 cord_uid: gytebbua file: cache/cord-283168-kl1hoa1x.json key: cord-283168-kl1hoa1x authors: Farkas, Tibor; Fey, Brittney; Hargitt, Edwin; Parcells, Mark; Ladman, Brian; Murgia, Maria; Saif, Yehia title: Molecular detection of novel picornaviruses in chickens and turkeys date: 2011-12-13 journal: Virus Genes DOI: 10.1007/s11262-011-0695-4 sha: doc_id: 283168 cord_uid: kl1hoa1x file: cache/cord-283439-hqdq2qrh.json key: cord-283439-hqdq2qrh authors: Rahman, Mohammad Tariqur; Idid, Syed Zahir title: Can Zn Be a Critical Element in COVID-19 Treatment? date: 2020-05-26 journal: Biol Trace Elem Res DOI: 10.1007/s12011-020-02194-9 sha: doc_id: 283439 cord_uid: hqdq2qrh file: cache/cord-287093-9mertwj7.json key: cord-287093-9mertwj7 authors: Netherton, Christopher L; Wileman, Tom title: Virus factories, double membrane vesicles and viroplasm generated in animal cells date: 2011-10-12 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2011.09.008 sha: doc_id: 287093 cord_uid: 9mertwj7 file: cache/cord-283097-rlf5nv5q.json key: cord-283097-rlf5nv5q authors: Ganar, Ketan; Das, Moushumee; Sinha, Sugandha; Kumar, Sachin title: Newcastle disease virus: Current status and our understanding date: 2014-05-12 journal: Virus Research DOI: 10.1016/j.virusres.2014.02.016 sha: doc_id: 283097 cord_uid: rlf5nv5q file: cache/cord-287501-7it4kh0e.json key: cord-287501-7it4kh0e authors: Roh, Changhyun title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date: 2012-05-03 journal: Int J Nanomedicine DOI: 10.2147/ijn.s31379 sha: doc_id: 287501 cord_uid: 7it4kh0e file: cache/cord-283895-1p5uog38.json key: cord-283895-1p5uog38 authors: Trottier, J.; Darques, R.; Ait Mouheb, N.; Partiot, E.; Bakhache, W.; Deffieu, M. S.; Gaudin, R. title: Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date: 2020-07-09 journal: nan DOI: 10.1101/2020.07.08.20148882 sha: doc_id: 283895 cord_uid: 1p5uog38 file: cache/cord-281281-knelqmzx.json key: cord-281281-knelqmzx authors: Villas-Boas, Gustavo R.; Rescia, Vanessa C.; Paes, Marina M.; Lavorato, Stefânia N.; de Magalhães-Filho, Manoel F.; Cunha, Mila S.; Simões, Rafael da C.; de Lacerda, Roseli B.; de Freitas-Júnior, Renilson S.; Ramos, Bruno H. da S.; Mapeli, Ana M.; Henriques, Matheus da S. T.; de Freitas, William R.; Lopes, Luiz A. F.; Oliveira, Luiz G. R.; da Silva, Jonatas G.; Silva-Filho, Saulo E.; da Silveira, Ana P. S.; Leão, Katyuscya V.; Matos, Maria M. de S.; Fernandes, Jamille S.; Cuman, Roberto K. N.; Silva-Comar, Francielli M. de S.; Comar, Jurandir F.; Brasileiro, Luana do A.; dos Santos, Jussileide N.; Oesterreich, Silvia A. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 journal: Molecules DOI: 10.3390/molecules25184086 sha: doc_id: 281281 cord_uid: knelqmzx file: cache/cord-286416-8eu6wp9b.json key: cord-286416-8eu6wp9b authors: Valiente-Echeverría, Fernando; Melnychuk, Luca; Mouland, Andrew J. title: Viral modulation of stress granules date: 2012-06-14 journal: Virus Res DOI: 10.1016/j.virusres.2012.06.004 sha: doc_id: 286416 cord_uid: 8eu6wp9b file: cache/cord-281565-v8s2ski3.json key: cord-281565-v8s2ski3 authors: Belmonte-Reche, Efres; Serrano-Chacón, Israel; Gonzalez, Carlos; Gallo, Juan; Bañobre-López, Manuel title: Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2 date: 2020-08-20 journal: bioRxiv DOI: 10.1101/2020.08.19.257493 sha: doc_id: 281565 cord_uid: v8s2ski3 file: cache/cord-282618-tjvjlyn9.json key: cord-282618-tjvjlyn9 authors: Luke, J M; Vincent, J M; Du, S X; Gerdemann, U; Leen, A M; Whalen, R G; Hodgson, C P; Williams, J A title: Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers date: 2010-11-25 journal: Gene Ther DOI: 10.1038/gt.2010.149 sha: doc_id: 282618 cord_uid: tjvjlyn9 file: cache/cord-287153-jbuuph6w.json key: cord-287153-jbuuph6w authors: Lund, Morten; Røsæg, Magnus Vikan; Krasnov, Aleksei; Timmerhaus, Gerrit; Nyman, Ingvild Berg; Aspehaug, Vidar; Rimstad, Espen; Dahle, Maria Krudtaa title: Experimental Piscine orthoreovirus infection mediates protection against pancreas disease in Atlantic salmon (Salmo salar) date: 2016-10-21 journal: Vet Res DOI: 10.1186/s13567-016-0389-y sha: doc_id: 287153 cord_uid: jbuuph6w file: cache/cord-287228-0qm939ve.json key: cord-287228-0qm939ve authors: Hong, Ke; Cao, Wei; Liu, Zhengyin; Lin, Ling; Zhou, Xing; Zeng, Yan; Wei, Yuan; Chen, Li; Liu, Xiaosheng; Han, Yang; Ruan, Lianguo; Li, Taisheng title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1827983 sha: doc_id: 287228 cord_uid: 0qm939ve file: cache/cord-287396-18p171nr.json key: cord-287396-18p171nr authors: Schroyen, Martine; Tuggle, Christopher K. title: Current transcriptomics in pig immunity research date: 2014-11-15 journal: Mamm Genome DOI: 10.1007/s00335-014-9549-4 sha: doc_id: 287396 cord_uid: 18p171nr file: cache/cord-287275-vwyny1vt.json key: cord-287275-vwyny1vt authors: Zhang, Meng-Jia; Liu, De-Jian; Liu, Xiao-Li; Ge, Xing-Yi; Jongkaewwattana, Anan; He, Qi-Gai; Luo, Rui title: Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China date: 2018-10-30 journal: Arch Virol DOI: 10.1007/s00705-018-4081-6 sha: doc_id: 287275 cord_uid: vwyny1vt file: cache/cord-282742-eyukbot7.json key: cord-282742-eyukbot7 authors: Diosa-Toro, Mayra; Urcuqui-Inchima, Silvio; Smit, Jolanda M. title: Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date: 2013-02-20 journal: Adv Virus Res DOI: 10.1016/b978-0-12-408116-1.00004-5 sha: doc_id: 282742 cord_uid: eyukbot7 file: cache/cord-287324-ecpicv5v.json key: cord-287324-ecpicv5v authors: Qiu, Yuan; Chen, Ji-Ming; Wang, Tong; Hou, Guang-Yu; Zhuang, Qing-Ye; Wu, Run; Wang, Kai-Cheng title: Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods date: 2017-06-02 journal: Virus Res DOI: 10.1016/j.virusres.2017.05.003 sha: doc_id: 287324 cord_uid: ecpicv5v file: cache/cord-287372-ya5uvoki.json key: cord-287372-ya5uvoki authors: Böszörményi, Kinga P.; Stammes, Marieke A.; Fagrouch, Zahra C.; Kiemenyi-Kayere, Gwendoline; Niphuis, Henk; Mortier, Daniella; van Driel, Nikki; Nieuwenhuis, Ivonne; Zuiderwijk-Sick, Ella; Meijer, Lisette; Mooij, Petra; Remarque, Ed J.; Koopman, Gerrit; Hoste, Alexis C. R.; Sastre, Patricia; Haagmans, Bart L.; Bontrop, Ronald E.; Langermans, Jan A.M.; Bogers, Willy M.; Verschoor, Ernst J.; Verstrepen, Babs E. title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date: 2020-11-05 journal: bioRxiv DOI: 10.1101/2020.11.05.369413 sha: doc_id: 287372 cord_uid: ya5uvoki file: cache/cord-287488-h102xn29.json key: cord-287488-h102xn29 authors: Araujo, Danielle Bastos; Machado, Rafael Rahal Guaragna; Amgarten, Deyvid Emanuel; Malta, Fernanda de Mello; de Araujo, Gabriel Guarany; Monteiro, Cairo Oliveira; Candido, Erika Donizetti; Soares, Camila Pereira; de Menezes, Fernando Gatti; Pires, Ana Carolina Cornachioni; Santana, Rúbia Anita Ferraz; Viana, Amanda de Oliveira; Dorlass, Erick; Thomazelli, Luciano; Ferreira, Luis Carlos de Sousa; Botosso, Viviane Fongaro; Carvalho, Cristiane Rodrigues Guzzo; Oliveira, Danielle Bruna Leal; Pinho, João Renato Rebello; Durigon, Edison Luiz title: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date: 2020-10-23 journal: Mem Inst Oswaldo Cruz DOI: 10.1590/0074-02760200342 sha: doc_id: 287488 cord_uid: h102xn29 file: cache/cord-286877-0h5vgi5c.json key: cord-286877-0h5vgi5c authors: Dahiya, Shyam S.; Saini, Mohini; Kumar, Pankaj; Gupta, Praveen K. title: Immunogenicity of a DNA-launched replicon-based canine parvovirus DNA vaccine expressing VP2 antigen in dogs date: 2012-10-31 journal: Research in Veterinary Science DOI: 10.1016/j.rvsc.2012.01.017 sha: doc_id: 286877 cord_uid: 0h5vgi5c file: cache/cord-284609-1q75zw6b.json key: cord-284609-1q75zw6b authors: King, Andrew M.Q.; McCahon, David; Slade, William R.; Newman, John W.I. title: Recombination in RNA date: 1982-07-31 journal: Cell DOI: 10.1016/0092-8674(82)90454-8 sha: doc_id: 284609 cord_uid: 1q75zw6b file: cache/cord-284933-flbibrcm.json key: cord-284933-flbibrcm authors: Kim, Jong-Oh; Kim, Jae-Ok; Kim, Wi-Sik; Oh, Myung-Joo title: Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection date: 2017-01-13 journal: Genes (Basel) DOI: 10.3390/genes8010031 sha: doc_id: 284933 cord_uid: flbibrcm file: cache/cord-287487-qeltdch7.json key: cord-287487-qeltdch7 authors: Graepel, Kevin W.; 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Poon, Leo L.M.; Choi, Su-Jin; Choe, Pyoeng Gyun; Song, Kyoung-Ho; Bang, Ji Hwan; Kim, Eu Suk; Kim, Hong Bin; Park, Sang Won; Kim, Nam Joong; Peiris, Malik; Oh, Myoung-don title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date: 2018-05-09 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2018.05.003 sha: doc_id: 288167 cord_uid: 976qxja2 file: cache/cord-283880-lrrkuist.json key: cord-283880-lrrkuist authors: Kumar, Arvind; Murthy, Satyapramod; Kapoor, Amit title: Evolution of selective-sequencing approaches for virus discovery and virome analysis date: 2017-07-15 journal: Virus Research DOI: 10.1016/j.virusres.2017.06.005 sha: doc_id: 283880 cord_uid: lrrkuist file: cache/cord-288962-jgtoehcr.json key: cord-288962-jgtoehcr authors: Andréoletti, Laurent; Lesay, Manuella; Deschildre, Antoine; Lambert, Valérie; Dewilde, Anny; Wattré, Pierre title: Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date: 2000-06-06 journal: J Med Virol DOI: 10.1002/1096-9071(200007)61:3<341::aid-jmv10>3.0.co;2-0 sha: doc_id: 288962 cord_uid: jgtoehcr file: cache/cord-286243-ddpemgqt.json key: cord-286243-ddpemgqt authors: Whitaker, Amy M.; Freudenthal, Bret D. title: APE1: A skilled nucleic acid surgeon date: 2018-11-30 journal: DNA Repair DOI: 10.1016/j.dnarep.2018.08.012 sha: doc_id: 286243 cord_uid: ddpemgqt file: cache/cord-283998-whwksoxt.json key: cord-283998-whwksoxt authors: Tannock, Gregory A.; Hierholzer, John C. title: The RNA of human coronavirus OC-43 date: 1977-12-31 journal: Virology DOI: 10.1016/0042-6822(77)90126-x sha: doc_id: 283998 cord_uid: whwksoxt file: cache/cord-288093-012ipcdr.json key: cord-288093-012ipcdr authors: Bouvette, Jonathan; Korkut, Dursun Nizam; Fouillen, Aurélien; Amellah, Soumiya; Nanci, Antonio; Durocher, Yves; Omichinski, James G.; Legault, Pascale title: High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date: 2018-12-06 journal: BMC Biotechnol DOI: 10.1186/s12896-018-0485-3 sha: doc_id: 288093 cord_uid: 012ipcdr file: cache/cord-283590-xvnv17zy.json key: cord-283590-xvnv17zy authors: Chen, Dabiao; Xu, Wenxiong; Lei, Ziying; Huang, Zhanlian; Liu, Jing; Gao, Zhiliang; Peng, Liang title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.03.003 sha: doc_id: 283590 cord_uid: xvnv17zy file: cache/cord-285868-fz5utxss.json key: cord-285868-fz5utxss authors: Jheng, Jia-Rong; Ho, Jin-Yuan; Horng, Jim-Tong title: ER stress, autophagy, and RNA viruses date: 2014-08-05 journal: Front Microbiol DOI: 10.3389/fmicb.2014.00388 sha: doc_id: 285868 cord_uid: fz5utxss file: cache/cord-283346-0v4b6do2.json key: cord-283346-0v4b6do2 authors: Ansari, Abdul Wahid; Bhatnagar, Nupur; Dittrich-Breiholz, Oliver; Kracht, Michael; Schmidt, Reinhold E.; Heiken, Hans title: Host chemokine (C-C motif) ligand-2 (CCL2) is differentially regulated in HIV type 1 (HIV-1)-infected individuals date: 2006-08-17 journal: Int Immunol DOI: 10.1093/intimm/dxl078 sha: doc_id: 283346 cord_uid: 0v4b6do2 file: cache/cord-288390-p1q3v1ie.json key: cord-288390-p1q3v1ie authors: Habjan, Matthias; 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Lucente, Maria Stella; Lorusso, Eleonora; Elia, Gabriella; Martella, Vito; Patruno, Giovanni; Buonavoglia, Domenico; Decaro, Nicola title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 journal: J Virol Methods DOI: 10.1016/j.jviromet.2015.12.003 sha: doc_id: 288701 cord_uid: nx9fg4yn file: cache/cord-285262-690kpupt.json key: cord-285262-690kpupt authors: Imre, Gergely title: The involvement of regulated cell death forms in modulating the bacterial and viral pathogenesis date: 2020-01-27 journal: Int Rev Cell Mol Biol DOI: 10.1016/bs.ircmb.2019.12.008 sha: doc_id: 285262 cord_uid: 690kpupt file: cache/cord-289093-si8btsab.json key: cord-289093-si8btsab authors: Beard, Philippa M.; Griffiths, Samantha J.; Gonzalez, Orland; Haga, Ismar R.; Pechenick Jowers, Tali; Reynolds, Danielle K.; Wildenhain, Jan; Tekotte, Hille; Auer, Manfred; Tyers, Mike; Ghazal, Peter; Zimmer, Ralf; Haas, Jürgen title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 journal: PLoS One DOI: 10.1371/journal.pone.0098431 sha: doc_id: 289093 cord_uid: si8btsab file: cache/cord-288651-bgo8istm.json key: cord-288651-bgo8istm authors: SHI, Yi; YANG, De Hua; XIONG, Jie; JIA, Jie; HUANG, Bing; JIN, You Xin title: Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date: 2005-03-17 journal: Cell Res DOI: 10.1038/sj.cr.7290286 sha: doc_id: 288651 cord_uid: bgo8istm file: cache/cord-289192-1ecr16a3.json key: cord-289192-1ecr16a3 authors: Fujita, Motomichi; Adachi, Koji; Nagasawa, Michiaki title: Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA date: 2019-02-01 journal: Anal Biochem DOI: 10.1016/j.ab.2018.10.021 sha: doc_id: 289192 cord_uid: 1ecr16a3 file: cache/cord-288960-v6l6o5va.json key: cord-288960-v6l6o5va authors: Li, Yang; Wilson, Heather L.; Kiss-Toth, Endre title: Regulating STING in health and disease date: 2017-06-07 journal: J Inflamm (Lond) DOI: 10.1186/s12950-017-0159-2 sha: doc_id: 288960 cord_uid: v6l6o5va file: cache/cord-286711-nr6vnl9h.json key: cord-286711-nr6vnl9h authors: nan title: Other viruses causing gastroenteritis date: 2003-12-31 journal: Perspectives in Medical Virology DOI: 10.1016/s0168-7069(03)09037-2 sha: doc_id: 286711 cord_uid: nr6vnl9h file: cache/cord-288879-rj03dsib.json key: cord-288879-rj03dsib authors: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 journal: Mol Neurobiol DOI: 10.1007/s12035-018-1269-4 sha: doc_id: 288879 cord_uid: rj03dsib file: cache/cord-289321-ahl46ql9.json key: cord-289321-ahl46ql9 authors: van Buuren, Nicholas; Tellinghuisen, Timothy L; Richardson, Christopher D; Kirkegaard, Karla title: Transmission genetics of drug-resistant hepatitis C virus date: 2018-03-28 journal: eLife DOI: 10.7554/elife.32579 sha: doc_id: 289321 cord_uid: ahl46ql9 file: cache/cord-284156-btb4oodz.json key: cord-284156-btb4oodz authors: Liu, Yiliu; Olagnier, David; Lin, Rongtuan title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date: 2017-01-03 journal: Front Immunol DOI: 10.3389/fimmu.2016.00662 sha: doc_id: 284156 cord_uid: btb4oodz file: cache/cord-284707-72vx11aq.json key: cord-284707-72vx11aq authors: Leibowitz, Julian L.; Devries, James R. title: Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells date: 1988-09-30 journal: Virology DOI: 10.1016/0042-6822(88)90147-x sha: doc_id: 284707 cord_uid: 72vx11aq file: cache/cord-285505-8norumv6.json key: cord-285505-8norumv6 authors: Vere Hodge, R. Anthony title: Meeting report: 27th International conference on antiviral research, in Raleigh, NC, USA date: 2014-09-16 journal: Antiviral Res DOI: 10.1016/j.antiviral.2014.08.009 sha: doc_id: 285505 cord_uid: 8norumv6 file: cache/cord-289407-8fje16z1.json key: cord-289407-8fje16z1 authors: Moore, G.; Rickard, H.; Stevenson, D.; Aranega Bou, P.; Pitman, J.; Crook, A.; Davies, K.; Spencer, A.; Burton, C.; Easterbrook, L.; Love, H. E.; Summers, S.; Welch, S. R.; Wand, N.; Thompson, K.-A.; Pottage, T.; Richards, K. S.; Dunning, J.; Bennett, A. title: Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date: 2020-09-25 journal: nan DOI: 10.1101/2020.09.24.20191411 sha: doc_id: 289407 cord_uid: 8fje16z1 file: cache/cord-290472-w77cmljm.json key: cord-290472-w77cmljm authors: Sharon, Donald; Chen, Rui; Snyder, Michael title: Systems Biology Approaches to Disease Marker Discovery date: 2010-06-09 journal: Dis Markers DOI: 10.3233/dma-2010-0707 sha: doc_id: 290472 cord_uid: w77cmljm file: cache/cord-290481-i2ppvsh5.json key: cord-290481-i2ppvsh5 authors: Dolja, Valerian V.; Kreuze, Jan F.; Valkonen, Jari P.T. title: Comparative and functional genomics of closteroviruses date: 2006-03-09 journal: Virus Res DOI: 10.1016/j.virusres.2006.02.002 sha: doc_id: 290481 cord_uid: i2ppvsh5 file: cache/cord-285676-4kgy20o9.json key: cord-285676-4kgy20o9 authors: de Vries, Antoine A.F.; Horzinek, Marian C.; Rottier, Peter J.M.; de Groot, Raoul J. title: The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses date: 1997-02-28 journal: Seminars in Virology DOI: 10.1006/smvy.1997.0104 sha: doc_id: 285676 cord_uid: 4kgy20o9 file: cache/cord-286103-cgky6ar6.json key: cord-286103-cgky6ar6 authors: Otaki, Momoko; Sada, Kiyonao; Kadoya, Hiroyasu; Nagano-Fujii, Motoko; Hotta, Hak title: Inhibition of measles virus and subacute sclerosing panencephalitis virus by RNA interference date: 2006-02-13 journal: Antiviral Res DOI: 10.1016/j.antiviral.2006.01.009 sha: doc_id: 286103 cord_uid: cgky6ar6 file: cache/cord-286719-1xjmlwqr.json key: cord-286719-1xjmlwqr authors: Draz, Mohamed Shehata; Shafiee, Hadi title: Applications of gold nanoparticles in virus detection date: 2018-02-15 journal: Theranostics DOI: 10.7150/thno.23856 sha: doc_id: 286719 cord_uid: 1xjmlwqr file: cache/cord-290550-u8x9drva.json key: cord-290550-u8x9drva authors: Radford, Alan D.; Chapman, David; Dixon, Linda; Chantrey, Julian; Darby, Alistair C.; Hall, Neil title: Application of next-generation sequencing technologies in virology date: 2012-09-17 journal: J Gen Virol DOI: 10.1099/vir.0.043182-0 sha: doc_id: 290550 cord_uid: u8x9drva file: cache/cord-291026-99cit4ig.json key: cord-291026-99cit4ig authors: Lung, O.; Pasick, J.; Fisher, M.; Buchanan, C.; Erickson, A.; Ambagala, A. title: Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date: 2015-01-27 journal: Transbound Emerg Dis DOI: 10.1111/tbed.12318 sha: doc_id: 291026 cord_uid: 99cit4ig file: cache/cord-285785-29ohzeug.json key: cord-285785-29ohzeug authors: Chen, Xiaolan; Ali Abdalla, Bahareldin; Li, Zhenhui; Nie, Qinghua title: Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System date: 2020-08-12 journal: Life (Basel) DOI: 10.3390/life10080148 sha: doc_id: 285785 cord_uid: 29ohzeug file: cache/cord-286343-s8n1ldol.json key: cord-286343-s8n1ldol authors: Martin, Javier; Klapsa, Dimitra; Wilton, Thomas; Zambon, Maria; Bentley, Emma; Bujaki, Erika; Fritzsche, Martin; Mate, Ryan; Majumdar, Manasi title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 journal: Viruses DOI: 10.3390/v12101144 sha: doc_id: 286343 cord_uid: s8n1ldol file: cache/cord-290744-m0vpizuh.json key: cord-290744-m0vpizuh authors: Kindler, E.; Thiel, V.; Weber, F. title: Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date: 2016-09-09 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2016.08.006 sha: doc_id: 290744 cord_uid: m0vpizuh file: cache/cord-291029-oldket3n.json key: cord-291029-oldket3n authors: Sefers, Susan E.; Rickmyre, Jamie; Blackman, Amondrea; Li, Haijing; Edwards, Kathryn; Tang, Yi-Wei title: QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date: 2005-07-21 journal: J Clin Virol DOI: 10.1016/j.jcv.2005.05.011 sha: doc_id: 291029 cord_uid: oldket3n file: cache/cord-291765-97lk5qfo.json key: cord-291765-97lk5qfo authors: Eckerle, Lance D.; Brockway, Sarah M.; Sperry, Steven M.; Lu, Xiaotao; Denison, Mark R. title: Effects of Mutagenesis of Murine Hepatitis Virus NSP1 and NSP14 on Replication in Culture date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_8 sha: doc_id: 291765 cord_uid: 97lk5qfo file: cache/cord-291063-de7v4e5s.json key: cord-291063-de7v4e5s authors: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 journal: J Biomed Biotechnol DOI: 10.1155/2009/419539 sha: doc_id: 291063 cord_uid: de7v4e5s file: cache/cord-287658-c2lljdi7.json key: cord-287658-c2lljdi7 authors: Lopez-Rincon, Alejandro; Tonda, Alberto; Mendoza-Maldonado, Lucero; Mulders, Daphne G.J.C.; Molenkamp, Richard; Perez-Romero, Carmina A.; Claassen, Eric; Garssen, Johan; Kraneveld, Aletta D. title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date: 2020-09-10 journal: bioRxiv DOI: 10.1101/2020.03.13.990242 sha: doc_id: 287658 cord_uid: c2lljdi7 file: cache/cord-290801-dv6aak01.json key: cord-290801-dv6aak01 authors: Ivanyi-Nagy, Roland; Darlix, Jean-Luc title: Reprint of: Core protein-mediated 5′–3′ annealing of the West Nile virus genomic RNA in vitro() date: 2012-09-27 journal: Virus Res DOI: 10.1016/j.virusres.2012.09.009 sha: doc_id: 290801 cord_uid: dv6aak01 file: cache/cord-291513-vpehn6nx.json key: cord-291513-vpehn6nx authors: Minich, Jeremiah; Ali, Farhana; Marotz, Clarisse; Belda-Ferre, Pedro; Chiang, Leslie; Shaffer, Justin P.; Carpenter, Carolina S.; McDonald, Daniel; Gilbert, Jack; Allard, Sarah M.; Allen, Eric E; Knight, Rob; Sweeney, Daniel A.; Swafford, Austin D. title: Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date: 2020-08-18 journal: Res Sq DOI: 10.21203/rs.3.rs-56028/v1 sha: doc_id: 291513 cord_uid: vpehn6nx file: cache/cord-291749-revhbd0q.json key: cord-291749-revhbd0q authors: Mongan, Arthur Elia; Tuda, Josef Sem Berth; Runtuwene, Lucky Ronald title: Portable sequencer in the fight against infectious disease date: 2019-10-03 journal: J Hum Genet DOI: 10.1038/s10038-019-0675-4 sha: doc_id: 291749 cord_uid: revhbd0q file: cache/cord-290254-m9l8ntur.json key: cord-290254-m9l8ntur authors: Rodriguez-Manzano, J.; Malpartida-Cardenas, K.; Moser, N.; Pennisi, I.; Cavuto, M.; Miglietta, L.; Moniri, A.; Penn, R.; Satta, G.; Randell, P.; Davies, F.; Bolt, F.; Barclay, W.; Holmes, A.; Georgiou, P. title: A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date: 2020-06-30 journal: nan DOI: 10.1101/2020.06.29.20142349 sha: doc_id: 290254 cord_uid: m9l8ntur file: cache/cord-290813-6ylwj5je.json key: cord-290813-6ylwj5je authors: Ng, Enders K. O.; Lo, Y. M. Dennis title: Molecular Diagnosis of Severe Acute Respiratory Syndrome date: 2006 journal: Clinical Applications of PCR DOI: 10.1385/1-59745-074-x:163 sha: doc_id: 290813 cord_uid: 6ylwj5je file: cache/cord-291677-zcbyhsf1.json key: cord-291677-zcbyhsf1 authors: Wilamowski, M.; Sherrell, D.A.; Minasov, G.; Kim, Y.; Shuvalova, L.; Lavens, A.; Chard, R.; Maltseva, N.; Jedrzejczak, R.; Rosas-Lemus, M.; Saint, N.; Foster, I.T.; Michalska, K.; Satchell, K.J.F.; Joachimiak, A title: Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date: 2020-08-16 journal: bioRxiv DOI: 10.1101/2020.08.14.251421 sha: doc_id: 291677 cord_uid: zcbyhsf1 file: cache/cord-286603-4p3t0vre.json key: cord-286603-4p3t0vre authors: Duan, Zhiqiang; Yuan, Chao; Han, Yifan; Zhou, Lei; Zhao, Jiafu; Ruan, Yong; Chen, Jiaqi; Ni, Mengmeng; Ji, Xinqin title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein date: 2020-06-27 journal: Virulence DOI: 10.1080/21505594.2020.1770482 sha: doc_id: 286603 cord_uid: 4p3t0vre file: cache/cord-291860-dw1sfzqx.json key: cord-291860-dw1sfzqx authors: van Boheemen, Sander; van Rijn, Anneloes L.; Pappas, Nikos; Carbo, Ellen C.; Vorderman, Ruben H.P.; Sidorov, Igor; van `t Hof, Peter J.; Mei, Hailiang; Claas, Eric C.J.; Kroes, Aloys C.M.; de Vries, Jutte J.C. title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 journal: J Mol Diagn DOI: 10.1016/j.jmoldx.2019.10.007 sha: doc_id: 291860 cord_uid: dw1sfzqx file: cache/cord-287018-g4y5kjju.json key: cord-287018-g4y5kjju authors: Konstantinova, P; de Vries, W; Haasnoot, J; ter Brake, O; de Haan, P; Berkhout, B title: Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA date: 2006-05-18 journal: Gene Ther DOI: 10.1038/sj.gt.3302786 sha: doc_id: 287018 cord_uid: g4y5kjju file: cache/cord-287931-cxqzac4a.json key: cord-287931-cxqzac4a authors: Huang, Weiwei; Yang, Yinhui; Zhang, Xinlei; Zhao, Changan; Yin, Aihua; Zhang, Xiaozhuang; He, Zhengxin; Jiang, Yongqiang; Zhang, Liang title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date: 2013-09-20 journal: BMC Infect Dis DOI: 10.1186/1471-2334-13-437 sha: doc_id: 287931 cord_uid: cxqzac4a file: cache/cord-291962-rp172ugk.json key: cord-291962-rp172ugk authors: Jing, Huiyuan; Song, Tao; Cao, Sufang; Sun, Yanting; Wang, Jinhe; Dong, Wang; Zhang, Yan; Ding, Zhen; Wang, Ting; Xing, Zhao; Bao, Wenqi title: Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 date: 2019-07-15 journal: Virus Res DOI: 10.1016/j.virusres.2019.05.011 sha: doc_id: 291962 cord_uid: rp172ugk file: cache/cord-286842-04cuk2cn.json key: cord-286842-04cuk2cn authors: Plyusnina, Angelina; Plyusnin, Alexander title: Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture date: 2005-02-22 journal: Virol J DOI: 10.1186/1743-422x-2-12 sha: doc_id: 286842 cord_uid: 04cuk2cn file: cache/cord-289965-qcezqpze.json key: cord-289965-qcezqpze authors: Lehmann, Kathleen C.; Hooghiemstra, Lisa; Gulyaeva, Anastasia; Samborskiy, Dmitry V.; Zevenhoven-Dobbe, Jessika C.; Snijder, Eric J.; Gorbalenya, Alexander E.; Posthuma, Clara C. title: Arterivirus nsp12 versus the coronavirus nsp16 2′-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins date: 2015-09-01 journal: Journal of General Virology DOI: 10.1099/vir.0.000209 sha: doc_id: 289965 cord_uid: qcezqpze file: cache/cord-293215-6flf5ig0.json key: cord-293215-6flf5ig0 authors: Eriksson, Klara Kristin; Makia, Divine; Thiel, Volker title: Generation of Recombinant Coronaviruses Using Vaccinia Virus as the Cloning Vector and Stable Cell Lines Containing Coronaviral Replicon RNAs date: 2007-11-28 journal: SARS- and Other Coronaviruses DOI: 10.1007/978-1-59745-181-9_18 sha: doc_id: 293215 cord_uid: 6flf5ig0 file: cache/cord-294138-h7sfd1wa.json key: cord-294138-h7sfd1wa authors: McIver, David J.; Silithammavong, Soubanh; Theppangna, Watthana; Gillis, Amethyst; Douangngeun, Bounlom; Khammavong, Kongsy; Singhalath, Sinpakone; Duong, Veasna; Buchy, Philippe; Olson, Sarah H.; Keatts, Lucy; Fine, Amanda E.; Greatorex, Zoe; Gilbert, Martin; LeBreton, Matthew; Saylors, Karen; Joly, Damien O.; Rubin, Edward M.; Lange, Christian E. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 journal: Arch Virol DOI: 10.1007/s00705-020-04683-7 sha: doc_id: 294138 cord_uid: h7sfd1wa file: cache/cord-291727-4wfhuvww.json key: cord-291727-4wfhuvww authors: Ketteler, Robin title: On programmed ribosomal frameshifting: the alternative proteomes date: 2012-11-19 journal: Front Genet DOI: 10.3389/fgene.2012.00242 sha: doc_id: 291727 cord_uid: 4wfhuvww file: cache/cord-291754-1zxztadu.json key: cord-291754-1zxztadu authors: Zhao, Ye; Cheng, Jinlong; Xu, Gang; Thiel, Volker; Zhang, Guozhong title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 journal: Virus Res DOI: 10.1016/j.virusres.2019.197726 sha: doc_id: 291754 cord_uid: 1zxztadu file: cache/cord-287748-co9j3uig.json key: cord-287748-co9j3uig authors: Kobayashi, Tomoya; Murakami, Shin; Yamamoto, Terumasa; Mineshita, Ko; Sakuyama, Muneki; Sasaki, Reiko; Maeda, Ken; Horimoto, Taisuke title: Detection of bat hepatitis E virus RNA in microbats in Japan date: 2018-05-29 journal: Virus Genes DOI: 10.1007/s11262-018-1577-9 sha: doc_id: 287748 cord_uid: co9j3uig file: cache/cord-290948-cuu78cvl.json key: cord-290948-cuu78cvl authors: Imbert, Isabelle; Snijder, Eric J.; Dimitrova, Maria; Guillemot, Jean-Claude; Lécine, Patrick; Canard, Bruno title: The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date: 2008-02-05 journal: Virus Res DOI: 10.1016/j.virusres.2007.11.017 sha: doc_id: 290948 cord_uid: cuu78cvl file: cache/cord-291965-9r9ll83m.json key: cord-291965-9r9ll83m authors: Pfefferle, Susanne; Oppong, Samuel; Drexler, Jan Felix; Gloza-Rausch, Florian; Ipsen, Anne; Seebens, Antje; Müller, Marcel A.; Annan, Augustina; Vallo, Peter; Adu-Sarkodie, Yaw; Kruppa, Thomas F.; Drosten, Christian title: Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date: 2009-09-17 journal: Emerg Infect Dis DOI: 10.3201/eid1509.090224 sha: doc_id: 291965 cord_uid: 9r9ll83m file: cache/cord-292353-z86rjwle.json key: cord-292353-z86rjwle authors: Hussein, Islam T.M.; Haseeb, Abdul; Haque, Absarul; Mir, Mohammad A. title: Recent Advances in Hantavirus Molecular Biology and Disease date: 2011-04-01 journal: Adv Appl Microbiol DOI: 10.1016/b978-0-12-387022-3.00006-9 sha: doc_id: 292353 cord_uid: z86rjwle file: cache/cord-287758-da11ypiy.json key: cord-287758-da11ypiy authors: Mônica Vitalino de Almeida, Sinara; Cleberson Santos Soares, José; Lima dos Santos, Keriolaine; Emanuel Ferreira Alves, Josival; Galdino Ribeiro, Amélia; Trindade Tenório Jacob, Íris; Juliane da Silva Ferreira, Cindy; Celerino dos Santos, Jéssica; Ferreira de Oliveira, Jamerson; Bezerra de Carvalho Junior, Luiz; do Carmo Alves de Lima, Maria title: COVID-19 therapy: what weapons do we bring into battle? date: 2020-09-10 journal: Bioorg Med Chem DOI: 10.1016/j.bmc.2020.115757 sha: doc_id: 287758 cord_uid: da11ypiy file: cache/cord-288669-46tkedw7.json key: cord-288669-46tkedw7 authors: Lee, Changhee; Yoo, Dongwan title: The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties date: 2006-11-10 journal: Virology DOI: 10.1016/j.virol.2006.07.013 sha: doc_id: 288669 cord_uid: 46tkedw7 file: cache/cord-289612-4x5t4c5u.json key: cord-289612-4x5t4c5u authors: Alsuliman, Tamim; Sulaiman, Rand; Ismail, Sawsan; Srour, Micha; Alrstom, Ali title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 journal: Curr Res Transl Med DOI: 10.1016/j.retram.2020.06.001 sha: doc_id: 289612 cord_uid: 4x5t4c5u file: cache/cord-290218-dvyeg5fk.json key: cord-290218-dvyeg5fk authors: Jiang, Yi; Yin, Wanchao; Xu, H. Eric title: RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date: 2020-09-04 journal: Biochem Biophys Res Commun DOI: 10.1016/j.bbrc.2020.08.116 sha: doc_id: 290218 cord_uid: dvyeg5fk file: cache/cord-292045-pnid9dmq.json key: cord-292045-pnid9dmq authors: Kumar, Manish; Patel, Arbind Kumar; Shah, Anil V.; Raval, Janvi; Rajpara, Neha; Joshi, Madhvi; Joshi, Chaitanya G. title: First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date: 2020-07-28 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.141326 sha: doc_id: 292045 cord_uid: pnid9dmq file: cache/cord-293038-pjjvfdnq.json key: cord-293038-pjjvfdnq authors: Fontana, Juan; López‐Montero, Noelia; Elliott, Richard M.; Fernández, José Jesús; Risco, Cristina title: The unique architecture of Bunyamwera virus factories around the Golgi complex date: 2008-06-10 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2008.01184.x sha: doc_id: 293038 cord_uid: pjjvfdnq file: cache/cord-293375-qcy56ui7.json key: cord-293375-qcy56ui7 authors: Strauss, Ellen G.; De Groot, Raoul J.; Levinson, Randy; Strauss, James H. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 journal: Virology DOI: 10.1016/0042-6822(92)90268-t sha: doc_id: 293375 cord_uid: qcy56ui7 file: cache/cord-293747-ds8rhbkv.json key: cord-293747-ds8rhbkv authors: Lani, Rafidah; Hassandarvish, Pouya; Chiam, Chun Wei; Moghaddam, Ehsan; Chu, Justin Jang Hann; Rausalu, Kai; Merits, Andres; Higgs, Stephen; Vanlandingham, Dana; Abu Bakar, Sazaly; Zandi, Keivan title: Antiviral activity of silymarin against chikungunya virus date: 2015-06-16 journal: Sci Rep DOI: 10.1038/srep11421 sha: doc_id: 293747 cord_uid: ds8rhbkv file: cache/cord-293988-f5gvwjyh.json key: cord-293988-f5gvwjyh authors: Musso, Nicolò; Costantino, Angelita; La Spina, Sebastiano; Finocchiaro, Alessandra; Andronico, Francesca; Stracquadanio, Stefano; Liotta, Luigi; Visalli, Rosanna; Emmanuele, Giovanni title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date: 2020-09-11 journal: Pathogens DOI: 10.3390/pathogens9090746 sha: doc_id: 293988 cord_uid: f5gvwjyh file: cache/cord-294056-7e477y1x.json key: cord-294056-7e477y1x authors: La Monica, Nicola; Yokomori, Kyoko; Lai, Michael M.C. title: Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences date: 1992-05-31 journal: Virology DOI: 10.1016/0042-6822(92)90774-j sha: doc_id: 294056 cord_uid: 7e477y1x file: cache/cord-295733-f3rt1fyk.json key: cord-295733-f3rt1fyk authors: Ge, Tianxiang; Lu, Ye; Zheng, Shufa; Zhuo, Lixin; Yu, Ling; Ni, Zuowei; Zhou, Yanan; Ni, Lingmei; Qu, Tingting; Zhong, Zifeng title: Evaluation of disinfection procedures in a designated hospital for COVID-19 date: 2020-08-22 journal: Am J Infect Control DOI: 10.1016/j.ajic.2020.08.028 sha: doc_id: 295733 cord_uid: f3rt1fyk file: cache/cord-296309-i1mpov7k.json key: cord-296309-i1mpov7k authors: Houldcroft, Charlotte J.; Beale, Mathew A.; Breuer, Judith title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro.2016.182 sha: doc_id: 296309 cord_uid: i1mpov7k file: cache/cord-296847-r752bcsu.json key: cord-296847-r752bcsu authors: Campanini, Giulia; Percivalle, Elena; Baldanti, Fausto; Rovida, Francesca; Bertaina, Alice; Marchi, Antonietta; Stronati, Mauro; Gerna, Giuseppe title: Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants date: 2007-04-23 journal: J Clin Virol DOI: 10.1016/j.jcv.2007.03.009 sha: doc_id: 296847 cord_uid: r752bcsu file: cache/cord-294800-akr4f5p8.json key: cord-294800-akr4f5p8 authors: Kabir, Md. Tanvir; Uddin, Md. Sahab; Hossain, Md. Farhad; Abdulhakim, Jawaher A.; Alam, Md. Asraful; Ashraf, Ghulam Md; Bungau, Simona G.; Bin-Jumah, May N.; Abdel-Daim, Mohamed M.; Aleya, Lotfi title: nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date: 2020-07-10 journal: Front Cell Dev Biol DOI: 10.3389/fcell.2020.00616 sha: doc_id: 294800 cord_uid: akr4f5p8 file: cache/cord-293646-d4qcckh1.json key: cord-293646-d4qcckh1 authors: Meanwell, Nicholas A.; Serrano-Wu, Michael H.; Snyder, Lawrence B. title: Chapter 22. Non-HIV antiviral agents date: 2003-12-31 journal: Annual Reports in Medicinal Chemistry DOI: 10.1016/s0065-7743(03)38023-6 sha: doc_id: 293646 cord_uid: d4qcckh1 file: cache/cord-293481-bmfj50fb.json key: cord-293481-bmfj50fb authors: Malin, Jakob J.; Suárez, Isabelle; Priesner, Vanessa; Fätkenheuer, Gerd; Rybniker, Jan title: Remdesivir against COVID-19 and Other Viral Diseases date: 2020-10-14 journal: Clin Microbiol Rev DOI: 10.1128/cmr.00162-20 sha: doc_id: 293481 cord_uid: bmfj50fb file: cache/cord-293766-vpfda3pd.json key: cord-293766-vpfda3pd authors: Ji, Jingjing; Zhang, Jinxia; Shao, Ziyun; Xie, Qifeng; Zhong, Li; Liu, Zhifeng title: Glucocorticoid therapy does not delay viral clearance in COVID-19 patients date: 2020-09-21 journal: Crit Care DOI: 10.1186/s13054-020-03287-6 sha: doc_id: 293766 cord_uid: vpfda3pd file: cache/cord-294890-93ldjyi5.json key: cord-294890-93ldjyi5 authors: Chen, Yan; Li, Xue; Su, Liyao; Chen, Xu; Zhang, Shuting; Xu, Xiaoping; Zhang, Zihao; Chen, Yukun; XuHan, Xu; Lin, Yuling; Lai, Zhongxiong title: Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour date: 2018-11-06 journal: BMC Genomics DOI: 10.1186/s12864-018-5158-z sha: doc_id: 294890 cord_uid: 93ldjyi5 file: cache/cord-292673-00s3wgem.json key: cord-292673-00s3wgem authors: Buonaguro, Luigi; Tagliamonte, Maria; Tornesello, Maria Lina; Buonaguro, Franco M. title: SARS-CoV-2 RNA polymerase as target for antiviral therapy date: 2020-05-05 journal: J Transl Med DOI: 10.1186/s12967-020-02355-3 sha: doc_id: 292673 cord_uid: 00s3wgem file: cache/cord-294483-mozabpcs.json key: cord-294483-mozabpcs authors: Choudhary, Manohar Lal; Vipat, Veena; Jadhav, Sheetal; Basu, Atanu; Cherian, Sarah; Abraham, Priya; Potdar, Varsha A. title: Development of in vitro transcribed RNA as positive control for laboratory diagnosis of SARS-CoV-2 in India date: 2020-04-28 journal: Indian J Med Res DOI: 10.4103/ijmr.ijmr_671_20 sha: doc_id: 294483 cord_uid: mozabpcs file: cache/cord-293852-r72c6584.json key: cord-293852-r72c6584 authors: Greco, S.; Madè, A.; Gaetano, C.; Devaux, Y.; Emanueli, C.; Martelli, F. title: Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date: 2020-10-31 journal: J Transl Med DOI: 10.1186/s12967-020-02582-8 sha: doc_id: 293852 cord_uid: r72c6584 file: cache/cord-289926-y1rjgbui.json key: cord-289926-y1rjgbui authors: Veretnik, S.; Gribskov, M. title: RNA binding domain of HDV antigen is homologous to the HMG box of SRY date: 2014-05-18 journal: Arch Virol DOI: 10.1007/s007050050575 sha: doc_id: 289926 cord_uid: y1rjgbui file: cache/cord-292643-n6xp5mlz.json key: cord-292643-n6xp5mlz authors: Hall, Richard J.; Wang, Jing; Todd, Angela K.; Bissielo, Ange B.; Yen, Seiha; Strydom, Hugo; Moore, Nicole E.; Ren, Xiaoyun; Huang, Q. Sue; Carter, Philip E.; Peacey, Matthew title: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date: 2013-09-13 journal: J Virol Methods DOI: 10.1016/j.jviromet.2013.08.035 sha: doc_id: 292643 cord_uid: n6xp5mlz file: cache/cord-289248-6mx4o0eb.json key: cord-289248-6mx4o0eb authors: Wang, Yilong; Liu, Rongxian; Lu, Mijia; Yang, Yingzhi; Zhou, Duo; Hao, Xiaoqiang; Zhou, Dongming; Wang, Bin; Li, Jianrong; Huang, Yao-Wei; Zhao, Zhengyan title: Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date: 2018-05-01 journal: Virology DOI: 10.1016/j.virol.2018.02.022 sha: doc_id: 289248 cord_uid: 6mx4o0eb file: cache/cord-291916-5yqc3zcx.json key: cord-291916-5yqc3zcx authors: Hozhabri, Hossein; Piceci Sparascio, Francesca; Sohrabi, Hamidreza; Mousavifar, Leila; Roy, René; Scribano, Daniela; De Luca, Alessandro; Ambrosi, Cecilia; Sarshar, Meysam title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 journal: Int J Environ Res Public Health DOI: 10.3390/ijerph17165648 sha: doc_id: 291916 cord_uid: 5yqc3zcx file: cache/cord-297078-pxggjaby.json key: cord-297078-pxggjaby authors: Poole, Anthony M.; Logan, Derek T. title: Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome? date: 2005-03-16 journal: Mol Biol Evol DOI: 10.1093/molbev/msi132 sha: doc_id: 297078 cord_uid: pxggjaby file: cache/cord-291590-24psoaer.json key: cord-291590-24psoaer authors: Ogando, Natacha S.; Zevenhoven-Dobbe, Jessika C.; Posthuma, Clara C.; Snijder, Eric J. title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date: 2020-06-20 journal: bioRxiv DOI: 10.1101/2020.06.19.162529 sha: doc_id: 291590 cord_uid: 24psoaer file: cache/cord-293355-0v71xwqy.json key: cord-293355-0v71xwqy authors: Aguiar, Eric Roberto Guimarães Rocha; Olmo, Roenick Proveti; Marques, João Trindade title: Virus‐derived small RNAs: molecular footprints of host–pathogen interactions date: 2016-05-12 journal: Wiley Interdiscip Rev RNA DOI: 10.1002/wrna.1361 sha: doc_id: 293355 cord_uid: 0v71xwqy file: cache/cord-297323-l3f12hg4.json key: cord-297323-l3f12hg4 authors: Amor, Sandra; Fernández Blanco, Laura; Baker, David title: Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date: 2020-09-26 journal: Clin Exp Immunol DOI: 10.1111/cei.13523 sha: doc_id: 297323 cord_uid: l3f12hg4 file: cache/cord-298847-szezd2vb.json key: cord-298847-szezd2vb authors: Jacomy, Hélène; Talbot, Pierre J title: Vacuolating encephalitis in mice infected by human coronavirus OC43 date: 2003-10-10 journal: Virology DOI: 10.1016/s0042-6822(03)00323-4 sha: doc_id: 298847 cord_uid: szezd2vb file: cache/cord-290802-761wqgbe.json key: cord-290802-761wqgbe authors: Zhao, Zheng; Bourne, Philip E. title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date: 2020-09-18 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00623 sha: doc_id: 290802 cord_uid: 761wqgbe file: cache/cord-289535-srrfr1es.json key: cord-289535-srrfr1es authors: Tregoning, J. S.; Brown, E. S.; Cheeseman, H. M.; Flight, K. E.; Higham, S. L.; Lemm, N.‐M.; Pierce, B. F.; Stirling, D. C.; Wang, Z.; Pollock, K. M. title: Vaccines for COVID‐19 date: 2020-10-18 journal: Clin Exp Immunol DOI: 10.1111/cei.13517 sha: doc_id: 289535 cord_uid: srrfr1es file: cache/cord-292831-oihcay6w.json key: cord-292831-oihcay6w authors: Choudhary, Manohar L.; Anand, Siddharth P.; Heydari, Mostafa; Rane, Grishma; Potdar, Varsha A.; Chadha, Mandeep S.; Mishra, Akhilesh C. title: Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR date: 2013-01-08 journal: J Virol Methods DOI: 10.1016/j.jviromet.2012.12.017 sha: doc_id: 292831 cord_uid: oihcay6w file: cache/cord-294363-bv6xa8v8.json key: cord-294363-bv6xa8v8 authors: Zhou, Hong; Fang, Yan; Xu, Tao; Ni, Wei‐Jian; Shen, Ai‐Zong; Meng, Xiao‐Ming title: Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date: 2020-05-05 journal: Br J Pharmacol DOI: 10.1111/bph.15092 sha: doc_id: 294363 cord_uid: bv6xa8v8 file: cache/cord-293913-frkb8iso.json key: cord-293913-frkb8iso authors: Gao, Hong-Qiang; Schiller, Jennifer J.; Baker, Susan C. title: Identification of the polymerase polyprotein products p72 and p65 of the murine coronavirus MHV-JHM date: 1996-12-31 journal: Virus Research DOI: 10.1016/s0168-1702(96)01368-8 sha: doc_id: 293913 cord_uid: frkb8iso file: cache/cord-294764-v28wbrqp.json key: cord-294764-v28wbrqp authors: Deval, Jerome; Jin, Zhinan; Chuang, Ying-Chih; Kao, C. Cheng title: Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses date: 2017-04-15 journal: Virus Res DOI: 10.1016/j.virusres.2016.12.018 sha: doc_id: 294764 cord_uid: v28wbrqp file: cache/cord-298032-3zlu8g8y.json key: cord-298032-3zlu8g8y authors: Nan, Yuchen; Zhang, Yan-Jin title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 journal: Front Microbiol DOI: 10.3389/fmicb.2018.00750 sha: doc_id: 298032 cord_uid: 3zlu8g8y file: cache/cord-298036-2zurc60t.json key: cord-298036-2zurc60t authors: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 journal: Cell Signal DOI: 10.1016/j.cellsig.2020.109772 sha: doc_id: 298036 cord_uid: 2zurc60t file: cache/cord-293163-udcw1mx5.json key: cord-293163-udcw1mx5 authors: Lu, Patrick Y.; Xie, Frank Y.; Woodle, Martin C. title: Modulation of angiogenesis with siRNA inhibitors for novel therapeutics date: 2005-02-04 journal: Trends Mol Med DOI: 10.1016/j.molmed.2005.01.005 sha: doc_id: 293163 cord_uid: udcw1mx5 file: cache/cord-293417-oqusfhei.json key: cord-293417-oqusfhei authors: Ma, Yanlin; Tong, Xiaohang; Xu, Xiaoling; Li, Xuemei; Lou, Zhiyong; Rao, Zihe title: Structures of the N- and C-terminal domains of MHV-A59 nucleocapsid protein corroborate a conserved RNA-protein binding mechanism in coronavirus date: 2010-07-01 journal: Protein & Cell DOI: 10.1007/s13238-010-0079-x sha: doc_id: 293417 cord_uid: oqusfhei file: cache/cord-295351-0zr2e8lh.json key: cord-295351-0zr2e8lh authors: Mohd Ropidi, Muhammad Izzuddin; Khazali, Ahmad Suhail; Nor Rashid, Nurshamimi; Yusof, Rohana title: Endoplasmic reticulum: a focal point of Zika virus infection date: 2020-01-20 journal: J Biomed Sci DOI: 10.1186/s12929-020-0618-6 sha: doc_id: 295351 cord_uid: 0zr2e8lh file: cache/cord-297974-sduz0j35.json key: cord-297974-sduz0j35 authors: Bokelmann, L.; Nickel, O.; Maricic, T.; Paabo, S.; Meyer, M.; Borte, S.; Riesenberg, S. title: Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date: 2020-08-06 journal: nan DOI: 10.1101/2020.08.04.20168617 sha: doc_id: 297974 cord_uid: sduz0j35 file: cache/cord-299509-7xjdryoq.json key: cord-299509-7xjdryoq authors: Scholte, Florine E. M.; Tas, Ali; Martina, Byron E. E.; Cordioli, Paolo; Narayanan, Krishna; Makino, Shinji; Snijder, Eric J.; van Hemert, Martijn J. title: Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates date: 2013-08-01 journal: PLoS One DOI: 10.1371/journal.pone.0071047 sha: doc_id: 299509 cord_uid: 7xjdryoq file: cache/cord-293790-7hyelm88.json key: cord-293790-7hyelm88 authors: Guévin, Carl; Manna, David; Bélanger, Claudia; Konan, Kouacou V.; Mak, Paul; Labonté, Patrick title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection date: 2010-09-01 journal: Virology DOI: 10.1016/j.virol.2010.05.032 sha: doc_id: 293790 cord_uid: 7hyelm88 file: cache/cord-297834-me1ajoyb.json key: cord-297834-me1ajoyb authors: Schountz, Tony; Prescott, Joseph title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 journal: Viruses DOI: 10.3390/v6031317 sha: doc_id: 297834 cord_uid: me1ajoyb file: cache/cord-294108-uvnh0s9r.json key: cord-294108-uvnh0s9r authors: Dube, Taru; Ghosh, Amrito; Mishra, Jibanananda; Kompella, Uday B.; Panda, Jiban Jyoti title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 journal: Adv Ther (Weinh) DOI: 10.1002/adtp.202000172 sha: doc_id: 294108 cord_uid: uvnh0s9r file: cache/cord-294842-aesiff1f.json key: cord-294842-aesiff1f authors: Romero-Brey, Inés; Bartenschlager, Ralf title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 journal: Viruses DOI: 10.3390/v6072826 sha: doc_id: 294842 cord_uid: aesiff1f file: cache/cord-291225-75ys908n.json key: cord-291225-75ys908n authors: Martins, Nelson; Lemoine, Aurélie; Santiago, Estelle; Paro, Simona; Imler, Jean-Luc; Meignin, Carine title: A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells date: 2018-12-12 journal: G3 (Bethesda) DOI: 10.1534/g3.118.200872 sha: doc_id: 291225 cord_uid: 75ys908n file: cache/cord-293651-96cmduez.json key: cord-293651-96cmduez authors: Callison, Scott A.; Hilt, Deborah A.; Boynton, Tye O.; Sample, Brenda F.; Robison, Robert; Swayne, David E.; Jackwood, Mark W. title: Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens date: 2006-08-28 journal: J Virol Methods DOI: 10.1016/j.jviromet.2006.07.018 sha: doc_id: 293651 cord_uid: 96cmduez file: cache/cord-299943-wzkh04dv.json key: cord-299943-wzkh04dv authors: Santhanam, Manikandan; Algov, Itay; Alfonta, Lital title: DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment date: 2020-08-18 journal: Sensors (Basel) DOI: 10.3390/s20164648 sha: doc_id: 299943 cord_uid: wzkh04dv file: cache/cord-294718-n3gx862b.json key: cord-294718-n3gx862b authors: Tam, Patrick C K; Ly, Kathleen M; Kernich, Max L; Spurrier, Nicola; Lawrence, Diana; Gordon, David L; Tucker, Emily C title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa673 sha: doc_id: 294718 cord_uid: n3gx862b file: cache/cord-300884-rqfxe0x1.json key: cord-300884-rqfxe0x1 authors: Zhang, Jianqiang; Guy, James S.; Snijder, Eric J.; Denniston, Doug A.; Timoney, Peter J.; Balasuriya, Udeni B.R. title: Genomic characterization of equine coronavirus date: 2007-12-05 journal: Virology DOI: 10.1016/j.virol.2007.06.035 sha: doc_id: 300884 cord_uid: rqfxe0x1 file: cache/cord-299754-tgexahwd.json key: cord-299754-tgexahwd authors: van Tol, Sarah; Hage, Adam; Giraldo, Maria Isabel; Bharaj, Preeti; Rajsbaum, Ricardo title: The TRIMendous Role of TRIMs in Virus–Host Interactions date: 2017-08-22 journal: Vaccines (Basel) DOI: 10.3390/vaccines5030023 sha: doc_id: 299754 cord_uid: tgexahwd file: cache/cord-295217-z2erqkr9.json key: cord-295217-z2erqkr9 authors: Seow, Justine Jia Wen; Wong, Regina Men Men; Pai, Rhea; Sharma, Ankur title: Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art date: 2020-06-02 journal: J Indian Inst Sci DOI: 10.1007/s41745-020-00178-1 sha: doc_id: 295217 cord_uid: z2erqkr9 file: cache/cord-297790-tpjxt0w5.json key: cord-297790-tpjxt0w5 authors: Mandl, Judith N.; Schneider, Caitlin; Schneider, David S.; Baker, Michelle L. title: Going to Bat(s) for Studies of Disease Tolerance date: 2018-09-20 journal: Front Immunol DOI: 10.3389/fimmu.2018.02112 sha: doc_id: 297790 cord_uid: tpjxt0w5 file: cache/cord-292751-tk1oggi9.json key: cord-292751-tk1oggi9 authors: Hosseini, Elahe Seyed; Kashani, Narjes Riahi; Nikzad, Hossein; Azadbakht, Javid; Bafrani, Hassan Hassani; Kashani, Hamed Haddad title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date: 2020-09-24 journal: Virology DOI: 10.1016/j.virol.2020.08.011 sha: doc_id: 292751 cord_uid: tk1oggi9 file: cache/cord-295019-8tf8ah6g.json key: cord-295019-8tf8ah6g authors: Weber, Wilfried; Fussenegger, Martin title: Emerging biomedical applications of synthetic biology date: 2011-11-29 journal: Nat Rev Genet DOI: 10.1038/nrg3094 sha: doc_id: 295019 cord_uid: 8tf8ah6g file: cache/cord-292112-dejrksum.json key: cord-292112-dejrksum authors: Wang, Jinglu; 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Wong, On Kei; Luk, Winsie; Yuen, Kwok Yung; Peiris, Joseph S M; Guan, Yi title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 journal: Clin Chem DOI: 10.1373/49.6.953 sha: doc_id: 300685 cord_uid: bcjnujlj file: cache/cord-297092-oq14cwka.json key: cord-297092-oq14cwka authors: Tan, Shaoyuan; Dvorak, Cheryl M. T.; Murtaugh, Michael P. title: Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model date: 2020-10-07 journal: Viruses DOI: 10.3390/v12101136 sha: doc_id: 297092 cord_uid: oq14cwka file: cache/cord-293525-c7nwygl1.json key: cord-293525-c7nwygl1 authors: Saldanha, I. F.; Lawson, B.; Goharriz, H.; Rodriguez-Ramos Fernandez, J.; John, S. K.; Fooks, A. R.; Cunningham, A. A.; Johnson, N.; Horton, D. L. title: Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date: 2019-04-03 journal: Epidemiol Infect DOI: 10.1017/s0950268819000207 sha: doc_id: 293525 cord_uid: c7nwygl1 file: cache/cord-300399-21xozruq.json key: cord-300399-21xozruq authors: Jayamohan, Harikrishnan; Lambert, Christopher J.; Sant, Himanshu J.; Jafek, Alexander; Patel, Dhruv; Feng, Haidong; Beeman, Michael; Mahmood, Tawsif; Nze, Ugochukwu; Gale, Bruce K. title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 journal: Anal Bioanal Chem DOI: 10.1007/s00216-020-02958-1 sha: doc_id: 300399 cord_uid: 21xozruq file: cache/cord-301226-hmc2wmst.json key: cord-301226-hmc2wmst authors: Randazzo, Walter; Cuevas-Ferrando, Enric; Sanjuan, Rafael; Domingo-Calap, Pilar; Sanchez, Gloria title: Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date: 2020-04-27 journal: nan DOI: 10.1101/2020.04.23.20076679 sha: doc_id: 301226 cord_uid: hmc2wmst file: cache/cord-296250-7ln7p715.json key: cord-296250-7ln7p715 authors: Wang, Sheng-Fan; Chen, Kuan-Hsuan; Wang, Szu-Yu; Yarmishyn, Aliaksandr A.; Lai, Wei-Yi; Lin, Yi-Ying; Wang, Mong-Lien; Chou, Shih-Jie; Yang, Yi-Ping; Chang, Yuh-Lih title: The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2 date: 2020-05-20 journal: J Chin Med Assoc DOI: 10.1097/jcma.0000000000000353 sha: doc_id: 296250 cord_uid: 7ln7p715 file: cache/cord-299747-qovrstak.json key: cord-299747-qovrstak authors: Deval, Jerome; Symons, Julian A; Beigelman, Leo title: Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus date: 2014-09-17 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2014.08.004 sha: doc_id: 299747 cord_uid: qovrstak file: cache/cord-292347-d7xq7x5g.json key: cord-292347-d7xq7x5g authors: Carter, Linda J.; Garner, Linda V.; Smoot, Jeffrey W.; Li, Yingzhu; Zhou, Qiongqiong; Saveson, Catherine J.; Sasso, Janet M.; Gregg, Anne C.; Soares, Divya J.; Beskid, Tiffany R.; Jervey, Susan R.; Liu, Cynthia title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 journal: ACS Cent Sci DOI: 10.1021/acscentsci.0c00501 sha: doc_id: 292347 cord_uid: d7xq7x5g file: cache/cord-297579-ohpm5ys0.json key: cord-297579-ohpm5ys0 authors: Netzler, Natalie E.; Enosi Tuipulotu, Daniel; White, Peter A. title: Norovirus antivirals: Where are we now? date: 2018-12-25 journal: Med Res Rev DOI: 10.1002/med.21545 sha: doc_id: 297579 cord_uid: ohpm5ys0 file: cache/cord-297880-jlnv90vn.json key: cord-297880-jlnv90vn authors: Stewart, Hazel; Brown, Katherine; Dinan, Adam M.; Irigoyen, Nerea; Snijder, Eric J.; Firth, Andrew E. title: Transcriptional and Translational Landscape of Equine Torovirus date: 2018-08-16 journal: J Virol DOI: 10.1128/jvi.00589-18 sha: doc_id: 297880 cord_uid: jlnv90vn file: cache/cord-300470-vgd1ol2z.json key: cord-300470-vgd1ol2z authors: Conradie, Andelé M.; Stassen, Liesel; Huismans, Henk; Potgieter, Christiaan A.; Theron, Jacques title: Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus date: 2016-09-19 journal: Virology DOI: 10.1016/j.virol.2016.07.010 sha: doc_id: 300470 cord_uid: vgd1ol2z file: cache/cord-298078-uqrwq5qk.json key: cord-298078-uqrwq5qk authors: Kwak, Hoyun; Park, Min Woo; Jeong, Sunjoo title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date: 2011-08-30 journal: PLoS One DOI: 10.1371/journal.pone.0024067 sha: doc_id: 298078 cord_uid: uqrwq5qk file: cache/cord-298938-xemarhlv.json key: cord-298938-xemarhlv authors: Goswami, Biswendu B.; Kulka, Michael; Ngo, Diana; Cebula, Thomas A. title: Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase date: 2004-04-07 journal: Antiviral Res DOI: 10.1016/j.antiviral.2004.02.004 sha: doc_id: 298938 cord_uid: xemarhlv file: cache/cord-300023-2dg7njki.json key: cord-300023-2dg7njki authors: Pillet, S.; Berthelot, P.; Gagneux-Brunon, A.; Mory, O.; Gay, C.; Viallon, A.; Lucht, F.; Pozzetto, B.; Botelho-Nevers, E. title: Contamination of healthcare workers' mobile phones by epidemic viruses() date: 2015-12-20 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2015.12.008 sha: doc_id: 300023 cord_uid: 2dg7njki file: cache/cord-300963-1n1f8mf2.json key: cord-300963-1n1f8mf2 authors: Gajendran, Mahesh; Perisetti, Abhilash; Aziz, Muhammad; Raghavapuram, Saikiran; Bansal, Pardeep; Tharian, Benjamin; Goyal, Hemant title: Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date: 2020-10-12 journal: Ann Gastroenterol DOI: 10.20524/aog.2020.0547 sha: doc_id: 300963 cord_uid: 1n1f8mf2 file: cache/cord-301233-nenw0f81.json key: cord-301233-nenw0f81 authors: Naydenova, Katerina; Muir, Kyle W.; Wu, Long-Fei; Zhang, Ziguo; Coscia, Francesca; Peet, Mathew J.; Castro-Hartmann, Pablo; Qian, Pu; Sader, Kasim; Dent, Kyle; Kimanius, Dari; Sutherland, John D.; Löwe, Jan; Barford, David; Russo, Christopher J. title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date: 2020-10-21 journal: bioRxiv DOI: 10.1101/2020.10.21.347690 sha: doc_id: 301233 cord_uid: nenw0f81 file: cache/cord-298905-c2uuvfm5.json key: cord-298905-c2uuvfm5 authors: Horzinek, M. C. title: Molecular pathogenesis of virus infections date: 1987 journal: Experientia DOI: 10.1007/bf01945522 sha: doc_id: 298905 cord_uid: c2uuvfm5 file: cache/cord-297039-vfuem6bk.json key: cord-297039-vfuem6bk authors: Beltrán-García, Jesús; Osca-Verdegal, Rebeca; Nacher-Sendra, Elena; Pallardó, Federico V.; García-Giménez, José Luis title: Circular RNAs in Sepsis: Biogenesis, Function, and Clinical Significance date: 2020-06-25 journal: Cells DOI: 10.3390/cells9061544 sha: doc_id: 297039 cord_uid: vfuem6bk file: cache/cord-297760-uzzuoy9v.json key: cord-297760-uzzuoy9v authors: Naito, Yuki; Ui-Tei, Kumiko; Nishikawa, Toru; Takebe, Yutaka; Saigo, Kaoru title: siVirus: web-based antiviral siRNA design software for highly divergent viral sequences date: 2006-07-01 journal: Nucleic Acids Res DOI: 10.1093/nar/gkl214 sha: doc_id: 297760 cord_uid: uzzuoy9v file: cache/cord-296977-yzhsdz9c.json key: cord-296977-yzhsdz9c authors: Soares, R. R. G.; Akhtar, A. S.; Pinto, I. F.; Lapins, N.; Barrett, D.; Sandh, G.; Yin, X.; Pelechano, V.; Russom, A. title: Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date: 2020-11-06 journal: nan DOI: 10.1101/2020.11.04.20225888 sha: doc_id: 296977 cord_uid: yzhsdz9c file: cache/cord-297776-k38jssr0.json key: cord-297776-k38jssr0 authors: Volk, Aaron; Hackbart, Matthew; Deng, Xufang; Cruz-Pulido, Yazmin; O’Brien, Amornrat; Baker, Susan C. title: Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages date: 2020-05-18 journal: J Virol DOI: 10.1128/jvi.00178-20 sha: doc_id: 297776 cord_uid: k38jssr0 file: cache/cord-298820-nogoqyxl.json key: cord-298820-nogoqyxl authors: Zhang, Qi; Lai, Mei-Mei; Lou, Yun-Yan; Guo, Bin-Han; Wang, Hui-Yan; Zheng, Xiao-Qun title: Transcriptome altered by latent human cytomegalovirus infection on THP-1 cells using RNA-seq date: 2016-12-05 journal: Gene DOI: 10.1016/j.gene.2016.09.014 sha: doc_id: 298820 cord_uid: nogoqyxl file: cache/cord-298281-wkje5jyt.json key: cord-298281-wkje5jyt authors: Chan, Vinson Wai-Shun; Chiu, Peter Ka-Fung; Yee, Chi-Hang; Yuan, Yuhong; Ng, Chi-Fai; Teoh, Jeremy Yuen-Chun title: A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date: 2020-05-27 journal: World J Urol DOI: 10.1007/s00345-020-03246-4 sha: doc_id: 298281 cord_uid: wkje5jyt file: cache/cord-298779-0mjizsoo.json key: cord-298779-0mjizsoo authors: Narendrula, Rashmi; Mispel-Beyer, Kyle; Guo, Baoqing; Parissenti, Amadeo M.; Pritzker, Laura B.; Pritzker, Ken; Masilamani, Twinkle; Wang, Xiaohui; Lannér, Carita title: RNA disruption is associated with response to multiple classes of chemotherapy drugs in tumor cell lines date: 2016-02-24 journal: BMC Cancer DOI: 10.1186/s12885-016-2197-1 sha: doc_id: 298779 cord_uid: 0mjizsoo file: cache/cord-298233-qqhgmqrg.json key: cord-298233-qqhgmqrg authors: Nan, Yuchen; Zhang, Yan-Jin title: Molecular Biology and Infection of Hepatitis E Virus date: 2016-09-07 journal: Front Microbiol DOI: 10.3389/fmicb.2016.01419 sha: doc_id: 298233 cord_uid: qqhgmqrg file: cache/cord-300489-gzcb6uqw.json key: cord-300489-gzcb6uqw authors: Martinez, Mitzi L.; Weiss, Richard C. title: Detection of feline infectious peritonitis virus infection in cell cultures and peripheral blood mononuclear leukocytes of experimentally infected cats using a biotinylated cDNA probe date: 1993-03-31 journal: Veterinary Microbiology DOI: 10.1016/0378-1135(93)90016-z sha: doc_id: 300489 cord_uid: gzcb6uqw file: cache/cord-298934-vtrfqozl.json key: cord-298934-vtrfqozl authors: Makino, Shinji; Shieh, Chien-Kou; Soe, Lisa H.; Baker, Susan C.; Lai, Michael M.C. title: Primary structure and translation of a defective interfering rna of murine coronavirus date: 1988-10-31 journal: Virology DOI: 10.1016/0042-6822(88)90526-0 sha: doc_id: 298934 cord_uid: vtrfqozl file: cache/cord-299560-np6nfvf2.json key: cord-299560-np6nfvf2 authors: Hendaus, Mohamed A. title: Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary date: 2020-05-20 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1767691 sha: doc_id: 299560 cord_uid: np6nfvf2 file: cache/cord-301904-mjfbvl5n.json key: cord-301904-mjfbvl5n authors: Schultz-Cherry, S. title: Astroviruses date: 2014-11-28 journal: Reference Module in Biomedical Sciences DOI: 10.1016/b978-0-12-801238-3.02539-3 sha: doc_id: 301904 cord_uid: mjfbvl5n file: cache/cord-301115-sedfbjlw.json key: cord-301115-sedfbjlw authors: Han, Mingfeng; Xu, Mengyuan; Zhang, Yafei; Liu, Zhongping; Li, Shasha; He, Tengfei; Li, Jinsong; Gao, Yong; Liu, Wanjun; Li, Tuantuan; Chen, Zixiang; Huang, Xin; Cheng, Guoling; Wang, Jun; Dittmer, Ulf; Witzke, Oliver; Zou, Guizhou; Li, Xiuyong; Lu, Mengji; Zhang, Zhenhua title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date: 2020-08-28 journal: Med Microbiol Immunol DOI: 10.1007/s00430-020-00693-z sha: doc_id: 301115 cord_uid: sedfbjlw file: cache/cord-294260-g410mavp.json key: cord-294260-g410mavp authors: Sztuba-Solińska, Joanna; Stollar, Victor; Bujarski, Jozef J. title: Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle date: 2011-04-10 journal: Virology DOI: 10.1016/j.virol.2011.02.007 sha: doc_id: 294260 cord_uid: g410mavp file: cache/cord-295467-9fnis6ci.json key: cord-295467-9fnis6ci authors: Botella, Leticia; Tuomivirta, Tero T.; Hantula, Jarkko; Diez, Julio J.; Jankovsky, Libor title: The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history date: 2014-12-12 journal: Fungal Biol DOI: 10.1016/j.funbio.2014.12.001 sha: doc_id: 295467 cord_uid: 9fnis6ci file: cache/cord-301285-p83ondy8.json key: cord-301285-p83ondy8 authors: Kautz, Tiffany F; Guerbois, Mathilde; Khanipov, Kamil; Patterson, Edward I; Langsjoen, Rose M; Yun, Ruimei; Warmbrod, Kelsey L; Fofanov, Yuriy; Weaver, Scott C; Forrester, Naomi L title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 journal: Virus Evol DOI: 10.1093/ve/vey004 sha: doc_id: 301285 cord_uid: p83ondy8 file: cache/cord-302425-aaxvlktp.json key: cord-302425-aaxvlktp authors: Cortey, Martí; Díaz, Ivan; Vidal, Anna; Martín-Valls, Gerard; Franzo, Giovanni; Gómez de Nova, Pedro José; Darwich, Laila; Puente, Héctor; Carvajal, Ana; Martín, Marga; Mateu, Enric title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date: 2019-12-05 journal: BMC Vet Res DOI: 10.1186/s12917-019-2204-2 sha: doc_id: 302425 cord_uid: aaxvlktp file: cache/cord-302195-25gjbyi1.json key: cord-302195-25gjbyi1 authors: Al Huraimel, Khalid; Alhosani, Mohamed; Kunhabdulla, Shabana; Stietiya, Mohammed Hashem title: SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date: 2020-07-15 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.140946 sha: doc_id: 302195 cord_uid: 25gjbyi1 file: cache/cord-302355-3se1wp8o.json key: cord-302355-3se1wp8o authors: Chen, Yi-Shiuan; Fan, Yi-Hsin; Tien, Chih-Feng; Yueh, Andrew; Chang, Ruey-Yi title: The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 journal: PLoS One DOI: 10.1371/journal.pone.0201250 sha: doc_id: 302355 cord_uid: 3se1wp8o file: cache/cord-301997-63160t7f.json key: cord-301997-63160t7f authors: Schwer, Beate; Visca, Paolo; Vos, Jan C.; Stunnenberg, Hendrik G. title: Discontinuous transcription or RNA processing of vaccinia virus late messengers results in a 5′ poly(A) leader date: 1987-07-17 journal: Cell DOI: 10.1016/0092-8674(87)90212-1 sha: doc_id: 301997 cord_uid: 63160t7f file: cache/cord-302020-ypsh3rjv.json key: cord-302020-ypsh3rjv authors: Kim, Dongwan; Lee, Joo-Yeon; Yang, Jeong-Sun; Kim, Jun Won; Kim, V. Narry; Chang, Hyeshik title: The Architecture of SARS-CoV-2 Transcriptome date: 2020-04-23 journal: Cell DOI: 10.1016/j.cell.2020.04.011 sha: doc_id: 302020 cord_uid: ypsh3rjv file: cache/cord-303111-iv4lzpev.json key: cord-303111-iv4lzpev authors: Almazán, Fernando; Sola, Isabel; Zuñiga, Sonia; Marquez-Jurado, Silvia; Morales, Lucia; Becares, Martina; Enjuanes, Luis title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date: 2014-12-19 journal: Virus Res DOI: 10.1016/j.virusres.2014.09.006 sha: doc_id: 303111 cord_uid: iv4lzpev file: cache/cord-301535-eui41zyg.json key: cord-301535-eui41zyg authors: Chandler-Brown, Devon; Bueno, Anna M.; Atay, Oguzhan; Tsao, David S. title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date: 2020-04-10 journal: bioRxiv DOI: 10.1101/2020.04.07.029199 sha: doc_id: 301535 cord_uid: eui41zyg file: cache/cord-302316-raf5rlkq.json key: cord-302316-raf5rlkq authors: Brüssow, Harald title: COVID‐19: From pathogenesis models to the first drug trials date: 2020-06-23 journal: Microb Biotechnol DOI: 10.1111/1751-7915.13611 sha: doc_id: 302316 cord_uid: raf5rlkq file: cache/cord-302085-xyru2q9o.json key: cord-302085-xyru2q9o authors: Shepard, Samuel S.; Meno, Sarah; Bahl, Justin; Wilson, Malania M.; Barnes, John; Neuhaus, Elizabeth title: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler date: 2016-09-05 journal: BMC Genomics DOI: 10.1186/s12864-016-3030-6 sha: doc_id: 302085 cord_uid: xyru2q9o file: cache/cord-303265-v6ci69n0.json key: cord-303265-v6ci69n0 authors: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 journal: Virus as Populations DOI: 10.1016/b978-0-12-816331-3.00001-5 sha: doc_id: 303265 cord_uid: v6ci69n0 file: cache/cord-302368-uhhtvdif.json key: cord-302368-uhhtvdif authors: Longhini, Andrew P.; LeBlanc, Regan M.; Becette, Owen; Salguero, Carolina; Wunderlich, Christoph H.; Johnson, Bruce A.; D'Souza, Victoria M.; Kreutz, Christoph; Dayie, T. Kwaku title: Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations date: 2016-04-07 journal: Nucleic Acids Res DOI: 10.1093/nar/gkv1333 sha: doc_id: 302368 cord_uid: uhhtvdif file: cache/cord-302980-2jlz4c58.json key: cord-302980-2jlz4c58 authors: Crucière, C.; Laporte, J. title: Sequence and analysis of bovine enteritic coronavirus (F15) genome I.—Sequence of the gene coding for the nucleocapsid protein; analysis of the predicted protein date: 1988-03-31 journal: Annales de l'Institut Pasteur / Virologie DOI: 10.1016/s0769-2617(88)80012-1 sha: doc_id: 302980 cord_uid: 2jlz4c58 file: cache/cord-303153-z7bdiuvx.json key: cord-303153-z7bdiuvx authors: Ulasli, Mustafa; Verheije, Monique H.; de Haan, Cornelis A. M.; Reggiori, Fulvio title: Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus date: 2010-01-20 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2010.01437.x sha: doc_id: 303153 cord_uid: z7bdiuvx file: cache/cord-304306-rxjahqwh.json key: cord-304306-rxjahqwh authors: Vlachakis, Dimitrios; Papakonstantinou, Eleni; Mitsis, Thanasis; Pierouli, Katerina; Diakou, Io; Chrousos, George; Bacopoulou, Flora title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date: 2020-10-08 journal: Food Chem Toxicol DOI: 10.1016/j.fct.2020.111805 sha: doc_id: 304306 cord_uid: rxjahqwh file: cache/cord-301362-f3lp10lm.json key: cord-301362-f3lp10lm authors: Delgui, Laura R.; Colombo, María I. title: A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases date: 2017-01-20 journal: Front Cell Infect Microbiol DOI: 10.3389/fcimb.2017.00005 sha: doc_id: 301362 cord_uid: f3lp10lm file: cache/cord-302409-40ktyt5q.json key: cord-302409-40ktyt5q authors: Wang, Jie; Feng, Haiting; Zhang, Sheng; Ni, Zuowei; Ni, Lingmei; Chen, Yu; Zhuo, Lixin; Zhong, Zifeng; Qu, Tingting title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 journal: Int J Infect Dis DOI: 10.1016/j.ijid.2020.04.024 sha: doc_id: 302409 cord_uid: 40ktyt5q file: cache/cord-302047-vv5gpldi.json key: cord-302047-vv5gpldi authors: Willemsen, Anouk; Zwart, Mark P title: On the stability of sequences inserted into viral genomes date: 2019-11-14 journal: Virus Evol DOI: 10.1093/ve/vez045 sha: doc_id: 302047 cord_uid: vv5gpldi file: cache/cord-303408-coesfldm.json key: cord-303408-coesfldm authors: Konstantinova, Pavlina; ter Brake, Olivier; Haasnoot, Joost; de Haan, Peter; Berkhout, Ben title: Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome date: 2007-03-01 journal: Retrovirology DOI: 10.1186/1742-4690-4-15 sha: doc_id: 303408 cord_uid: coesfldm file: cache/cord-304044-i1ikf96b.json key: cord-304044-i1ikf96b authors: Wu, Yue; Lü, Ling; Yang, Li-Shi; Weng, Shao-Ping; Chan, Sui-Ming; He, Jian-Guo title: Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date: 2007-10-03 journal: Aquaculture DOI: 10.1016/j.aquaculture.2007.06.029 sha: doc_id: 304044 cord_uid: i1ikf96b file: cache/cord-304356-jyp9gjh9.json key: cord-304356-jyp9gjh9 authors: Grant, Rogan A.; Morales-Nebreda, Luisa; Markov, Nikolay S.; Swaminathan, Suchitra; Guzman, Estefany R.; Abbott, Darryl A.; Donnelly, Helen K.; Donayre, Alvaro; Goldberg, Isaac A.; Klug, Zasu M.; Borkowski, Nicole; Lu, Ziyan; Kihshen, Hermon; Politanska, Yuliya; Sichizya, Lango; Kang, Mengjia; Shilatifard, Ali; Qi, Chao; Argento, A. Christine; Kruser, Jacqueline M.; Malsin, Elizabeth S.; Pickens, Chiagozie O.; Smith, Sean; Walter, James M.; Pawlowski, Anna E.; Schneider, Daniel; Nannapaneni, Prasanth; Abdala-Valencia, Hiam; Bharat, Ankit; Gottardi, Cara J.; Budinger, GR Scott; Misharin, Alexander V.; Singer, Benjamin D.; Wunderink, Richard G. title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date: 2020-08-05 journal: bioRxiv DOI: 10.1101/2020.08.05.238188 sha: doc_id: 304356 cord_uid: jyp9gjh9 file: cache/cord-303319-v3iyur78.json key: cord-303319-v3iyur78 authors: Abe, Takayuki; Marutani, Yuki; Shoji, Ikuo title: Cytosolic DNA‐sensing immune response and viral infection date: 2019-02-26 journal: Microbiol Immunol DOI: 10.1111/1348-0421.12669 sha: doc_id: 303319 cord_uid: v3iyur78 file: cache/cord-302895-471zei5o.json key: cord-302895-471zei5o authors: Deng, Zengqin; Lehmann, Kathleen C.; Li, Xiaorong; Feng, Chong; Wang, Guoqiang; Zhang, Qi; Qi, Xiaoxuan; Yu, Lin; Zhang, Xingliang; Feng, Wenhai; Wu, Wei; Gong, Peng; Tao, Ye; Posthuma, Clara C.; Snijder, Eric J.; Gorbalenya, Alexander E.; Chen, Zhongzhou title: Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase date: 2013-12-24 journal: Nucleic Acids Res DOI: 10.1093/nar/gkt1310 sha: doc_id: 302895 cord_uid: 471zei5o file: cache/cord-304058-i8cywew0.json key: cord-304058-i8cywew0 authors: Pfefferle, Susanne; Krähling, Verena; Ditt, Vanessa; Grywna, Klaus; Mühlberger, Elke; Drosten, Christian title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 journal: Virol J DOI: 10.1186/1743-422x-6-131 sha: doc_id: 304058 cord_uid: i8cywew0 file: cache/cord-303377-lkewcf8a.json key: cord-303377-lkewcf8a authors: Dimke, H.; Larsen, S. L.; Skov, M. N.; Larsen, H.; Hartmeyer, G. N.; Moeller, J. B. title: Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date: 2020-05-27 journal: nan DOI: 10.1101/2020.05.26.20099440 sha: doc_id: 303377 cord_uid: lkewcf8a file: cache/cord-306948-wkisfz1m.json key: cord-306948-wkisfz1m authors: Han, Mingyuan; Yoo, Dongwan title: Engineering the PRRS virus genome: Updates and perspectives date: 2014-12-05 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2014.10.007 sha: doc_id: 306948 cord_uid: wkisfz1m file: cache/cord-304553-gbwb7fqi.json key: cord-304553-gbwb7fqi authors: Christopher, Mary E.; Wong, Jonathan P. title: Broad-Spectrum Drugs Against Viral Agents date: 2008-09-01 journal: Int J Mol Sci DOI: 10.3390/ijms9091561 sha: doc_id: 304553 cord_uid: gbwb7fqi file: cache/cord-303189-ktl4jw8v.json key: cord-303189-ktl4jw8v authors: Coccia, Eliana M.; Battistini, Angela title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 journal: Seminars in Immunology DOI: 10.1016/j.smim.2015.03.005 sha: doc_id: 303189 cord_uid: ktl4jw8v file: cache/cord-302830-5psqxxc8.json key: cord-302830-5psqxxc8 authors: Ávila‐Pérez, Ginés; Rejas, María Teresa; Rodríguez, Dolores title: Ultrastructural characterization of membranous torovirus replication factories date: 2016-07-05 journal: Cell Microbiol DOI: 10.1111/cmi.12620 sha: doc_id: 302830 cord_uid: 5psqxxc8 file: cache/cord-304876-txaoz7oh.json key: cord-304876-txaoz7oh authors: Jordan, Paul C; Stevens, Sarah K; Deval, Jerome title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 journal: Antivir Chem Chemother DOI: 10.1177/2040206618764483 sha: doc_id: 304876 cord_uid: txaoz7oh file: cache/cord-305811-987dhnf7.json key: cord-305811-987dhnf7 authors: Cho, Che-Pei; Lin, Szu-Chieh; Chou, Ming-Yuan; Hsu, Hsiu-Ting; Chang, Kung-Yao title: Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date: 2013-04-29 journal: PLoS One DOI: 10.1371/journal.pone.0062283 sha: doc_id: 305811 cord_uid: 987dhnf7 file: cache/cord-308216-s6rd8p41.json key: cord-308216-s6rd8p41 authors: Duan, Fang; Ni, Shiming; Nie, Yuhong; Huang, Qiang; Wu, Kaili title: Small interfering RNA targeting for infected‐cell polypeptide 4 inhibits herpes simplex virus type 1 replication in retinal pigment epithelial cells date: 2011-10-20 journal: Clin Exp Ophthalmol DOI: 10.1111/j.1442-9071.2011.02668.x sha: doc_id: 308216 cord_uid: s6rd8p41 file: cache/cord-308835-999kewdw.json key: cord-308835-999kewdw authors: Leibowitz, Julian L.; Wilhelmsen, Kirk C.; Bond, Clifford W. title: The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM date: 1981-10-15 journal: Virology DOI: 10.1016/0042-6822(81)90250-6 sha: doc_id: 308835 cord_uid: 999kewdw file: cache/cord-305591-ir3wz6nr.json key: cord-305591-ir3wz6nr authors: Ji, Danyang; Juhas, Mario; Tsang, Chi Man; Kwok, Chun Kit; Li, Yongshu; Zhang, Yang title: Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date: 2020-06-01 journal: Brief Bioinform DOI: 10.1093/bib/bbaa114 sha: doc_id: 305591 cord_uid: ir3wz6nr file: cache/cord-303403-9th2jiq6.json key: cord-303403-9th2jiq6 authors: Qing, Jie; Wang, Yaxin; Sun, Yuna; Huang, Jiaoyan; Yan, Wenzhong; Wang, Jinglan; Su, Dan; Ni, Cheng; Li, Jian; Rao, Zihe; Liu, Lei; Lou, Zhiyong title: Cyclophilin A Associates with Enterovirus-71 Virus Capsid and Plays an Essential Role in Viral Infection as an Uncoating Regulator date: 2014-10-02 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1004422 sha: doc_id: 303403 cord_uid: 9th2jiq6 file: cache/cord-304014-k62mtr9j.json key: cord-304014-k62mtr9j authors: Ma, Xuelian; Zhao, Xiaomin; Wang, Kaili; Tang, Xiaoyi; Guo, Jianxiong; Mi, Mi; Qi, Yanping; Chang, Lingling; Huang, Yong; Tong, Dewen title: Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection date: 2019-11-04 journal: BMC Genomics DOI: 10.1186/s12864-019-6156-5 sha: doc_id: 304014 cord_uid: k62mtr9j file: cache/cord-305859-vt8vwo3y.json key: cord-305859-vt8vwo3y authors: Jung, Kwonil; Hu, Hui; Saif, Linda J. title: Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus date: 2017-04-03 journal: Arch Virol DOI: 10.1007/s00705-017-3351-z sha: doc_id: 305859 cord_uid: vt8vwo3y file: cache/cord-307860-iqk1yiw4.json key: cord-307860-iqk1yiw4 authors: Ionescu, Mihaela Ileana title: An Overview of the Crystallized Structures of the SARS-CoV-2 date: 2020-10-24 journal: Protein J DOI: 10.1007/s10930-020-09933-w sha: doc_id: 307860 cord_uid: iqk1yiw4 file: cache/cord-303915-14yfs4pa.json key: cord-303915-14yfs4pa authors: Almazán, Fernando; DeDiego, Marta L.; Sola, Isabel; Zuñiga, Sonia; Nieto-Torres, Jose L.; Marquez-Jurado, Silvia; Andrés, German; Enjuanes, Luis title: Engineering a Replication-Competent, Propagation-Defective Middle East Respiratory Syndrome Coronavirus as a Vaccine Candidate date: 2013-09-10 journal: mBio DOI: 10.1128/mbio.00650-13 sha: doc_id: 303915 cord_uid: 14yfs4pa file: cache/cord-304873-ppb9k3zu.json key: cord-304873-ppb9k3zu authors: Kang, Hunseung title: Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1 date: 1998-04-01 journal: Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression DOI: 10.1016/s0167-4781(98)00004-9 sha: doc_id: 304873 cord_uid: ppb9k3zu file: cache/cord-305290-xnjwv0d7.json key: cord-305290-xnjwv0d7 authors: Atkins, John F.; Weiss, Robert B.; Gesteland, Raymond F. title: Ribosome gymnastics—Degree of difficulty 9.5, style 10.0 date: 1990-08-10 journal: Cell DOI: 10.1016/0092-8674(90)90007-2 sha: doc_id: 305290 cord_uid: xnjwv0d7 file: cache/cord-310141-2jofy8fo.json key: cord-310141-2jofy8fo authors: Qureshi, Abid; Tantray, Vaqar Gani; Kirmani, Altaf Rehman; Ahangar, Abdul Ghani title: A review on current status of antiviral siRNA date: 2018-04-15 journal: Rev Med Virol DOI: 10.1002/rmv.1976 sha: doc_id: 310141 cord_uid: 2jofy8fo file: cache/cord-310748-ao29zx1u.json key: cord-310748-ao29zx1u authors: Banner, Lisa R.; Mc Lai, Michael title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 journal: Virology DOI: 10.1016/0042-6822(91)90795-d sha: doc_id: 310748 cord_uid: ao29zx1u file: cache/cord-306076-ygfnkgqp.json key: cord-306076-ygfnkgqp authors: Fujita, Yu; Takeshita, Fumitaka; Kuwano, Kazuyoshi; Ochiya, Takahiro title: RNAi Therapeutic Platforms for Lung Diseases date: 2013-02-06 journal: Pharmaceuticals (Basel) DOI: 10.3390/ph6020223 sha: doc_id: 306076 cord_uid: ygfnkgqp file: cache/cord-305393-96mrxt8a.json key: cord-305393-96mrxt8a authors: Lai, Yvonne; Yi, Guanghui; Chen, Alice; Bhardwaj, Kanchan; Tragesser, Brady J.; Rodrigo A. Valverde,; Zlotnick, Adam; Mukhopadhyay, Suchetana; Ranjith-Kumar, C. T.; Kao, C. Cheng title: Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3 date: 2011-10-10 journal: PLoS One DOI: 10.1371/journal.pone.0025837 sha: doc_id: 305393 cord_uid: 96mrxt8a file: cache/cord-307893-mvl0wrsj.json key: cord-307893-mvl0wrsj authors: Goulter-Thorsen, R.M.; Jaykus, L-A title: Disciplines Associated with Food Safety: Food Virology date: 2014-01-13 journal: Encyclopedia of Food Safety DOI: 10.1016/b978-0-12-378612-8.00024-x sha: doc_id: 307893 cord_uid: mvl0wrsj file: cache/cord-308034-9b219k0v.json key: cord-308034-9b219k0v authors: Murray, James L.; Sheng, Jinsong; Rubin, Donald H. title: A Role for H/ACA and C/D Small Nucleolar RNAs in Viral Replication date: 2014-01-30 journal: Mol Biotechnol DOI: 10.1007/s12033-013-9730-0 sha: doc_id: 308034 cord_uid: 9b219k0v file: cache/cord-310192-8x37nx4s.json key: cord-310192-8x37nx4s authors: Zhang, Huaqun; Keane, Sarah C. title: Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date: 2019-04-25 journal: Wiley Interdiscip Rev RNA DOI: 10.1002/wrna.1541 sha: doc_id: 310192 cord_uid: 8x37nx4s file: cache/cord-307934-84zfabti.json key: cord-307934-84zfabti authors: Lai, Chao-Kuen; Saxena, Vikas; Tseng, Chung-Hsin; Jeng, King-Song; Kohara, Michinori; Lai, Michael M. C. title: Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport date: 2014-06-06 journal: PLoS One DOI: 10.1371/journal.pone.0099022 sha: doc_id: 307934 cord_uid: 84zfabti file: cache/cord-304283-nv4ret1f.json key: cord-304283-nv4ret1f authors: Hung, Chuan-Fu; Lu, Kuang-Chu; Cheng, Tsung-Lin; Wu, Ren-Huang; Huang, Lin-Ya; Teng, Chiao-Fang; Chang, Wen-Tsan title: A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells date: 2006-08-04 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2006.05.164 sha: doc_id: 304283 cord_uid: nv4ret1f file: cache/cord-304498-ty41xob0.json key: cord-304498-ty41xob0 authors: Denison, Mark R; Graham, Rachel L; Donaldson, Eric F; Eckerle, Lance D; Baric, Ralph S title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 journal: RNA Biology DOI: 10.4161/rna.8.2.15013 sha: doc_id: 304498 cord_uid: ty41xob0 file: cache/cord-306535-j26eqmxt.json key: cord-306535-j26eqmxt authors: Robertson, Matthew J.; Kent, Katarzyna; Tharp, Nathan; Nozawa, Kaori; Dean, Laura; Mathew, Michelle; Grimm, Sandra L.; Yu, Zhifeng; Légaré, Christine; Fujihara, Yoshitaka; Ikawa, Masahito; Sullivan, Robert; Coarfa, Cristian; Matzuk, Martin M.; Garcia, Thomas X. title: Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets date: 2020-08-19 journal: BMC Biol DOI: 10.1186/s12915-020-00826-z sha: doc_id: 306535 cord_uid: j26eqmxt file: cache/cord-307354-dkwcheu0.json key: cord-307354-dkwcheu0 authors: Abernathy, Emma; Glaunsinger, Britt title: Emerging roles for RNA degradation in viral replication and antiviral defense date: 2015-05-31 journal: Virology DOI: 10.1016/j.virol.2015.02.007 sha: doc_id: 307354 cord_uid: dkwcheu0 file: cache/cord-310086-9e4txeck.json key: cord-310086-9e4txeck authors: Fu, Wei; Chen, Qian; Wang, Tao title: Letter to the Editor: Three cases of re‐detectable positive SARS‐CoV‐2 RNA in recovered COVID‐19 patients with antibodies date: 2020-05-05 journal: J Med Virol DOI: 10.1002/jmv.25968 sha: doc_id: 310086 cord_uid: 9e4txeck file: cache/cord-306921-3afgpunj.json key: cord-306921-3afgpunj authors: Owino, Collins Oduor; Chu, Justin Jang Hann title: Recent advances on the role of host factors during non-poliovirus enteroviral infections date: 2019-06-19 journal: J Biomed Sci DOI: 10.1186/s12929-019-0540-y sha: doc_id: 306921 cord_uid: 3afgpunj file: cache/cord-312544-vip4jtlv.json key: cord-312544-vip4jtlv authors: Ng, Lisa FP; Barr, Ian; Nguyen, Tung; Noor, Suriani Mohd; Tan, Rosemary Sok-Pin; Agathe, Lora V; Gupta, Sanjay; Khalil, Hassuzana; To, Thanh Long; Hassan, Sharifah Syed; Ren, Ee-Chee title: Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay date: 2006-03-02 journal: BMC Infect Dis DOI: 10.1186/1471-2334-6-40 sha: doc_id: 312544 cord_uid: vip4jtlv file: cache/cord-310771-tnwfp1je.json key: cord-310771-tnwfp1je authors: Revilla-Fernández, Sandra; Wallner, Barbara; Truschner, Klaus; Benczak, Alexandra; Brem, Gottfried; Schmoll, Friedrich; Mueller, Mathias; Steinborn, Ralf title: The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date: 2005-02-23 journal: J Virol Methods DOI: 10.1016/j.jviromet.2005.01.018 sha: doc_id: 310771 cord_uid: tnwfp1je file: cache/cord-304794-z2kx314h.json key: cord-304794-z2kx314h authors: Métifiot, Mathieu; Amrane, Samir; Litvak, Simon; Andreola, Marie-Line title: G-quadruplexes in viruses: function and potential therapeutic applications date: 2014-11-10 journal: Nucleic Acids Res DOI: 10.1093/nar/gku999 sha: doc_id: 304794 cord_uid: z2kx314h file: cache/cord-311982-wkg56xeq.json key: cord-311982-wkg56xeq authors: Dye, Charlotte; Siddell, Stuart G. title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 journal: J Feline Med Surg DOI: 10.1016/j.jfms.2006.12.002 sha: doc_id: 311982 cord_uid: wkg56xeq file: cache/cord-304424-048xo7jn.json key: cord-304424-048xo7jn authors: Greninger, Alexander L. title: A decade of RNA virus metagenomics is (not) enough date: 2018-01-15 journal: Virus Res DOI: 10.1016/j.virusres.2017.10.014 sha: doc_id: 304424 cord_uid: 048xo7jn file: cache/cord-305336-wxiazglk.json key: cord-305336-wxiazglk authors: Li, Ji Lian; Cornman, R. Scott; Evans, Jay D.; Pettis, Jeffery S.; Zhao, Yan; Murphy, Charles; Peng, Wen Jun; Wu, Jie; Hamilton, Michele; Boncristiani, Humberto F.; Zhou, Liang; Hammond, John; Chen, Yan Ping title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 journal: mBio DOI: 10.1128/mbio.00898-13 sha: doc_id: 305336 cord_uid: wxiazglk file: cache/cord-306288-w43wec48.json key: cord-306288-w43wec48 authors: Jang, Sungho; Jang, Sungyeon; Yang, Jina; Seo, Sang Woo; Jung, Gyoo Yeol title: RNA-based dynamic genetic controllers: development strategies and applications date: 2017-11-10 journal: Curr Opin Biotechnol DOI: 10.1016/j.copbio.2017.10.005 sha: doc_id: 306288 cord_uid: w43wec48 file: cache/cord-306688-po4p1466.json key: cord-306688-po4p1466 authors: Wang, X.; Ahlquist, P. title: Brome Mosaic Virus date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00560-4 sha: doc_id: 306688 cord_uid: po4p1466 file: cache/cord-305737-bnzd7b25.json key: cord-305737-bnzd7b25 authors: Rehwinkel, Jan; Reis e Sousa, Caetano title: Targeting the viral Achilles’ heel: recognition of 5′-triphosphate RNA in innate anti-viral defence date: 2013-05-23 journal: Curr Opin Microbiol DOI: 10.1016/j.mib.2013.04.009 sha: doc_id: 305737 cord_uid: bnzd7b25 file: cache/cord-305871-w1quh4fx.json key: cord-305871-w1quh4fx authors: Hindawi, Salwa I.; Hashem, Anwar M.; Damanhouri, Ghazi A.; El‐Kafrawy, Sherif A.; Tolah, Ahmed M.; Hassan, Ahmed M.; Azhar , Esam I. title: Inactivation of Middle East respiratory syndrome‐coronavirus in human plasma using amotosalen and ultraviolet A light date: 2017-12-14 journal: Transfusion DOI: 10.1111/trf.14422 sha: doc_id: 305871 cord_uid: w1quh4fx file: cache/cord-310371-pylrg91h.json key: cord-310371-pylrg91h authors: Bishop, R.F.; Kirkwood, C.D. title: Enteric Viruses date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00386-1 sha: doc_id: 310371 cord_uid: pylrg91h file: cache/cord-306934-29ljbl7g.json key: cord-306934-29ljbl7g authors: Tonelli, Michele; Vazzana, Iana; Tasso, Bruno; Boido, Vito; Sparatore, Fabio; Fermeglia, Maurizio; Paneni, Maria Silvia; Posocco, Paola; Pricl, Sabrina; Colla, Paolo La; Ibba, Cristina; Secci, Barbara; Collu, Gabriella; Loddo, Roberta title: Antiviral and cytotoxic activities of aminoarylazo compounds and aryltriazene derivatives date: 2009-07-01 journal: Bioorganic & Medicinal Chemistry DOI: 10.1016/j.bmc.2009.05.020 sha: doc_id: 306934 cord_uid: 29ljbl7g file: cache/cord-312431-de7zhswl.json key: cord-312431-de7zhswl authors: Ganesh, Atheesha; Lin, Johnson; Singh, Moganavelli title: Detecting Virus‐Like Particles from the Umgeni River, South Africa date: 2013-08-30 journal: Clean (Weinh) DOI: 10.1002/clen.201200564 sha: doc_id: 312431 cord_uid: de7zhswl file: cache/cord-307603-uqr6r14u.json key: cord-307603-uqr6r14u authors: Kauppinen, S.; Vester, B.; Wengel, J. title: Locked Nucleic Acid: High-Affinity Targeting of Complementary RNA for RNomics date: 2006 journal: RNA Towards Medicine DOI: 10.1007/3-540-27262-3_21 sha: doc_id: 307603 cord_uid: uqr6r14u file: cache/cord-307904-lnagg1uw.json key: cord-307904-lnagg1uw authors: Johnson, Jennifer A; Bragg, Jennifer N; Lawrence, Diane M; Jackson, Andrew O title: Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo date: 2003-08-15 journal: Virology DOI: 10.1016/s0042-6822(03)00285-x sha: doc_id: 307904 cord_uid: lnagg1uw file: cache/cord-310605-r63sg73c.json key: cord-310605-r63sg73c authors: Dorward, D. A.; Russell, C. D.; Um, I. H.; Elshani, M.; Armstrong, S. D.; Penrice-Randal, R.; Millar, T.; Lerpiniere, C. E.; Tagliavini, G.; Hartley, C. S.; Randall, N. P.; Gachanja, N. N.; Potey, P. M.; Anderson, A. M.; Campbell, V. L.; Duguid, A. J.; Al Qsous, W.; BouHaidar, R.; Baillie, J. K.; Dhaliwal, K.; Wallace, W. A.; Bellamy, C. O.; Prost, S.; Smith, C.; Hiscox, J. A.; Harrison, D. J.; Lucas, C. D.; ICECAP, title: Tissue-specific tolerance in fatal Covid-19 date: 2020-07-04 journal: nan DOI: 10.1101/2020.07.02.20145003 sha: doc_id: 310605 cord_uid: r63sg73c file: cache/cord-309048-emmtplv3.json key: cord-309048-emmtplv3 authors: Lomonossoff, George P.; Wege, Christina title: TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date: 2018-07-26 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2018.06.003 sha: doc_id: 309048 cord_uid: emmtplv3 file: cache/cord-311625-d7iycdyh.json key: cord-311625-d7iycdyh authors: Choong, Oi Kuan; Mehrbod, Parvaneh; Tejo, Bimo Ario; Omar, Abdul Rahman title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication date: 2014-02-20 journal: Biomed Res Int DOI: 10.1155/2014/654712 sha: doc_id: 311625 cord_uid: d7iycdyh file: cache/cord-311628-ep795pil.json key: cord-311628-ep795pil authors: Fu, Yu; Li, Jinming title: A novel delivery platform based on Bacteriophage MS2 virus-like particles date: 2016-01-04 journal: Virus Res DOI: 10.1016/j.virusres.2015.08.022 sha: doc_id: 311628 cord_uid: ep795pil file: cache/cord-308331-55ge7kmr.json key: cord-308331-55ge7kmr authors: Routh, Andrew; Johnson, John E. title: Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data date: 2013-10-09 journal: Nucleic Acids Res DOI: 10.1093/nar/gkt916 sha: doc_id: 308331 cord_uid: 55ge7kmr file: cache/cord-311007-0i1abjfa.json key: cord-311007-0i1abjfa authors: Schwarz, Megan C.; Sourisseau, Marion; Espino, Michael M.; Gray, Essanna S.; Chambers, Matthew T.; Tortorella, Domenico; Evans, Matthew J. title: Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone date: 2016-09-28 journal: mSphere DOI: 10.1128/msphere.00246-16 sha: doc_id: 311007 cord_uid: 0i1abjfa file: cache/cord-308884-erofmh39.json key: cord-308884-erofmh39 authors: Yang, Seung Won; Jang, Yo Han; Kwon, Soon Bin; Lee, Yoon Jae; Chae, Wonil; Byun, Young Ho; Kim, Paul; Park, Chan; Lee, Young Jae; Kim, Choon Kang; Kim, Young Seok; Choi, Seong Il; Seong, Baik Lin title: Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date: 2018-01-08 journal: FASEB J DOI: 10.1096/fj.201700747rr sha: doc_id: 308884 cord_uid: erofmh39 file: cache/cord-306424-gf0bglm0.json key: cord-306424-gf0bglm0 authors: Scutigliani, Enzo Maxim; Kikkert, Marjolein title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2017.05.007 sha: doc_id: 306424 cord_uid: gf0bglm0 file: cache/cord-307817-2vy28i4m.json key: cord-307817-2vy28i4m authors: Lou, Zhiyong; Sun, Yuna; Rao, Zihe title: Current progress in antiviral strategies date: 2014-01-14 journal: Trends Pharmacol Sci DOI: 10.1016/j.tips.2013.11.006 sha: doc_id: 307817 cord_uid: 2vy28i4m file: cache/cord-310268-8q4tk6fd.json key: cord-310268-8q4tk6fd authors: Zhu, Qinchang; Liu, Ge; Kai, Masaaki title: DNA Aptamers in the Diagnosis and Treatment of Human Diseases date: 2015-11-25 journal: Molecules DOI: 10.3390/molecules201219739 sha: doc_id: 310268 cord_uid: 8q4tk6fd file: cache/cord-312332-rwmuucsp.json key: cord-312332-rwmuucsp authors: Dicker, Kate; Järvelin, Aino I.; Garcia-Moreno, Manuel; Castello, Alfredo title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2020.08.002 sha: doc_id: 312332 cord_uid: rwmuucsp file: cache/cord-309043-dlmx12vt.json key: cord-309043-dlmx12vt authors: von Brunn, Albrecht; Teepe, Carola; Simpson, Jeremy C.; Pepperkok, Rainer; Friedel, Caroline C.; Zimmer, Ralf; Roberts, Rhonda; Baric, Ralph; Haas, Jürgen title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 journal: PLoS One DOI: 10.1371/journal.pone.0000459 sha: doc_id: 309043 cord_uid: dlmx12vt file: cache/cord-306754-qohrnpgq.json key: cord-306754-qohrnpgq authors: Lee, Justin S.; Mackie, Ryan S.; Harrison, Thomas; Shariat, Basir; Kind, Trey; Kehl, Timo; Löchelt, Martin; Boucher, Christina; VandeWoude, Sue title: Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species date: 2017-05-23 journal: J Clin Microbiol DOI: 10.1128/jcm.01463-16 sha: doc_id: 306754 cord_uid: qohrnpgq file: cache/cord-312240-0k8y86pf.json key: cord-312240-0k8y86pf authors: Schlaberg, Robert; Queen, Krista; Simmon, Keith; Tardif, Keith; Stockmann, Chris; Flygare, Steven; Kennedy, Brett; Voelkerding, Karl; Bramley, Anna; Zhang, Jing; Eilbeck, Karen; Yandell, Mark; Jain, Seema; Pavia, Andrew T.; Tong, Suxiang; Ampofo, Krow title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date: 2017-05-01 journal: The Journal of Infectious Diseases DOI: 10.1093/infdis/jix148 sha: doc_id: 312240 cord_uid: 0k8y86pf file: cache/cord-309722-04pp3lv0.json key: cord-309722-04pp3lv0 authors: Qiu, Yingshan; Lam, Jenny K. W.; Leung, Susan W. S.; Liang, Wanling title: Delivery of RNAi Therapeutics to the Airways—From Bench to Bedside date: 2016-09-20 journal: Molecules DOI: 10.3390/molecules21091249 sha: doc_id: 309722 cord_uid: 04pp3lv0 file: cache/cord-309469-2naxn580.json key: cord-309469-2naxn580 authors: An, Hongliu; Cai, Zhichao; Yang, Yuying; Wang, Zhaoxiong; Liu, Ding Xiang; Fang, Shouguo title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date: 2019-01-05 journal: Virology DOI: 10.1016/j.virol.2018.12.019 sha: doc_id: 309469 cord_uid: 2naxn580 file: cache/cord-310920-itqwhi6a.json key: cord-310920-itqwhi6a authors: Haddad, Christina; Davila-Calderon, Jesse; Tolbert, Blanton S. title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 journal: Methods DOI: 10.1016/j.ymeth.2020.06.013 sha: doc_id: 310920 cord_uid: itqwhi6a file: cache/cord-313138-y485ev30.json key: cord-313138-y485ev30 authors: Magor, Katharine E.; Miranzo Navarro, Domingo; Barber, Megan R.W.; Petkau, Kristina; Fleming-Canepa, Ximena; Blyth, Graham A.D.; Blaine, Alysson H. title: Defense genes missing from the flight division date: 2013-04-24 journal: Dev Comp Immunol DOI: 10.1016/j.dci.2013.04.010 sha: doc_id: 313138 cord_uid: y485ev30 file: cache/cord-314254-9ye8tfvz.json key: cord-314254-9ye8tfvz authors: Pfaender, Stephanie; Brown, Richard JP; Pietschmann, Thomas; Steinmann, Eike title: Natural reservoirs for homologs of hepatitis C virus date: 2014-03-26 journal: Emerg Microbes Infect DOI: 10.1038/emi.2014.19 sha: doc_id: 314254 cord_uid: 9ye8tfvz file: cache/cord-307914-lgprrwee.json key: cord-307914-lgprrwee authors: Bartok, Eva; Hartmann, Gunther title: Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids date: 2020-07-14 journal: Immunity DOI: 10.1016/j.immuni.2020.06.014 sha: doc_id: 307914 cord_uid: lgprrwee file: cache/cord-310947-aqau2n7q.json key: cord-310947-aqau2n7q authors: Pan, Ji'An; Peng, Xiaoxue; Gao, Yajing; Li, Zhilin; Lu, Xiaolu; Chen, Yingzhao; Ishaq, Musarat; Liu, Dan; DeDiego, Marta L.; Enjuanes, Luis; Guo, Deyin title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 journal: PLoS One DOI: 10.1371/journal.pone.0003299 sha: doc_id: 310947 cord_uid: aqau2n7q file: cache/cord-313161-07iwwsfz.json key: cord-313161-07iwwsfz authors: Lundstrom, Kenneth title: Alphavirus-Based Vaccines date: 2014-06-16 journal: Viruses DOI: 10.3390/v6062392 sha: doc_id: 313161 cord_uid: 07iwwsfz file: cache/cord-314369-o4nis91y.json key: cord-314369-o4nis91y authors: Lopez-Lopes, G. I. S.; Ahagon, C. M.; Bonega, M. A.; Santos, F. P. d.; Santos, K. C. d. O.; Cilli, A.; Prado, L. S. d.; Silva, D. B. B. d.; Luz, N. B. d.; Saraceni, C. P.; Afonso, A. M. S.; Timenetsky, M. d. C.; Brigido, L. F. d. M. title: Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date: 2020-08-01 journal: nan DOI: 10.1101/2020.07.29.20163998 sha: doc_id: 314369 cord_uid: o4nis91y file: cache/cord-313439-cadyykks.json key: cord-313439-cadyykks authors: Felten, Sandra; Hartmann, Katrin title: Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date: 2019-11-15 journal: Viruses DOI: 10.3390/v11111068 sha: doc_id: 313439 cord_uid: cadyykks file: cache/cord-314560-rswa5zdn.json key: cord-314560-rswa5zdn authors: Manjunath, N.; Kumar, Priti; Lee, Sang Kyung; Shankar, Premlata title: Interfering antiviral immunity: application, subversion, hope? date: 2006-06-06 journal: Trends Immunol DOI: 10.1016/j.it.2006.05.006 sha: doc_id: 314560 cord_uid: rswa5zdn file: cache/cord-314753-xflhxb13.json key: cord-314753-xflhxb13 authors: Manso, Carmen F.; Bibby, David F.; Mbisa, Jean L. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 journal: Sci Rep DOI: 10.1038/s41598-017-02239-5 sha: doc_id: 314753 cord_uid: xflhxb13 file: cache/cord-310967-15mv5yx7.json key: cord-310967-15mv5yx7 authors: Morris, Vincent L.; Tieszer, Christina; MacKinnon, Joanne; Percy, Dean title: Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease date: 1989-03-31 journal: Virology DOI: 10.1016/0042-6822(89)90048-2 sha: doc_id: 310967 cord_uid: 15mv5yx7 file: cache/cord-307598-p54p7enk.json key: cord-307598-p54p7enk authors: Schlee, Martin title: Master sensors of pathogenic RNA – RIG-I like receptors date: 2013-07-01 journal: Immunobiology DOI: 10.1016/j.imbio.2013.06.007 sha: doc_id: 307598 cord_uid: p54p7enk file: cache/cord-310861-9kb0b6rq.json key: cord-310861-9kb0b6rq authors: Koo, Bonhan; Jin, Choong Eun; Lee, Tae Yoon; Lee, Jeong Hoon; Park, Mi Kyoung; Sung, Heungsup; Park, Se Yoon; Lee, Hyun Jung; Kim, Sun Mi; Kim, Ji Yeun; Kim, Sung-Han; Shin, Yong title: An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections date: 2017-04-15 journal: Biosens Bioelectron DOI: 10.1016/j.bios.2016.11.051 sha: doc_id: 310861 cord_uid: 9kb0b6rq file: cache/cord-312392-8zxl48af.json key: cord-312392-8zxl48af authors: Buonavoglia, Canio; Decaro, Nicola; Martella, Vito; Elia, Gabriella; Campolo, Marco; Desario, Costantina; Castagnaro, Massimo; Tempesta, Maria title: Canine Coronavirus Highly Pathogenic for Dogs date: 2006-03-17 journal: Emerg Infect Dis DOI: 10.3201/eid1203.050839 sha: doc_id: 312392 cord_uid: 8zxl48af file: cache/cord-312741-0au4nctt.json key: cord-312741-0au4nctt authors: Lin, Panpan; Wang, Manni; Wei, Yuquan; Kim, Taewan; Wei, Xiawei title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 journal: MedComm (Beijing) DOI: 10.1002/mco2.26 sha: doc_id: 312741 cord_uid: 0au4nctt file: cache/cord-315069-xo4mbxei.json key: cord-315069-xo4mbxei authors: Knorr, D. A.; Mullin, R. H.; Hearne, P. Q.; Morris, T. J. title: De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage date: 1991-03-31 journal: Virology DOI: 10.1016/0042-6822(91)90484-s sha: doc_id: 315069 cord_uid: xo4mbxei file: cache/cord-312223-qgwzgazd.json key: cord-312223-qgwzgazd authors: Shafagati, Nazly; Narayanan, Aarthi; Baer, Alan; Fite, Katherine; Pinkham, Chelsea; Bailey, Charles; Kashanchi, Fatah; Lepene, Benjamin; Kehn-Hall, Kylene title: The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date: 2013-07-04 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0002296 sha: doc_id: 312223 cord_uid: qgwzgazd file: cache/cord-314572-1pou702r.json key: cord-314572-1pou702r authors: Lin, Ya-Hui; Chang, Kung-Yao title: Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date: 2016-10-14 journal: Nucleic Acids Res DOI: 10.1093/nar/gkw718 sha: doc_id: 314572 cord_uid: 1pou702r file: cache/cord-313684-61hkogdh.json key: cord-313684-61hkogdh authors: Samaddar, Arghadip; Grover, Malika; Nag, Vijaya Lakshmi title: Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date: 2020-09-17 journal: Front Pharmacol DOI: 10.3389/fphar.2020.585888 sha: doc_id: 313684 cord_uid: 61hkogdh file: cache/cord-314891-brgtwxhe.json key: cord-314891-brgtwxhe authors: Fumian, Tulio M.; Tuipulotu, Daniel Enosi; Netzler, Natalie E.; Lun, Jennifer H.; Russo, Alice G.; Yan, Grace J. H.; White, Peter A. title: Potential Therapeutic Agents for Feline Calicivirus Infection date: 2018-08-16 journal: Viruses DOI: 10.3390/v10080433 sha: doc_id: 314891 cord_uid: brgtwxhe file: cache/cord-315909-vwugf0wp.json key: cord-315909-vwugf0wp authors: Letko, Michael; Munster, Vincent title: Studying Evolutionary Adaptation of MERS-CoV date: 2019-09-14 journal: MERS Coronavirus DOI: 10.1007/978-1-0716-0211-9_1 sha: doc_id: 315909 cord_uid: vwugf0wp file: cache/cord-316134-lkd2mj27.json key: cord-316134-lkd2mj27 authors: Sungsuwan, Suttipun; Jongkaewwattana, Anan; Jaru-Ampornpan, Peera title: Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication date: 2020-01-15 journal: Virology DOI: 10.1016/j.virol.2019.11.007 sha: doc_id: 316134 cord_uid: lkd2mj27 file: cache/cord-317244-4su5on6s.json key: cord-317244-4su5on6s authors: Maganga, Gael D.; Bourgarel, Mathieu; Obame Nkoghe, Judicael; N'Dilimabaka, Nadine; Drosten, Christian; Paupy, Christophe; Morand, Serge; Drexler, Jan Felix; Leroy, Eric M. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 journal: PLoS One DOI: 10.1371/journal.pone.0115588 sha: doc_id: 317244 cord_uid: 4su5on6s file: cache/cord-315072-b28yikvj.json key: cord-315072-b28yikvj authors: Giotis, Efstathios S.; Robey, Rebecca C.; Skinner, Natalie G.; Tomlinson, Christopher D.; Goodbourn, Stephen; Skinner, Michael A. title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) date: 2016-08-05 journal: Vet Res DOI: 10.1186/s13567-016-0363-8 sha: doc_id: 315072 cord_uid: b28yikvj file: cache/cord-315483-l6dm82pp.json key: cord-315483-l6dm82pp authors: Santhakumar, Diwakar; Rohaim, Mohammed Abdel Mohsen Shahaat; Hussein, Hussein A.; Hawes, Pippa; Ferreira, Helena Lage; Behboudi, Shahriar; Iqbal, Munir; Nair, Venugopal; Arns, Clarice W.; Munir, Muhammad title: Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses date: 2018-05-01 journal: Sci Rep DOI: 10.1038/s41598-018-24905-y sha: doc_id: 315483 cord_uid: l6dm82pp file: cache/cord-303533-6s01qplg.json key: cord-303533-6s01qplg authors: Neuman, Benjamin W.; Angelini, Megan M.; Buchmeier, Michael J. title: Does form meet function in the coronavirus replicative organelle? date: 2014-07-15 journal: Trends Microbiol DOI: 10.1016/j.tim.2014.06.003 sha: doc_id: 303533 cord_uid: 6s01qplg file: cache/cord-312517-b24zlaqt.json key: cord-312517-b24zlaqt authors: Kim, Denny; Robertson, James S.; Excler, Jean-Louis; Condit, Richard C.; Fast, Patricia E.; Gurwith, Marc; Pavlakis, George; Monath, Thomas P.; Smith, Jonathan; Wood, David; Smith, Emily R.; Chen, Robert T.; Kochhar, Sonali title: The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines date: 2020-06-19 journal: Vaccine DOI: 10.1016/j.vaccine.2020.06.017 sha: doc_id: 312517 cord_uid: b24zlaqt file: cache/cord-313301-7mkadtp9.json key: cord-313301-7mkadtp9 authors: Duffy, Siobain; Burch, Christina L.; Turner, Paul E. title: EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date: 2007-08-23 journal: Evolution DOI: 10.1111/j.1558-5646.2007.00226.x sha: doc_id: 313301 cord_uid: 7mkadtp9 file: cache/cord-314877-db7tze8j.json key: cord-314877-db7tze8j authors: Chkuaseli, Tamari; White, K Andrew title: Activation of viral transcription by stepwise largescale folding of an RNA virus genome date: 2020-08-12 journal: Nucleic Acids Res DOI: 10.1093/nar/gkaa675 sha: doc_id: 314877 cord_uid: db7tze8j file: cache/cord-315611-xbj41ekc.json key: cord-315611-xbj41ekc authors: Ahmad, Mohammed; Dwivedy, Abhisek; Mariadasse, Richard; Tiwari, Satish; Kar, Deepsikha; Jeyakanthan, Jeyaraman; Biswal, Bichitra K. title: Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date: 2020-07-14 journal: ACS Omega DOI: 10.1021/acsomega.0c02096 sha: doc_id: 315611 cord_uid: xbj41ekc file: cache/cord-316179-kmdxltie.json key: cord-316179-kmdxltie authors: Fozouni, P.; Son, S.; Diaz de Leon Derby, M.; Knott, G. J.; Gray, C. N.; D'Ambrosio, M. V.; Zhao, C.; Switz, N. A.; Kumar, G. R.; Stephens, S. I.; Boehm, D.; Tsou, C.-L.; Shu, J.; Bhuiya, A.; Armstrong, M.; Harris, A.; Osterloh, J. M.; Meyer-Franke, A.; Langelier, C.; Pollard, K. S.; Crawford, E. D.; Puschnik, A. S.; Phelps, M.; Kistler, A.; DeRisi, J. L.; Doudna, J. A.; Fletcher, D. A.; Ott, M. title: Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date: 2020-09-30 journal: nan DOI: 10.1101/2020.09.28.20201947 sha: doc_id: 316179 cord_uid: kmdxltie file: cache/cord-316503-wtmmewiz.json key: cord-316503-wtmmewiz authors: Warren, Travis K.; Shurtleff, Amy C.; Bavari, Sina title: Advanced morpholino oligomers: A novel approach to antiviral therapy date: 2012-02-14 journal: Antiviral Res DOI: 10.1016/j.antiviral.2012.02.004 sha: doc_id: 316503 cord_uid: wtmmewiz file: cache/cord-312001-8p7scli8.json key: cord-312001-8p7scli8 authors: Majzoub, Karim; Wrensch, Florian; Baumert, Thomas F. title: The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans date: 2019-08-16 journal: Viruses DOI: 10.3390/v11080758 sha: doc_id: 312001 cord_uid: 8p7scli8 file: cache/cord-312461-5qzpo6l1.json key: cord-312461-5qzpo6l1 authors: Adalja, Amesh A.; Watson, Matthew; Toner, Eric S.; Cicero, Anita; Inglesby, Thomas V. title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date: 2019-08-30 journal: Global Catastrophic Biological Risks DOI: 10.1007/82_2019_176 sha: doc_id: 312461 cord_uid: 5qzpo6l1 file: cache/cord-312688-12san3m7.json key: cord-312688-12san3m7 authors: Martin, Baptiste; Hoenen, Thomas; Canard, Bruno; Decroly, Etienne title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date: 2016-09-14 journal: Antiviral Res DOI: 10.1016/j.antiviral.2016.09.001 sha: doc_id: 312688 cord_uid: 12san3m7 file: cache/cord-315384-eqiokrub.json key: cord-315384-eqiokrub authors: van der Hoek, Lia; Sure, Klaus; Ihorst, Gabriele; Stang, Alexander; Pyrc, Krzysztof; Jebbink, Maarten F; Petersen, Gudula; Forster, Johannes; Berkhout, Ben; Überla, Klaus title: Croup Is Associated with the Novel Coronavirus NL63 date: 2005-08-23 journal: PLoS Med DOI: 10.1371/journal.pmed.0020240 sha: doc_id: 315384 cord_uid: eqiokrub file: cache/cord-317037-1qydcc5e.json key: cord-317037-1qydcc5e authors: Kumar, Asit; Kodidela, Sunitha; Tadrous, Erene; Cory, Theodore James; Walker, Crystal Martin; Smith, Amber Marie; Mukherjee, Ahona; Kumar, Santosh title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 journal: Viruses DOI: 10.3390/v12080887 sha: doc_id: 317037 cord_uid: 1qydcc5e file: cache/cord-317591-qa6oxy4j.json key: cord-317591-qa6oxy4j authors: Fukushima, Akiko; Fukuda, Noboru; Lai, Yimu; Ueno, Takahiro; Moriyama, Mitsuhiko; Taguchi, Fumihiro; Iguchi, Akifumi; Shimizu, Kazushi; Kuroda, Kazumichi title: Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date: 2009-05-07 journal: Intervirology DOI: 10.1159/000215946 sha: doc_id: 317591 cord_uid: qa6oxy4j file: cache/cord-317851-lj07947c.json key: cord-317851-lj07947c authors: Elena, S F; Agudelo-Romero, P; Carrasco, P; Codoñer, F M; Martín, S; Torres-Barceló, C; Sanjuán, R title: Experimental evolution of plant RNA viruses date: 2008-02-06 journal: Heredity (Edinb) DOI: 10.1038/sj.hdy.6801088 sha: doc_id: 317851 cord_uid: lj07947c file: cache/cord-318359-41h90h05.json key: cord-318359-41h90h05 authors: Irigoyen, Nerea; Dinan, Adam M.; Brierley, Ian; Firth, Andrew E. title: Ribosome profiling of the retrovirus murine leukemia virus date: 2018-01-22 journal: Retrovirology DOI: 10.1186/s12977-018-0394-5 sha: doc_id: 318359 cord_uid: 41h90h05 file: cache/cord-313541-fpqwzf9k.json key: cord-313541-fpqwzf9k authors: Ulloa, S.; Bravo, C.; Parra, B.; Ramirez, E.; Acevedo, A.; Fasce, R.; Fernandez, J. title: A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date: 2020-08-22 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113960 sha: doc_id: 313541 cord_uid: fpqwzf9k file: cache/cord-314019-8n0jafsk.json key: cord-314019-8n0jafsk authors: Feng, Qian; Langereis, Martijn A.; van Kuppeveld, Frank J.M. title: Induction and suppression of innate antiviral responses by picornaviruses date: 2014-07-18 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2014.07.003 sha: doc_id: 314019 cord_uid: 8n0jafsk file: cache/cord-312886-o3ipzn05.json key: cord-312886-o3ipzn05 authors: Onomoto, Koji; Yoneyama, Mitsutoshi; Fung, Gabriel; Kato, Hiroki; Fujita, Takashi title: Antiviral innate immunity and stress granule responses date: 2014-08-19 journal: Trends Immunol DOI: 10.1016/j.it.2014.07.006 sha: doc_id: 312886 cord_uid: o3ipzn05 file: cache/cord-314567-purplsjn.json key: cord-314567-purplsjn authors: Fernández-Ponce, Cecilia; Durán-Ruiz, Maria C.; Narbona-Sánchez, Isaac; Muñoz-Miranda, Juan P.; Arbulo-Echevarria, Mikel M.; Serna-Sanz, Antonio; Baumann, Christian; Litrán, Rocío; Aguado, Enrique; Bloch, Wilhelm; García-Cozar, Francisco title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 journal: Front Microbiol DOI: 10.3389/fmicb.2017.02595 sha: doc_id: 314567 cord_uid: purplsjn file: cache/cord-314833-6fue84x6.json key: cord-314833-6fue84x6 authors: Chang, Chung-ke; Hou, Ming-Hon; Chang, Chi-Fon; Hsiao, Chwan-Deng; Huang, Tai-huang title: The SARS coronavirus nucleocapsid protein – Forms and functions date: 2014-01-11 journal: Antiviral Res DOI: 10.1016/j.antiviral.2013.12.009 sha: doc_id: 314833 cord_uid: 6fue84x6 file: cache/cord-315616-pvt0amth.json key: cord-315616-pvt0amth authors: Poole, Anthony; Penny, David; Sjöberg, Britt-Marie title: Methyl-RNA: an evolutionary bridge between RNA and DNA? date: 2004-06-17 journal: Chem Biol DOI: 10.1016/s1074-5521(00)00042-9 sha: doc_id: 315616 cord_uid: pvt0amth file: cache/cord-319664-gyktrd36.json key: cord-319664-gyktrd36 authors: Mancini, Fabiola; Barbanti, Fabrizio; Scaturro, Maria; Errico, Giulia; Iacobino, Angelo; Bella, Antonino; Riccardo, Flavia; Marsili, Giulia; Stefanelli, Paola; Pezzotti, Patrizio; Rezza, Giovanni; Ciervo, Alessandra title: Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date: 2020-06-18 journal: Emerging microbes & infections DOI: 10.1080/22221751.2020.1775500 sha: doc_id: 319664 cord_uid: gyktrd36 file: cache/cord-318853-mxyxwkhx.json key: cord-318853-mxyxwkhx authors: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 journal: Virol J DOI: 10.1186/1743-422x-2-70 sha: doc_id: 318853 cord_uid: mxyxwkhx file: cache/cord-319100-3gdawhfn.json key: cord-319100-3gdawhfn authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date: 2020-06-10 journal: bioRxiv DOI: 10.1101/2020.06.09.142323 sha: doc_id: 319100 cord_uid: 3gdawhfn file: cache/cord-312892-p72zwmtb.json key: cord-312892-p72zwmtb authors: Chen, Nanhua; Xia, Pengpeng; Li, Shuangjie; Zhang, Tangjie; Wang, Tony T.; Zhu, Jianzhong title: RNA sensors of the innate immune system and their detection of pathogens date: 2017-04-04 journal: IUBMB Life DOI: 10.1002/iub.1625 sha: doc_id: 312892 cord_uid: p72zwmtb file: cache/cord-314316-hsspggp8.json key: cord-314316-hsspggp8 authors: Sirinarumitr, Theerapol; Paul, Prem S.; Halbur, Patrick G.; Kluge, John P. title: Rapid in situ hybridization technique for the detection of ribonucleic acids in tissues using radiolabelled and fluorescein-labelled riboprobes date: 1997-08-31 journal: Molecular and Cellular Probes DOI: 10.1006/mcpr.1997.0114 sha: doc_id: 314316 cord_uid: hsspggp8 file: cache/cord-315054-kji2kfek.json key: cord-315054-kji2kfek authors: Chakraborty, Nabarun; Schmitt, Connie W.; Honnold, Cary L.; Moyler, Candace; Butler, Stephen; Nachabe, Hisham; Gautam, Aarti; Hammamieh, Rasha title: Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration date: 2020-07-22 journal: Front Mol Biosci DOI: 10.3389/fmolb.2020.00142 sha: doc_id: 315054 cord_uid: kji2kfek file: cache/cord-317455-6qx0v28w.json key: cord-317455-6qx0v28w authors: Brown, Paul A.; Courtillon, Céline; Weerts, Erik A. W. S.; Andraud, Mathieu; Allée, Chantal; Vendembeuche, Anthony; Amelot, Michel; Rose, Nicolas; Verheije, Monique H.; Eterradossi, Nicolas title: Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date: 2018-09-10 journal: Transbound Emerg Dis DOI: 10.1111/tbed.13006 sha: doc_id: 317455 cord_uid: 6qx0v28w file: cache/cord-317720-gbi11oxx.json key: cord-317720-gbi11oxx authors: Lefferts, Joel A.; Gutmann, Edward J.; Martin, Isabella W.; Wells, Wendy A.; Tsongalis, Gregory J. title: Implementation of an Emergency Use Authorization Test During an Impending National Crisis date: 2020-05-14 journal: J Mol Diagn DOI: 10.1016/j.jmoldx.2020.05.001 sha: doc_id: 317720 cord_uid: gbi11oxx file: cache/cord-318164-6rqi17oz.json key: cord-318164-6rqi17oz authors: Paoli, D.; Pallotti, F.; Nigro, G.; Aureli, A.; Perlorca, A.; Mazzuti, L.; Di Carlo, D.; Turriziani, O.; Lenzi, A.; Lombardo, F. title: Sperm cryopreservation during the SARS-CoV-2 pandemic date: 2020-10-10 journal: J Endocrinol Invest DOI: 10.1007/s40618-020-01438-8 sha: doc_id: 318164 cord_uid: 6rqi17oz file: cache/cord-318495-1w74wf02.json key: cord-318495-1w74wf02 authors: Vignuzzi, Marco; López, Carolina B. title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 journal: Nat Microbiol DOI: 10.1038/s41564-019-0465-y sha: doc_id: 318495 cord_uid: 1w74wf02 file: cache/cord-318551-c1qr27lg.json key: cord-318551-c1qr27lg authors: Boguszewska‐Chachulska, Anna M.; Haenni, Anne‐Lise title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 journal: Adv Virus Res DOI: 10.1016/s0065-3527(05)65002-6 sha: doc_id: 318551 cord_uid: c1qr27lg file: cache/cord-318576-dc5n6ni4.json key: cord-318576-dc5n6ni4 authors: Jitobaom, Kunlakanya; Phakaratsakul, Supinya; Sirihongthong, Thanyaporn; Chotewutmontri, Sasithorn; Suriyaphol, Prapat; Suptawiwat, Ornpreya; Auewarakul, Prasert title: Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation date: 2020-05-08 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e03915 sha: doc_id: 318576 cord_uid: dc5n6ni4 file: cache/cord-318749-k91oku7h.json key: cord-318749-k91oku7h authors: Dong, Hui-Jun; Zhang, Rui; Kuang, Yu; Wang, Xiao-Jia title: Selective regulation in ribosome biogenesis and protein production for efficient viral translation date: 2020-10-29 journal: Arch Microbiol DOI: 10.1007/s00203-020-02094-5 sha: doc_id: 318749 cord_uid: k91oku7h file: cache/cord-319179-gqaxf7mz.json key: cord-319179-gqaxf7mz authors: Denison, M.; Perlman, S. title: Identification of putative polymerase gene product in cells infected with murine coronavirus A59 date: 1987-04-30 journal: Virology DOI: 10.1016/0042-6822(87)90303-5 sha: doc_id: 319179 cord_uid: gqaxf7mz file: cache/cord-319501-a2x1hvkk.json key: cord-319501-a2x1hvkk authors: Wong, Lok-Yin Roy; Lui, Pak-Yin; Jin, Dong-Yan title: A molecular arms race between host innate antiviral response and emerging human coronaviruses date: 2016-01-15 journal: Virol Sin DOI: 10.1007/s12250-015-3683-3 sha: doc_id: 319501 cord_uid: a2x1hvkk file: cache/cord-319729-6lzjhn8j.json key: cord-319729-6lzjhn8j authors: Tian, Bin; Zhou, Ming; Yang, Yu; Yu, Lan; Luo, Zhaochen; Tian, Dayong; Wang, Ke; Cui, Min; Chen, Huanchun; Fu, Zhen F.; Zhao, Ling title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway date: 2018-01-19 journal: Front Immunol DOI: 10.3389/fimmu.2017.02011 sha: doc_id: 319729 cord_uid: 6lzjhn8j file: cache/cord-319780-rfj9t99r.json key: cord-319780-rfj9t99r authors: Alexander, S.P.H.; Armstrong, J.; Davenport, A.P.; Davies, J.; Faccenda, E.; Harding, S.D.; Levi‐Schaffer, F.; Maguire, J.J.; Pawson, A.J.; Southan, C.; Spedding, M.J. title: A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date: 2020-05-01 journal: Br J Pharmacol DOI: 10.1111/bph.15094 sha: doc_id: 319780 cord_uid: rfj9t99r file: cache/cord-319842-4mnaicki.json key: cord-319842-4mnaicki authors: Jackson, William T; Giddings, Thomas H; Taylor, Matthew P; Mulinyawe, Sara; Rabinovitch, Marlene; Kopito, Ron R; Kirkegaard, Karla title: Subversion of Cellular Autophagosomal Machinery by RNA Viruses date: 2005-04-26 journal: PLoS Biol DOI: 10.1371/journal.pbio.0030156 sha: doc_id: 319842 cord_uid: 4mnaicki file: cache/cord-315085-rucfowvv.json key: cord-315085-rucfowvv authors: Sekulic, Miroslav; Harper, Holly; Nezami, Behtash G; Shen, Daniel L; Sekulic, Simona Pichler; Koeth, Aaron T; Harding, Clifford V; Gilmore, Hannah; Sadri, Navid title: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date: 2020-05-26 journal: Am J Clin Pathol DOI: 10.1093/ajcp/aqaa091 sha: doc_id: 315085 cord_uid: rucfowvv file: cache/cord-317537-wgu5cd0y.json key: cord-317537-wgu5cd0y authors: Lu, Hsiang-Chia; Chen, Cheng-En; Tsai, Meng-Hsiun; Wang, Hsiang-iu; Su, Hong-Ji; Yeh, Hsin-Hung title: Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant date: 2009-05-25 journal: Virology DOI: 10.1016/j.virol.2009.02.049 sha: doc_id: 317537 cord_uid: wgu5cd0y file: cache/cord-317715-xtsi663k.json key: cord-317715-xtsi663k authors: Ortiz-Riaño, Emilio; Cheng, Benson Y. H.; de la Torre, Juan C.; Martínez-Sobrido, Luis title: D471G Mutation in LCMV-NP Affects its Ability to Self-associate and Results in a Dominant Negative Effect in Viral RNA Synthesis date: 2012-10-16 journal: Viruses DOI: 10.3390/v4102137 sha: doc_id: 317715 cord_uid: xtsi663k file: cache/cord-318478-fn0gcxbb.json key: cord-318478-fn0gcxbb authors: Ziv, Omer; Price, Jonathan; Shalamova, Lyudmila; Kamenova, Tsveta; Goodfellow, Ian; Weber, Friedemann; Miska, Eric A. title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.07.19.211110 sha: doc_id: 318478 cord_uid: fn0gcxbb file: cache/cord-319116-2ts6zpdb.json key: cord-319116-2ts6zpdb authors: Ruggiero, Emanuela; Richter, Sara N title: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy date: 2018-04-20 journal: Nucleic Acids Res DOI: 10.1093/nar/gky187 sha: doc_id: 319116 cord_uid: 2ts6zpdb file: cache/cord-319681-kjet3e50.json key: cord-319681-kjet3e50 authors: Lin, Zhaoru; Gilbert, Robert J. C.; Brierley, Ian title: Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U(6)A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting date: 2012-06-28 journal: Nucleic Acids Res DOI: 10.1093/nar/gks629 sha: doc_id: 319681 cord_uid: kjet3e50 file: cache/cord-317773-jdq1d98i.json key: cord-317773-jdq1d98i authors: Meng, Qing-Wen; Zhang, Zai-Ping; Wang, Wei; Tian, Jin; Xiao, Zhi-Guang title: Enhanced inhibition of Avian leukosis virus subgroup J replication by multi-target miRNAs date: 2011-12-22 journal: Virol J DOI: 10.1186/1743-422x-8-556 sha: doc_id: 317773 cord_uid: jdq1d98i file: cache/cord-318751-4v2tl0gi.json key: cord-318751-4v2tl0gi authors: Arias, Armando; Emmott, Edward; Vashist, Surender; Goodfellow, Ian title: Progress towards the prevention and treatment of norovirus infections date: 2013-11-17 journal: Future Microbiol DOI: 10.2217/fmb.13.109 sha: doc_id: 318751 cord_uid: 4v2tl0gi file: cache/cord-319906-s7kzp795.json key: cord-319906-s7kzp795 authors: Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L title: StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase date: 2011-06-02 journal: BMC Bioinformatics DOI: 10.1186/1471-2105-12-226 sha: doc_id: 319906 cord_uid: s7kzp795 file: cache/cord-320169-dtv7to3l.json key: cord-320169-dtv7to3l authors: Liu, Yen-Chin; Kuo, Rei-Lin; Shih, Shin-Ru title: COVID-19: the First Documented Coronavirus Pandemic in History date: 2020-05-05 journal: Biomed J DOI: 10.1016/j.bj.2020.04.007 sha: doc_id: 320169 cord_uid: dtv7to3l file: cache/cord-321053-lgae22f8.json key: cord-321053-lgae22f8 authors: Gerold, Gisa; Pietschmann, Thomas title: Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date: 2013-10-04 journal: Curr Hepat Rep DOI: 10.1007/s11901-013-0187-1 sha: doc_id: 321053 cord_uid: lgae22f8 file: cache/cord-319635-kh99n7q2.json key: cord-319635-kh99n7q2 authors: Chiang, Wei-Wei; Chuang, Ching-Kai; Chao, Mei; Chen, Wei-June title: Cell Type-Dependent RNA Recombination Frequency in the Japanese Encephalitis Virus date: 2014-07-22 journal: Biomed Res Int DOI: 10.1155/2014/471323 sha: doc_id: 319635 cord_uid: kh99n7q2 file: cache/cord-320501-xqgqq55q.json key: cord-320501-xqgqq55q authors: Theobald, Nigel title: Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine date: 2020-06-24 journal: Drug Discov Today DOI: 10.1016/j.drudis.2020.06.020 sha: doc_id: 320501 cord_uid: xqgqq55q file: cache/cord-320921-eumuid3r.json key: cord-320921-eumuid3r authors: Widagdo, W.; Okba, Nisreen M. A.; Richard, Mathilde; de Meulder, Dennis; Bestebroer, Theo M.; Lexmond, Pascal; Farag, Elmoubasher A. B. A.; Al-Hajri, Mohammed; Stittelaar, Koert J.; de Waal, Leon; van Amerongen, Geert; van den Brand, Judith M. A.; Haagmans, Bart L.; Herfst, Sander title: Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits date: 2019-04-24 journal: Viruses DOI: 10.3390/v11040381 sha: doc_id: 320921 cord_uid: eumuid3r file: cache/cord-321505-m40s6uw9.json key: cord-321505-m40s6uw9 authors: Sakamoto, Naoya; Tanabe, Yoko; Yokota, Takanori; Satoh, Kenichi; Sekine‐Osajima, Yuko; Nakagawa, Mina; Itsui, Yasuhiro; Tasaka, Megumi; Sakurai, Yuki; Cheng‐Hsin, Chen; Yano, Masahiko; Ohkoshi, Shogo; Aoyagi, Yutaka; Maekawa, Shinya; Enomoto, Nobuyuki; Kohara, Michinori; Watanabe, Mamoru title: Inhibition of hepatitis C virus infection and expression in vitro and in vivo by recombinant adenovirus expressing short hairpin RNA date: 2007-08-07 journal: J Gastroenterol Hepatol DOI: 10.1111/j.1440-1746.2007.05076.x sha: doc_id: 321505 cord_uid: m40s6uw9 file: cache/cord-319781-6thdg2up.json key: cord-319781-6thdg2up authors: Payne, Kelly; Kenny, Peter; Scovell, Jason M.; Khodamoradi, Kajal; Ramasamy, Ranjith title: Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date: 2020-07-24 journal: Sex Med Rev DOI: 10.1016/j.sxmr.2020.06.003 sha: doc_id: 319781 cord_uid: 6thdg2up file: cache/cord-319821-ij34t1ae.json key: cord-319821-ij34t1ae authors: Bauer, Lisa; Lyoo, Heyrhyoung; van der Schaar, Hilde M; Strating, Jeroen RPM; van Kuppeveld, Frank JM title: Direct-acting antivirals and host-targeting strategies to combat enterovirus infections date: 2017-04-12 journal: Curr Opin Virol DOI: 10.1016/j.coviro.2017.03.009 sha: doc_id: 319821 cord_uid: ij34t1ae file: cache/cord-320709-2pnqpljt.json key: cord-320709-2pnqpljt authors: Munster, Vincent J.; Adney, Danielle R.; van Doremalen, Neeltje; Brown, Vienna R.; Miazgowicz, Kerri L.; Milne-Price, Shauna; Bushmaker, Trenton; Rosenke, Rebecca; Scott, Dana; Hawkinson, Ann; de Wit, Emmie; Schountz, Tony; Bowen, Richard A. title: Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis) date: 2016-02-22 journal: Sci Rep DOI: 10.1038/srep21878 sha: doc_id: 320709 cord_uid: 2pnqpljt file: cache/cord-320935-3n157yl4.json key: cord-320935-3n157yl4 authors: Kumar, Manish; Mohapatra, Sanjeeb; Mazumder, Payal; Singh, Ashwin; Honda, Ryo; Lin, Chuxia; Kumari, Rina; Goswami, Ritusmita; Jha, Pawan Kumar; Vithanage, Meththika; Kuroda, Keisuke title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 journal: Curr Pollut Rep DOI: 10.1007/s40726-020-00161-5 sha: doc_id: 320935 cord_uid: 3n157yl4 file: cache/cord-318276-so5jooj0.json key: cord-318276-so5jooj0 authors: Bertholet, Christine; Van Meir, Erwin; ten Heggeler-Bordier, Béatrice; Wittek, Riccardo title: Vaccinia virus produces late mRNAs by discontinuous synthesis date: 1987-07-17 journal: Cell DOI: 10.1016/0092-8674(87)90211-x sha: doc_id: 318276 cord_uid: so5jooj0 file: cache/cord-319194-ukuia48s.json key: cord-319194-ukuia48s authors: Liò, Pietro; Goldman, Nick title: Phylogenomics and bioinformatics of SARS-CoV date: 2004-02-04 journal: Trends Microbiol DOI: 10.1016/j.tim.2004.01.005 sha: doc_id: 319194 cord_uid: ukuia48s file: cache/cord-319649-d6dqr03e.json key: cord-319649-d6dqr03e authors: Yang, Jie; Cheng, Zhenyun; Zhang, Songliu; Xiong, Wei; Xia, Hongjie; Qiu, Yang; Wang, Zhaowei; Wu, Feige; Qin, Cheng-Feng; Yin, Lei; Hu, Yuanyang; Zhou, Xi title: A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing date: 2013-12-05 journal: Nucleic Acids Res DOI: 10.1093/nar/gkt1256 sha: doc_id: 319649 cord_uid: d6dqr03e file: cache/cord-320212-fw51w4nm.json key: cord-320212-fw51w4nm authors: Friedman, Stephanie D.; Snellgrove, Wyatt C.; Genthner, Fred J. title: Genomic Sequences of two Novel Levivirus Single-Stranded RNA Coliphages (Family Leviviridae): Evidence for Recombinationin Environmental Strains date: 2012-09-13 journal: Viruses DOI: 10.3390/v4091548 sha: doc_id: 320212 cord_uid: fw51w4nm file: cache/cord-320325-sjab8zsk.json key: cord-320325-sjab8zsk authors: Mendez, Aaron S; Vogt, Carolin; Bohne, Jens; Glaunsinger, Britt A title: Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX date: 2018-12-14 journal: Nucleic Acids Res DOI: 10.1093/nar/gky932 sha: doc_id: 320325 cord_uid: sjab8zsk file: cache/cord-320713-b37c8aye.json key: cord-320713-b37c8aye authors: Roberts, Lisa O.; Jopling, Catherine L.; Jackson, Richard J.; Willis, Anne E. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 journal: Prog Mol Biol Transl Sci DOI: 10.1016/s1877-1173(09)90009-6 sha: doc_id: 320713 cord_uid: b37c8aye file: cache/cord-321013-8pkrg0mx.json key: cord-321013-8pkrg0mx authors: McBride, Ruth; van Zyl, Marjorie; Fielding, Burtram C. title: The Coronavirus Nucleocapsid Is a Multifunctional Protein date: 2014-08-07 journal: Viruses DOI: 10.3390/v6082991 sha: doc_id: 321013 cord_uid: 8pkrg0mx file: cache/cord-321957-ybtk9cp1.json key: cord-321957-ybtk9cp1 authors: Carey, Brian D.; Akhrymuk, Ivan; Dahal, Bibha; Pinkham, Chelsea L.; Bracci, Nicole; Finstuen-Magro, Sarah; Lin, Shih-Chao; Lehman, Caitlin W.; Sokoloski, Kevin J.; Kehn-Hall, Kylene title: Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation date: 2020-03-09 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008282 sha: doc_id: 321957 cord_uid: ybtk9cp1 file: cache/cord-320351-47d0nby0.json key: cord-320351-47d0nby0 authors: Li, Zhouxiao; Cheng, Ye; Wu, Fan; Wu, Liangliang; Cao, Hongyong; Wang, Qian; Tang, Weiwei title: The emerging landscape of circular RNAs in immunity: breakthroughs and challenges date: 2020-07-10 journal: Biomark Res DOI: 10.1186/s40364-020-00204-5 sha: doc_id: 320351 cord_uid: 47d0nby0 file: cache/cord-321938-pda4a5n7.json key: cord-321938-pda4a5n7 authors: Weisshoff, Hardy; Krylova, Oxana; Nikolenko, Heike; Düngen, Hans-Dirk; Dallmann, Andre; Becker, Susanne; Göttel, Peter; Müller, Johannes; Haberland, Annekathrin title: Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date: 2020-11-02 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e05421 sha: doc_id: 321938 cord_uid: pda4a5n7 file: cache/cord-322084-gkg1059v.json key: cord-322084-gkg1059v authors: JEONG, YONG SEOK; REPASS, JOHN F.; KIM, YOUNG-NAM; HWANG, SUN-MIN; MAKINO, SHINJI title: Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence date: 1996-03-01 journal: Virology DOI: 10.1006/viro.1996.0118 sha: doc_id: 322084 cord_uid: gkg1059v file: cache/cord-322240-z8zkl2xh.json key: cord-322240-z8zkl2xh authors: Maeda, Ken; Hondo, Eiichi; Terakawa, Junpei; Kiso, Yasuo; Nakaichi, Numekazu; Endoh, Daiji; Sakai, Kouji; Morikawa, Shigeru; Mizutani, Tetsuya title: Isolation of Novel Adenovirus from Fruit Bat (Pteropus dasymallus yayeyamae) date: 2008-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1402.070932 sha: doc_id: 322240 cord_uid: z8zkl2xh file: cache/cord-321155-dty18esg.json key: cord-321155-dty18esg authors: Zhang, Rongxin; Ke, Xiao; Gu, Yu; Liu, Hongde; Sun, Xiao title: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date: 2020-06-05 journal: bioRxiv DOI: 10.1101/2020.06.05.135749 sha: doc_id: 321155 cord_uid: dty18esg file: cache/cord-321607-3r736dnk.json key: cord-321607-3r736dnk authors: Ezelle, Heather J.; Malathi, Krishnamurthy; Hassel, Bret A. title: The Roles of RNase-L in Antimicrobial Immunity and the Cytoskeleton-Associated Innate Response date: 2016-01-08 journal: Int J Mol Sci DOI: 10.3390/ijms17010074 sha: doc_id: 321607 cord_uid: 3r736dnk file: cache/cord-322062-nnefbeo6.json key: cord-322062-nnefbeo6 authors: Tam, Albert W.; Smith, Matthew M.; Guerra, Martha E.; Huang, Chiao-Chain; Bradley, Daniel W.; Fry, Kirk E.; Reyes, Gregory R. title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome date: 1991-11-30 journal: Virology DOI: 10.1016/0042-6822(91)90760-9 sha: doc_id: 322062 cord_uid: nnefbeo6 file: cache/cord-321773-5fw9abzl.json key: cord-321773-5fw9abzl authors: Cheng, Wenyu; Chen, Guohua; Jia, Huaijie; He, Xiaobing; Jing, Zhizhong title: DDX5 RNA Helicases: Emerging Roles in Viral Infection date: 2018-04-09 journal: Int J Mol Sci DOI: 10.3390/ijms19041122 sha: doc_id: 321773 cord_uid: 5fw9abzl file: cache/cord-323585-iv2dcpqj.json key: cord-323585-iv2dcpqj authors: Li, Su; Feng, Shuo; Wang, Jing-Han; He, Wen-Rui; Qin, Hua-Yang; Dong, Hong; Li, Lian-Feng; Yu, Shao-Xiong; Li, Yongfeng; Qiu, Hua-Ji title: eEF1A Interacts with the NS5A Protein and Inhibits the Growth of Classical Swine Fever Virus date: 2015-08-10 journal: Viruses DOI: 10.3390/v7082833 sha: doc_id: 323585 cord_uid: iv2dcpqj file: cache/cord-322234-1zyy536y.json key: cord-322234-1zyy536y authors: Lorusso, Alessio; Faaberg, Kay S.; Killian, Mary Lea; Koster, Leo; Vincent, Amy L. title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 journal: J Virol Methods DOI: 10.1016/j.jviromet.2009.12.002 sha: doc_id: 322234 cord_uid: 1zyy536y file: cache/cord-322756-ouvn71r9.json key: cord-322756-ouvn71r9 authors: Chow, Michael Y.T.; Qiu, Yingshan; Lam, Jenny K.W. title: Inhaled RNA Therapy: From Promise to Reality date: 2020-09-04 journal: Trends Pharmacol Sci DOI: 10.1016/j.tips.2020.08.002 sha: doc_id: 322756 cord_uid: ouvn71r9 file: cache/cord-322206-roxa3ix6.json key: cord-322206-roxa3ix6 authors: I. Sardi, Silvia; H. Carvalho, Rejane; C. Pacheco, Luis G.; P. d. Almeida, João P.; M. d. A. Belitardo, Emilia M.; S. Pinheiro, Carina; S. Campos, Gúbio; R. G. R. Aguiar, Eric title: High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date: 2020-07-21 journal: Viruses DOI: 10.3390/v12070782 sha: doc_id: 322206 cord_uid: roxa3ix6 file: cache/cord-322410-k23engcx.json key: cord-322410-k23engcx authors: Naguib, Mahmoud M.; El-Kady, Magdy F.; Lüschow, Dörte; Hassan, Kareem E.; Arafa, Abdel-Satar; El-Zanaty, Ali; Hassan, Mohamed K.; Hafez, Hafez M.; Grund, Christian; Harder, Timm C. title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses date: 2017-03-21 journal: J Virol Methods DOI: 10.1016/j.jviromet.2017.02.018 sha: doc_id: 322410 cord_uid: k23engcx file: cache/cord-323668-evzzfu04.json key: cord-323668-evzzfu04 authors: Yin, Zhixin; Guan, Dawei; Fan, Qin; Su, Juan; Zheng, Wenling; Ma, Wenli; Ke, Changwen title: lncRNA expression signatures in response to enterovirus 71 infection date: 2013-01-11 journal: Biochemical and Biophysical Research Communications DOI: 10.1016/j.bbrc.2012.11.101 sha: doc_id: 323668 cord_uid: evzzfu04 file: cache/cord-323691-5s5almd2.json key: cord-323691-5s5almd2 authors: Mishin, Vasiliy P; Cominelli, Fabio; Yamshchikov, Vladimir F title: A ‘minimal’ approach in design of flavivirus infectious DNA date: 2001-12-04 journal: Virus Research DOI: 10.1016/s0168-1702(01)00371-9 sha: doc_id: 323691 cord_uid: 5s5almd2 file: cache/cord-323737-6ajqy0ch.json key: cord-323737-6ajqy0ch authors: Jiang, Yuanyuan; Liu, Lanxin; Manning, Morenci; Bonahoom, Madison; Lotvola, Aaron; Yang, Zhe; Yang, Zeng-Quan title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus date: 2020-10-04 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1828172 sha: doc_id: 323737 cord_uid: 6ajqy0ch file: cache/cord-323756-atnrw9ew.json key: cord-323756-atnrw9ew authors: Vabret, Nicolas; Blander, J. Magarian title: Sensing Microbial RNA in the Cytosol date: 2013-12-25 journal: Front Immunol DOI: 10.3389/fimmu.2013.00468 sha: doc_id: 323756 cord_uid: atnrw9ew file: cache/cord-323029-7hqp8xuq.json key: cord-323029-7hqp8xuq authors: Bognár, Zsófia; Gyurcsányi, Róbert E. title: Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date: 2020-08-11 journal: Int J Mol Sci DOI: 10.3390/ijms21165748 sha: doc_id: 323029 cord_uid: 7hqp8xuq file: cache/cord-323845-s78t5qxj.json key: cord-323845-s78t5qxj authors: Soliman, H.; El-Matbouli, M. title: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) date: 2006-05-31 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2005.11.063 sha: doc_id: 323845 cord_uid: s78t5qxj file: cache/cord-323973-wszo9s3d.json key: cord-323973-wszo9s3d authors: Zhu, Hanliang; Zhang, Haoqing; Ni, Sheng; Korabečná, Marie; Yobas, Levent; Neuzil, Pavel title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 journal: Trends Analyt Chem DOI: 10.1016/j.trac.2020.115984 sha: doc_id: 323973 cord_uid: wszo9s3d file: cache/cord-323987-gh1m05gi.json key: cord-323987-gh1m05gi authors: Dziąbowska, Karolina; Czaczyk, Elżbieta; Nidzworski, Dawid title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 journal: Biosensors (Basel) DOI: 10.3390/bios8040094 sha: doc_id: 323987 cord_uid: gh1m05gi file: cache/cord-324137-nau83mjv.json key: cord-324137-nau83mjv authors: Saranathan, Nandhini; Vivekanandan, Perumal title: G-Quadruplexes: More Than Just a Kink in Microbial Genomes date: 2018-09-14 journal: Trends Microbiol DOI: 10.1016/j.tim.2018.08.011 sha: doc_id: 324137 cord_uid: nau83mjv file: cache/cord-324212-aqp73hi9.json key: cord-324212-aqp73hi9 authors: Wyszko, Eliza; Nowak, Monika; Pospieszny, Henryk; Szymanski, Maciej; Pas, Jakub; Barciszewska, Mirosława Z.; Barciszewski, Jan title: Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum date: 2006-10-09 journal: FEBS J DOI: 10.1111/j.1742-4658.2006.05497.x sha: doc_id: 324212 cord_uid: aqp73hi9 file: cache/cord-324324-8ybfiz8f.json key: cord-324324-8ybfiz8f authors: Decaro, Nicola; Lorusso, Alessio title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 journal: Vet Microbiol DOI: 10.1016/j.vetmic.2020.108693 sha: doc_id: 324324 cord_uid: 8ybfiz8f file: cache/cord-324638-gwd8qin6.json key: cord-324638-gwd8qin6 authors: Chiu, Rossa WK; Jin, Yongjie; Chung, Grace TY; Lui, Wing-bong; Chan, Anthony TC; Lim, Wilina; Dennis Lo, YM title: Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date: 2006-02-09 journal: BMC Infect Dis DOI: 10.1186/1471-2334-6-20 sha: doc_id: 324638 cord_uid: gwd8qin6 file: cache/cord-324495-0pee1i3o.json key: cord-324495-0pee1i3o authors: Kang, Hyeonjeong; Lee, Changhee title: Sasa quelpaertensis Nakai extract suppresses porcine reproductive and respiratory syndrome virus replication and modulates virus-induced cytokine production date: 2015-06-06 journal: Arch Virol DOI: 10.1007/s00705-015-2469-0 sha: doc_id: 324495 cord_uid: 0pee1i3o file: cache/cord-324928-cpryxa6p.json key: cord-324928-cpryxa6p authors: Lello, Laura Sandra; Utt, Age; Bartholomeeusen, Koen; Wang, Sainan; Rausalu, Kai; Kendall, Catherine; Coppens, Sandra; Fragkoudis, Rennos; Tuplin, Andrew; Alphey, Luke; Ariën, Kevin K.; Merits, Andres title: Cross-utilisation of template RNAs by alphavirus replicases date: 2020-09-04 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008825 sha: doc_id: 324928 cord_uid: cpryxa6p file: cache/cord-324640-2zhaknbi.json key: cord-324640-2zhaknbi authors: Munday, Diane C.; Emmott, Edward; Surtees, Rebecca; Lardeau, Charles-Hugues; Wu, Weining; Duprex, W. Paul; Dove, Brian K.; Barr, John N.; Hiscox, Julian A. title: Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus date: 2010-07-20 journal: Mol Cell Proteomics DOI: 10.1074/mcp.m110.001859 sha: doc_id: 324640 cord_uid: 2zhaknbi file: cache/cord-324697-c0dv1zmi.json key: cord-324697-c0dv1zmi authors: Rodriguez, William; Macveigh-Fierro, Daniel; Miles, Jacob; Muller, Mandy title: Fated for decay: RNA elements targeted by viral endonucleases date: 2020-06-07 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2020.05.010 sha: doc_id: 324697 cord_uid: c0dv1zmi file: cache/cord-324984-ojrpsdt9.json key: cord-324984-ojrpsdt9 authors: Ji, Xingyue; Li, Zhuorong title: Medicinal chemistry strategies toward host targeting antiviral agents date: 2020-02-14 journal: Med Res Rev DOI: 10.1002/med.21664 sha: doc_id: 324984 cord_uid: ojrpsdt9 file: cache/cord-325043-vqjhiv7p.json key: cord-325043-vqjhiv7p authors: Gorbalenya, Alexander E.; Blinov, Vladimir M.; Donchenko, Alexei P.; Koonin, Eugene V. title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication date: 1989 journal: J Mol Evol DOI: 10.1007/bf02102483 sha: doc_id: 325043 cord_uid: vqjhiv7p file: cache/cord-324944-ixh3ykrc.json key: cord-324944-ixh3ykrc authors: Mitsakakis, Konstantinos; D'Acremont, Valérie; Hin, Sebastian; von Stetten, Felix; Zengerle, Roland title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 journal: Microelectron Eng DOI: 10.1016/j.mee.2018.10.001 sha: doc_id: 324944 cord_uid: ixh3ykrc file: cache/cord-325113-sou8xyld.json key: cord-325113-sou8xyld authors: Kuiper, Johannes W. P.; Baade, Timo; Kremer, Marcel; Kranaster, Ramon; Irmisch, Linda; Schuchmann, Marcus; Zander, Johannes; Marx, Andreas; Hauck, Christof R. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 journal: PLoS One DOI: 10.1371/journal.pone.0241740 sha: doc_id: 325113 cord_uid: sou8xyld file: cache/cord-325137-6c6er06a.json key: cord-325137-6c6er06a authors: Moser, Lindsey A.; Ramirez-Carvajal, Lisbeth; Puri, Vinita; Pauszek, Steven J.; Matthews, Krystal; Dilley, Kari A.; Mullan, Clancy; McGraw, Jennifer; Khayat, Michael; Beeri, Karen; Yee, Anthony; Dugan, Vivien; Heise, Mark T.; Frieman, Matthew B.; Rodriguez, Luis L.; Bernard, Kristen A.; Wentworth, David E.; Stockwell, Timothy B.; Shabman, Reed S. title: A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date: 2016-06-07 journal: mSystems DOI: 10.1128/msystems.00039-15 sha: doc_id: 325137 cord_uid: 6c6er06a file: cache/cord-325197-j1uo8qmf.json key: cord-325197-j1uo8qmf authors: Crimi, Ettore; Benincasa, Giuditta; Figueroa-Marrero, Neisaliz; Galdiero, Massimiliano; Napoli, Claudio title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date: 2020-08-20 journal: Br J Anaesth DOI: 10.1016/j.bja.2020.06.060 sha: doc_id: 325197 cord_uid: j1uo8qmf file: cache/cord-325280-4whzcmqv.json key: cord-325280-4whzcmqv authors: Takizawa, Naoki; Yamasaki, Manabu title: Current landscape and future prospects of antiviral drugs derived from microbial products date: 2017-10-11 journal: J Antibiot (Tokyo) DOI: 10.1038/ja.2017.115 sha: doc_id: 325280 cord_uid: 4whzcmqv file: cache/cord-325326-2bbqz4o7.json key: cord-325326-2bbqz4o7 authors: Beitzel, Brett F.; Bakken, Russell R.; Smith, Jeffrey M.; Schmaljohn, Connie S. title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date: 2010-10-14 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1001146 sha: doc_id: 325326 cord_uid: 2bbqz4o7 file: cache/cord-325230-3kg4oe4g.json key: cord-325230-3kg4oe4g authors: Agol, Vadim I.; Gmyl, Anatoly P. title: Viral security proteins: counteracting host defences date: 2010-11-09 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro2452 sha: doc_id: 325230 cord_uid: 3kg4oe4g file: cache/cord-325529-pid58g2r.json key: cord-325529-pid58g2r authors: Ben-Ami, Roni; Klochendler, Agnes; Seidel, Matan; Sido, Tal; Gurel-Gurevich, Ori; Yassour, Moran; Meshorer, Eran; Benedek, Gil; Fogel, Irit; Oiknine-Djian, Esther; Gertler, Asaf; Rotstein, Zeev; Lavi, Bruno; Dor, Yuval; Wolf, Dana G.; Salton, Maayan; Drier, Yotam title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 journal: Clin Microbiol Infect DOI: 10.1016/j.cmi.2020.06.009 sha: doc_id: 325529 cord_uid: pid58g2r file: cache/cord-325328-3l3jznkj.json key: cord-325328-3l3jznkj authors: Holbrook, Stephen R title: RNA structure: the long and the short of it date: 2005-05-16 journal: Curr Opin Struct Biol DOI: 10.1016/j.sbi.2005.04.005 sha: doc_id: 325328 cord_uid: 3l3jznkj file: cache/cord-325479-2r4oomdp.json key: cord-325479-2r4oomdp authors: Torii, Shotaro; Furumai, Hiroaki; Katayama, Hiroyuki title: Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date: 2020-10-17 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.143067 sha: doc_id: 325479 cord_uid: 2r4oomdp file: cache/cord-325624-6anybxnk.json key: cord-325624-6anybxnk authors: Ireland, Derek D. C.; Stohlman, Stephen A.; Hinton, David R.; Kapil, Parul; Silverman, Robert H.; Atkinson, Roscoe A.; Bergmann, Cornelia C. title: RNase L Mediated Protection from Virus Induced Demyelination date: 2009-10-02 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1000602 sha: doc_id: 325624 cord_uid: 6anybxnk file: cache/cord-325736-gs9d8y55.json key: cord-325736-gs9d8y55 authors: Marin, J; Jeler-Kačar, D; Levstek, V; Maček, V title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date: 2000-07-31 journal: Journal of Infection DOI: 10.1053/jinf.2000.0688 sha: doc_id: 325736 cord_uid: gs9d8y55 file: cache/cord-325820-tnyzmrm8.json key: cord-325820-tnyzmrm8 authors: Kovacikova, Kristina; Morren, Bas M.; Tas, Ali; Albulescu, Irina C.; van Rijswijk, Robin; Jarhad, Dnyandev B.; Shin, Young Sup; Jang, Min Hwan; Kim, Gyudong; Lee, Hyuk Woo; Jeong, Lak Shin; Snijder, Eric J.; van Hemert, Martijn J. title: 6′-β-Fluoro-Homoaristeromycin and 6′-Fluoro-Homoneplanocin A Are Potent Inhibitors of Chikungunya Virus Replication through Their Direct Effect on Viral Nonstructural Protein 1 date: 2020-03-24 journal: Antimicrob Agents Chemother DOI: 10.1128/aac.02532-19 sha: doc_id: 325820 cord_uid: tnyzmrm8 file: cache/cord-325925-010xj69x.json key: cord-325925-010xj69x authors: Mordecai, Gideon J; Miller, Kristina M; Di Cicco, Emiliano; Schulze, Angela D; Kaukinen, Karia H; Ming, Tobi J; Li, Shaorong; Tabata, Amy; Teffer, Amy; Patterson, David A; Ferguson, Hugh W; Suttle, Curtis A title: Endangered wild salmon infected by newly discovered viruses date: 2019-09-03 journal: eLife DOI: 10.7554/elife.47615 sha: doc_id: 325925 cord_uid: 010xj69x file: cache/cord-325954-rhrkr97h.json key: cord-325954-rhrkr97h authors: Han, Mi Seon; Seong, Moon-Woo; Kim, Namhee; Shin, Sue; Cho, Sung Im; Park, Hyunwoong; Kim, Taek Soo; Park, Sung Sup; Choi, Eun Hwa title: Viral RNA Load in Mildly Symptomatic and Asymptomatic Children with COVID-19, Seoul, South Korea date: 2020-10-17 journal: Emerg Infect Dis DOI: 10.3201/eid2610.202449 sha: doc_id: 325954 cord_uid: rhrkr97h file: cache/cord-325958-1v1pg2z0.json key: cord-325958-1v1pg2z0 authors: Lange, Clemens; Wolf, Julian; Auw‐Haedrich, Claudia; Schlecht, Anja; Boneva, Stefaniya; Lapp, Thabo; Horres, Ralf; Agostini, Hansjürgen; Martin, Gottfried; Reinhard, Thomas; Schlunck, Günther title: Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date: 2020-05-06 journal: J Med Virol DOI: 10.1002/jmv.25981 sha: doc_id: 325958 cord_uid: 1v1pg2z0 file: cache/cord-325966-0g7a9s5z.json key: cord-325966-0g7a9s5z authors: Shih, Hsin-I.; Wu, Chi-Jung; Tu, Yi-Fang; Chi, Chia-Yu title: Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date: 2020-05-30 journal: Biomed J DOI: 10.1016/j.bj.2020.05.021 sha: doc_id: 325966 cord_uid: 0g7a9s5z file: cache/cord-326017-qw4qynqv.json key: cord-326017-qw4qynqv authors: Laskar, Partha; Yallapu, Murali M.; Chauhan, Subhash C. title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 journal: Diseases DOI: 10.3390/diseases8030030 sha: doc_id: 326017 cord_uid: qw4qynqv file: cache/cord-326225-crtpzad7.json key: cord-326225-crtpzad7 authors: Neill, John D.; Bayles, Darrell O.; Ridpath, Julia F. title: Simultaneous rapid sequencing of multiple RNA virus genomes date: 2014-06-01 journal: J Virol Methods DOI: 10.1016/j.jviromet.2014.02.016 sha: doc_id: 326225 cord_uid: crtpzad7 file: cache/cord-326217-ji0njeha.json key: cord-326217-ji0njeha authors: Saleh, Maged; Rüschenbaum, Sabrina; Welsch, Christoph; Zeuzem, Stefan; Moradpour, Darius; Gouttenoire, Jérôme; Lange, Christian M. title: Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date: 2018-11-27 journal: Front Microbiol DOI: 10.3389/fmicb.2018.02949 sha: doc_id: 326217 cord_uid: ji0njeha file: cache/cord-326257-rcv8sh22.json key: cord-326257-rcv8sh22 authors: Simmonds, P. title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date: 2020-05-01 journal: bioRxiv DOI: 10.1101/2020.05.01.072330 sha: doc_id: 326257 cord_uid: rcv8sh22 file: cache/cord-326719-p1ma4akz.json key: cord-326719-p1ma4akz authors: Enjuanes, Luis; Almazán, Fernando; Ortego, Javier title: Virus-based vectors for gene expression in mammalian cells: Coronavirus date: 2003-12-31 journal: New Comprehensive Biochemistry DOI: 10.1016/s0167-7306(03)38010-x sha: doc_id: 326719 cord_uid: p1ma4akz file: cache/cord-326911-va3x6au2.json key: cord-326911-va3x6au2 authors: Ramos-Mandujano, G.; Salunke, R.; Mfarrej, S.; Rachmadi, A.; Hala, S.; Xu, J.; Alofi, F. S.; Khogeer, A.; Hashem, A. M.; Almontashiri, N. A.; Alsomali, A.; Hamdan, S.; Hong, P.; Pain, A.; Li, M. title: A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date: 2020-06-29 journal: nan DOI: 10.1101/2020.06.28.20141945 sha: doc_id: 326911 cord_uid: va3x6au2 file: cache/cord-327024-1k5jucae.json key: cord-327024-1k5jucae authors: Zhang, Qingshui; Cao, Yanxin; Wang, Jun; Fu, Guanghua; Sun, Mengxu; Zhang, Lijiao; Meng, Li; Cui, Guolin; Huang, Yu; Hu, Xueying; Su, Jingliang title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date: 2018-04-19 journal: Emerg Microbes Infect DOI: 10.1038/s41426-018-0074-5 sha: doc_id: 327024 cord_uid: 1k5jucae file: cache/cord-327259-7o7fs4yb.json key: cord-327259-7o7fs4yb authors: Correa, I. A.; Rodrigues, T. d. S.; Queiroz, A.; Nascimento, L. d. F.; Wolff, T.; Akamine, R. N.; Kuriyama, S. N.; Costa, L.; Fidalgo-Neto, A. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 journal: nan DOI: 10.1101/2020.08.16.20167536 sha: doc_id: 327259 cord_uid: 7o7fs4yb file: cache/cord-327272-fspxett8.json key: cord-327272-fspxett8 authors: Buonaguro, Luigi; Buonaguro, Franco M. title: Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date: 2020-05-12 journal: Infect Agent Cancer DOI: 10.1186/s13027-020-00302-x sha: doc_id: 327272 cord_uid: fspxett8 file: cache/cord-327660-p1b07b4t.json key: cord-327660-p1b07b4t authors: Wolf, Yuri I.; Kazlauskas, Darius; Iranzo, Jaime; Lucía-Sanz, Adriana; Kuhn, Jens H.; Krupovic, Mart; Dolja, Valerian V.; Koonin, Eugene V. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 journal: mBio DOI: 10.1128/mbio.02329-18 sha: doc_id: 327660 cord_uid: p1b07b4t file: cache/cord-327000-oyg3oyx1.json key: cord-327000-oyg3oyx1 authors: Li, Shasha; Yang, Jinping; Zhu, Zixiang; Zheng, Haixue title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 journal: Pathogens DOI: 10.3390/pathogens9050367 sha: doc_id: 327000 cord_uid: oyg3oyx1 file: cache/cord-327855-txryqil7.json key: cord-327855-txryqil7 authors: Kulka, M.; Chen, A.; Ngo, D.; Bhattacharya, S. S.; Cebula, T. A.; Goswami, B. B. title: The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date: 2003 journal: Arch Virol DOI: 10.1007/s00705-003-0110-0 sha: doc_id: 327855 cord_uid: txryqil7 file: cache/cord-327518-yilv9z2m.json key: cord-327518-yilv9z2m authors: nan title: Coronaviridae date: 2011-11-23 journal: Virus Taxonomy DOI: 10.1016/b978-0-12-384684-6.00068-9 sha: doc_id: 327518 cord_uid: yilv9z2m file: cache/cord-328300-zehltghv.json key: cord-328300-zehltghv authors: Lin, Shing-Yen; Liu, Chia-Ling; Chang, Yu-Ming; Zhao, Jincun; Perlman, Stanley; Hou, Ming-Hon title: Structural Basis for the Identification of the N-Terminal Domain of Coronavirus Nucleocapsid Protein as an Antiviral Target date: 2014-02-24 journal: J Med Chem DOI: 10.1021/jm500089r sha: doc_id: 328300 cord_uid: zehltghv file: cache/cord-327997-noqbcxua.json key: cord-327997-noqbcxua authors: Wu, Kevin E.; Fazal, Furqan M.; Parker, Kevin R.; Zou, James; Chang, Howard Y. title: RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date: 2020-06-20 journal: Cell Syst DOI: 10.1016/j.cels.2020.06.008 sha: doc_id: 327997 cord_uid: noqbcxua file: cache/cord-328042-e1is656g.json key: cord-328042-e1is656g authors: Klein, Steffen; Müller, Thorsten G.; Khalid, Dina; Sonntag-Buck, Vera; Heuser, Anke-Mareil; Glass, Bärbel; Meurer, Matthias; Morales, Ivonne; Schillak, Angelika; Freistaedter, Andrew; Ambiel, Ina; Winter, Sophie L.; Zimmermann, Liv; Naumoska, Tamara; Bubeck, Felix; Kirrmaier, Daniel; Ullrich, Stephanie; Barreto Miranda, Isabel; Anders, Simon; Grimm, Dirk; Schnitzler, Paul; Knop, Michael; Kräusslich, Hans-Georg; Dao Thi, Viet Loan; Börner, Kathleen; Chlanda, Petr title: SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date: 2020-08-07 journal: Viruses DOI: 10.3390/v12080863 sha: doc_id: 328042 cord_uid: e1is656g file: cache/cord-328259-3g4klpyg.json key: cord-328259-3g4klpyg authors: Guajardo-Leiva, Sergio; Chnaiderman, Jonás; Gaggero, Aldo; Díez, Beatriz title: Metagenomic Insights into the Sewage RNA Virosphere of a Large City date: 2020-09-21 journal: Viruses DOI: 10.3390/v12091050 sha: doc_id: 328259 cord_uid: 3g4klpyg file: cache/cord-328085-7wp18qb6.json key: cord-328085-7wp18qb6 authors: Barage, Sagar; Karthic, A.; Bavi, Rohit; Desai, Neetin; Kumar, Raj; Kumar, Vikas; Lee, Keun Woo title: Identification and characterization of novel RdRp and Nsp15 inhibitors for SARS-COV2 using computational approach date: 2020-11-06 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1841026 sha: doc_id: 328085 cord_uid: 7wp18qb6 file: cache/cord-328252-dk54w8z9.json key: cord-328252-dk54w8z9 authors: Kikkert, Marjolein title: Innate Immune Evasion by Human Respiratory RNA Viruses date: 2019-10-14 journal: Journal of Innate Immunity DOI: 10.1159/000503030 sha: doc_id: 328252 cord_uid: dk54w8z9 file: cache/cord-328471-oz99upzz.json key: cord-328471-oz99upzz authors: Ahmad, Jamshaid; Ikram, Saima; Ahmad, Fawad; Rehman, Irshad Ur; Mushtaq, Maryam title: SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date: 2020-07-23 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e04502 sha: doc_id: 328471 cord_uid: oz99upzz file: cache/cord-328686-5ik5em5a.json key: cord-328686-5ik5em5a authors: Zhao, L.; Atoni, E.; Du, Y.; Zhang, H.; Donde, O.; Huang, D.; Xiao, S.; Ma, T.; Shu, Z.; Yuan, Z.; Tong, L.; Xia, H. title: First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date: 2020-08-21 journal: nan DOI: 10.1101/2020.08.19.20172924 sha: doc_id: 328686 cord_uid: 5ik5em5a file: cache/cord-328633-c31xsyeo.json key: cord-328633-c31xsyeo authors: Moser, Michael J.; DiFrancesco, Robert A.; Gowda, Krishne; Klingele, Audrey J.; Sugar, Darby R.; Stocki, Stacy; Mead, David A.; Schoenfeld, Thomas W. title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date: 2012-06-04 journal: PLoS One DOI: 10.1371/journal.pone.0038371 sha: doc_id: 328633 cord_uid: c31xsyeo file: cache/cord-328659-miujzgtd.json key: cord-328659-miujzgtd authors: Mishra, Akhilesh; Pandey, Ashutosh Kumar; Gupta, Parul; Pradhan, Prashant; Dhamija, Sonam; Gomes, James; Kundu, Bishwajit; Vivekanandan, Perumal; Menon, Manoj B. title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date: 2020-07-27 journal: bioRxiv DOI: 10.1101/2020.05.07.082768 sha: doc_id: 328659 cord_uid: miujzgtd file: cache/cord-328460-thx9zh11.json key: cord-328460-thx9zh11 authors: Zanoli, Laura Maria; Spoto, Giuseppe title: Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices date: 2012-12-27 journal: Biosensors (Basel) DOI: 10.3390/bios3010018 sha: doc_id: 328460 cord_uid: thx9zh11 file: cache/cord-328737-6mcefqn5.json key: cord-328737-6mcefqn5 authors: Lee, Eun Yeong; Kim, Yeseul; Koo, Bonhan; Noh, Geun Su; Lee, Hansuek; Shin, Yong title: A novel nucleic acid amplification system based on nano-gap embedded active disk resonators date: 2020-05-26 journal: Sens Actuators B Chem DOI: 10.1016/j.snb.2020.128351 sha: doc_id: 328737 cord_uid: 6mcefqn5 file: cache/cord-328768-2qk884x2.json key: cord-328768-2qk884x2 authors: Sabatier, Marina; Bal, Antonin; Destras, Grégory; Regue, Hadrien; Quéromès, Grégory; Cheynet, Valérie; Lina, Bruno; Bardel, Claire; Brengel-Pesce, Karen; Navratil, Vincent; Josset, Laurence title: Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses date: 2020-10-06 journal: Microorganisms DOI: 10.3390/microorganisms8101539 sha: doc_id: 328768 cord_uid: 2qk884x2 file: cache/cord-328947-3l9ydspz.json key: cord-328947-3l9ydspz authors: Webb, L. G.; Veloz, J.; Pintado-Silva, J.; Zhu, T.; Rangel, M. V.; Mutetwa, T.; Zhang, L.; Bernal-Rubio, D.; Figueroa, D.; Carrau, L.; Fenutria, R.; Potla, U.; Reid, St. P.; Yount, J. S.; Stapleford, K. A.; Aguirre, S.; Fernandez-Sesma, A. title: Chikungunya virus antagonizes cGAS-STING mediated type-I interferon responses by degrading cGAS date: 2020-10-15 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008999 sha: doc_id: 328947 cord_uid: 3l9ydspz file: cache/cord-329041-coryaz2s.json key: cord-329041-coryaz2s authors: Brown, Ariane J.; Won, John J.; Graham, Rachel L.; Dinnon, Kenneth H.; Sims, Amy C.; Feng, Joy Y.; Cihlar, Tomas; Denison, Mark R.; Baric, Ralph S.; Sheahan, Timothy P. title: Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date: 2019-09-30 journal: Antiviral Research DOI: 10.1016/j.antiviral.2019.104541 sha: doc_id: 329041 cord_uid: coryaz2s file: cache/cord-328960-46zui1sl.json key: cord-328960-46zui1sl authors: Hillen, Hauke S.; Kokic, Goran; Farnung, Lucas; Dienemann, Christian; Tegunov, Dimitry; Cramer, Patrick title: Structure of replicating SARS-CoV-2 polymerase date: 2020-04-27 journal: bioRxiv DOI: 10.1101/2020.04.27.063180 sha: doc_id: 328960 cord_uid: 46zui1sl file: cache/cord-329102-2y49kcwu.json key: cord-329102-2y49kcwu authors: Lan, Tammy C. T.; Allan, Matthew F.; Malsick, Lauren E.; Khandwala, Stuti; Nyeo, Sherry S. Y.; Bathe, Mark; Griffiths, Anthony; Rouskin, Silvi title: Structure of the full SARS-CoV-2 RNA genome in infected cells date: 2020-06-30 journal: bioRxiv DOI: 10.1101/2020.06.29.178343 sha: doc_id: 329102 cord_uid: 2y49kcwu file: cache/cord-329107-43e2lkht.json key: cord-329107-43e2lkht authors: Pawlicka, Kamila; Kalathiya, Umesh; Alfaro, Javier title: Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics date: 2020-03-24 journal: Cancers (Basel) DOI: 10.3390/cancers12030765 sha: doc_id: 329107 cord_uid: 43e2lkht file: cache/cord-329311-p68kr4ga.json key: cord-329311-p68kr4ga authors: Prebensen, Christian; hre, Peder L My; Jonassen, Christine; Rangberg, Anbjørg; Blomfeldt, Anita; Svensson, My; Omland, Torbjørn; Berdal, Jan-Erik title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 journal: Clin Infect Dis DOI: 10.1093/cid/ciaa1338 sha: doc_id: 329311 cord_uid: p68kr4ga file: cache/cord-329361-0mpbau1b.json key: cord-329361-0mpbau1b authors: Bennasser, Yamina; Yeung, Man Lung; Jeang, Kuan-Teh title: RNAi Therapy for HIV Infection: Principles and Practicalities date: 2012-08-16 journal: BioDrugs DOI: 10.2165/00063030-200721010-00003 sha: doc_id: 329361 cord_uid: 0mpbau1b file: cache/cord-329504-91te3nu8.json key: cord-329504-91te3nu8 authors: Croll, Tristan; Diederichs, Kay; Fischer, Florens; Fyfe, Cameron; Gao, Yunyun; Horrell, Sam; Joseph, Agnel Praveen; Kandler, Luise; Kippes, Oliver; Kirsten, Ferdinand; Müller, Konstantin; Nolte, Kristoper; Payne, Alex; Reeves, Matthew G.; Richardson, Jane; Santoni, Gianluca; Stäb, Sabrina; Tronrud, Dale; Williams, Christopher; Thorn, Andrea title: Making the invisible enemy visible date: 2020-10-07 journal: bioRxiv DOI: 10.1101/2020.10.07.307546 sha: doc_id: 329504 cord_uid: 91te3nu8 file: cache/cord-329366-xuszdrsa.json key: cord-329366-xuszdrsa authors: Hackbart, Matthew; Deng, Xufang; Baker, Susan C. title: Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors date: 2020-04-07 journal: Proc Natl Acad Sci U S A DOI: 10.1073/pnas.1921485117 sha: doc_id: 329366 cord_uid: xuszdrsa file: cache/cord-329429-ur8g68vp.json key: cord-329429-ur8g68vp authors: Miłek, Justyna; Blicharz-Domańska, Katarzyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 journal: J Vet Res DOI: 10.2478/jvetres-2018-0035 sha: doc_id: 329429 cord_uid: ur8g68vp file: cache/cord-329493-ueqlhgn0.json key: cord-329493-ueqlhgn0 authors: Stadler, Konrad; Masignani, Vega; Eickmann, Markus; Becker, Stephan; Abrignani, Sergio; Klenk, Hans-Dieter; Rappuoli, Rino title: SARS — beginning to understand a new virus date: 2003 journal: Nat Rev Microbiol DOI: 10.1038/nrmicro775 sha: doc_id: 329493 cord_uid: ueqlhgn0 file: cache/cord-329494-cdn52epy.json key: cord-329494-cdn52epy authors: Artuso, María C.; Ellenberg, Paula C.; Scolaro, Luis A.; Damonte, Elsa B.; García, Cybele C. title: Inhibition of Junín virus replication by small interfering RNAs date: 2009-07-08 journal: Antiviral Res DOI: 10.1016/j.antiviral.2009.07.001 sha: doc_id: 329494 cord_uid: cdn52epy file: cache/cord-329618-kywhulpc.json key: cord-329618-kywhulpc authors: Xu, Cheng; Evensen, Øystein; Munang’andu, Hetron Mweemba title: A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells date: 2016-05-23 journal: BMC Genomics DOI: 10.1186/s12864-016-2739-6 sha: doc_id: 329618 cord_uid: kywhulpc file: cache/cord-329687-vhi4tbnc.json key: cord-329687-vhi4tbnc authors: Verdugo, C.; Plaza, A.; Acosta-Jamett, G.; Castro, N.; Gutierrez, J.; Hernandez, C.; Lopez-Joven, C.; Loncoman, C.; Navarrete, C.; Ramirez-Reveco, A.; Romero, A.; Silva, A.; Vega, M.; Vergara, J. title: A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing. date: 2020-06-03 journal: nan DOI: 10.1101/2020.05.30.20117721 sha: doc_id: 329687 cord_uid: vhi4tbnc file: cache/cord-329527-0rlotyz3.json key: cord-329527-0rlotyz3 authors: Bohmwald, Karen; Gálvez, Nicolás M. S.; Ríos, Mariana; Kalergis, Alexis M. title: Neurologic Alterations Due to Respiratory Virus Infections date: 2018-10-26 journal: Front Cell Neurosci DOI: 10.3389/fncel.2018.00386 sha: doc_id: 329527 cord_uid: 0rlotyz3 parallel: Warning: No more processes: Decreasing number of running jobs to 95. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-329707-89zyu8bl.json key: cord-329707-89zyu8bl authors: Zhang, Xue; Wu, Kailang; Yue, Xin; Zhu, Ying; Wu, Jianguo title: Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date: 2006-11-30 journal: Intervirology DOI: 10.1159/000097391 sha: doc_id: 329707 cord_uid: 89zyu8bl file: cache/cord-329710-vqorb6j7.json key: cord-329710-vqorb6j7 authors: Kumar, Krishna; Lupoli, Tania J. title: Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date: 2020-05-27 journal: ACS Med Chem Lett DOI: 10.1021/acsmedchemlett.0c00254 sha: doc_id: 329710 cord_uid: vqorb6j7 file: cache/cord-330045-4gj9d181.json key: cord-330045-4gj9d181 authors: Sun, Jiufeng; Xiao, Jianpeng; Sun, Ruilin; Tang, Xi; Liang, Chumin; Lin, Huifang; Zeng, Lilian; Hu, Jianxiong; Yuan, Runyu; Zhou, Pingping; Peng, Jinju; Xiong, Qianlin; Cui, Fengfu; Liu, Zhe; Lu, Jing; Tian, Junzhang; Ma, Wenjun; Ke, Changwen title: Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date: 2020-08-17 journal: Emerg Infect Dis DOI: 10.3201/eid2608.201097 sha: doc_id: 330045 cord_uid: 4gj9d181 file: cache/cord-330131-yfhrmbvx.json key: cord-330131-yfhrmbvx authors: Danchin, Antoine; Marlière, Philippe title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 journal: Environ Microbiol DOI: 10.1111/1462-2920.15025 sha: doc_id: 330131 cord_uid: yfhrmbvx file: cache/cord-330200-l6bnxi40.json key: cord-330200-l6bnxi40 authors: Huang, Jianping; Mao, Tingting; Li, Shufei; Wu, Lianpeng; Xu, Xueqin; Li, Huanzheng; xu, Chenyang; Su, Feifei; Dai, Jianyi; Shi, Jichan; Cai, Jing; Huang, Chongquan; Lin, Xuan; Chen, Dong; Lin, Xiaoling; Sun, Baochang; Tang, Shaohua title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date: 2020-04-27 journal: nan DOI: 10.1101/2020.04.22.20071258 sha: doc_id: 330200 cord_uid: l6bnxi40 file: cache/cord-329866-io9fvy58.json key: cord-329866-io9fvy58 authors: Lorusso, Eleonora; Mari, Viviana; Losurdo, Michele; Lanave, Gianvito; Trotta, Adriana; Dowgier, Giulia; Colaianni, Maria Loredana; Zatelli, Andrea; Elia, Gabriella; Buonavoglia, Domenico; Decaro, Nicola title: Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis date: 2019-08-31 journal: Research in Veterinary Science DOI: 10.1016/j.rvsc.2017.10.004 sha: doc_id: 329866 cord_uid: io9fvy58 file: cache/cord-330213-reb9vo7x.json key: cord-330213-reb9vo7x authors: Miladi, Milad; Fuchs, Jonas; Maier, Wolfgang; Weigang, Sebastian; Pedrosa, Núria Díaz i; Weiss, Lisa; Lother, Achim; Nekrutenko, Anton; Ruzsics, Zsolt; Panning, Marcus; Kochs, Georg; Gilsbach, Ralf; Grüning, Björn title: The landscape of SARS-CoV-2 RNA modifications date: 2020-07-18 journal: bioRxiv DOI: 10.1101/2020.07.18.204362 sha: doc_id: 330213 cord_uid: reb9vo7x file: cache/cord-331066-ediowz4s.json key: cord-331066-ediowz4s authors: Chechetkin, Vladimir R.; Lobzin, Vasily V. title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date: 2020-09-09 journal: Journal of biomolecular structure & dynamics DOI: 10.1080/07391102.2020.1815581 sha: doc_id: 331066 cord_uid: ediowz4s file: cache/cord-330847-a84pcc9z.json key: cord-330847-a84pcc9z authors: Edwards, M. C.; Petty, I.T.D.; Jackson, A. O. title: RNA recombination in the genome of Barley stripe mosaic virus date: 1992-07-31 journal: Virology DOI: 10.1016/0042-6822(92)90722-2 sha: doc_id: 330847 cord_uid: a84pcc9z file: cache/cord-330954-ft14aa2n.json key: cord-330954-ft14aa2n authors: Liu, B. M.; Yang, Q. Q.; Zhao, L. Y.; Xie, W.; Si, X. Y. title: Epidemiological characteristics of COVID-19 patients in convalescence period date: 2020-06-03 journal: Epidemiol Infect DOI: 10.1017/s0950268820001181 sha: doc_id: 330954 cord_uid: ft14aa2n file: cache/cord-331076-ak481qew.json key: cord-331076-ak481qew authors: Eskier, Doğa; Suner, Aslı; Oktay, Yavuz; Karakülah, Gökhan title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-10-12 journal: PeerJ DOI: 10.7717/peerj.10181 sha: doc_id: 331076 cord_uid: ak481qew file: cache/cord-329794-msxrdhb3.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-329794-msxrdhb3 authors: Lu, Aili; Zhang, Huanqing; Zhang, Xiaoyan; Wang, Hongxia; Hu, Qikuan; Shen, Li; Schaffhausen, Brian S.; Hou, Weimin; Li, Linsong title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date: 2004-06-20 journal: Virology DOI: 10.1016/j.virol.2004.03.031 sha: doc_id: 329794 cord_uid: msxrdhb3 file: cache/cord-330800-s91zfzfi.json key: cord-330800-s91zfzfi authors: Reta, Daniel Hussien; Tessema, Tesfaye Sisay; Ashenef, Addis Simachew; Desta, Adey Feleke; Labisso, Wajana Lako; Gizaw, Solomon Tebeje; Abay, Solomon Mequanente; Melka, Daniel Seifu; Reta, Fisseha Alemu title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 journal: Int J Microbiol DOI: 10.1155/2020/8832728 sha: doc_id: 330800 cord_uid: s91zfzfi file: cache/cord-331414-i0oxm5mr.json key: cord-331414-i0oxm5mr authors: Kautz, Tiffany F.; Jaworski, Elizabeth; Routh, Andrew; Forrester, Naomi L. title: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene date: 2020-06-19 journal: Viruses DOI: 10.3390/v12060660 sha: doc_id: 331414 cord_uid: i0oxm5mr parallel: Warning: No more processes: Decreasing number of running jobs to 94. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-331509-p19dg1jw.json key: cord-331509-p19dg1jw authors: Bigault, Lionel; Brown, Paul; Bernard, Cécilia; Blanchard, Yannick; Grasland, Béatrice title: Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR date: 2020-05-31 journal: J Virol Methods DOI: 10.1016/j.jviromet.2020.113906 sha: doc_id: 331509 cord_uid: p19dg1jw file: cache/cord-331607-2h56vb0n.json key: cord-331607-2h56vb0n authors: Jin, Xuejiao; Cao, Xiuling; Wang, Xueting; Jiang, Jun; Wan, Juan; Laliberté, Jean-François; Zhang, Yongliang title: Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication date: 2018-01-30 journal: Front Plant Sci DOI: 10.3389/fpls.2018.00057 sha: doc_id: 331607 cord_uid: 2h56vb0n parallel: Warning: No more processes: Decreasing number of running jobs to 93. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-331916-n744pymd.json key: cord-331916-n744pymd authors: Liu, Jue; Chen, Isabelle; Chua, Huikheng; Du, Qingyun; Kwang, Jimmy title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference date: 2006-04-10 journal: Virology DOI: 10.1016/j.virol.2005.12.006 sha: doc_id: 331916 cord_uid: n744pymd parallel: Warning: No more processes: Decreasing number of running jobs to 92. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-331680-qlzhtxs0.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-331680-qlzhtxs0 authors: Goryachev, A.N.; Kalantarov, S.A.; Severova, A.G.; Goryacheva, A.S. title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date: 2020-11-03 journal: bioRxiv DOI: 10.1101/2020.11.02.363598 sha: doc_id: 331680 cord_uid: qlzhtxs0 file: cache/cord-331802-wo462anq.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-331802-wo462anq authors: Xia, Hongjie; Wang, Peipei; Wang, Guang-Chuan; Yang, Jie; Sun, Xianlin; Wu, Wenzhe; Qiu, Yang; Shu, Ting; Zhao, Xiaolu; Yin, Lei; Qin, Cheng-Feng; Hu, Yuanyang; Zhou, Xi title: Human Enterovirus Nonstructural Protein 2C(ATPase) Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone date: 2015-07-28 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1005067 sha: doc_id: 331802 cord_uid: wo462anq file: cache/cord-332270-fusfdkjw.json key: cord-332270-fusfdkjw authors: Lukiw, Walter J.; Vergallo, Andrea; Lista, Simone; Hampel, Harald; Zhao, Yuhai title: Biomarkers for Alzheimer’s Disease (AD) and the Application of Precision Medicine date: 2020-09-21 journal: J Pers Med DOI: 10.3390/jpm10030138 sha: doc_id: 332270 cord_uid: fusfdkjw file: cache/cord-332003-67e9fchy.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-332003-67e9fchy authors: Boisguérin, Prisca; Deshayes, Sébastien; Gait, Michael J.; O'Donovan, Liz; Godfrey, Caroline; Betts, Corinne A.; Wood, Matthew J.A.; Lebleu, Bernard title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 journal: Adv Drug Deliv Rev DOI: 10.1016/j.addr.2015.02.008 sha: doc_id: 332003 cord_uid: 67e9fchy file: cache/cord-332006-if46jycd.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-332006-if46jycd authors: Whitehead, Kathryn A.; Langer, Robert; Anderson, Daniel G. title: Knocking down barriers: advances in siRNA delivery date: 2009 journal: Nat Rev Drug Discov DOI: 10.1038/nrd2742 sha: doc_id: 332006 cord_uid: if46jycd file: cache/cord-332356-au7s3dmp.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-332356-au7s3dmp authors: Strandin, Tomas; Hepojoki, Jussi; Wang, Hao; Vaheri, Antti; Lankinen, Hilkka title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date: 2011-09-15 journal: Virology DOI: 10.1016/j.virol.2011.06.030 sha: doc_id: 332356 cord_uid: au7s3dmp file: cache/cord-332024-jk983q4p.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-332024-jk983q4p authors: Briese, Thomas; Palacios, Gustavo; Kokoris, Mark; Jabado, Omar; Liu, Zhiqiang; Renwick, Neil; Kapoor, Vishal; Casas, Inmaculada; Pozo, Francisco; Limberger, Ron; Perez-Brena, Pilar; Ju, Jingyue; Lipkin, W. Ian title: Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date: 2005-02-17 journal: Emerg Infect Dis DOI: 10.3201/eid1102.040492 sha: doc_id: 332024 cord_uid: jk983q4p file: cache/cord-333261-knj2rrut.json key: cord-333261-knj2rrut authors: Albright, Catherine J.; Hall, David J. title: An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date: 2011-11-11 journal: Biochem Mol Biol Educ DOI: 10.1002/bmb.20530 sha: doc_id: 333261 cord_uid: knj2rrut file: cache/cord-332632-u2ud0vmq.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-332632-u2ud0vmq authors: Lussi, Carmela; Schweizer, Matthias title: What can pestiviral endonucleases teach us about innate immunotolerance? date: 2016-03-17 journal: Cytokine Growth Factor Rev DOI: 10.1016/j.cytogfr.2016.03.003 sha: doc_id: 332632 cord_uid: u2ud0vmq file: cache/cord-332992-8rmqg4rf.json key: cord-332992-8rmqg4rf authors: de Vries, A. 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F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 journal: Neth Heart J DOI: 10.1007/s12471-020-01475-1 sha: doc_id: 332992 cord_uid: 8rmqg4rf file: cache/cord-333429-bq7kfpby.json key: cord-333429-bq7kfpby authors: Shi, Ding; Wu, Wenrui; Wang, Qing; Xu, Kaijin; Xie, Jiaojiao; Wu, Jingjing; Lv, Longxian; Sheng, Jifang; Guo, Jing; Wang, Kaicen; Fang, Daiqiong; Li, Yating; Li, Lanjuan title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date: 2020-07-02 journal: J Infect Dis DOI: 10.1093/infdis/jiaa388 sha: doc_id: 333429 cord_uid: bq7kfpby file: cache/cord-333473-c1lykari.json key: cord-333473-c1lykari authors: Irigoyen, Nerea; Firth, Andrew E.; Jones, Joshua D.; Chung, Betty Y.-W.; Siddell, Stuart G.; Brierley, Ian title: High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling date: 2016-02-26 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1005473 sha: doc_id: 333473 cord_uid: c1lykari file: cache/cord-333636-h2sg6shp.json key: cord-333636-h2sg6shp authors: Kochan, G.; Gonzalez, D.; Rodriguez, J. F. title: Characterization of the RNA-binding activity of VP3, a major structural protein of Infectious bursal disease virus date: 2003 journal: Arch Virol DOI: 10.1007/s00705-002-0949-5 sha: doc_id: 333636 cord_uid: h2sg6shp file: cache/cord-333524-a6p6ma8r.json key: cord-333524-a6p6ma8r authors: Khan, Pavana; Aufdembrink, Lauren M.; Engelhart, Aaron E. title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 journal: ACS Synth Biol DOI: 10.1021/acssynbio.0c00359 sha: doc_id: 333524 cord_uid: a6p6ma8r file: cache/cord-333547-88dkh6xd.json key: cord-333547-88dkh6xd authors: Hasan, Shadi W.; Ibrahim, Yazan; Daou, Marianne; Kannout, Hussein; Jan, Nila; Lopes, Alvaro; Alsafar, Habiba; Yousef, Ahmed F. title: Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date: 2020-10-19 journal: Sci Total Environ DOI: 10.1016/j.scitotenv.2020.142929 sha: doc_id: 333547 cord_uid: 88dkh6xd file: cache/cord-333979-bx2xspbe.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-333979-bx2xspbe authors: Kalikiri, Mahesh K R; Hasan, Mohammad Rubayet; Mirza, Faheem; Xaba, Thabisile; Tang, Patrick; Lorenz, Stephan title: High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads date: 2020-04-11 journal: nan DOI: 10.1101/2020.04.08.20055731 sha: doc_id: 333979 cord_uid: bx2xspbe file: cache/cord-332747-u46xryoo.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-332747-u46xryoo authors: Mingorance, Lidia; Castro, Victoria; Ávila-Pérez, Ginés; Calvo, Gema; Rodriguez, María Josefa; Carrascosa, José L.; Pérez-del-Pulgar, Sofía; Forns, Xavier; Gastaminza, Pablo title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date: 2018-09-18 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1007284 sha: doc_id: 332747 cord_uid: u46xryoo file: cache/cord-333515-llqpfhwg.json key: cord-333515-llqpfhwg authors: Zhao, Juanjuan; Yuan, Quan; Wang, Haiyan; Liu, Wei; Liao, Xuejiao; Su, Yingying; Wang, Xin; Yuan, Jing; Li, Tingdong; Li, Jinxiu; Qian, Shen; Hong, Congming; Wang, Fuxiang; Liu, Yingxia; Wang, Zhaoqin; He, Qing; Li, Zhiyong; He, Bin; Zhang, Tianying; Ge, Shengxiang; Liu, Lei; Zhang, Jun; Xia, Ningshao; Zhang, Zheng title: Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date: 2020-03-03 journal: nan DOI: 10.1101/2020.03.02.20030189 sha: doc_id: 333515 cord_uid: llqpfhwg file: cache/cord-334082-fyxn0g3v.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-334082-fyxn0g3v authors: O’Carroll, I.P.; Rein, A. title: Viral Nucleic Acids date: 2015-08-20 journal: Encyclopedia of Cell Biology DOI: 10.1016/b978-0-12-394447-4.10061-6 sha: doc_id: 334082 cord_uid: fyxn0g3v file: cache/cord-333080-qytwbsne.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-333080-qytwbsne authors: Alahari, Suresh K.; Yousefi, Hassan; Poursheikhani, Arash; bahmanpour, Zahra; Vatanmakanian, Mousa; Taheri, Mohammad; Mashouri, Ladan title: SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date: 2020-07-28 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110548 sha: doc_id: 333080 cord_uid: qytwbsne file: cache/cord-334123-wb45ww7f.json key: cord-334123-wb45ww7f authors: Schimmel, Paul title: RNA pseudoknots that interact with components of the translation apparatus date: 1989-07-14 journal: Cell DOI: 10.1016/0092-8674(89)90395-4 sha: doc_id: 334123 cord_uid: wb45ww7f file: cache/cord-332484-qy8vj6uu.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-332484-qy8vj6uu authors: Pierini, Roberto; Cottam, Eleanor; Roberts, Rebecca; Wileman, Thomas title: Modulation of membrane traffic between endoplasmic reticulum, ERGIC and Golgi to generate compartments for the replication of bacteria and viruses date: 2009-04-01 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2009.03.015 sha: doc_id: 332484 cord_uid: qy8vj6uu file: cache/cord-332844-2se4d1yp.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-332844-2se4d1yp authors: Yun, Sang-Im; Song, Byung-Hak; Kim, Jin-Kyoung; Lee, Young-Min title: Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses date: 2015-12-29 journal: J Vis Exp DOI: 10.3791/53164 sha: doc_id: 332844 cord_uid: 2se4d1yp file: cache/cord-335040-1qa6pe4v.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-335040-1qa6pe4v authors: Rogstam, Annika; Nyblom, Maria; Christensen, Signe; Sele, Celeste; Talibov, Vladimir O.; Lindvall, Therese; Rasmussen, Anna Andersson; André, Ingemar; Fisher, Zoë; Knecht, Wolfgang; Kozielski, Frank title: Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-10-06 journal: Int J Mol Sci DOI: 10.3390/ijms21197375 sha: doc_id: 335040 cord_uid: 1qa6pe4v file: cache/cord-334771-uy3s6443.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-334771-uy3s6443 authors: Rao, BL; Basu, Atanu; Wairagkar, Niteen S; Gore, Milind M; Arankalle, Vidya A; Thakare, Jyotsna P; Jadi, Ramesh S; Rao, KA; Mishra, AC title: A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date: 2004-09-09 journal: Lancet DOI: 10.1016/s0140-6736(04)16982-1 sha: doc_id: 334771 cord_uid: uy3s6443 file: cache/cord-335443-iv2gs3kg.json key: cord-335443-iv2gs3kg authors: Kim, Youngchang; Wower, Jacek; Maltseva, Natalia; Chang, Changsoo; Jedrzejczak, Robert; Wilamowski, Mateusz; Kang, Soowon; Nicolaescu, Vlad; Randall, Glenn; Michalska, Karolina; Joachimiak, Andrzej title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date: 2020-06-28 journal: bioRxiv DOI: 10.1101/2020.06.26.173872 sha: doc_id: 335443 cord_uid: iv2gs3kg file: cache/cord-335482-nx7odchj.json key: cord-335482-nx7odchj authors: Makino, Shinji; Taguchi, Fumihiro; Fujiwara, Kosaku title: Defective interfering particles of mouse hepatitis virus date: 1984-02-29 journal: Virology DOI: 10.1016/0042-6822(84)90420-3 sha: doc_id: 335482 cord_uid: nx7odchj file: cache/cord-332710-2s14knw6.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-332710-2s14knw6 authors: Lai, Michael M.C. title: Recombination in large RNA viruses: Coronaviruses date: 1996-12-31 journal: Seminars in Virology DOI: 10.1006/smvy.1996.0046 sha: doc_id: 332710 cord_uid: 2s14knw6 file: cache/cord-335614-qh98622y.json key: cord-335614-qh98622y authors: Xu, Puzhi; Liu, Ping; Zhou, Changming; Shi, Yan; Wu, Qingpeng; Yang, Yitian; Li, Guyue; Hu, Guoliang; Guo, Xiaoquan title: A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date: 2019-11-16 journal: Viruses DOI: 10.3390/v11111070 sha: doc_id: 335614 cord_uid: qh98622y file: cache/cord-335864-392xmrq0.json key: cord-335864-392xmrq0 authors: Sun, Yu-Meng; Chen, Yue-Qin title: Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application date: 2020-08-10 journal: J Hematol Oncol DOI: 10.1186/s13045-020-00945-8 sha: doc_id: 335864 cord_uid: 392xmrq0 file: cache/cord-334463-nvu5tqxb.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-334463-nvu5tqxb authors: Kim, Chonsaeng; Bergelson, Jeffrey M. title: Echovirus 7 Entry into Polarized Intestinal Epithelial Cells Requires Clathrin and Rab7 date: 2012-04-10 journal: mBio DOI: 10.1128/mbio.00304-11 sha: doc_id: 334463 cord_uid: nvu5tqxb file: cache/cord-334394-qgyzk7th.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-334394-qgyzk7th authors: Edgar, Robert C.; Taylor, Jeff; Altman, Tomer; Barbera, Pierre; Meleshko, Dmitry; Lin, Victor; Lohr, Dan; Novakovsky, Gherman; Al-Shayeb, Basem; Banfield, Jillian F.; Korobeynikov, Anton; Chikhi, Rayan; Babaian, Artem title: Petabase-scale sequence alignment catalyses viral discovery date: 2020-08-10 journal: bioRxiv DOI: 10.1101/2020.08.07.241729 sha: doc_id: 334394 cord_uid: qgyzk7th file: cache/cord-334299-0zn1z7rc.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-334299-0zn1z7rc authors: Ahmed, Warish; Bivins, Aaron; Bertsch, Paul M.; Bibby, Kyle; Choi, Phil M.; Farkas, Kata; Gyawali, Pradip; Hamilton, Kerry A.; Haramoto, Eiji; Kitajima, Masaaki; Simpson, Stuart L.; Tandukar, Sarmila; Thomas, Kevin; Mueller, Jochen F. title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date: 2020-09-30 journal: Curr Opin Environ Sci Health DOI: 10.1016/j.coesh.2020.09.003 sha: doc_id: 334299 cord_uid: 0zn1z7rc file: cache/cord-336093-ic6q6ke8.json key: cord-336093-ic6q6ke8 authors: Sun, Ying; Wang, Zidao; Tao, Jiali; Wang, Yi; Wu, Andong; Yang, Ziwen; Wang, Kaimei; Shi, Liqiao; Chen, Yu; Guo, Deyin title: Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date: 2014-02-11 journal: Antiviral Res DOI: 10.1016/j.antiviral.2014.02.002 sha: doc_id: 336093 cord_uid: ic6q6ke8 file: cache/cord-336319-8068s9a3.json key: cord-336319-8068s9a3 authors: Graci, Jason D.; Cameron, Craig E. title: Mechanisms of action of ribavirin against distinct viruses date: 2005-11-15 journal: Rev Med Virol DOI: 10.1002/rmv.483 sha: doc_id: 336319 cord_uid: 8068s9a3 file: cache/cord-336560-m5u6ryy9.json key: cord-336560-m5u6ryy9 authors: Boudewijns, Robbert; Thibaut, Hendrik Jan; Kaptein, Suzanne J. F.; Li, Rong; Vergote, Valentijn; Seldeslachts, Laura; De Keyzer, Carolien; Bervoets, Lindsey; Sharma, Sapna; Van Weyenbergh, Johan; Liesenborghs, Laurens; Ma, Ji; Jansen, Sander; Van Looveren, Dominique; Vercruysse, Thomas; Jochmans, Dirk; Wang, Xinyu; Martens, Erik; Roose, Kenny; De Vlieger, Dorien; Schepens, Bert; Van Buyten, Tina; Jacobs, Sofie; Liu, Yanan; Martí-Carreras, Joan; Vanmechelen, Bert; Wawina-Bokalanga, Tony; Delang, Leen; Rocha-Pereira, Joana; Coelmont, Lotte; Chiu, Winston; Leyssen, Pieter; Heylen, Elisabeth; Schols, Dominique; Wang, Lanjiao; Close, Lila; Matthijnssens, Jelle; Van Ranst, Marc; Compernolle, Veerle; Schramm, Georg; Van Laere, Koen; Saelens, Xavier; Callewaert, Nico; Opdenakker, Ghislain; Maes, Piet; Weynand, Birgit; Cawthorne, Christopher; Velde, Greetje Vande; Wang, Zhongde; Neyts, Johan; Dallmeier, Kai title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date: 2020-07-02 journal: bioRxiv DOI: 10.1101/2020.04.23.056838 sha: doc_id: 336560 cord_uid: m5u6ryy9 file: cache/cord-334315-ymkrgj0h.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-334315-ymkrgj0h authors: Moon, Stephanie L.; Wilusz, Jeffrey title: Cytoplasmic Viruses: Rage against the (Cellular RNA Decay) Machine date: 2013-12-05 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003762 sha: doc_id: 334315 cord_uid: ymkrgj0h file: cache/cord-335067-tg66h99q.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-335067-tg66h99q authors: Woolhouse, Mark E.J.; Adair, Kyle title: Ecological and taxonomic variation among human RNA viruses date: 2013-03-19 journal: J Clin Virol DOI: 10.1016/j.jcv.2013.02.019 sha: doc_id: 335067 cord_uid: tg66h99q file: cache/cord-336012-8klkojpo.json key: cord-336012-8klkojpo authors: Harilal, Divinlal; Ramaswamy, Sathishkumar; Loney, Tom; Suwaidi, Hanan Al; Khansaheb, Hamda; Alkhaja, Abdulmajeed; Varghese, Rupa; Deesi, Zulfa; Nowotny, Norbert; Alsheikh-Ali, Alawi; Tayoun, Ahmad Abou title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date: 2020-06-18 journal: bioRxiv DOI: 10.1101/2020.06.06.138339 sha: doc_id: 336012 cord_uid: 8klkojpo file: cache/cord-335377-zrbn637z.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-335377-zrbn637z authors: Ishimaru, Daniella; Plant, Ewan P.; Sims, Amy C.; Yount, Boyd L.; Roth, Braden M.; Eldho, Nadukkudy V.; Pérez-Alvarado, Gabriela C.; Armbruster, David W.; Baric, Ralph S.; Dinman, Jonathan D.; Taylor, Deborah R.; Hennig, Mirko title: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date: 2012-12-26 journal: Nucleic Acids Res DOI: 10.1093/nar/gks1361 sha: doc_id: 335377 cord_uid: zrbn637z file: cache/cord-335441-bj3me7p8.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-335441-bj3me7p8 authors: Jourdain, Elsa; Gunnarsson, Gunnar; Wahlgren, John; Latorre-Margalef, Neus; Bröjer, Caroline; Sahlin, Sofie; Svensson, Lovisa; Waldenström, Jonas; Lundkvist, Åke; Olsen, Björn title: Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data date: 2010-01-28 journal: PLoS One DOI: 10.1371/journal.pone.0008935 sha: doc_id: 335441 cord_uid: bj3me7p8 file: cache/cord-336554-n8n5ii5k.json key: cord-336554-n8n5ii5k authors: Singh, Thakur Uttam; Parida, Subhashree; Lingaraju, Madhu Cholenahalli; Kesavan, Manickam; Kumar, Dinesh; Singh, Raj Kumar title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 journal: Pharmacol Rep DOI: 10.1007/s43440-020-00155-6 sha: doc_id: 336554 cord_uid: n8n5ii5k file: cache/cord-336775-d4hi9myk.json key: cord-336775-d4hi9myk authors: Kirtipal, Nikhil; Bharadwaj, Shiv; Kang, Sang Gu title: From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date: 2020-08-13 journal: Infection, Genetics and Evolution DOI: 10.1016/j.meegid.2020.104502 sha: doc_id: 336775 cord_uid: d4hi9myk file: cache/cord-337339-0vkigjv2.json key: cord-337339-0vkigjv2 authors: Osterrieder, Nikolaus; Bertzbach, Luca D.; Dietert, Kristina; Abdelgawad, Azza; Vladimirova, Daria; Kunec, Dusan; Hoffmann, Donata; Beer, Martin; Gruber, Achim D.; Trimpert, Jakob title: Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date: 2020-07-20 journal: Viruses DOI: 10.3390/v12070779 sha: doc_id: 337339 cord_uid: 0vkigjv2 file: cache/cord-337026-osgi06o4.json key: cord-337026-osgi06o4 authors: Panoutsopoulos, Alexios A. title: Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date: 2020-06-19 journal: SN Compr Clin Med DOI: 10.1007/s42399-020-00360-7 sha: doc_id: 337026 cord_uid: osgi06o4 file: cache/cord-334947-pa0p5dif.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-334947-pa0p5dif authors: Rozen-Gagnon, Kathryn; Stapleford, Kenneth A.; Mongelli, Vanesa; Blanc, Hervé; Failloux, Anna-Bella; Saleh, Maria-Carla; Vignuzzi, Marco title: Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date: 2014-01-16 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003877 sha: doc_id: 334947 cord_uid: pa0p5dif file: cache/cord-336447-hpnkou41.json key: cord-336447-hpnkou41 authors: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 journal: Rambam Maimonides Med J DOI: 10.5041/rmmj.10418 sha: doc_id: 336447 cord_uid: hpnkou41 file: cache/cord-337673-1nau263l.json key: cord-337673-1nau263l authors: Wu, Chang-Jer; Chan, Yi-Lin title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 journal: Expert Opin Investig Drugs DOI: 10.1517/13543784.15.2.89 sha: doc_id: 337673 cord_uid: 1nau263l file: cache/cord-337879-liqhbqxl.json key: cord-337879-liqhbqxl authors: Kriesel, John D.; Hobbs, Maurine R.; Jones, Brandt B.; Milash, Brett; Nagra, Rashed M.; Fischer, Kael F. title: Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain date: 2012-03-08 journal: PLoS One DOI: 10.1371/journal.pone.0031886 sha: doc_id: 337879 cord_uid: liqhbqxl file: cache/cord-337361-salby0fu.json key: cord-337361-salby0fu authors: Bujarski, Jozef J. title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date: 2013-03-26 journal: Front Plant Sci DOI: 10.3389/fpls.2013.00068 sha: doc_id: 337361 cord_uid: salby0fu file: cache/cord-337199-mbv8kd1k.json key: cord-337199-mbv8kd1k authors: Ballarín-González, Borja; Thomsen, Troels Bo; Howard, Kenneth Alan title: Clinical translation of RNAi-based treatments for respiratory diseases date: 2012-09-07 journal: Drug Deliv Transl Res DOI: 10.1007/s13346-012-0098-7 sha: doc_id: 337199 cord_uid: mbv8kd1k file: cache/cord-337998-08tknscm.json key: cord-337998-08tknscm authors: Sztuba-Solinska, Joanna; Diaz, Larissa; Kumar, Mia R.; Kolb, Gaëlle; Wiley, Michael R.; Jozwick, Lucas; Kuhn, Jens H.; Palacios, Gustavo; Radoshitzky, Sheli R.; J. Le Grice, Stuart F.; Johnson, Reed F. title: A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8 date: 2016-11-16 journal: Nucleic Acids Res DOI: 10.1093/nar/gkw825 sha: doc_id: 337998 cord_uid: 08tknscm file: cache/cord-337508-nfzaw8gg.json key: cord-337508-nfzaw8gg authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 date: 2020-10-05 journal: Pathology DOI: 10.1016/j.pathol.2020.09.013 sha: doc_id: 337508 cord_uid: nfzaw8gg file: cache/cord-337976-c2auspti.json key: cord-337976-c2auspti authors: Weiss, Susan R. title: Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date: 1983-04-30 journal: Virology DOI: 10.1016/s0042-6822(83)80022-1 sha: doc_id: 337976 cord_uid: c2auspti file: cache/cord-334891-4jgtxg07.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-334891-4jgtxg07 authors: Choudhury, Abhigyan; Chandra Das, Nabarun; Patra, Ritwik; Bhattacharya, Manojit; Mukherjee, Suprabhat title: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date: 2020-11-11 journal: bioRxiv DOI: 10.1101/2020.11.11.377713 sha: doc_id: 334891 cord_uid: 4jgtxg07 file: cache/cord-336986-rmxin1da.json key: cord-336986-rmxin1da authors: De Clercq, Erik title: New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date: 2019-08-07 journal: Chem Asian J DOI: 10.1002/asia.201900841 sha: doc_id: 336986 cord_uid: rmxin1da file: cache/cord-337285-t6qr41wc.json key: cord-337285-t6qr41wc authors: Ikeda, Masanori; Kato, Nobuyuki title: Modulation of host metabolism as a target of new antivirals() date: 2007-10-10 journal: Adv Drug Deliv Rev DOI: 10.1016/j.addr.2007.03.021 sha: doc_id: 337285 cord_uid: t6qr41wc file: cache/cord-338083-77re4l0w.json key: cord-338083-77re4l0w authors: Bolin, Steven R.; Grooms, Daniel L. title: Origination and consequences of bovine viral diarrhea virus diversity date: 2005-03-04 journal: Vet Clin North Am Food Anim Pract DOI: 10.1016/j.cvfa.2003.11.009 sha: doc_id: 338083 cord_uid: 77re4l0w file: cache/cord-338345-mr1orklo.json key: cord-338345-mr1orklo authors: Adedeji, Adeyemi O.; Lazarus, Hilary title: Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase date: 2016-09-07 journal: mSphere DOI: 10.1128/msphere.00235-16 sha: doc_id: 338345 cord_uid: mr1orklo file: cache/cord-335231-617e5dcy.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-335231-617e5dcy authors: Pettersson, Lisa; Klingström, Jonas; Hardestam, Jonas; Lundkvist, Åke; Ahlm, Clas; Evander, Magnus title: Hantavirus RNA in Saliva from Patients with Hemorrhagic Fever with Renal Syndrome date: 2008-03-17 journal: Emerg Infect Dis DOI: 10.3201/eid1403.071242 sha: doc_id: 335231 cord_uid: 617e5dcy file: cache/cord-337899-w5zh40gv.json key: cord-337899-w5zh40gv authors: Bissoyi, Akalabya; Pattanayak, Subrat K.; Bit, Arindam; Patel, Ashish; Singh, Abhishek K.; Behera, Sudhanshu S.; Satpathy, Debabrata title: Alphavirus Nonstructural Proteases and Their Inhibitors date: 2017-07-14 journal: Viral Proteases and Their Inhibitors DOI: 10.1016/b978-0-12-809712-0.00004-6 sha: doc_id: 337899 cord_uid: w5zh40gv file: cache/cord-338307-vfutmwxq.json key: cord-338307-vfutmwxq authors: Sturman, Lawrence S.; Holmes, Kathryn V. title: The Molecular Biology of Coronaviruses date: 1983-12-31 journal: Advances in Virus Research DOI: 10.1016/s0065-3527(08)60721-6 sha: doc_id: 338307 cord_uid: vfutmwxq file: cache/cord-338358-ppjxo2di.json key: cord-338358-ppjxo2di authors: Whitworth, Kristin M.; Benne, Joshua A.; Spate, Lee D.; Murphy, Stephanie L.; Samuel, Melissa S.; Murphy, Clifton N.; Richt, Jürgen A.; Walters, Eric; Prather, Randall S.; Wells, Kevin D. title: Zygote injection of CRISPR/Cas9 RNA successfully modifies the target gene without delaying blastocyst development or altering the sex ratio in pigs date: 2016-10-15 journal: Transgenic Res DOI: 10.1007/s11248-016-9989-6 sha: doc_id: 338358 cord_uid: ppjxo2di file: cache/cord-338680-wwlttymp.json key: cord-338680-wwlttymp authors: Khonyongwa, K.; Taori, S. K.; Soares, A.; Desai, N.; Sudhanva, M.; Bernal, W.; Schelenz, S.; Curran, L. A. title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-07-30 journal: nan DOI: 10.1101/2020.07.24.20148262 sha: doc_id: 338680 cord_uid: wwlttymp file: cache/cord-338727-1kodz527.json key: cord-338727-1kodz527 authors: Ilinskaya, O. N.; Mahmud, R. Shah title: Ribonucleases as antiviral agents date: 2014-10-11 journal: Mol Biol DOI: 10.1134/s0026893314040050 sha: doc_id: 338727 cord_uid: 1kodz527 file: cache/cord-339456-82iks0xf.json key: cord-339456-82iks0xf authors: Mikel, P.; Vasickova, P.; Kralik, P. title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date: 2015-02-25 journal: Food Environ Virol DOI: 10.1007/s12560-015-9188-2 sha: doc_id: 339456 cord_uid: 82iks0xf file: cache/cord-338901-1kzy7rts.json key: cord-338901-1kzy7rts authors: Li, Heng; Yang, Li; Liu, Fei-fei; Ma, Xin-na; He, Pei-lan; Tang, Wei; Tong, Xian-kun; Zuo, Jian-ping title: Overview of therapeutic drug research for COVID-19 in China date: 2020-06-17 journal: Acta Pharmacol Sin DOI: 10.1038/s41401-020-0438-y sha: doc_id: 338901 cord_uid: 1kzy7rts file: cache/cord-339288-y8woqsii.json key: cord-339288-y8woqsii authors: Tews, Birke Andrea; Meyers, Gregor title: Self-Replicating RNA date: 2016-06-11 journal: RNA Vaccines DOI: 10.1007/978-1-4939-6481-9_2 sha: doc_id: 339288 cord_uid: y8woqsii file: cache/cord-339782-rybjc58j.json key: cord-339782-rybjc58j authors: Carmo, Anália; Pereira‐Vaz, João; Mota, Vanda; Mendes, Alexandra; Morais, Célia; da Silva, Andreia Coelho; Camilo, Elisabete; Pinto, Catarina Silva; Cunha, Elizabete; Pereira, Janet; Coucelo, Margarida; Martinho, Patrícia; Correia, Lurdes; Marques, Gilberto; Araújo, Lucília; Rodrigues, Fernando title: Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date: 2020-06-02 journal: J Med Virol DOI: 10.1002/jmv.26103 sha: doc_id: 339782 cord_uid: rybjc58j file: cache/cord-338582-o976nab9.json key: cord-338582-o976nab9 authors: Dahlhausen, Bob title: Future Veterinary Diagnostics date: 2010-09-19 journal: J Exot Pet Med DOI: 10.1053/j.jepm.2010.05.006 sha: doc_id: 338582 cord_uid: o976nab9 file: cache/cord-340189-jo38hjqa.json key: cord-340189-jo38hjqa authors: Bar-On, Yinon M; Flamholz, Avi; Phillips, Rob; Milo, Ron title: SARS-CoV-2 (COVID-19) by the numbers date: 2020-04-02 journal: eLife DOI: 10.7554/elife.57309 sha: doc_id: 340189 cord_uid: jo38hjqa file: cache/cord-336628-0evl3wnd.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-336628-0evl3wnd authors: Neufeldt, Christopher J.; Cerikan, Berati; Cortese, Mirko; Frankish, Jamie; Lee, Ji-Young; Plociennikowska, Agnieszka; Heigwer, Florian; Joecks, Sebastian; Burkart, Sandy S.; Zander, David Y.; Gendarme, Mathieu; El Debs, Bachir; Halama, Niels; Merle, Uta; Boutros, Michael; Binder, Marco; Bartenschlager, Ralf title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date: 2020-07-21 journal: bioRxiv DOI: 10.1101/2020.07.21.212639 sha: doc_id: 336628 cord_uid: 0evl3wnd file: cache/cord-339976-tg2jkss7.json key: cord-339976-tg2jkss7 authors: Wang, Haibin; Mao, Yuanli; Ju, Liancai; Zhang, Jing; Liu, Zhiguo; Zhou, Xianzhi; Li, Qinghong; Wang, Yuedong; Kim, Sunghee; Zhang, Lurong title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 journal: Clin Chem DOI: 10.1373/clinchem.2004.031237 sha: doc_id: 339976 cord_uid: tg2jkss7 file: cache/cord-339431-kyr5lv15.json key: cord-339431-kyr5lv15 authors: Saçar Demirci, Müşerref Duygu; Adan, Aysun title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date: 2020-03-17 journal: bioRxiv DOI: 10.1101/2020.03.15.992438 sha: doc_id: 339431 cord_uid: kyr5lv15 file: cache/cord-338812-q24jycgk.json key: cord-338812-q24jycgk authors: Zakaryan, H.; Stamminger, T. title: Nuclear remodelling during viral infections date: 2011-04-28 journal: Cell Microbiol DOI: 10.1111/j.1462-5822.2011.01596.x sha: doc_id: 338812 cord_uid: q24jycgk file: cache/cord-339209-oe8onyr9.json key: cord-339209-oe8onyr9 authors: Vasilakis, Nikos; Guzman, Hilda; Firth, Cadhla; Forrester, Naomi L; Widen, Steven G; Wood, Thomas G; Rossi, Shannan L; Ghedin, Elodie; Popov, Vsevolov; Blasdell, Kim R; Walker, Peter J; Tesh, Robert B title: Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date: 2014-05-20 journal: Virol J DOI: 10.1186/1743-422x-11-97 sha: doc_id: 339209 cord_uid: oe8onyr9 file: cache/cord-339172-210dwhgj.json key: cord-339172-210dwhgj authors: Knoops, Kèvin; Kikkert, Marjolein; van den Worm, Sjoerd H. E.; Zevenhoven-Dobbe, Jessika C; van der Meer, Yvonne; Koster, Abraham J; Mommaas, A. Mieke; Snijder, Eric J title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 journal: PLoS Biol DOI: 10.1371/journal.pbio.0060226 sha: doc_id: 339172 cord_uid: 210dwhgj file: cache/cord-340046-kgbvld0y.json key: cord-340046-kgbvld0y authors: Houspie, Lieselot; De Coster, Sarah; Keyaerts, Els; Narongsack, Phouthalack; De Roy, Rikka; Talboom, Ive; Sisk, Maura; Maes, Piet; Verbeeck, Jannick; Van Ranst, Marc title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 journal: Virol J DOI: 10.1186/1743-422x-8-98 sha: doc_id: 340046 cord_uid: kgbvld0y file: cache/cord-340325-0oh40b6r.json key: cord-340325-0oh40b6r authors: Witzigmann, Dominik; Kulkarni, Jayesh A.; Leung, Jerry; Chen, Sam; Cullis, Pieter R.; van der Meel, Roy title: Lipid nanoparticle technology for therapeutic gene regulation in the liver date: 2020-07-02 journal: Adv Drug Deliv Rev DOI: 10.1016/j.addr.2020.06.026 sha: doc_id: 340325 cord_uid: 0oh40b6r file: cache/cord-340423-f8ab7413.json key: cord-340423-f8ab7413 authors: Barr, J.N.; Fearns, R. title: Genetic Instability of RNA Viruses date: 2016-09-09 journal: Genome Stability DOI: 10.1016/b978-0-12-803309-8.00002-1 sha: doc_id: 340423 cord_uid: f8ab7413 file: cache/cord-341029-49360l2a.json key: cord-341029-49360l2a authors: Nasir, Arshan; Caetano-Anollés, Gustavo title: A phylogenomic data-driven exploration of viral origins and evolution date: 2015-09-25 journal: Sci Adv DOI: 10.1126/sciadv.1500527 sha: doc_id: 341029 cord_uid: 49360l2a file: cache/cord-340489-yo3cp5vs.json key: cord-340489-yo3cp5vs authors: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 journal: Innere Medizin DOI: 10.1016/b978-3-437-42831-9.10013-0 sha: doc_id: 340489 cord_uid: yo3cp5vs file: cache/cord-340554-7cwp2xbw.json key: cord-340554-7cwp2xbw authors: Yamasaki, Satoshi; Amemiya, Takayuki; Yabuki, Yukimitsu; Horimoto, Katsuhisa; Fukui, Kazuhiko title: ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow date: 2019-03-06 journal: J Comput Aided Mol Des DOI: 10.1007/s10822-019-00195-y sha: doc_id: 340554 cord_uid: 7cwp2xbw file: cache/cord-341050-hnuogpqn.json key: cord-341050-hnuogpqn authors: Acharya, Dhiraj; Bai, Fengwei title: An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection date: 2016-05-18 journal: West Nile Virus DOI: 10.1007/978-1-4939-3670-0_19 sha: doc_id: 341050 cord_uid: hnuogpqn file: cache/cord-341171-s8vkgdhf.json key: cord-341171-s8vkgdhf authors: Kojima, Mizuki; Mawatari, Kazuaki; Emoto, Takahiro; Nishisaka-Nonaka, Risa; Bui, Thi Kim Ngan; Shimohata, Takaaki; Uebanso, Takashi; Akutagawa, Masatake; Kinouchi, Yohsuke; Wada, Takahiro; Okamoto, Masayuki; Ito, Hiroshi; Tojo, Kenji; Daidoji, Tomo; Nakaya, Takaaki; Takahashi, Akira title: Irradiation by a Combination of Different Peak-Wavelength Ultraviolet-Light Emitting Diodes Enhances the Inactivation of Influenza A Viruses date: 2020-07-08 journal: Microorganisms DOI: 10.3390/microorganisms8071014 sha: doc_id: 341171 cord_uid: s8vkgdhf file: cache/cord-341071-nwrl1qws.json key: cord-341071-nwrl1qws authors: Berzal-Herranz, Alfredo; Romero-López, Cristina title: Two Examples of RNA Aptamers with Antiviral Activity. Are Aptamers the Wished Antiviral Drugs? date: 2020-07-22 journal: Pharmaceuticals (Basel) DOI: 10.3390/ph13080157 sha: doc_id: 341071 cord_uid: nwrl1qws file: cache/cord-341034-2oigu75k.json key: cord-341034-2oigu75k authors: Moser, Theresa S.; Schieffer, Daniel; Cherry, Sara title: AMP-Activated Kinase Restricts Rift Valley Fever Virus Infection by Inhibiting Fatty Acid Synthesis date: 2012-04-19 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1002661 sha: doc_id: 341034 cord_uid: 2oigu75k file: cache/cord-341541-3l6tjf3t.json key: cord-341541-3l6tjf3t authors: Hajijafari Anaraki, Mozafar; Sheikhi, Nariman; Haghbin Nazarpak, Hadi; Nikbakht Brujeni, Gholamreza title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene date: 2020-05-26 journal: Microbiol Immunol DOI: 10.1111/1348-0421.12825 sha: doc_id: 341541 cord_uid: 3l6tjf3t file: cache/cord-340475-h0q1m3ed.json key: cord-340475-h0q1m3ed authors: Carnero, Elena; Barriocanal, Marina; Segura, Victor; Guruceaga, Elizabeth; Prior, Celia; Börner, Kathleen; Grimm, Dirk; Fortes, Puri title: Type I Interferon Regulates the Expression of Long Non-Coding RNAs date: 2014-11-06 journal: Front Immunol DOI: 10.3389/fimmu.2014.00548 sha: doc_id: 340475 cord_uid: h0q1m3ed file: cache/cord-341321-paucodwz.json key: cord-341321-paucodwz authors: Finkbeiner, Stacy R; Kirkwood, Carl D; Wang, David title: Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea date: 2008-10-14 journal: Virol J DOI: 10.1186/1743-422x-5-117 sha: doc_id: 341321 cord_uid: paucodwz file: cache/cord-341330-31ngknq4.json key: cord-341330-31ngknq4 authors: Sarma, Phulen; Shekhar, Nishant; Prajapat, Manisha; Avti, Pramod; Kaur, Hardeep; Kumar, Subodh; Singh, Sanjay; Kumar, Harish; Prakash, Ajay; Dhibar, Deba Prasad; Medhi, Bikash title: In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain) date: 2020-05-18 journal: J Biomol Struct Dyn DOI: 10.1080/07391102.2020.1753580 sha: doc_id: 341330 cord_uid: 31ngknq4 file: cache/cord-341324-f9g9gitn.json key: cord-341324-f9g9gitn authors: Rojas, José M.; Alejo, Alí; Martín, Verónica; Sevilla, Noemí title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date: 2020-10-21 journal: Cell Mol Life Sci DOI: 10.1007/s00018-020-03671-z sha: doc_id: 341324 cord_uid: f9g9gitn file: cache/cord-341342-kyavg4vu.json key: cord-341342-kyavg4vu authors: Masters, P. S. title: Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date: 1992 journal: Arch Virol DOI: 10.1007/bf01309634 sha: doc_id: 341342 cord_uid: kyavg4vu file: cache/cord-341176-83khavoh.json key: cord-341176-83khavoh authors: Lotfi, Melika; Rezaei, Nima title: CRISPR/Cas13: A potential therapeutic option of COVID-19 date: 2020-09-17 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110738 sha: doc_id: 341176 cord_uid: 83khavoh file: cache/cord-340422-8f5xe4zc.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-340422-8f5xe4zc authors: Rowland, R. R. R.; Robinson, B.; Stefanick, J.; Kim, T. S.; Guanghua, L.; Lawson, S. R.; Benfield, D. A. title: Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine date: 2001 journal: Arch Virol DOI: 10.1007/s007050170161 sha: doc_id: 340422 cord_uid: 8f5xe4zc file: cache/cord-341502-jlzufa28.json key: cord-341502-jlzufa28 authors: Lee, Sungyul; Lee, Young-suk; Choi, Yeon; Son, Ahyeon; Park, Youngran; Lee, Kyung-Min; Kim, Jeesoo; Kim, Jong-Seo; Kim, V. Narry title: The SARS-CoV-2 RNA interactome date: 2020-11-02 journal: bioRxiv DOI: 10.1101/2020.11.02.364497 sha: doc_id: 341502 cord_uid: jlzufa28 file: cache/cord-342117-r2chpw7y.json key: cord-342117-r2chpw7y authors: Wu, Xinwei; Hong, Hua; Yue, Jinya; Wu, Yejian; Li, Xiangzhong; Jiang, Liyun; Li, Lei; Li, Qiaoyan; Gao, Guoquan; Yang, Xia title: Inhibitory effect of small interfering RNA on dengue virus replication in mosquito cells date: 2010-10-14 journal: Virol J DOI: 10.1186/1743-422x-7-270 sha: doc_id: 342117 cord_uid: r2chpw7y file: cache/cord-342189-ya05m58o.json key: cord-342189-ya05m58o authors: Banerjee, Abhik K.; Blanco, Mario R.; Bruce, Emily A.; Honson, Drew D.; Chen, Linlin M.; Chow, Amy; Bhat, Prashant; Ollikainen, Noah; Quinodoz, Sofia A.; Loney, Colin; Thai, Jasmine; Miller, Zachary D.; Lin, Aaron E.; Schmidt, Madaline M.; Stewart, Douglas G.; Goldfarb, Daniel; De Lorenzo, Giuditta; Rihn, Suzannah J.; Voorhees, Rebecca; Botten, Jason W.; Majumdar, Devdoot; Guttman, Mitchell title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 journal: Cell DOI: 10.1016/j.cell.2020.10.004 sha: doc_id: 342189 cord_uid: ya05m58o file: cache/cord-342456-5gp3cry0.json key: cord-342456-5gp3cry0 authors: Hoagland, Daisy A.; Clarke, Daniel J.B.; Møller, Rasmus; Han, Yuling; Yang, Liuliu; Wojciechowicz, Megan L.; Lachmann, Alexander; Oguntuyo, Kasopefoluwa Y.; Stevens, Christian; Lee, Benhur; Chen, Shuibing; Ma’ayan, Avi; tenOever, Benjamin R title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date: 2020-07-13 journal: bioRxiv DOI: 10.1101/2020.07.12.199687 sha: doc_id: 342456 cord_uid: 5gp3cry0 file: cache/cord-341804-rnj3wtg4.json key: cord-341804-rnj3wtg4 authors: Jin, Zhe; Liu, Jing-Yi; Feng, Rang; Ji, Lu; Jin, Zi-Li; Li, Hai-Bo title: Drug treatment of coronavirus disease 2019 (COVID-19) in China. date: 2020-06-27 journal: Eur J Pharmacol DOI: 10.1016/j.ejphar.2020.173326 sha: doc_id: 341804 cord_uid: rnj3wtg4 file: cache/cord-342344-jjnf4yje.json key: cord-342344-jjnf4yje authors: Mello, C. J.; Kamitaki, N.; de Rivera, H.; McCarroll, S. A. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 journal: nan DOI: 10.1101/2020.06.24.20139584 sha: doc_id: 342344 cord_uid: jjnf4yje file: cache/cord-342412-azkamnpa.json key: cord-342412-azkamnpa authors: Ecker, David J; Sampath, Rangarajan; Willett, Paul; Wyatt, Jacqueline R; Samant, Vivek; Massire, Christian; Hall, Thomas A; Hari, Kumar; McNeil, John A; Büchen-Osmond, Cornelia; Budowle, Bruce title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date: 2005-04-25 journal: BMC Microbiol DOI: 10.1186/1471-2180-5-19 sha: doc_id: 342412 cord_uid: azkamnpa file: cache/cord-343470-w215pzdc.json key: cord-343470-w215pzdc authors: Tsai, Kevin; Cullen, Bryan R. title: Epigenetic and epitranscriptomic regulation of viral replication date: 2020-06-12 journal: Nat Rev Microbiol DOI: 10.1038/s41579-020-0382-3 sha: doc_id: 343470 cord_uid: w215pzdc file: cache/cord-342145-cq6xe5r7.json key: cord-342145-cq6xe5r7 authors: Dao Thi, Viet Loan; Herbst, Konrad; Boerner, Kathleen; Meurer, Matthias; Kremer, Lukas PM; Kirrmaier, Daniel; Freistaedter, Andrew; Papagiannidis, Dimitrios; Galmozzi, Carla; Stanifer, Megan L.; Boulant, Steeve; Klein, Steffen; Chlanda, Petr; Khalid, Dina; Barreto Miranda, Isabel; Schnitzler, Paul; Kräusslich, Hans-Georg; Knop, Michael; Anders, Simon title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date: 2020-08-12 journal: Sci Transl Med DOI: 10.1126/scitranslmed.abc7075 sha: doc_id: 342145 cord_uid: cq6xe5r7 file: cache/cord-342676-ykog278j.json key: cord-342676-ykog278j authors: Stewart, H.; Bingham, R.J.; White, S. J.; Dykeman, E. C.; Zothner, C.; Tuplin, A. K.; Stockley, P. G.; Twarock, R.; Harris, M. title: Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging date: 2016-03-14 journal: Sci Rep DOI: 10.1038/srep22952 sha: doc_id: 342676 cord_uid: ykog278j file: cache/cord-342649-ysossker.json key: cord-342649-ysossker authors: Scagnolari, Carolina; Midulla, Fabio; Selvaggi, Carla; Monteleone, Katia; Bonci, Enea; Papoff, Paola; Cangiano, Giulia; Marco, Paola Di; Moretti, Corrado; Pierangeli, Alessandra; Antonelli, Guido title: Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus date: 2012-03-10 journal: Med Microbiol Immunol DOI: 10.1007/s00430-012-0233-6 sha: doc_id: 342649 cord_uid: ysossker file: cache/cord-343448-xhm97wy2.json key: cord-343448-xhm97wy2 authors: Rinaldi, Andrea title: RNA to the rescue: RNA is one of the most promising targets for drug development given its wide variety of uses date: 2020-06-26 journal: EMBO Rep DOI: 10.15252/embr.202051013 sha: doc_id: 343448 cord_uid: xhm97wy2 file: cache/cord-342681-pqzcy9wu.json key: cord-342681-pqzcy9wu authors: Pongpirul, Wannarat A.; Mott, Joshua A.; Woodring, Joseph V.; Uyeki, Timothy M.; MacArthur, John R.; Vachiraphan, Apichart; Suwanvattana, Pawita; Uttayamakul, Sumonmal; Chunsuttiwat, Supamit; Chotpitayasunondh, Tawee; Pongpirul, Krit; Prasithsirikul, Wisit title: Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date: 2020-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid2607.200598 sha: doc_id: 342681 cord_uid: pqzcy9wu file: cache/cord-342902-y1v8wzxq.json key: cord-342902-y1v8wzxq authors: Yuan, Shuofeng; Yin, Xin; Meng, XiangZhi; Chan, Jasper; Ye, Zi-Wei; Riva, Laura; Pache, Lars; Chan, Chris Chun-Yiu; Lai, Pok-Man; Chan, Chris; Poon, Vincent; Matsunaga, Naoko; Pu, Yuan; Yuen, Chun-Kit; Cao, Jianli; Liang, Ronghui; Tang, Kaiming; Sheng, Li; Du, Yushen; Xu, Wan; Sze, Kong-Hung; Zhang, Jinxia; Chu, Hin; Kok, Kin-Hang; To, Kelvin; Jin, Dong-Yan; Sun, Ren; Chanda, Sumit; Yuen, Kwok-Yung title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date: 2020-10-07 journal: Res Sq DOI: 10.21203/rs.3.rs-86169/v1 sha: doc_id: 342902 cord_uid: y1v8wzxq file: cache/cord-343963-99rd3o79.json key: cord-343963-99rd3o79 authors: Wong, Mun-Teng; Chen, Steve S-L title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 journal: Cell Mol Immunol DOI: 10.1038/cmi.2014.127 sha: doc_id: 343963 cord_uid: 99rd3o79 parallel: Warning: No more processes: Decreasing number of running jobs to 91. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-342901-ca2xxkb2.json key: cord-342901-ca2xxkb2 authors: Lloyd, Richard E. title: Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses date: 2015-05-31 journal: Virology DOI: 10.1016/j.virol.2015.03.001 sha: doc_id: 342901 cord_uid: ca2xxkb2 file: cache/cord-343350-04e6wvov.json key: cord-343350-04e6wvov authors: Liu, Haipeng; Söderhäll, Kenneth; Jiravanichpaisal, Pikul title: Antiviral immunity in crustaceans date: 2009-02-15 journal: Fish Shellfish Immunol DOI: 10.1016/j.fsi.2009.02.009 sha: doc_id: 343350 cord_uid: 04e6wvov file: cache/cord-344714-0cam9ipf.json key: cord-344714-0cam9ipf authors: Russo, Maria; Moccia, Stefania; Spagnuolo, Carmela; Tedesco, Idolo; Russo, Gian Luigi title: Roles of flavonoids against coronavirus infection date: 2020-07-28 journal: Chem Biol Interact DOI: 10.1016/j.cbi.2020.109211 sha: doc_id: 344714 cord_uid: 0cam9ipf file: cache/cord-342653-bpyc2gbl.json key: cord-342653-bpyc2gbl authors: Wang, Hai-Tao; Hur, Sun title: Substrate recognition by TRIM and TRIM-like proteins in innate immunity date: 2020-10-20 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2020.09.013 sha: doc_id: 342653 cord_uid: bpyc2gbl file: cache/cord-343221-e29of29o.json key: cord-343221-e29of29o authors: Kindler, Eveline; Gil-Cruz, Cristina; Spanier, Julia; Li, Yize; Wilhelm, Jochen; Rabouw, Huib H.; Züst, Roland; Hwang, Mihyun; V’kovski, Philip; Stalder, Hanspeter; Marti, Sabrina; Habjan, Matthias; Cervantes-Barragan, Luisa; Elliot, Ruth; Karl, Nadja; Gaughan, Christina; van Kuppeveld, Frank J. M.; Silverman, Robert H.; Keller, Markus; Ludewig, Burkhard; Bergmann, Cornelia C.; Ziebuhr, John; Weiss, Susan R.; Kalinke, Ulrich; Thiel, Volker title: Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication date: 2017-02-03 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1006195 sha: doc_id: 343221 cord_uid: e29of29o file: cache/cord-343632-cv3qgno3.json key: cord-343632-cv3qgno3 authors: Zhang, Yinhua; Odiwuor, Nelson; Xiong, Jin; Sun, Luo; Nyaruaba, Raphael Ohuru; Wei, Hongping; Tanner, Nathan A title: Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP date: 2020-02-29 journal: nan DOI: 10.1101/2020.02.26.20028373 sha: doc_id: 343632 cord_uid: cv3qgno3 file: cache/cord-344006-0iq9s94n.json key: cord-344006-0iq9s94n authors: Atzrodt, Cassandra L.; Maknojia, Insha; McCarthy, Robert D.P.; Oldfield, Tiara M.; Po, Jonathan; Ta, Kenny T.L.; Stepp, Hannah E.; Clements, Thomas P. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 journal: FEBS J DOI: 10.1111/febs.15375 sha: doc_id: 344006 cord_uid: 0iq9s94n parallel: Warning: No more processes: Decreasing number of running jobs to 90. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-344410-yo9libo0.json key: cord-344410-yo9libo0 authors: Zhou, Yan; Zheng, HaiHong; Gao, Fei; Tian, DeBin; Yuan, ShiShan title: Mutational analysis of the SDD sequence motif of a PRRSV RNA-dependent RNA polymerase date: 2011-09-16 journal: Sci China Life Sci DOI: 10.1007/s11427-011-4216-4 sha: doc_id: 344410 cord_uid: yo9libo0 file: cache/cord-344464-if6js43s.json key: cord-344464-if6js43s authors: Cowley, J. A.; Walker, P. J. title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date: 2002 journal: Arch Virol DOI: 10.1007/s00705-002-0847-x sha: doc_id: 344464 cord_uid: if6js43s file: cache/cord-342756-rgm9ffpk.json key: cord-342756-rgm9ffpk authors: Senger, Mario Roberto; Evangelista, Tereza Cristina Santos; Dantas, Rafael Ferreira; Santana, Marcos Vinicius da Silva; Gonçalves, Luiz Carlos Saramago; de Souza Neto, Lauro Ribeiro; Ferreira, Sabrina Baptista; Silva-Junior, Floriano Paes title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date: 2020-10-02 journal: Mem Inst Oswaldo Cruz DOI: 10.1590/0074-02760200254 sha: doc_id: 342756 cord_uid: rgm9ffpk file: cache/cord-343604-v986m9jd.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-343604-v986m9jd authors: Vijayakumar, Balaji Gowrivel; Ramesh, Deepthi; Joji, Annu; Jayachandra prakasan, Jayadharini; Kannan, Tharanikkarasu title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date: 2020-08-06 journal: Eur J Pharmacol DOI: 10.1016/j.ejphar.2020.173448 sha: doc_id: 343604 cord_uid: v986m9jd file: cache/cord-341513-e6p3lrlf.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-341513-e6p3lrlf authors: Li, Yunchuan; Zhang, Hao; Zhu, Bibo; Ashraf, Usama; Chen, Zheng; Xu, Qiuping; Zhou, Dengyuan; Zheng, Bohan; Song, Yunfeng; Chen, Huanchun; Ye, Jing; Cao, Shengbo title: Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection date: 2017-09-29 journal: Front Immunol DOI: 10.3389/fimmu.2017.01237 sha: doc_id: 341513 cord_uid: e6p3lrlf file: cache/cord-344749-omzhhr0k.json key: cord-344749-omzhhr0k authors: Kaya, Sariye Irem; Karadurmus, Leyla; Ozcelikay, Goksu; Bakirhan, Nurgul K.; Ozkan, Sibel A. title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 journal: Nanosensors for Smart Cities DOI: 10.1016/b978-0-12-819870-4.00017-7 sha: doc_id: 344749 cord_uid: omzhhr0k file: cache/cord-344782-ond1ziu5.json key: cord-344782-ond1ziu5 authors: Zhang, Jing; Finlaison, Deborah S.; Frost, Melinda J.; Gestier, Sarah; Gu, Xingnian; Hall, Jane; Jenkins, Cheryl; Parrish, Kate; Read, Andrew J.; Srivastava, Mukesh; Rose, Karrie; Kirkland, Peter D. title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 journal: PLoS One DOI: 10.1371/journal.pone.0205209 sha: doc_id: 344782 cord_uid: ond1ziu5 file: cache/cord-342800-62jklwiy.json key: cord-342800-62jklwiy authors: Xu, Shuqin; Yang, Kunpeng; Li, Rose; Zhang, Lu title: mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection date: 2020-09-09 journal: Int J Mol Sci DOI: 10.3390/ijms21186582 sha: doc_id: 342800 cord_uid: 62jklwiy file: cache/cord-344636-go5cw92q.json key: cord-344636-go5cw92q authors: Huang, Wei E.; Lim, Boon; Hsu, Chia‐Chen; Xiong, Dan; Wu, Wei; Yu, Yejiong; Jia, Huidong; Wang, Yun; Zeng, Yida; Ji, Mengmeng; Chang, Hong; Zhang, Xiuming; Wang, Hui; Cui, Zhanfeng title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date: 2020-04-25 journal: Microb Biotechnol DOI: 10.1111/1751-7915.13586 sha: doc_id: 344636 cord_uid: go5cw92q file: cache/cord-345204-ch0e6lzl.json key: cord-345204-ch0e6lzl authors: Scarlata, S.; Yerramilli, V. S. title: Design Of A Rapid And Reversible Fluorescence Assay To Detect COVID-19 And Other Pathogens date: 2020-10-05 journal: nan DOI: 10.1101/2020.10.02.20196113 sha: doc_id: 345204 cord_uid: ch0e6lzl file: cache/cord-345647-h3imwhss.json key: cord-345647-h3imwhss authors: Gao, Wen-Hua; Lin, Xian-Dan; Chen, Yan-Mei; Xie, Chun-Gang; Tan, Zhi-Zhou; Zhou, Jia-Jun; Chen, Shuai; Holmes, Edward C; Zhang, Yong-Zhen title: Newly identified viral genomes in pangolins with fatal disease date: 2020-04-12 journal: Virus Evol DOI: 10.1093/ve/veaa020 sha: doc_id: 345647 cord_uid: h3imwhss file: cache/cord-344321-fjer281d.json key: cord-344321-fjer281d authors: Ning, Yi; Hu, Jue; Lu, Fangguo title: Aptamers used for biosensors and targeted therapy date: 2020-10-20 journal: Biomed Pharmacother DOI: 10.1016/j.biopha.2020.110902 sha: doc_id: 344321 cord_uid: fjer281d file: cache/cord-345302-wbkfjz8r.json key: cord-345302-wbkfjz8r authors: Devaney, Ryan; Trudgett, James; Trudgett, Alan; Meharg, Caroline; Smyth, Victoria title: A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date: 2016-10-04 journal: Avian Pathol DOI: 10.1080/03079457.2016.1193123 sha: doc_id: 345302 cord_uid: wbkfjz8r file: cache/cord-345863-j01l71dh.json key: cord-345863-j01l71dh authors: Drechsler, Yvonne; Vasconcelos, Elton J. R.; Griggs, Lisa M.; Diniz, Pedro P. P. V.; Collisson, Ellen title: Host Gene Expression of Macrophages in Response to Feline Coronavirus Infection date: 2020-06-09 journal: Cells DOI: 10.3390/cells9061431 sha: doc_id: 345863 cord_uid: j01l71dh file: cache/cord-345157-fhmhpobi.json key: cord-345157-fhmhpobi authors: Qi, Dan; Guan, Jitian; Wu, Erxi title: Virus infection-induced host mRNA degradation and potential application of live cell imaging date: 2018-12-12 journal: Radiol Infect Dis DOI: 10.1016/j.jrid.2018.12.002 sha: doc_id: 345157 cord_uid: fhmhpobi file: cache/cord-343662-scn7b4c6.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-343662-scn7b4c6 authors: Delli Ponti, Riccardo; Armaos, Alexandros; Marti, Stefanie; Tartaglia, Gian Gaetano title: A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs date: 2018-12-03 journal: Front Mol Biosci DOI: 10.3389/fmolb.2018.00111 sha: doc_id: 343662 cord_uid: scn7b4c6 file: cache/cord-345898-a6vt8kso.json key: cord-345898-a6vt8kso authors: Ren, Linzhu; Peng, Zhiyuan; Chen, Xinrong; Ouyang, Hongsheng title: Live Cell Reporter Systems for Positive-Sense Single Strand RNA Viruses date: 2016-01-04 journal: Appl Biochem Biotechnol DOI: 10.1007/s12010-015-1968-5 sha: doc_id: 345898 cord_uid: a6vt8kso file: cache/cord-342634-4ouhdjsr.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-342634-4ouhdjsr authors: Semrad, Katharina title: Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding date: 2010-12-26 journal: Biochem Res Int DOI: 10.1155/2011/532908 sha: doc_id: 342634 cord_uid: 4ouhdjsr file: cache/cord-345654-vyz6f3he.json key: cord-345654-vyz6f3he authors: Dennehy, John J. title: Evolutionary ecology of virus emergence date: 2016-12-30 journal: Ann N Y Acad Sci DOI: 10.1111/nyas.13304 sha: doc_id: 345654 cord_uid: vyz6f3he file: cache/cord-343918-5yk1j4ms.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-343918-5yk1j4ms authors: Gorbalenya, A.E. title: Phylogeny of Viruses date: 2008-07-30 journal: Encyclopedia of Virology DOI: 10.1016/b978-012374410-4.00712-3 sha: doc_id: 343918 cord_uid: 5yk1j4ms file: cache/cord-345957-wuk2arf9.json key: cord-345957-wuk2arf9 authors: Mohamed, Fakry F.; Mansour, Shimaa M. G.; Orabi, Ahmed; El-Araby, Iman E.; Ng, Terry Fei Fan; Mor, Sunil K.; Goyal, Sagar M. title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt date: 2018-02-08 journal: Arch Virol DOI: 10.1007/s00705-018-3758-1 sha: doc_id: 345957 cord_uid: wuk2arf9 file: cache/cord-346544-kk7qyn4w.json key: cord-346544-kk7qyn4w authors: Andersson, M.; Arancibia - Carcamo, C. V.; Auckland, K.; Baillie, J. K.; Barnes, E.; Beneke, T.; Bibi, S.; Carroll, M.; Crook, D.; Dingle, K.; Dold, C.; Downs, L. O.; Dunn, L.; Eyre, D. W.; Gilbert Jaramillo, J.; Harvala Simmonds, H.; Hoosdally, S.; Ijaz, S.; James, T.; James, W.; Jeffery, K.; Justice, A.; Klenerman, P.; Knight, J. C.; Knight, M.; Liu, X.; Lumley, S. F.; Matthews, P. C.; McNaughton, A. L.; Mentzer, A. J.; Mongkolsapaya, J.; Oakley, S.; Oliveira, M. S.; Peto, T.; Ploeg, R. J.; Ratcliff, J.; Roberts, D. J.; Rudkin, J.; Screaton, G.; Semple, M. G.; Skelley, D. T.; Simmonds, P. title: SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date: 2020-05-26 journal: nan DOI: 10.1101/2020.05.21.20105486 sha: doc_id: 346544 cord_uid: kk7qyn4w file: cache/cord-345413-bsd32j8r.json key: cord-345413-bsd32j8r authors: Terada, Yutaka; Kuroda, Yudai; Morikawa, Shigeru; Matsuura, Yoshiharu; Maeda, Ken; Kamitani, Wataru title: Establishment of a Virulent Full-Length cDNA Clone for Type I Feline Coronavirus Strain C3663 date: 2019-08-02 journal: Journal of Virology DOI: 10.1128/jvi.01208-19 sha: doc_id: 345413 cord_uid: bsd32j8r file: cache/cord-346267-l08ld2cy.json key: cord-346267-l08ld2cy authors: Wertheim, Joel O.; Kosakovsky Pond, Sergei L. title: Purifying Selection Can Obscure the Ancient Age of Viral Lineages date: 2011-06-24 journal: Molecular Biology and Evolution DOI: 10.1093/molbev/msr170 sha: doc_id: 346267 cord_uid: l08ld2cy file: cache/cord-345630-bam3pa70.json key: cord-345630-bam3pa70 authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 journal: Virology DOI: 10.1016/0042-6822(91)90071-i sha: doc_id: 345630 cord_uid: bam3pa70 file: cache/cord-344421-rmnck42f.json key: cord-344421-rmnck42f authors: Theuns, Sebastiaan; Vanmechelen, Bert; Bernaert, Quinten; Deboutte, Ward; Vandenhole, Marilou; Beller, Leen; Matthijnssens, Jelle; Maes, Piet; Nauwynck, Hans J. title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus date: 2018-06-29 journal: Sci Rep DOI: 10.1038/s41598-018-28180-9 sha: doc_id: 344421 cord_uid: rmnck42f file: cache/cord-346697-ixho9t5g.json key: cord-346697-ixho9t5g authors: Guo, Hua; Cai, Chunlin; Wang, Bo; Zhuo, Fei; Jiang, Rendi; Wang, Ning; Li, Bei; Zhang, Wei; Zhu, Yan; Fan, Yi; Chen, Wushen; Chen, Weihong; Yang, Xinglou; Shi, Zhengli title: Novel hepacivirus in Asian house shrew, China date: 2019-01-28 journal: Sci China Life Sci DOI: 10.1007/s11427-018-9435-7 sha: doc_id: 346697 cord_uid: ixho9t5g file: cache/cord-346978-ubkqny8j.json key: cord-346978-ubkqny8j authors: Ranoa, Diana Rose E.; Holland, Robin L.; Alnaji, Fadi G.; Green, Kelsie J.; Wang, Leyi; Brooke, Christopher B.; Burke, Martin D.; Fan, Timothy M.; Hergenrother, Paul J. title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date: 2020-06-18 journal: bioRxiv DOI: 10.1101/2020.06.18.159434 sha: doc_id: 346978 cord_uid: ubkqny8j file: cache/cord-346314-o9fjpqaj.json key: cord-346314-o9fjpqaj authors: Jarboui, Mohamed Ali; Bidoia, Carlo; Woods, Elena; Roe, Barbara; Wynne, Kieran; Elia, Giuliano; Hall, William W.; Gautier, Virginie W. title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 journal: PLoS One DOI: 10.1371/journal.pone.0048702 sha: doc_id: 346314 cord_uid: o9fjpqaj file: cache/cord-346853-0c1qdjb5.json key: cord-346853-0c1qdjb5 authors: Holmes, E. C.; Drummond, A. J. title: The Evolutionary Genetics of Viral Emergence date: 2007 journal: Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission DOI: 10.1007/978-3-540-70962-6_3 sha: doc_id: 346853 cord_uid: 0c1qdjb5 file: cache/cord-346930-gl573ip9.json key: cord-346930-gl573ip9 authors: Hussain, Azhar; Kaler, Jasndeep; Dubey, Arun Kumar title: Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date: 2020-05-24 journal: Cureus DOI: 10.7759/cureus.8260 sha: doc_id: 346930 cord_uid: gl573ip9 file: cache/cord-346514-vyo8l14p.json key: cord-346514-vyo8l14p authors: Chen, I-Hsuan; Cheng, Jai-Hong; Huang, Ying-Wen; Lin, Na-Sheng; Hsu, Yau-Heiu; Tsai, Ching-Hsiu title: Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date: 2013-06-13 journal: Virology DOI: 10.1016/j.virol.2013.05.032 sha: doc_id: 346514 cord_uid: vyo8l14p file: cache/cord-347302-ylnb6qfl.json key: cord-347302-ylnb6qfl authors: van der Schaar, Hilde M.; Dorobantu, Cristina M.; Albulescu, Lucian; Strating, Jeroen R.P.M.; van Kuppeveld, Frank J.M. title: Fat(al) attraction: Picornaviruses Usurp Lipid Transfer at Membrane Contact Sites to Create Replication Organelles date: 2016-03-22 journal: Trends Microbiol DOI: 10.1016/j.tim.2016.02.017 sha: doc_id: 347302 cord_uid: ylnb6qfl file: cache/cord-345371-pjbviagq.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-345371-pjbviagq authors: Lisi, Lucia; Lacal, Pedro Miguel; Barbaccia, Maria Luisa; Graziani, Grazia title: Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date: 2020-07-23 journal: Biochem Pharmacol DOI: 10.1016/j.bcp.2020.114169 sha: doc_id: 345371 cord_uid: pjbviagq file: cache/cord-346138-ip42zcld.json key: cord-346138-ip42zcld authors: Zhurakivska, Khrystyna; Troiano, Giuseppe; Pannone, Giuseppe; Caponio, Vito Carlo Alberto; Lo Muzio, Lorenzo title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 journal: Front Public Health DOI: 10.3389/fpubh.2020.00487 sha: doc_id: 346138 cord_uid: ip42zcld file: cache/cord-348204-365z3qxz.json key: cord-348204-365z3qxz authors: Harun, Mohammad Syamsul Reza; Kuan, Choong Oi; Selvarajah, Gayathri Thevi; Wei, Tan Sheau; Arshad, Siti Suri; Bejo, Mohd Hair; Omar, Abdul Rahman title: Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats date: 2013-11-09 journal: Virol J DOI: 10.1186/1743-422x-10-329 sha: doc_id: 348204 cord_uid: 365z3qxz file: cache/cord-348669-mizygp4j.json key: cord-348669-mizygp4j authors: Beall, Anne; Yount, Boyd; Lin, Chun-Ming; Hou, Yixuan; Wang, Qiuhong; Saif, Linda; Baric, Ralph title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date: 2016-01-05 journal: mBio DOI: 10.1128/mbio.01451-15 sha: doc_id: 348669 cord_uid: mizygp4j file: cache/cord-347221-g98q9cga.json key: cord-347221-g98q9cga authors: Piyush, Ravikant; Rajarshi, Keshav; Chatterjee, Aroni; Khan, Rajni; Ray, Shashikant title: Nucleic acid-based therapy for coronavirus disease 2019 date: 2020-09-19 journal: Heliyon DOI: 10.1016/j.heliyon.2020.e05007 sha: doc_id: 347221 cord_uid: g98q9cga parallel: Warning: No more processes: Decreasing number of running jobs to 89. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. file: cache/cord-347992-coby2m6e.json key: cord-347992-coby2m6e authors: Marton, Soledad; Reyes-Darias, José A.; Sánchez-Luque, Francisco J.; Romero-López, Cristina; Berzal-Herranz, Alfredo title: In Vitro and Ex Vivo Selection Procedures for Identifying Potentially Therapeutic DNA and RNA Molecules date: 2010-06-28 journal: Molecules DOI: 10.3390/molecules15074610 sha: doc_id: 347992 cord_uid: coby2m6e file: cache/cord-347532-n51qv9pp.json key: cord-347532-n51qv9pp authors: Wacharapluesadee, Supaporn; Sintunawa, Chirapol; Kaewpom, Thongchai; Khongnomnan, Kritsada; Olival, Kevin J.; Epstein, Jonathan H.; Rodpan, Apaporn; Sangsri, Paiboon; Intarut, Nirun; Chindamporn, Ariya; Suksawa, Kanyarat; Hemachudha, Thiravat title: Group C Betacoronavirus in Bat Guano Fertilizer, Thailand date: 2013-08-17 journal: Emerg Infect Dis DOI: 10.3201/eid1908.130119 sha: doc_id: 347532 cord_uid: n51qv9pp file: cache/cord-349249-jwvz1ux2.json key: cord-349249-jwvz1ux2 authors: Singh, Gagandeep; Singh, Pankaj; Pillatzki, Angela; Nelson, Eric; Webb, Brett; Dillberger-Lawson, Steven; Ramamoorthy, Sheela title: A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus date: 2019-10-22 journal: Front Vet Sci DOI: 10.3389/fvets.2019.00347 sha: doc_id: 349249 cord_uid: jwvz1ux2 file: cache/cord-345817-rrf3dbnb.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-345817-rrf3dbnb authors: WOOD, Lisa G.; POWELL, Heather; GRISSELL, Terry V.; DAVIES, Bronwyn; SHAFREN, Darren R.; WHITEHEAD, Bruce F.; HENSLEY, Michael J.; GIBSON, Peter G. title: Persistence of rhinovirus RNA and IP‐10 gene expression after acute asthma date: 2011-01-27 journal: Respirology DOI: 10.1111/j.1440-1843.2010.01897.x sha: doc_id: 345817 cord_uid: rrf3dbnb file: cache/cord-347917-fmb5nyxu.json key: cord-347917-fmb5nyxu authors: Liu, Junli; Wang, Fangfang; Du, Liuyang; Li, Juan; Yu, Tianqi; Jin, Yulan; Yan, Yan; Zhou, Jiyong; Gu, Jinyan title: Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection date: 2020-01-28 journal: Front Microbiol DOI: 10.3389/fmicb.2019.03036 sha: doc_id: 347917 cord_uid: fmb5nyxu file: cache/cord-349011-kxhpdvri.json key: cord-349011-kxhpdvri authors: Grandvaux, Nathalie; McCormick, Craig title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 journal: Viruses DOI: 10.3390/v11010079 sha: doc_id: 349011 cord_uid: kxhpdvri file: cache/cord-347128-6lyoz8nn.json key: cord-347128-6lyoz8nn authors: Kim, Cheorl-Ho title: SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date: 2020-06-26 journal: Int J Mol Sci DOI: 10.3390/ijms21124549 sha: doc_id: 347128 cord_uid: 6lyoz8nn file: cache/cord-348799-qu4zin3o.json key: cord-348799-qu4zin3o authors: Wu, Nannan; Nguyen, Xuan-Nhi; Wang, Li; Appourchaux, Romain; Zhang, Chengfei; Panthu, Baptiste; Gruffat, Henri; Journo, Chloé; Alais, Sandrine; Qin, Juliang; Zhang, Na; Tartour, Kevin; Catez, Frédéric; Mahieux, Renaud; Ohlmann, Theophile; Liu, Mingyao; Du, Bing; Cimarelli, Andrea title: The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation date: 2019-10-10 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008093 sha: doc_id: 348799 cord_uid: qu4zin3o file: cache/cord-347710-ff64y6ef.json key: cord-347710-ff64y6ef authors: Wan, Qianya; Song, Dan; Li, Huangcan; He, Ming-liang title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 journal: Signal Transduct Target Ther DOI: 10.1038/s41392-020-00233-4 sha: doc_id: 347710 cord_uid: ff64y6ef file: cache/cord-348243-e5tdb08v.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-348243-e5tdb08v authors: Schermer, Bernhard; Fabretti, Francesca; Damagnez, Maximilian; Di Cristanziano, Veronica; Heger, Eva; Arjune, Sita; Tanner, Nathan A.; Imhof, Thomas; Koch, Manuel; Ladha, Alim; Joung, Julia; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Burst, Volker; Zhang, Feng; Klein, Florian; Benzing, Thomas; Müller, Roman-Ulrich title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 journal: PLoS One DOI: 10.1371/journal.pone.0238612 sha: doc_id: 348243 cord_uid: e5tdb08v file: cache/cord-349684-2tioh80m.json key: cord-349684-2tioh80m authors: Pezzotti, Giuseppe; Ohgitani, Eriko; Shin-Ya, Masaharu; Adachi, Tetsuya; Marin, Elia; Boschetto, Francesco; Zhu, Wenliang; Mazda, Osam title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date: 2020-06-20 journal: bioRxiv DOI: 10.1101/2020.06.19.159970 sha: doc_id: 349684 cord_uid: 2tioh80m file: cache/cord-349839-s32d3di2.json key: cord-349839-s32d3di2 authors: Westhof, Eric; Jaeger, Luc title: RNA pseudoknots date: 1992-06-30 journal: Current Opinion in Structural Biology DOI: 10.1016/0959-440x(92)90221-r sha: doc_id: 349839 cord_uid: s32d3di2 file: cache/cord-349042-u9svz7pf.json key: cord-349042-u9svz7pf authors: Li, Jifen; Eberwine, James title: The successes and future prospects of the linear antisense RNA amplification methodology date: 2018-03-29 journal: Nat Protoc DOI: 10.1038/nprot.2018.011 sha: doc_id: 349042 cord_uid: u9svz7pf file: cache/cord-349341-ap5n6ijl.json key: cord-349341-ap5n6ijl authors: Kopek, Benjamin G; Perkins, Guy; Miller, David J; Ellisman, Mark H; Ahlquist, Paul title: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle date: 2007-08-14 journal: PLoS Biol DOI: 10.1371/journal.pbio.0050220 sha: doc_id: 349341 cord_uid: ap5n6ijl file: cache/cord-350342-j4p8235a.json key: cord-350342-j4p8235a authors: Brocato, Rebecca L.; Principe, Lucia M.; Kim, Robert K.; Zeng, Xiankun; Williams, Janice A.; Liu, Yanan; Li, Rong; Smith, Jeffrey M.; Golden, Joseph W.; Gangemi, Dave; Youssef, Sawsan; Wang, Zhongde; Glanville, Jacob; Hooper, Jay W. title: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date: 2020-10-27 journal: J Virol DOI: 10.1128/jvi.01683-20 sha: doc_id: 350342 cord_uid: j4p8235a file: cache/cord-348147-leni23pa.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-348147-leni23pa authors: Müller, B.; Klemm, U.; Mas Marques, A.; Schreier, E. title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice date: 2007-05-29 journal: Arch Virol DOI: 10.1007/s00705-007-0989-y sha: doc_id: 348147 cord_uid: leni23pa file: cache/cord-350189-2su7oqbz.json key: cord-350189-2su7oqbz authors: Elmén, Joacim; Thonberg, Håkan; Ljungberg, Karl; Frieden, Miriam; Westergaard, Majken; Xu, Yunhe; Wahren, Britta; Liang, Zicai; Ørum, Henrik; Koch, Troels; Wahlestedt, Claes title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date: 2005-01-14 journal: Nucleic Acids Res DOI: 10.1093/nar/gki193 sha: doc_id: 350189 cord_uid: 2su7oqbz file: cache/cord-348860-zaimorg0.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-348860-zaimorg0 authors: Ratra, Ruchi; Lal, Sunil K. title: Functional genomics as a tool in virus research date: 2008-06-01 journal: Indian Journal of Microbiology DOI: 10.1007/s12088-008-0032-3 sha: doc_id: 348860 cord_uid: zaimorg0 file: cache/cord-350906-ew04zzh6.json key: cord-350906-ew04zzh6 authors: Khambhati, Khushal; Bhattacharjee, Gargi; Singh, Vijai title: Current progress in CRISPR‐based diagnostic platforms date: 2018-10-26 journal: J Cell Biochem DOI: 10.1002/jcb.27690 sha: doc_id: 350906 cord_uid: ew04zzh6 file: cache/cord-349623-dw5o9i59.json key: cord-349623-dw5o9i59 authors: Miranda, José P.; Osorio, Javiera; Videla, Mauricio; Angel, Gladys; Camponovo, Rossana; Henríquez-Henríquez, Marcela title: Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date: 2020-10-15 journal: Front Med (Lausanne) DOI: 10.3389/fmed.2020.567572 sha: doc_id: 349623 cord_uid: dw5o9i59 file: cache/cord-348815-lthz75oc.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-348815-lthz75oc authors: Kurreck, Jens title: RNA Interference: From Basic Research to Therapeutic Applications date: 2009-01-19 journal: Angew Chem Int Ed Engl DOI: 10.1002/anie.200802092 sha: doc_id: 348815 cord_uid: lthz75oc file: cache/cord-346916-jj4l9ydl.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-346916-jj4l9ydl authors: Girardi, Erika; Pfeffer, Sebastien; Baumert, Thomas F.; Majzoub, Karim title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 journal: Semin Cell Dev Biol DOI: 10.1016/j.semcdb.2020.08.006 sha: doc_id: 346916 cord_uid: jj4l9ydl file: cache/cord-347351-emdj66vj.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-347351-emdj66vj authors: Kampf, Günter; Brüggemann, Yannick; Kaba, Hani E.J.; Steinmann, Joerg; Pfaender, Stephanie; Scheithauer, Simone; Steinmann, Eike title: Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date: 2020-09-18 journal: J Hosp Infect DOI: 10.1016/j.jhin.2020.09.022 sha: doc_id: 347351 cord_uid: emdj66vj file: cache/cord-347472-n6811ens.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-347472-n6811ens authors: Rosebrock, Adam P. title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date: 2020-05-15 journal: bioRxiv DOI: 10.1101/2020.05.13.094839 sha: doc_id: 347472 cord_uid: n6811ens file: cache/cord-351864-zozrj7w5.json key: cord-351864-zozrj7w5 authors: Chappleboim, A.; Joseph-Strauss, D.; Rahat, A.; Sharkia, I.; Adam, M.; Kitsberg, D.; Fialkoff, G.; Lotem, M.; Gershon, O.; Schmidtner, A.-K.; Oiknine-Djian, E.; Klochendler, A.; Sadeh, R.; Dor, Y.; Wolf, D.; Habib, N.; Friedman, N. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 journal: nan DOI: 10.1101/2020.08.08.20170746 sha: doc_id: 351864 cord_uid: zozrj7w5 file: cache/cord-350040-e8q7wq0h.json key: cord-350040-e8q7wq0h authors: Aronin, N title: Target selectivity in mRNA silencing date: 2006-02-16 journal: Gene Ther DOI: 10.1038/sj.gt.3302726 sha: doc_id: 350040 cord_uid: e8q7wq0h file: cache/cord-350747-5t5xthk6.json key: cord-350747-5t5xthk6 authors: Gmyl, A. P.; Agol, V. I. title: Diverse Mechanisms of RNA Recombination date: 2005 journal: Mol Biol DOI: 10.1007/s11008-005-0069-x sha: doc_id: 350747 cord_uid: 5t5xthk6 file: cache/cord-350019-4nlbu54e.json key: cord-350019-4nlbu54e authors: Robinson, Elektra K.; Covarrubias, Sergio; Carpenter, Susan title: The how and why of lncRNA function: An innate immune perspective() date: 2019-09-02 journal: Biochim Biophys Acta Gene Regul Mech DOI: 10.1016/j.bbagrm.2019.194419 sha: doc_id: 350019 cord_uid: 4nlbu54e file: cache/cord-348777-pk9y6vfp.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-348777-pk9y6vfp authors: Ding, Cheng; Feng, Xuewen; Chen, Yanfei; Yuan, Jing; Yi, Ping; Li, Yongtao; Ni, Qin; Zou, Rongrong; Li, Xiaohe; Sheng, Jifang; Li, Lanjuan; Xu, Kaijin title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date: 2020-09-28 journal: Infect Dis Ther DOI: 10.1007/s40121-020-00337-y sha: doc_id: 348777 cord_uid: pk9y6vfp file: cache/cord-350533-fp1ctpax.json key: cord-350533-fp1ctpax authors: Tchesnokov, Egor P.; Bailey-Elkin, Ben A.; Mark, Brian L.; Götte, Matthias title: Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein date: 2020-06-04 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0008283 sha: doc_id: 350533 cord_uid: fp1ctpax file: cache/cord-350836-1enteev7.json key: cord-350836-1enteev7 authors: Brisse, Morgan; Ly, Hinh title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date: 2019-07-17 journal: Front Immunol DOI: 10.3389/fimmu.2019.01586 sha: doc_id: 350836 cord_uid: 1enteev7 file: cache/cord-350600-73q8mve4.json key: cord-350600-73q8mve4 authors: Myint, S.; Siddell, S.; Tyrrell, D. title: Detection of human coronavirus 229E in nasal washings using RNA:RNA hybridization date: 2005-12-09 journal: J Med Virol DOI: 10.1002/jmv.1890290113 sha: doc_id: 350600 cord_uid: 73q8mve4 file: cache/cord-350697-u032yk0z.json key: cord-350697-u032yk0z authors: Roy, Anupam; Sarkar, Biswatrish; Celik, Cagla; Ghosh, Animesh; Basu, Utpal; Jana, Malabendu; Jana, Arundhati; Gencay, Ayse; Sezgin, Gulten Can; Ildiz, Nilay; Dam, Paulami; Mandal, Amit K.; Ocsoy, Ismail title: Can concomitant use of zinc and curcumin with other immunity‐boosting nutraceuticals be the arsenal against COVID‐19? date: 2020-06-02 journal: Phytother Res DOI: 10.1002/ptr.6766 sha: doc_id: 350697 cord_uid: u032yk0z file: cache/cord-350640-sz6xj5o3.json key: cord-350640-sz6xj5o3 authors: Menzel, Nicolas; Fischl, Wolfgang; Hueging, Kathrin; Bankwitz, Dorothea; Frentzen, Anne; Haid, Sibylle; Gentzsch, Juliane; Kaderali, Lars; Bartenschlager, Ralf; Pietschmann, Thomas title: MAP-Kinase Regulated Cytosolic Phospholipase A2 Activity Is Essential for Production of Infectious Hepatitis C Virus Particles date: 2012-07-26 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1002829 sha: doc_id: 350640 cord_uid: sz6xj5o3 file: cache/cord-349417-vn7q8wc4.json key: cord-349417-vn7q8wc4 authors: Ziebuhr, John title: The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_1 sha: doc_id: 349417 cord_uid: vn7q8wc4 file: cache/cord-349762-f5no10eq.json key: cord-349762-f5no10eq authors: Nagura-Ikeda, Mayu; Imai, Kazuo; Tabata, Sakiko; Miyoshi, Kazuyasu; Murahara, Nami; Mizuno, Tsukasa; Horiuchi, Midori; Kato, Kento; Imoto, Yoshitaka; Iwata, Maki; Mimura, Satoshi; Ito, Toshimitsu; Tamura, Kaku; Kato, Yasuyuki title: Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date: 2020-08-24 journal: J Clin Microbiol DOI: 10.1128/jcm.01438-20 sha: doc_id: 349762 cord_uid: f5no10eq file: cache/cord-350762-rh4zbehk.json key: cord-350762-rh4zbehk authors: Hutcheson, Jessica M.; Susta, Leonardo; Stice, Steven L.; Afonso, Claudio L.; West, Franklin D. title: Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date: 2015-06-04 journal: Biologicals DOI: 10.1016/j.biologicals.2015.03.004 sha: doc_id: 350762 cord_uid: rh4zbehk file: cache/cord-351377-xorj8tnz.json key: cord-351377-xorj8tnz authors: Kao, Chi-Fei; Chiou, Hue-Ying; Chang, Yen-Chen; Hsueh, Cheng-Shun; Jeng, Chian-Ren; Tsai, Pei-Shiue; Cheng, Ivan-Chen; Pang, Victor Fei; Chang, Hui-Wen title: The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date: 2018-10-04 journal: Viruses DOI: 10.3390/v10100543 sha: doc_id: 351377 cord_uid: xorj8tnz file: cache/cord-349358-leicos9j.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-349358-leicos9j authors: Ketzinel‐Gilad, Mali; Shaul, Yosef; Galun, Eithan title: RNA interference for antiviral therapy date: 2006-06-16 journal: J Gene Med DOI: 10.1002/jgm.929 sha: doc_id: 349358 cord_uid: leicos9j file: cache/cord-351489-tzmev77c.json key: cord-351489-tzmev77c authors: Yuan, Shuofeng; Chan, Chris Chun-Yiu; Chik, Kenn Ka-Heng; Tsang, Jessica Oi-Ling; Liang, Ronghui; Cao, Jianli; Tang, Kaiming; Cai, Jian-Piao; Ye, Zi-Wei; Yin, Feifei; To, Kelvin Kai-Wang; Chu, Hin; Jin, Dong-Yan; Hung, Ivan Fan-Ngai; Yuen, Kwok-Yung; Chan, Jasper Fuk-Woo title: Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date: 2020-06-10 journal: Viruses DOI: 10.3390/v12060628 sha: doc_id: 351489 cord_uid: tzmev77c file: cache/cord-350083-kldu8q8x.json key: cord-350083-kldu8q8x authors: Oany, Arafat Rahman; Sharmin, Tahmina; Chowdhury, Afrin Sultana; Jyoti, Tahmina Pervin; Hasan, Md. Anayet title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date: 2015-08-08 journal: In Silico Pharmacol DOI: 10.1186/s40203-015-0011-4 sha: doc_id: 350083 cord_uid: kldu8q8x file: cache/cord-351482-hzh5tyoo.json key: cord-351482-hzh5tyoo authors: Peng, Xinxia; Gralinski, Lisa; Ferris, Martin T.; Frieman, Matthew B.; Thomas, Matthew J.; Proll, Sean; Korth, Marcus J.; Tisoncik, Jennifer R.; Heise, Mark; Luo, Shujun; Schroth, Gary P.; Tumpey, Terrence M.; Li, Chengjun; Kawaoka, Yoshihiro; Baric, Ralph S.; Katze, Michael G. title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 journal: mBio DOI: 10.1128/mbio.00198-11 sha: doc_id: 351482 cord_uid: hzh5tyoo file: cache/cord-349672-2kt7xw8i.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-349672-2kt7xw8i authors: Dasgupta, Tumpa; Ferdous, Shomita; Tse-Dinh, Yuk-Ching title: Mechanism of Type IA Topoisomerases date: 2020-10-17 journal: Molecules DOI: 10.3390/molecules25204769 sha: doc_id: 349672 cord_uid: 2kt7xw8i file: cache/cord-351837-vasuu70k.json key: cord-351837-vasuu70k authors: Shannon, Ashleigh; Selisko, Barbara; Le, Nhung-Thi-Tuyet; Huchting, Johanna; Touret, Franck; Piorkowski, Géraldine; Fattorini, Véronique; Ferron, François; Decroly, Etienne; Meier, Chris; Coutard, Bruno; Peersen, Olve; Canard, Bruno title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date: 2020-09-17 journal: Nat Commun DOI: 10.1038/s41467-020-18463-z sha: doc_id: 351837 cord_uid: vasuu70k file: cache/cord-351115-dy81dtnk.json key: cord-351115-dy81dtnk authors: Wang, Chen; Konecki, Daniel M.; Marciano, David C.; Govindarajan, Harikumar; Williams, Amanda M.; Wastuwidyaningtyas, Brigitta; Bourquard, Thomas; Katsonis, Panagiotis; Lichtarge, Olivier title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date: 2020-10-20 journal: Res Sq DOI: 10.21203/rs.3.rs-95030/v1 sha: doc_id: 351115 cord_uid: dy81dtnk file: cache/cord-351520-c5fi2uoh.json key: cord-351520-c5fi2uoh authors: Zhong, Bo; Wang, Yan-Yi; Shu, Hong-Bing title: Regulation of virus-triggered type I interferon signaling by cellular and viral proteins date: 2010-02-01 journal: Front Biol (Beijing) DOI: 10.1007/s11515-010-0013-x sha: doc_id: 351520 cord_uid: c5fi2uoh file: cache/cord-352178-irjhmxsg.json key: cord-352178-irjhmxsg authors: Saxton-Shaw, Kali D.; Ledermann, Jeremy P.; Borland, Erin M.; Stovall, Janae L.; Mossel, Eric C.; Singh, Amber J.; Wilusz, Jeffrey; Powers, Ann M. title: O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date: 2013-01-24 journal: PLoS Negl Trop Dis DOI: 10.1371/journal.pntd.0001931 sha: doc_id: 352178 cord_uid: irjhmxsg file: cache/cord-352088-9k01ej6l.json key: cord-352088-9k01ej6l authors: Saiz, Juan-Carlos title: Vaccines against RNA Viruses date: 2020-08-27 journal: Vaccines (Basel) DOI: 10.3390/vaccines8030479 sha: doc_id: 352088 cord_uid: 9k01ej6l file: cache/cord-351559-az4pgi9k.json key: cord-351559-az4pgi9k authors: Turjya, Rafeed Rahman; Khan, Md. Abdullah-Al-Kamran; Islam, Abul Bashar Mir Md. Khademul title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 journal: bioRxiv DOI: 10.1101/2020.06.29.177204 sha: doc_id: 351559 cord_uid: az4pgi9k file: cache/cord-352361-jh31omg2.json key: cord-352361-jh31omg2 authors: Nobach, Daniel; Herden, Christiane title: No evidence for European bats serving as reservoir for Borna disease virus 1 or other known mammalian orthobornaviruses date: 2020-01-30 journal: Virol J DOI: 10.1186/s12985-020-1289-3 sha: doc_id: 352361 cord_uid: jh31omg2 file: cache/cord-351920-igmb2yfe.json key: cord-351920-igmb2yfe authors: Oma, Veslemøy Sunniva; Tråvén, Madeleine; Alenius, Stefan; Myrmel, Mette; Stokstad, Maria title: Bovine coronavirus in naturally and experimentally exposed calves; viral shedding and the potential for transmission date: 2016-06-13 journal: Virol J DOI: 10.1186/s12985-016-0555-x sha: doc_id: 351920 cord_uid: igmb2yfe file: cache/cord-351854-5s03f0pp.json key: cord-351854-5s03f0pp authors: Ben-Ami, Roni; Klochendler, Agnes; Seidel, Matan; Sido, Tal; Gurel-Gurevich, Ori; Yassour, Moran; Meshorer, Eran; Benedek, Gil; Fogel, Irit; Oiknine-Djian, Esther; Gertler, Asaf; Rotstein, Zeev; Lavi, Bruno; Dor, Yuval; Wolf, Dana G; Salton, Maayan; Drier, Yotam title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 journal: nan DOI: 10.1101/2020.04.17.20069062 sha: doc_id: 351854 cord_uid: 5s03f0pp file: cache/cord-350286-n7ylgqfu.json key: cord-350286-n7ylgqfu authors: Giri, Rajanish; Bhardwaj, Taniya; Shegane, Meenakshi; Gehi, Bhuvaneshwari R.; Kumar, Prateek; Gadhave, Kundlik; Oldfield, Christopher J.; Uversky, Vladimir N. title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 journal: bioRxiv DOI: 10.1101/2020.03.13.990598 sha: doc_id: 350286 cord_uid: n7ylgqfu file: cache/cord-351365-dc9t3vh3.json key: cord-351365-dc9t3vh3 authors: Todt, Daniel; Walter, Stephanie; Brown, Richard J. P.; Steinmann, Eike title: Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date: 2016-10-13 journal: Viruses DOI: 10.3390/v8100283 sha: doc_id: 351365 cord_uid: dc9t3vh3 file: cache/cord-352768-16vgnq14.json key: cord-352768-16vgnq14 authors: Tang, Qingquan; Li, Baojian; Woodle, Martin; Lu, Patrick Y. title: Application of siRNA Against SARS in the Rhesus Macaque Model date: 2008 journal: RNAi DOI: 10.1007/978-1-59745-191-8_11 sha: doc_id: 352768 cord_uid: 16vgnq14 file: cache/cord-353640-giznbcpd.json key: cord-353640-giznbcpd authors: Barza, Ruby; Patel, Parul; Sabatini, Linda; Singh, Kamaljit title: Use of a Simplified Sample Processing step without RNA Extraction for direct SARS-CoV-2 RT-PCR Detection date: 2020-08-11 journal: J Clin Virol DOI: 10.1016/j.jcv.2020.104587 sha: doc_id: 353640 cord_uid: giznbcpd file: cache/cord-351548-jvl63652.json key: cord-351548-jvl63652 authors: Juranic Lisnic, Vanda; Babic Cac, Marina; Lisnic, Berislav; Trsan, Tihana; Mefferd, Adam; Das Mukhopadhyay, Chitrangada; Cook, Charles H.; Jonjic, Stipan; Trgovcich, Joanne title: Dual Analysis of the Murine Cytomegalovirus and Host Cell Transcriptomes Reveal New Aspects of the Virus-Host Cell Interface date: 2013-09-26 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1003611 sha: doc_id: 351548 cord_uid: jvl63652 file: cache/cord-352664-heoj8ji8.json key: cord-352664-heoj8ji8 authors: Hubbard, Amelia; Lewis, Clare M; Yoshida, Kentaro; Ramirez-Gonzalez, Ricardo H; de Vallavieille-Pope, Claude; Thomas, Jane; Kamoun, Sophien; Bayles, Rosemary; Uauy, Cristobal; Saunders, Diane GO title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date: 2015-02-25 journal: Genome Biol DOI: 10.1186/s13059-015-0590-8 sha: doc_id: 352664 cord_uid: heoj8ji8 file: cache/cord-352891-ljmkqdzx.json key: cord-352891-ljmkqdzx authors: Parang, Keykavous; El-Sayed, Naglaa Salem; Kazeminy, Assad J.; Tiwari, Rakesh K. title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date: 2020-05-17 journal: Molecules DOI: 10.3390/molecules25102343 sha: doc_id: 352891 cord_uid: ljmkqdzx file: cache/cord-354465-5nqrrnqr.json key: cord-354465-5nqrrnqr authors: Haslinger, Christian; Stadler, Peter F. title: RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties date: 1999 journal: Bull Math Biol DOI: 10.1006/bulm.1998.0085 sha: doc_id: 354465 cord_uid: 5nqrrnqr file: cache/cord-352465-n746e8qt.json key: cord-352465-n746e8qt authors: Wang, Fei; Li, Juan; Fan, Shengjie; Jin, Zhigang; Huang, Cheng title: Targeting stress granules: A novel therapeutic strategy for human diseases date: 2020-08-16 journal: Pharmacol Res DOI: 10.1016/j.phrs.2020.105143 sha: doc_id: 352465 cord_uid: n746e8qt file: cache/cord-354536-c9v9kbw8.json key: cord-354536-c9v9kbw8 authors: Han, Yan-Jie; Ren, Zhi-Guang; Li, Xin-Xin; Yan, Ji-Liang; Ma, Chun-Yan; Wu, Dong-Dong; Ji, Xin-Ying title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 journal: Int J Med Sci DOI: 10.7150/ijms.47836 sha: doc_id: 354536 cord_uid: c9v9kbw8 file: cache/cord-354394-zojhdnlu.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-354394-zojhdnlu authors: Wang, Wei-Kung; Chen, Shey-Ying; Liu, I-Jung; Chen, Yee-Chun; Chen, Hui-Ling; Yang, Chao-Fu; Chen, Pei-Jer; Yeh, Shiou-Hwei; Kao, Chuan-Liang; Huang, Li-Min; Hsueh, Po-Ren; Wang, Jann-Tay; Sheng, Wang-Hwei; Fang, Chi-Tai; Hung, Chien-Ching; Hsieh, Szu-Min; Su, Chan-Ping; Chiang, Wen-Chu; Yang, Jyh-Yuan; Lin, Jih-Hui; Hsieh, Szu-Chia; Hu, Hsien-Ping; Chiang, Yu-Ping; Wang, Jin-Town; Yang, Pan-Chyr; Chang, Shan-Chwen title: Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date: 2004-07-17 journal: Emerg Infect Dis DOI: 10.3201/eid1007.031113 sha: doc_id: 354394 cord_uid: zojhdnlu file: cache/cord-352814-fcl2g5wr.json key: cord-352814-fcl2g5wr authors: Balboni, Andrea; Gallina, Laura; Palladini, Alessandra; Prosperi, Santino; Battilani, Mara title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 journal: ScientificWorldJournal DOI: 10.1100/2012/989514 sha: doc_id: 352814 cord_uid: fcl2g5wr file: cache/cord-353524-3w970ycx.json key: cord-353524-3w970ycx authors: Dömling, Alexander; Gao, Li title: Chemistry and Biology of SARS-CoV-2 date: 2020-05-22 journal: Chem DOI: 10.1016/j.chempr.2020.04.023 sha: doc_id: 353524 cord_uid: 3w970ycx file: cache/cord-354510-jlg5je0s.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-354510-jlg5je0s authors: de Carvalho, A. F.; Goncalves, A. P.; Silva, T. B.; Sato, H. I.; Vuitika, L.; Bagno, F. F.; Sergio, S. A.; Figueiredo, M. M.; Rocha, R. P.; Fernandes, A. P. S.; Alves, P. A.; Teixeira, S. M.; da Fonseca, F. G. title: THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date: 2020-06-20 journal: nan DOI: 10.1101/2020.06.18.20134304 sha: doc_id: 354510 cord_uid: jlg5je0s file: cache/cord-352379-q5inrxcm.json key: cord-352379-q5inrxcm authors: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 journal: J Biomed Sci DOI: 10.1007/bf02256318 sha: doc_id: 352379 cord_uid: q5inrxcm file: cache/cord-356013-pl3tmky8.json key: cord-356013-pl3tmky8 authors: Brian, D. A.; Baric, R. S. title: Coronavirus Genome Structure and Replication date: 2005 journal: Coronavirus Replication and Reverse Genetics DOI: 10.1007/3-540-26765-4_1 sha: doc_id: 356013 cord_uid: pl3tmky8 file: cache/cord-353576-f29kmtot.json key: cord-353576-f29kmtot authors: Maricic, T.; Nickel, O.; Aximu-Petri, A.; Essel, E.; Gansauge, M.; Kanis, P.; Macak, D.; Riesenberg, S.; Bokelmann, L.; Zeberg, H.; Meyer, M.; Borte, S.; Paabo, S. title: A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date: 2020-06-26 journal: nan DOI: 10.1101/2020.06.24.20139501 sha: doc_id: 353576 cord_uid: f29kmtot file: cache/cord-354051-ro3o27pv.json key: cord-354051-ro3o27pv authors: Peccia, J.; Zulli, A.; Brackney, D. E.; Grubaugh, N. D.; Kaplan, E. H.; Casanovas-Massana, A.; Ko, A. I.; Malik, A. A.; Wang, D.; Wang, M.; Weinberger, D. M.; Omer, S. B. title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date: 2020-05-22 journal: nan DOI: 10.1101/2020.05.19.20105999 sha: doc_id: 354051 cord_uid: ro3o27pv file: cache/cord-354824-7fdcu2f0.json key: cord-354824-7fdcu2f0 authors: Wu, Renyi; Wang, Lujing; Kuo, Hsiao-Chen Dina; Shannar, Ahmad; Peter, Rebecca; Chou, Pochung Jordan; Li, Shanyi; Hudlikar, Rasika; Liu, Xia; Liu, Zhigang; Poiani, George J.; Amorosa, Louis; Brunetti, Luigi; Kong, Ah-Ng title: An Update on Current Therapeutic Drugs Treating COVID-19 date: 2020-05-11 journal: Curr Pharmacol Rep DOI: 10.1007/s40495-020-00216-7 sha: doc_id: 354824 cord_uid: 7fdcu2f0 file: cache/cord-355676-2y8vowbi.json key: cord-355676-2y8vowbi authors: Liu, Pinghua; Millership, Jason J.; Li, Lichun; Giedroc, David P.; Leibowitz, Julian L. title: A Previously Unrecognized Unr Stem-Loop Structure in the Coronavirus 5’ Untranslated Region Plays a Functional role in Replication date: 2006 journal: The Nidoviruses DOI: 10.1007/978-0-387-33012-9_3 sha: doc_id: 355676 cord_uid: 2y8vowbi file: cache/cord-353274-wozwpvpq.json key: cord-353274-wozwpvpq authors: Borremans, B.; Gamble, A.; Prager, K. C.; Helman, S. K.; McClain, A. M.; Cox, C.; Savage, V.; Lloyd-Smith, J. O. title: Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date: 2020-05-20 journal: nan DOI: 10.1101/2020.05.15.20103275 sha: doc_id: 353274 cord_uid: wozwpvpq file: cache/cord-355743-vjiecd4k.json key: cord-355743-vjiecd4k authors: Ghosh, Sabyasachi; Rajwade, Ajit; Krishna, Srikar; Gopalkrishnan, Nikhil; Schaus, Thomas E.; Chakravarthy, Anirudh; Varahan, Sriram; Appu, Vidhya; Ramakrishnan, Raunak; Ch, Shashank; Jindal, Mohit; Bhupathi, Vadhir; Gupta, Aditya; Jain, Abhinav; Agarwal, Rishi; Pathak, Shreya; Rehan, Mohammed Ali; Consul, Sarthak; Gupta, Yash; Gupta, Nimay; Agarwal, Pratyush; Goyal, Ritika; Sagar, Vinay; Ramakrishnan, Uma; Krishna, Sandeep; Yin, Peng; Palakodeti, Dasaradhi; Gopalkrishnan, Manoj title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date: 2020-04-29 journal: nan DOI: 10.1101/2020.04.23.20077727 sha: doc_id: 355743 cord_uid: vjiecd4k file: cache/cord-353810-mf753ae9.json key: cord-353810-mf753ae9 authors: Tan, Cedric Chih Shen; Maurer-Stroh, Sebastian; Wan, Yue; Sessions, October Michael; de Sessions, Paola Florez title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 journal: AMB Express DOI: 10.1186/s13568-019-0772-y sha: doc_id: 353810 cord_uid: mf753ae9 file: cache/cord-354096-x2skguz8.json key: cord-354096-x2skguz8 authors: Ray, Pradipta R.; Wangzhou, Andi; Ghneim, Nizar; Yousuf, Muhammad S.; Paige, Candler; Tavares-Ferreira, Diana; Mwirigi, Juliet M.; Shiers, Stephanie; Sankaranarayanan, Ishwarya; McFarland, Amelia J.; Neerukonda, Sanjay V.; Davidson, Steve; Dussor, Gregory; Burton, Michael D.; Price, Theodore J. title: A pharmacological interactome between COVID-19 patient samples and human sensory neurons reveals potential drivers of neurogenic pulmonary dysfunction date: 2020-06-01 journal: Brain Behav Immun DOI: 10.1016/j.bbi.2020.05.078 sha: doc_id: 354096 cord_uid: x2skguz8 file: cache/cord-355499-5vj3oasa.json key: cord-355499-5vj3oasa authors: Song, Xiangjun; Zhao, Xiaomin; Huang, Yong; Xiang, Hailing; Zhang, Wenlong; Tong, Dewen title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date: 2015-06-07 journal: Int J Biol Sci DOI: 10.7150/ijbs.11585 sha: doc_id: 355499 cord_uid: 5vj3oasa file: cache/cord-354733-qxivrhj8.json key: cord-354733-qxivrhj8 authors: Gniazdowski, V.; Morris, C. P.; Wohl, S.; Mehoke, T.; Ramakrishnan, S.; Thielen, P.; Powell, H.; Smith, B. D.; Armstrong, D. T.; Herrera, M.; Reifsnyder, C.; Sevdali, M.; Carroll, K. C.; Pekosz, A.; Mostafa, H. H. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 journal: nan DOI: 10.1101/2020.08.05.20168963 sha: doc_id: 354733 cord_uid: qxivrhj8 file: cache/cord-354829-god79qzw.json key: cord-354829-god79qzw authors: Mao, Kaimin; Geng, Wei; Liao, Yuhan; Luo, Ping; Zhong, Hua; Ma, Pei; Xu, Juanjuan; Zhang, Shuai; Tan, Qi; Jin, Yang title: Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets date: 2020-09-23 journal: Aging (Albany NY) DOI: 10.18632/aging.104042 sha: doc_id: 354829 cord_uid: god79qzw file: cache/cord-353475-dtn7h1gj.json key: cord-353475-dtn7h1gj authors: Haddad, Hazem; Walid Al-Zyoud title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date: 2020-08-20 journal: Noncoding RNA Res DOI: 10.1016/j.ncrna.2020.08.002 sha: doc_id: 353475 cord_uid: dtn7h1gj file: cache/cord-354003-ko45l1qv.json key: cord-354003-ko45l1qv authors: Scarpin, M Regina; Leiboff, Samuel; Brunkard, Jacob O title: Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation date: 2020-10-15 journal: eLife DOI: 10.7554/elife.58795 sha: doc_id: 354003 cord_uid: ko45l1qv file: cache/cord-355179-wmfwl2bh.json key: cord-355179-wmfwl2bh authors: Jung, Eunhye; Nam, Sangwoo; Oh, Hyeryeon; Jun, Sangmi; Ro, Hyun-Joo; Kim, Baek; Kim, Meehyein; Go, Yun Young title: Neutralization of Acidic Intracellular Vesicles by Niclosamide Inhibits Multiple Steps of the Dengue Virus Life Cycle In Vitro date: 2019-06-18 journal: Sci Rep DOI: 10.1038/s41598-019-45095-1 sha: doc_id: 355179 cord_uid: wmfwl2bh file: cache/cord-353484-q7d0ysbo.json key: cord-353484-q7d0ysbo authors: Liu, Xue; Liu, Chao; Liu, Gang; Luo, Wenxin; Xia, Ningshao title: COVID-19: Progress in diagnostics, therapy and vaccination date: 2020-06-19 journal: Theranostics DOI: 10.7150/thno.47987 sha: doc_id: 353484 cord_uid: q7d0ysbo file: cache/cord-355758-tk7eturq.json key: cord-355758-tk7eturq authors: Berrio, Alejandro; Gartner, Valerie; Wray, Gregory A title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date: 2020-09-22 journal: bioRxiv DOI: 10.1101/2020.09.16.300038 sha: doc_id: 355758 cord_uid: tk7eturq file: cache/cord-355397-y69bk5jc.json key: cord-355397-y69bk5jc authors: Caruso, Ícaro P.; Sanches, Karoline; Da Poian, Andrea T.; Pinheiro, Anderson S.; Almeida, Fabio C. L. title: Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism date: 2020-09-06 journal: bioRxiv DOI: 10.1101/2020.08.24.264465 sha: doc_id: 355397 cord_uid: y69bk5jc file: cache/cord-355075-ieb35upi.json key: cord-355075-ieb35upi authors: Papenfuss, Anthony T; Baker, Michelle L; Feng, Zhi-Ping; Tachedjian, Mary; Crameri, Gary; Cowled, Chris; Ng, Justin; Janardhana, Vijaya; Field, Hume E; Wang, Lin-Fa title: The immune gene repertoire of an important viral reservoir, the Australian black flying fox date: 2012-06-20 journal: BMC Genomics DOI: 10.1186/1471-2164-13-261 sha: doc_id: 355075 cord_uid: ieb35upi file: cache/cord-355477-7xd93aqv.json key: cord-355477-7xd93aqv authors: SATIJA, NAMITA; LAL, SUNIL K. title: The Molecular Biology of SARS Coronavirus date: 2007-04-23 journal: Ann N Y Acad Sci DOI: 10.1196/annals.1408.002 sha: doc_id: 355477 cord_uid: 7xd93aqv file: cache/cord-356009-emn2w8if.json key: cord-356009-emn2w8if authors: Roshandel, M. R.; Nateqi, M.; Lak, R.; Aavani, P.; Sari Motlagh, R.; Aghaei Badr, T.; Sfakianos, J.; Kaplan, S. A.; Shariat, S.; Tewari, A. K. title: What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date: 2020-10-13 journal: nan DOI: 10.1101/2020.10.08.20209544 sha: doc_id: 356009 cord_uid: emn2w8if file: cache/cord-355357-b6aklh44.json key: cord-355357-b6aklh44 authors: Stapleford, Kenneth A.; Rozen-Gagnon, Kathryn; Das, Pratyush Kumar; Saul, Sirle; Poirier, Enzo Z.; Blanc, Hervé; Vidalain, Pierre-Olivier; Merits, Andres; Vignuzzi, Marco title: Viral Polymerase-Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion date: 2015-08-26 journal: J Virol DOI: 10.1128/jvi.01553-15 sha: doc_id: 355357 cord_uid: b6aklh44 file: cache/cord-356115-vblgotjn.json key: cord-356115-vblgotjn authors: Sawicki, Stanley G; Sawicki, Dorothea L; Younker, Diane; Meyer, Yvonne; Thiel, Volker; Stokes, Helen; Siddell, Stuart G title: Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins date: 2005-12-09 journal: PLoS Pathog DOI: 10.1371/journal.ppat.0010039 sha: doc_id: 356115 cord_uid: vblgotjn file: cache/cord-354529-k8p2u7iq.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-354529-k8p2u7iq authors: Wu, Yongran; Hong, Ke; Ruan, Lianguo; Yang, Xiaobo; Zhang, Jiancheng; Xu, Jiqian; Pan, Shangwen; Ren, Lehao; Chen, Lu; Huang, Chaolin; Shang, You title: Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date: 2020-08-31 journal: Virol Sin DOI: 10.1007/s12250-020-00281-8 sha: doc_id: 354529 cord_uid: k8p2u7iq file: cache/cord-352200-i05h8csb.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-352200-i05h8csb authors: Xu, Yi; Zhou, Wenwu; Zhou, Yijun; Wu, Jianxiang; Zhou, Xueping title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 journal: PLoS One DOI: 10.1371/journal.pone.0036238 sha: doc_id: 352200 cord_uid: i05h8csb file: cache/cord-353703-u86ggw11.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-353703-u86ggw11 authors: Gao, Peng; Chai, Yue; Song, Jiangwei; Liu, Teng; Chen, Peng; Zhou, Lei; Ge, Xinna; Guo, Xin; Han, Jun; Yang, Hanchun title: Reprogramming the unfolded protein response for replication by porcine reproductive and respiratory syndrome virus date: 2019-11-18 journal: PLoS Pathog DOI: 10.1371/journal.ppat.1008169 sha: doc_id: 353703 cord_uid: u86ggw11 file: cache/cord-355913-fhvt1ht1.json key: cord-355913-fhvt1ht1 authors: Burrell, Christopher J.; Howard, Colin R.; Murphy, Frederick A. title: Virus Replication date: 2016-11-11 journal: Fenner and White's Medical Virology DOI: 10.1016/b978-0-12-375156-0.00004-7 sha: doc_id: 355913 cord_uid: fhvt1ht1 file: cache/cord-353342-2n6kqyeo.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-353342-2n6kqyeo authors: Corman, Victor M.; Albarrak, Ali M.; Omrani, Ali Senosi; Albarrak, Mohammed M.; Farah, Mohamed Elamin; Almasri, Malak; Muth, Doreen; Sieberg, Andrea; Meyer, Benjamin; Assiri, Abdullah M.; Binger, Tabea; Steinhagen, Katja; Lattwein, Erik; Al-Tawfiq, Jaffar; Müller, Marcel A.; Drosten, Christian; Memish, Ziad A. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 journal: Clin Infect Dis DOI: 10.1093/cid/civ951 sha: doc_id: 353342 cord_uid: 2n6kqyeo file: cache/cord-353290-1wi1dhv6.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-353290-1wi1dhv6 authors: Kustin, Talia; Stern, Adi title: Biased mutation and selection in RNA viruses date: 2020-09-28 journal: Mol Biol Evol DOI: 10.1093/molbev/msaa247 sha: doc_id: 353290 cord_uid: 1wi1dhv6 file: cache/cord-354398-f3cg8gi1.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-354398-f3cg8gi1 authors: Al-Saud, Haya; Al-Romaih, Khaldoun; Bakheet, Razan; Mahmoud, Lina; Al-Harbi, Najla; Alshareef, Ibtihaj; Judia, Sara Bin; Aharbi, Layla; Alzayed, Abdulaziz; Jabaan, Amjad; Alhadrami, Hani; Albarrag, Ahmed; Azhar, Essam I.; Al-Mozaini, Maha Ahmad title: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date: 2020-09-20 journal: Ann Saudi Med DOI: 10.5144/0256-4947.2020.373 sha: doc_id: 354398 cord_uid: f3cg8gi1 file: cache/cord-352991-duqkpkll.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-352991-duqkpkll authors: Waghmare, Alpana; Campbell, Angela P.; Xie, Hu; Seo, Sachiko; Kuypers, Jane; Leisenring, Wendy; Jerome, Keith R.; Englund, Janet A.; Boeckh, Michael title: Respiratory Syncytial Virus Lower Respiratory Disease in Hematopoietic Cell Transplant Recipients: Viral RNA Detection in Blood, Antiviral Treatment, and Clinical Outcomes date: 2013-09-24 journal: Clinical Infectious Diseases DOI: 10.1093/cid/cit639 sha: doc_id: 352991 cord_uid: duqkpkll file: cache/cord-354407-zzxjv666.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: Resource temporarily unavailable key: cord-354407-zzxjv666 authors: Campanacci, Valérie; Egloff, Marie‐Pierre; Longhi, Sonia; Ferron, François; Rancurel, Corinne; Salomoni, Aurelia; Durousseau, Cécile; Tocque, Fabienne; Brémond, Nicolas; Dobbe, Jessika C.; Snijder, Eric J.; Canard, Bruno; Cambillau, Christian title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date: 2004-06-07 journal: Acta Crystallogr D Biol Crystallogr DOI: 10.1107/s0907444903016779 sha: doc_id: 354407 cord_uid: zzxjv666 file: cache/cord-354114-frdsct44.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-354114-frdsct44 authors: Vogel, Liesbeth; Van der Lubben, Mariken; Te Lintelo, Eddie G.; Bekker, Cornelis P.J.; Geerts, Tamara; Schuijff, Leontine S.; Grinwis, Guy C.M.; Egberink, Herman F.; Rottier, Peter J.M. title: Pathogenic characteristics of persistent feline enteric coronavirus infection in cats date: 2010-07-23 journal: Vet Res DOI: 10.1051/vetres/2010043 sha: doc_id: 354114 cord_uid: frdsct44 file: cache/cord-354582-fniymnmf.json /data-disk/reader-compute/reader-cord/bin/json2txt-carrel.sh: fork: retry: No child processes key: cord-354582-fniymnmf authors: Ma, Zhiqian; Li, Zhiwei; Dong, Linfang; Yang, Ting; Xiao, Shuqi title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 journal: Adv Virus Res DOI: 10.1016/bs.aivir.2020.06.003 sha: doc_id: 354582 cord_uid: fniymnmf Reading metadata file and updating bibliogrpahics === updating bibliographic database Building study carrel named keyword-rna-cord parallel: Warning: Only enough available processes to run 3 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 10 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 16 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 40 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 64 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: Only enough available processes to run 72 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: No more processes: Decreasing number of running jobs to 63. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordent2carrel.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/txt2urls.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/cordpos2carrel.sh: fork: retry: No child processes === file2bib.sh === id: cord-000322-8ctsa9sd author: Ninove, Laetitia title: RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date: 2011-02-09 pages: extension: .txt txt: ./txt/cord-000322-8ctsa9sd.txt cache: ./cache/cord-000322-8ctsa9sd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000322-8ctsa9sd.txt' === file2bib.sh === id: cord-000088-1xgjdhkx author: Faria, Nuno R title: Rooting human parechovirus evolution in time date: 2009-07-15 pages: extension: .txt txt: ./txt/cord-000088-1xgjdhkx.txt cache: ./cache/cord-000088-1xgjdhkx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000088-1xgjdhkx.txt' === file2bib.sh === id: cord-000159-8y8ho2x5 author: Bekaert, Michaël title: Recode-2: new design, new search tools, and many more genes date: 2009-09-25 pages: extension: .txt txt: ./txt/cord-000159-8y8ho2x5.txt cache: ./cache/cord-000159-8y8ho2x5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000159-8y8ho2x5.txt' === file2bib.sh === id: cord-000295-ft5wl70x author: Tomankova, Tereza title: Involvement of microRNAs in physiological and pathological processes in the lung date: 2010-11-23 pages: extension: .txt txt: ./txt/cord-000295-ft5wl70x.txt cache: ./cache/cord-000295-ft5wl70x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000295-ft5wl70x.txt' === file2bib.sh === id: cord-000265-llilwq1u author: Gao, Rongbao title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 pages: extension: .txt txt: ./txt/cord-000265-llilwq1u.txt cache: ./cache/cord-000265-llilwq1u.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000265-llilwq1u.txt' === file2bib.sh === id: cord-000715-zl1s82yi author: Shulman, Lester M. title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 pages: extension: .txt txt: ./txt/cord-000715-zl1s82yi.txt cache: ./cache/cord-000715-zl1s82yi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000715-zl1s82yi.txt' === file2bib.sh === id: cord-000482-wifs97yy author: Yu, Chien-Hung title: Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting date: 2011-07-29 pages: extension: .txt txt: ./txt/cord-000482-wifs97yy.txt cache: ./cache/cord-000482-wifs97yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000482-wifs97yy.txt' === file2bib.sh === id: cord-000269-v4jochbe author: Wittekindt, Nicola E. title: Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics date: 2010-10-18 pages: extension: .txt txt: ./txt/cord-000269-v4jochbe.txt cache: ./cache/cord-000269-v4jochbe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000269-v4jochbe.txt' === file2bib.sh === id: cord-000113-d0eur1hq author: Fooks, Anthony R. title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 pages: extension: .txt txt: ./txt/cord-000113-d0eur1hq.txt cache: ./cache/cord-000113-d0eur1hq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000113-d0eur1hq.txt' === file2bib.sh === id: cord-000435-2u49b7xo author: Firth, Andrew E. title: Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element date: 2011-04-27 pages: extension: .txt txt: ./txt/cord-000435-2u49b7xo.txt cache: ./cache/cord-000435-2u49b7xo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000435-2u49b7xo.txt' === file2bib.sh === id: cord-002045-m44fic4g author: Horie, Masayuki title: An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus date: 2016-05-13 pages: extension: .txt txt: ./txt/cord-002045-m44fic4g.txt cache: ./cache/cord-002045-m44fic4g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002045-m44fic4g.txt' === file2bib.sh === id: cord-001985-iwfidoer author: Urayama, Syun-ichi title: FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date: 2016-02-13 pages: extension: .txt txt: ./txt/cord-001985-iwfidoer.txt cache: ./cache/cord-001985-iwfidoer.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001985-iwfidoer.txt' === file2bib.sh === id: cord-000143-2xvd5ogf author: Napthine, Sawsan title: Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy date: 2009-12-22 pages: extension: .txt txt: ./txt/cord-000143-2xvd5ogf.txt cache: ./cache/cord-000143-2xvd5ogf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000143-2xvd5ogf.txt' === file2bib.sh === id: cord-001090-qg2r691d author: Twin, Jimmy title: The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis date: 2013-09-27 pages: extension: .txt txt: ./txt/cord-001090-qg2r691d.txt cache: ./cache/cord-001090-qg2r691d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001090-qg2r691d.txt' === file2bib.sh === id: cord-000532-e18licyc author: Tholstrup, Jesper title: mRNA pseudoknot structures can act as ribosomal roadblocks date: 2011-09-08 pages: extension: .txt txt: ./txt/cord-000532-e18licyc.txt cache: ./cache/cord-000532-e18licyc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000532-e18licyc.txt' === file2bib.sh === id: cord-000660-tsvzg0ax author: Fensterl, Volker title: Interferon-Induced Ifit2/ISG54 Protects Mice from Lethal VSV Neuropathogenesis date: 2012-05-17 pages: extension: .txt txt: ./txt/cord-000660-tsvzg0ax.txt cache: ./cache/cord-000660-tsvzg0ax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000660-tsvzg0ax.txt' === file2bib.sh === id: cord-000895-z5rdf0mi author: Belalov, Ilya S. title: Causes and Implications of Codon Usage Bias in RNA Viruses date: 2013-02-25 pages: extension: .txt txt: ./txt/cord-000895-z5rdf0mi.txt cache: ./cache/cord-000895-z5rdf0mi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000895-z5rdf0mi.txt' === file2bib.sh === id: cord-000128-t74b5j2j author: Laufer, S.D title: Peptide-Mediated Cellular Delivery of Oligonucleotide-Based Therapeutics In Vitro: Quantitative Evaluation of Overall Efficacy Employing Easy to Handle Reporter Systems date: 2008-12-17 pages: extension: .txt txt: ./txt/cord-000128-t74b5j2j.txt cache: ./cache/cord-000128-t74b5j2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000128-t74b5j2j.txt' === file2bib.sh === id: cord-002015-s3tdllby author: Burton, Aaron S. title: The elusive quest for RNA knots date: 2016-02-01 pages: extension: .txt txt: ./txt/cord-002015-s3tdllby.txt cache: ./cache/cord-002015-s3tdllby.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002015-s3tdllby.txt' === file2bib.sh === id: cord-002376-970934vm author: Mikel, Pavel title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 pages: extension: .txt txt: ./txt/cord-002376-970934vm.txt cache: ./cache/cord-002376-970934vm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002376-970934vm.txt' === file2bib.sh === id: cord-001397-nrq4ncdf author: Mlera, Luwanika title: The role of viral persistence in flavivirus biology date: 2014-05-12 pages: extension: .txt txt: ./txt/cord-001397-nrq4ncdf.txt cache: ./cache/cord-001397-nrq4ncdf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-001397-nrq4ncdf.txt' === file2bib.sh === id: cord-000556-uu1oz2ei author: Kumar, Ranjit title: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336” date: 2012-01-20 pages: extension: .txt txt: ./txt/cord-000556-uu1oz2ei.txt cache: ./cache/cord-000556-uu1oz2ei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000556-uu1oz2ei.txt' === file2bib.sh === id: cord-002423-1u44tdrj author: Geoghegan, Jemma L. title: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date: 2017-02-08 pages: extension: .txt txt: ./txt/cord-002423-1u44tdrj.txt cache: ./cache/cord-002423-1u44tdrj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002423-1u44tdrj.txt' === file2bib.sh === id: cord-002651-9r384oxd author: Pauly, Matthew D. title: Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity date: 2017-08-16 pages: extension: .txt txt: ./txt/cord-002651-9r384oxd.txt cache: ./cache/cord-002651-9r384oxd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002651-9r384oxd.txt' === file2bib.sh === id: cord-001257-t21l6i3f author: Kovalev, Nikolay title: The Expanding Functions of Cellular Helicases: The Tombusvirus RNA Replication Enhancer Co-opts the Plant eIF4AIII-Like AtRH2 and the DDX5-Like AtRH5 DEAD-Box RNA Helicases to Promote Viral Asymmetric RNA Replication date: 2014-04-17 pages: extension: .txt txt: ./txt/cord-001257-t21l6i3f.txt cache: ./cache/cord-001257-t21l6i3f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001257-t21l6i3f.txt' === file2bib.sh === id: cord-000578-jhetyd9t author: Kovalev, Nikolay title: A Co-Opted DEAD-Box RNA Helicase Enhances Tombusvirus Plus-Strand Synthesis date: 2012-02-16 pages: extension: .txt txt: ./txt/cord-000578-jhetyd9t.txt cache: ./cache/cord-000578-jhetyd9t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000578-jhetyd9t.txt' === file2bib.sh === id: cord-001228-4eh22ek7 author: Ofori, Leslie O. title: High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity date: 2014-01-05 pages: extension: .txt txt: ./txt/cord-001228-4eh22ek7.txt cache: ./cache/cord-001228-4eh22ek7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001228-4eh22ek7.txt' === file2bib.sh === id: cord-000125-uvf5qzfd author: Kenworthy, Rachael title: Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation date: 2009-09-03 pages: extension: .txt txt: ./txt/cord-000125-uvf5qzfd.txt cache: ./cache/cord-000125-uvf5qzfd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000125-uvf5qzfd.txt' === file2bib.sh === id: cord-000063-tex6bgab author: Sui, Hong-Yan title: Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication date: 2009-05-22 pages: extension: .txt txt: ./txt/cord-000063-tex6bgab.txt cache: ./cache/cord-000063-tex6bgab.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000063-tex6bgab.txt' === file2bib.sh === id: cord-002320-m99amd4y author: Mathur, Kalika title: Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity date: 2016-11-30 pages: extension: .txt txt: ./txt/cord-002320-m99amd4y.txt cache: ./cache/cord-002320-m99amd4y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002320-m99amd4y.txt' === file2bib.sh === id: cord-000238-om92cx5q author: Ogbunugafor, C. Brandon title: On the possible role of robustness in the evolution of infectious diseases date: 2010-06-30 pages: extension: .txt txt: ./txt/cord-000238-om92cx5q.txt cache: ./cache/cord-000238-om92cx5q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000238-om92cx5q.txt' === file2bib.sh === id: cord-001109-xs7df6a7 author: Tapia, Karla title: Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity date: 2013-10-31 pages: extension: .txt txt: ./txt/cord-001109-xs7df6a7.txt cache: ./cache/cord-001109-xs7df6a7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001109-xs7df6a7.txt' === file2bib.sh === id: cord-001542-f089bs8r author: Lai, Kang Yiu title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date: 2014-11-28 pages: extension: .txt txt: ./txt/cord-001542-f089bs8r.txt cache: ./cache/cord-001542-f089bs8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001542-f089bs8r.txt' === file2bib.sh === id: cord-000018-amvlm09p author: Pauli, Eva-K. title: Influenza A Virus Inhibits Type I IFN Signaling via NF-κB-Dependent Induction of SOCS-3 Expression date: 2008-11-07 pages: extension: .txt txt: ./txt/cord-000018-amvlm09p.txt cache: ./cache/cord-000018-amvlm09p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000018-amvlm09p.txt' === file2bib.sh === id: cord-001748-7e8px4vx author: Nobach, Daniel title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date: 2015-08-27 pages: extension: .txt txt: ./txt/cord-001748-7e8px4vx.txt cache: ./cache/cord-001748-7e8px4vx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001748-7e8px4vx.txt' === file2bib.sh === id: cord-002746-qn34eyul author: Antzin-Anduetza, Irati title: Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication date: 2017-11-09 pages: extension: .txt txt: ./txt/cord-002746-qn34eyul.txt cache: ./cache/cord-002746-qn34eyul.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002746-qn34eyul.txt' === file2bib.sh === id: cord-000830-jiy4cp4n author: Cobo, Fernando title: Application of Molecular Diagnostic Techniques for Viral Testing date: 2012-11-30 pages: extension: .txt txt: ./txt/cord-000830-jiy4cp4n.txt cache: ./cache/cord-000830-jiy4cp4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000830-jiy4cp4n.txt' === file2bib.sh === id: cord-000248-zueoyesj author: Berretta, Regina title: Cancer Biomarker Discovery: The Entropic Hallmark date: 2010-08-18 pages: extension: .txt txt: ./txt/cord-000248-zueoyesj.txt cache: ./cache/cord-000248-zueoyesj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000248-zueoyesj.txt' === file2bib.sh === id: cord-002238-fyztb8d9 author: Young, D. F. title: Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family date: 2016-09-29 pages: extension: .txt txt: ./txt/cord-002238-fyztb8d9.txt cache: ./cache/cord-002238-fyztb8d9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002238-fyztb8d9.txt' === file2bib.sh === id: cord-002413-795wuqz5 author: Balinsky, Corey A. title: IRAV (FLJ11286), an Interferon-Stimulated Gene with Antiviral Activity against Dengue Virus, Interacts with MOV10 date: 2017-02-14 pages: extension: .txt txt: ./txt/cord-002413-795wuqz5.txt cache: ./cache/cord-002413-795wuqz5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002413-795wuqz5.txt' === file2bib.sh === id: cord-000804-0hlj6r10 author: Brauburger, Kristina title: Forty-Five Years of Marburg Virus Research date: 2012-10-01 pages: extension: .txt txt: ./txt/cord-000804-0hlj6r10.txt cache: ./cache/cord-000804-0hlj6r10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000804-0hlj6r10.txt' === file2bib.sh === id: cord-000822-iuglkdcp author: Sperschneider, Jana title: Predicting pseudoknotted structures across two RNA sequences date: 2012-12-01 pages: extension: .txt txt: ./txt/cord-000822-iuglkdcp.txt cache: ./cache/cord-000822-iuglkdcp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000822-iuglkdcp.txt' === file2bib.sh === id: cord-000293-pc4x5e24 author: Yu, Chien-Hung title: Stimulation of ribosomal frameshifting by antisense LNA date: 2010-08-06 pages: extension: .txt txt: ./txt/cord-000293-pc4x5e24.txt cache: ./cache/cord-000293-pc4x5e24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-000293-pc4x5e24.txt' === file2bib.sh === id: cord-001655-uqw74ra0 author: Stenglein, Mark D. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 pages: extension: .txt txt: ./txt/cord-001655-uqw74ra0.txt cache: ./cache/cord-001655-uqw74ra0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001655-uqw74ra0.txt' === file2bib.sh === id: cord-000364-ikq38rm1 author: Rasmuson, J. title: Time to revise the paradigm of hantavirus syndromes? Hantavirus pulmonary syndrome caused by European hantavirus date: 2011-01-15 pages: extension: .txt txt: ./txt/cord-000364-ikq38rm1.txt cache: ./cache/cord-000364-ikq38rm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000364-ikq38rm1.txt' === file2bib.sh === id: cord-000937-8vk89i4h author: Law, John title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date: 2013-04-17 pages: extension: .txt txt: ./txt/cord-000937-8vk89i4h.txt cache: ./cache/cord-000937-8vk89i4h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000937-8vk89i4h.txt' === file2bib.sh === id: cord-000881-s90geszi author: Lang, Dorothy M. title: Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases date: 2012-12-25 pages: extension: .txt txt: ./txt/cord-000881-s90geszi.txt cache: ./cache/cord-000881-s90geszi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000881-s90geszi.txt' === file2bib.sh === id: cord-002720-lrkscs71 author: Kurosaki, Yohei title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification date: 2017-10-18 pages: extension: .txt txt: ./txt/cord-002720-lrkscs71.txt cache: ./cache/cord-002720-lrkscs71.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002720-lrkscs71.txt' === file2bib.sh === id: cord-002990-7flusgus author: Kitano, Mitsutaka title: Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro date: 2018-04-26 pages: extension: .txt txt: ./txt/cord-002990-7flusgus.txt cache: ./cache/cord-002990-7flusgus.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002990-7flusgus.txt' === file2bib.sh === id: cord-002222-rgqwm3vb author: Olarte-Castillo, Ximena A. title: Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date: 2016-09-23 pages: extension: .txt txt: ./txt/cord-002222-rgqwm3vb.txt cache: ./cache/cord-002222-rgqwm3vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002222-rgqwm3vb.txt' === file2bib.sh === id: cord-002102-0zbp3uqf author: Rasche, Andrea title: Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015 date: 2016-07-17 pages: extension: .txt txt: ./txt/cord-002102-0zbp3uqf.txt cache: ./cache/cord-002102-0zbp3uqf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002102-0zbp3uqf.txt' === file2bib.sh === id: cord-000372-wzwpyvll author: Castelló, Alfredo title: The Multifaceted Poliovirus 2A Protease: Regulation of Gene Expression by Picornavirus Proteases date: 2011-04-14 pages: extension: .txt txt: ./txt/cord-000372-wzwpyvll.txt cache: ./cache/cord-000372-wzwpyvll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000372-wzwpyvll.txt' === file2bib.sh === id: cord-000729-iq30z094 author: Marsh, Glenn A. title: Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date: 2012-08-02 pages: extension: .txt txt: ./txt/cord-000729-iq30z094.txt cache: ./cache/cord-000729-iq30z094.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000729-iq30z094.txt' === file2bib.sh === id: cord-002180-gsdk5x3e author: Davies, Colin title: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date: 2016-08-24 pages: extension: .txt txt: ./txt/cord-002180-gsdk5x3e.txt cache: ./cache/cord-002180-gsdk5x3e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002180-gsdk5x3e.txt' === file2bib.sh === id: cord-002006-pwlybr2h author: Liu, Yuan-yuan title: Specific interference shRNA-expressing plasmids inhibit Hantaan virus infection in vitro and in vivo date: 2016-03-14 pages: extension: .txt txt: ./txt/cord-002006-pwlybr2h.txt cache: ./cache/cord-002006-pwlybr2h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002006-pwlybr2h.txt' === file2bib.sh === id: cord-000981-6vloa2w3 author: Bálint, Zoltán title: Double-Stranded RNA Attenuates the Barrier Function of Human Pulmonary Artery Endothelial Cells date: 2013-06-03 pages: extension: .txt txt: ./txt/cord-000981-6vloa2w3.txt cache: ./cache/cord-000981-6vloa2w3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000981-6vloa2w3.txt' === file2bib.sh === id: cord-003254-yiqdsf9z author: Schlub, Timothy E title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date: 2018-08-07 pages: extension: .txt txt: ./txt/cord-003254-yiqdsf9z.txt cache: ./cache/cord-003254-yiqdsf9z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003254-yiqdsf9z.txt' === file2bib.sh === id: cord-002542-f7l4ty2j author: Jaworski, Elizabeth title: Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus date: 2017-05-05 pages: extension: .txt txt: ./txt/cord-002542-f7l4ty2j.txt cache: ./cache/cord-002542-f7l4ty2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002542-f7l4ty2j.txt' === file2bib.sh === id: cord-000640-t0y0b0gb author: Sumibcay, Laarni title: Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Côte d'Ivoire date: 2012-01-26 pages: extension: .txt txt: ./txt/cord-000640-t0y0b0gb.txt cache: ./cache/cord-000640-t0y0b0gb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-000640-t0y0b0gb.txt' === file2bib.sh === id: cord-000736-6f8vyziv author: Pripuzova, Natalia title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 pages: extension: .txt txt: ./txt/cord-000736-6f8vyziv.txt cache: ./cache/cord-000736-6f8vyziv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-000736-6f8vyziv.txt' === file2bib.sh === id: cord-000979-cav9n18w author: Hoppe, Sebastian title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 pages: extension: .txt txt: ./txt/cord-000979-cav9n18w.txt cache: ./cache/cord-000979-cav9n18w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000979-cav9n18w.txt' === file2bib.sh === id: cord-002312-jyk7f8hz author: Branton, W. G. title: Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis date: 2016-11-28 pages: extension: .txt txt: ./txt/cord-002312-jyk7f8hz.txt cache: ./cache/cord-002312-jyk7f8hz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002312-jyk7f8hz.txt' === file2bib.sh === id: cord-000547-adfigzc1 author: Beniac, Daniel R. title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date: 2012-01-11 pages: extension: .txt txt: ./txt/cord-000547-adfigzc1.txt cache: ./cache/cord-000547-adfigzc1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-000547-adfigzc1.txt' === file2bib.sh === id: cord-001152-v6uc0ijw author: Girardi, Erika title: Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells date: 2013-11-19 pages: extension: .txt txt: ./txt/cord-001152-v6uc0ijw.txt cache: ./cache/cord-001152-v6uc0ijw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001152-v6uc0ijw.txt' === file2bib.sh === id: cord-001963-4wjvykx7 author: Liu, Chia-Lin title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development date: 2016-02-26 pages: extension: .txt txt: ./txt/cord-001963-4wjvykx7.txt cache: ./cache/cord-001963-4wjvykx7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001963-4wjvykx7.txt' === file2bib.sh === id: cord-002398-0a3okta0 author: Myllykoski, Matti title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase date: 2017-01-31 pages: extension: .txt txt: ./txt/cord-002398-0a3okta0.txt cache: ./cache/cord-002398-0a3okta0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002398-0a3okta0.txt' === file2bib.sh === id: cord-002763-n952re94 author: Niu, Xiaosai title: Transcriptome analysis of avian reovirus-mediated changes in gene expression of normal chicken fibroblast DF-1 cells date: 2017-11-25 pages: extension: .txt txt: ./txt/cord-002763-n952re94.txt cache: ./cache/cord-002763-n952re94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002763-n952re94.txt' === file2bib.sh === id: cord-001829-rwnbxmt4 author: Lu, Yi-Fan title: IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance date: 2015-11-04 pages: extension: .txt txt: ./txt/cord-001829-rwnbxmt4.txt cache: ./cache/cord-001829-rwnbxmt4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001829-rwnbxmt4.txt' === file2bib.sh === id: cord-002179-v8lpw4r7 author: Viktorovskaya, Olga V. title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements date: 2016-08-24 pages: extension: .txt txt: ./txt/cord-002179-v8lpw4r7.txt cache: ./cache/cord-002179-v8lpw4r7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002179-v8lpw4r7.txt' === file2bib.sh === id: cord-002937-7xauocti author: Huang, Chung-Guei title: A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date: 2018-02-20 pages: extension: .txt txt: ./txt/cord-002937-7xauocti.txt cache: ./cache/cord-002937-7xauocti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002937-7xauocti.txt' === file2bib.sh === id: cord-002608-zn7tm1ww author: Sokoloski, Kevin J. title: Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants date: 2017-06-29 pages: extension: .txt txt: ./txt/cord-002608-zn7tm1ww.txt cache: ./cache/cord-002608-zn7tm1ww.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002608-zn7tm1ww.txt' === file2bib.sh === id: cord-001541-5d64esp4 author: Walker, Peter J. title: Evolution of Genome Size and Complexity in the Rhabdoviridae date: 2015-02-13 pages: extension: .txt txt: ./txt/cord-001541-5d64esp4.txt cache: ./cache/cord-001541-5d64esp4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001541-5d64esp4.txt' === file2bib.sh === id: cord-002994-1zjrunzc author: Faye, Martin title: Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus date: 2018-04-13 pages: extension: .txt txt: ./txt/cord-002994-1zjrunzc.txt cache: ./cache/cord-002994-1zjrunzc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002994-1zjrunzc.txt' === file2bib.sh === id: cord-003006-lk2ny1wd author: Cantoni, Diego title: Ebolaviruses: New roles for old proteins date: 2018-05-03 pages: extension: .txt txt: ./txt/cord-003006-lk2ny1wd.txt cache: ./cache/cord-003006-lk2ny1wd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003006-lk2ny1wd.txt' === file2bib.sh === id: cord-003158-mhlqnj52 author: Wang, Qi title: Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date: 2018-07-13 pages: extension: .txt txt: ./txt/cord-003158-mhlqnj52.txt cache: ./cache/cord-003158-mhlqnj52.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003158-mhlqnj52.txt' === file2bib.sh === id: cord-000866-dr2uow4m author: Picard-Jean, Frédéric title: The Immunosuppressive Agent Mizoribine Monophosphate Is an Inhibitor of the Human RNA Capping Enzyme date: 2013-01-17 pages: extension: .txt txt: ./txt/cord-000866-dr2uow4m.txt cache: ./cache/cord-000866-dr2uow4m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000866-dr2uow4m.txt' === file2bib.sh === id: cord-001453-l1r416w7 author: Hou, Linlin title: Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome date: 2014-11-10 pages: extension: .txt txt: ./txt/cord-001453-l1r416w7.txt cache: ./cache/cord-001453-l1r416w7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-001453-l1r416w7.txt' === file2bib.sh === id: cord-001964-iy6qzq58 author: Muñoz-González, Sara title: Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar date: 2016-02-26 pages: extension: .txt txt: ./txt/cord-001964-iy6qzq58.txt cache: ./cache/cord-001964-iy6qzq58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-001964-iy6qzq58.txt' === file2bib.sh === id: cord-003187-qdbcdn2j author: Bassi, Maria Rosaria title: Extinction of Zika Virus and Usutu Virus by Lethal Mutagenesis Reveals Different Patterns of Sensitivity to Three Mutagenic Drugs date: 2018-08-27 pages: extension: .txt txt: ./txt/cord-003187-qdbcdn2j.txt cache: ./cache/cord-003187-qdbcdn2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003187-qdbcdn2j.txt' === file2bib.sh === id: cord-002482-2t09zqqi author: Miras, Manuel title: Non-canonical Translation in Plant RNA Viruses date: 2017-04-06 pages: extension: .txt txt: ./txt/cord-002482-2t09zqqi.txt cache: ./cache/cord-002482-2t09zqqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002482-2t09zqqi.txt' === file2bib.sh === id: cord-002439-wesyiymn author: Le, My-Tra title: Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch date: 2017-02-13 pages: extension: .txt txt: ./txt/cord-002439-wesyiymn.txt cache: ./cache/cord-002439-wesyiymn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-002439-wesyiymn.txt' === file2bib.sh === id: cord-002676-zwkl1ywk author: Yu, Dong-Shan title: The lifecycle of the Ebola virus in host cells date: 2017-06-15 pages: extension: .txt txt: ./txt/cord-002676-zwkl1ywk.txt cache: ./cache/cord-002676-zwkl1ywk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002676-zwkl1ywk.txt' === file2bib.sh === id: cord-003070-6oca1mrm author: Shen, Wen-Jun title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date: 2018-02-28 pages: extension: .txt txt: ./txt/cord-003070-6oca1mrm.txt cache: ./cache/cord-003070-6oca1mrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003070-6oca1mrm.txt' === file2bib.sh === id: cord-002673-5a1rfi6k author: Knibb, Wayne title: Regional genetic diversity for NNV grouper viruses across the Indo-Asian region – implications for selecting virus resistance in farmed groupers date: 2017-09-06 pages: extension: .txt txt: ./txt/cord-002673-5a1rfi6k.txt cache: ./cache/cord-002673-5a1rfi6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-002673-5a1rfi6k.txt' === file2bib.sh === id: cord-002764-px0cz6qn author: Lin, Yuan title: Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs date: 2017-11-17 pages: extension: .txt txt: ./txt/cord-002764-px0cz6qn.txt cache: ./cache/cord-002764-px0cz6qn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-002764-px0cz6qn.txt' === file2bib.sh === id: cord-000794-l565gha4 author: Yan, Huan title: Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus date: 2012-11-13 pages: extension: .txt txt: ./txt/cord-000794-l565gha4.txt cache: ./cache/cord-000794-l565gha4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-000794-l565gha4.txt' === file2bib.sh === id: cord-003044-9uqa39j9 author: Cervera, Héctor title: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date: 2018-03-19 pages: extension: .txt txt: ./txt/cord-003044-9uqa39j9.txt cache: ./cache/cord-003044-9uqa39j9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003044-9uqa39j9.txt' === file2bib.sh === id: cord-003050-n25wnmq5 author: Nibert, Max L. title: A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date: 2018-03-07 pages: extension: .txt txt: ./txt/cord-003050-n25wnmq5.txt cache: ./cache/cord-003050-n25wnmq5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003050-n25wnmq5.txt' === file2bib.sh === id: cord-003104-9cx1gdze author: Fitzsimmons, William J. title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus date: 2018-06-28 pages: extension: .txt txt: ./txt/cord-003104-9cx1gdze.txt cache: ./cache/cord-003104-9cx1gdze.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003104-9cx1gdze.txt' === file2bib.sh === id: cord-003045-r707jl16 author: Bhuvaneshwar, Krithika title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date: 2018-06-05 pages: extension: .txt txt: ./txt/cord-003045-r707jl16.txt cache: ./cache/cord-003045-r707jl16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003045-r707jl16.txt' === file2bib.sh === id: cord-002687-ql6zo8ka author: Li, Dan title: A potent human neutralizing antibody Fc-dependently reduces established HBV infections date: 2017-09-26 pages: extension: .txt txt: ./txt/cord-002687-ql6zo8ka.txt cache: ./cache/cord-002687-ql6zo8ka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-002687-ql6zo8ka.txt' === file2bib.sh === id: cord-003130-p2h8p5bm author: Lindqvist, Richard title: Tick-Borne Flaviviruses and the Type I Interferon Response date: 2018-06-21 pages: extension: .txt txt: ./txt/cord-003130-p2h8p5bm.txt cache: ./cache/cord-003130-p2h8p5bm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-003130-p2h8p5bm.txt' === file2bib.sh === id: cord-003122-a3f4l6iu author: Dou, Dan title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 pages: extension: .txt txt: ./txt/cord-003122-a3f4l6iu.txt cache: ./cache/cord-003122-a3f4l6iu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003122-a3f4l6iu.txt' === file2bib.sh === id: cord-004827-bnf3mvaf author: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 pages: extension: .txt txt: ./txt/cord-004827-bnf3mvaf.txt cache: ./cache/cord-004827-bnf3mvaf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004827-bnf3mvaf.txt' === file2bib.sh === id: cord-003284-hjx2d5rq author: Márquez-Jurado, Silvia title: An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo date: 2018-10-07 pages: extension: .txt txt: ./txt/cord-003284-hjx2d5rq.txt cache: ./cache/cord-003284-hjx2d5rq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003284-hjx2d5rq.txt' === file2bib.sh === id: cord-003505-qr6ukfti author: Tabraue-Chávez, Mavys title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date: 2019-03-06 pages: extension: .txt txt: ./txt/cord-003505-qr6ukfti.txt cache: ./cache/cord-003505-qr6ukfti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003505-qr6ukfti.txt' === file2bib.sh === id: cord-003305-ya0siivm author: Liu, Weichi title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase date: 2018-11-16 pages: extension: .txt txt: ./txt/cord-003305-ya0siivm.txt cache: ./cache/cord-003305-ya0siivm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003305-ya0siivm.txt' === file2bib.sh === id: cord-003792-v48xeqdz author: Izquierdo-Suzán, Mónica title: Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date: 2019-08-17 pages: extension: .txt txt: ./txt/cord-003792-v48xeqdz.txt cache: ./cache/cord-003792-v48xeqdz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003792-v48xeqdz.txt' === file2bib.sh === id: cord-003711-l3brhmzq author: Munnur, Deeksha title: Reversible ADP-ribosylation of RNA date: 2019-06-20 pages: extension: .txt txt: ./txt/cord-003711-l3brhmzq.txt cache: ./cache/cord-003711-l3brhmzq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003711-l3brhmzq.txt' === file2bib.sh === id: cord-004280-c470nlie author: Coleman, Kristen K. title: Airborne Influenza A Virus Exposure in an Elementary School date: 2020-02-05 pages: extension: .txt txt: ./txt/cord-004280-c470nlie.txt cache: ./cache/cord-004280-c470nlie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004280-c470nlie.txt' === file2bib.sh === id: cord-003482-f1uvohf0 author: Malmlov, Ashley title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 pages: extension: .txt txt: ./txt/cord-003482-f1uvohf0.txt cache: ./cache/cord-003482-f1uvohf0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003482-f1uvohf0.txt' === file2bib.sh === id: cord-004848-2cfphi88 author: Carter, M. J. title: Transcription of feline calicivirus RNA date: 1990 pages: extension: .txt txt: ./txt/cord-004848-2cfphi88.txt cache: ./cache/cord-004848-2cfphi88.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004848-2cfphi88.txt' === file2bib.sh === id: cord-003382-v3w1wi5c author: Rahmatpanah, Farah title: Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors date: 2018-10-02 pages: extension: .txt txt: ./txt/cord-003382-v3w1wi5c.txt cache: ./cache/cord-003382-v3w1wi5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-003382-v3w1wi5c.txt' === file2bib.sh === id: cord-004656-n4h295e5 author: Olson, Ann Louise title: Developmental Regulation of Angiotensinogen Gene Expression in Sheep date: 1990 pages: extension: .txt txt: ./txt/cord-004656-n4h295e5.txt cache: ./cache/cord-004656-n4h295e5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-004656-n4h295e5.txt' === file2bib.sh === id: cord-005010-xg2bv9gy author: Dayer, Mohammad Reza title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date: 2015-01-30 pages: extension: .txt txt: ./txt/cord-005010-xg2bv9gy.txt cache: ./cache/cord-005010-xg2bv9gy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005010-xg2bv9gy.txt' === file2bib.sh === id: cord-005281-wy0zk9p8 author: Blinov, V. M. title: Viral component of the human genome date: 2017-05-09 pages: extension: .txt txt: ./txt/cord-005281-wy0zk9p8.txt cache: ./cache/cord-005281-wy0zk9p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005281-wy0zk9p8.txt' === file2bib.sh === id: cord-006331-s2qf98lj author: Spiridonova, V. A. title: Molecular recognition elements: DNA/RNA-aptamers to proteins date: 2010-05-23 pages: extension: .txt txt: ./txt/cord-006331-s2qf98lj.txt cache: ./cache/cord-006331-s2qf98lj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006331-s2qf98lj.txt' === file2bib.sh === id: cord-003707-fbe47bgi author: Russo, Alice G title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date: 2019-06-18 pages: extension: .txt txt: ./txt/cord-003707-fbe47bgi.txt cache: ./cache/cord-003707-fbe47bgi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003707-fbe47bgi.txt' === file2bib.sh === id: cord-003596-6dg7i06i author: Xiong, Qingqing title: Biomedical applications of mRNA nanomedicine date: 2018-07-27 pages: extension: .txt txt: ./txt/cord-003596-6dg7i06i.txt cache: ./cache/cord-003596-6dg7i06i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003596-6dg7i06i.txt' === file2bib.sh === id: cord-007819-51h2jrsy author: Schommer, Susan K. title: Use of a PRRSV Infectious Clone to Evaluate in Vitro Quasispecies Evolution date: 2006 pages: extension: .txt txt: ./txt/cord-007819-51h2jrsy.txt cache: ./cache/cord-007819-51h2jrsy.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007819-51h2jrsy.txt' === file2bib.sh === id: cord-006049-sw1hki4r author: Keefe, Anthony D. title: Aptamers as therapeutics date: 2010 pages: extension: .txt txt: ./txt/cord-006049-sw1hki4r.txt cache: ./cache/cord-006049-sw1hki4r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006049-sw1hki4r.txt' === file2bib.sh === id: cord-006452-mmdk2xom author: Chen, Jing title: Nucleic Acid-Based Therapeutics for Pulmonary Diseases date: 2018-10-18 pages: extension: .txt txt: ./txt/cord-006452-mmdk2xom.txt cache: ./cache/cord-006452-mmdk2xom.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006452-mmdk2xom.txt' === file2bib.sh === id: cord-003898-y6zpvw84 author: Tan, Kai Sen title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date: 2019-08-27 pages: extension: .txt txt: ./txt/cord-003898-y6zpvw84.txt cache: ./cache/cord-003898-y6zpvw84.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003898-y6zpvw84.txt' === file2bib.sh === id: cord-003676-kr4o8hoc author: Tan, Chee Wah title: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans date: 2019-05-28 pages: extension: .txt txt: ./txt/cord-003676-kr4o8hoc.txt cache: ./cache/cord-003676-kr4o8hoc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-003676-kr4o8hoc.txt' === file2bib.sh === id: cord-004851-h9ppa064 author: Plagemann, P. G. W. title: Hepatitis C virus date: 1991 pages: extension: .txt txt: ./txt/cord-004851-h9ppa064.txt cache: ./cache/cord-004851-h9ppa064.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004851-h9ppa064.txt' === file2bib.sh === id: cord-005654-n9u2em10 author: Campbell, David A. title: Apparent discontinuous transcription of Trypanosoma brucei variant surface antigen genes date: 1984 pages: extension: .txt txt: ./txt/cord-005654-n9u2em10.txt cache: ./cache/cord-005654-n9u2em10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005654-n9u2em10.txt' === file2bib.sh === id: cord-007714-n3omlvfl author: Brown, J. W. S. title: The Role of the Plant Nucleolus in Pre-mRNA Processing date: 2008 pages: extension: .txt txt: ./txt/cord-007714-n3omlvfl.txt cache: ./cache/cord-007714-n3omlvfl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007714-n3omlvfl.txt' === file2bib.sh === id: cord-004507-ezuyjcxs author: Tomazatos, Alexandru title: Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix) date: 2020-02-21 pages: extension: .txt txt: ./txt/cord-004507-ezuyjcxs.txt cache: ./cache/cord-004507-ezuyjcxs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004507-ezuyjcxs.txt' === file2bib.sh === id: cord-007009-4wbvdg1r author: Takahashi, Toru title: The First Identification and Retrospective Study of Severe Fever With Thrombocytopenia Syndrome in Japan date: 2014-03-15 pages: extension: .txt txt: ./txt/cord-007009-4wbvdg1r.txt cache: ./cache/cord-007009-4wbvdg1r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-007009-4wbvdg1r.txt' === file2bib.sh === id: cord-007236-8hiymqyb author: Sun, Ji-Min title: Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway date: 2011-11-09 pages: extension: .txt txt: ./txt/cord-007236-8hiymqyb.txt cache: ./cache/cord-007236-8hiymqyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007236-8hiymqyb.txt' === file2bib.sh === id: cord-004274-cot05vx7 author: Jackson, Nicholas A. C. title: The promise of mRNA vaccines: a biotech and industrial perspective date: 2020-02-04 pages: extension: .txt txt: ./txt/cord-004274-cot05vx7.txt cache: ./cache/cord-004274-cot05vx7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-004274-cot05vx7.txt' === file2bib.sh === id: cord-003435-ke0az7nf author: Schlake, Thomas title: mRNA as novel technology for passive immunotherapy date: 2018-10-17 pages: extension: .txt txt: ./txt/cord-003435-ke0az7nf.txt cache: ./cache/cord-003435-ke0az7nf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003435-ke0az7nf.txt' === file2bib.sh === id: cord-007463-8g0zklzy author: Pocock, D.H. title: Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis date: 2002-11-13 pages: extension: .txt txt: ./txt/cord-007463-8g0zklzy.txt cache: ./cache/cord-007463-8g0zklzy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007463-8g0zklzy.txt' === file2bib.sh === id: cord-007041-rloey02j author: Harel, Noam title: Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations date: 2019-12-16 pages: extension: .txt txt: ./txt/cord-007041-rloey02j.txt cache: ./cache/cord-007041-rloey02j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007041-rloey02j.txt' === file2bib.sh === id: cord-004509-jkzqmkz6 author: Thirion, Laurence title: Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology date: 2020-01-30 pages: extension: .txt txt: ./txt/cord-004509-jkzqmkz6.txt cache: ./cache/cord-004509-jkzqmkz6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004509-jkzqmkz6.txt' === file2bib.sh === id: cord-006129-5rog0s98 author: Hemida, Maged Gomaa title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date: 2012-08-16 pages: extension: .txt txt: ./txt/cord-006129-5rog0s98.txt cache: ./cache/cord-006129-5rog0s98.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006129-5rog0s98.txt' === file2bib.sh === id: cord-004719-3stcx0dd author: Mushegian, A. R. title: Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date: 1993 pages: extension: .txt txt: ./txt/cord-004719-3stcx0dd.txt cache: ./cache/cord-004719-3stcx0dd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-004719-3stcx0dd.txt' === file2bib.sh === id: cord-003597-zj3w9ptj author: Altman, Matthew C. title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children date: 2019-04-08 pages: extension: .txt txt: ./txt/cord-003597-zj3w9ptj.txt cache: ./cache/cord-003597-zj3w9ptj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-003597-zj3w9ptj.txt' === file2bib.sh === id: cord-009662-ntjngiem author: Moulton, Jon D. title: Using Morpholinos to Control Gene Expression date: 2007-01-15 pages: extension: .txt txt: ./txt/cord-009662-ntjngiem.txt cache: ./cache/cord-009662-ntjngiem.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-009662-ntjngiem.txt' === file2bib.sh === id: cord-005865-7lohh5ty author: Pipper, Juergen title: Catching bird flu in a droplet date: 2007-09-23 pages: extension: .txt txt: ./txt/cord-005865-7lohh5ty.txt cache: ./cache/cord-005865-7lohh5ty.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005865-7lohh5ty.txt' === file2bib.sh === id: cord-007474-ckqghr3b author: Johnson, Michael E. title: Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes date: 2002-11-13 pages: extension: .txt txt: ./txt/cord-007474-ckqghr3b.txt cache: ./cache/cord-007474-ckqghr3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007474-ckqghr3b.txt' === file2bib.sh === id: cord-009376-a35a92gh author: Lovatt, Archie title: Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date: 2002-01-07 pages: extension: .txt txt: ./txt/cord-009376-a35a92gh.txt cache: ./cache/cord-009376-a35a92gh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-009376-a35a92gh.txt' === file2bib.sh === id: cord-007621-rapinodd author: Vidovic, Maria title: Induction and regulation of class II major histocompatibility complex mRNA expression in astrocytes by interferon-γ and tumor necrosis factor-α date: 2002-11-13 pages: extension: .txt txt: ./txt/cord-007621-rapinodd.txt cache: ./cache/cord-007621-rapinodd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007621-rapinodd.txt' === file2bib.sh === id: cord-007066-zn10rnrm author: Park, Noh Jin title: Characterization of RNA in Saliva date: 2006-06-01 pages: extension: .txt txt: ./txt/cord-007066-zn10rnrm.txt cache: ./cache/cord-007066-zn10rnrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007066-zn10rnrm.txt' === file2bib.sh === id: cord-005392-0pgcfk6b author: Sidoti, Francesca title: Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes date: 2011-07-05 pages: extension: .txt txt: ./txt/cord-005392-0pgcfk6b.txt cache: ./cache/cord-005392-0pgcfk6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005392-0pgcfk6b.txt' === file2bib.sh === id: cord-007382-5kb16qb7 author: Hartmann, G. title: Nucleic Acid Immunity date: 2016-12-15 pages: extension: .txt txt: ./txt/cord-007382-5kb16qb7.txt cache: ./cache/cord-007382-5kb16qb7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-007382-5kb16qb7.txt' === file2bib.sh === id: cord-006951-tj22dh5o author: Li, Siyu title: The effect of RNA stiffness on the self-assembly of virus particles date: 2018-01-31 pages: extension: .txt txt: ./txt/cord-006951-tj22dh5o.txt cache: ./cache/cord-006951-tj22dh5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006951-tj22dh5o.txt' === file2bib.sh === id: cord-005378-u2bbgn8k author: Yun, Sang-Im title: Overview: Replication of porcine reproductive and respiratory syndrome virus date: 2013-12-19 pages: extension: .txt txt: ./txt/cord-005378-u2bbgn8k.txt cache: ./cache/cord-005378-u2bbgn8k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005378-u2bbgn8k.txt' === file2bib.sh === id: cord-006960-9pho3hk6 author: Prakash, R. title: Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date: 2013-12-27 pages: extension: .txt txt: ./txt/cord-006960-9pho3hk6.txt cache: ./cache/cord-006960-9pho3hk6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006960-9pho3hk6.txt' === file2bib.sh === id: cord-005377-36io7zsm author: Sidoti, Francesca title: Alternative Molecular Tests for Virological Diagnosis date: 2012-04-09 pages: extension: .txt txt: ./txt/cord-005377-36io7zsm.txt cache: ./cache/cord-005377-36io7zsm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-005377-36io7zsm.txt' === file2bib.sh === id: cord-008556-oetrdm8g author: Kozak, Marilyn title: Regulation of Protein Synthesis in Virus-Infected Animal Cells date: 2008-03-01 pages: extension: .txt txt: ./txt/cord-008556-oetrdm8g.txt cache: ./cache/cord-008556-oetrdm8g.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-008556-oetrdm8g.txt' === file2bib.sh === id: cord-008541-0u2fatbg author: Bujarski, Jozef J. title: Molecular Studies of Genetic RNA–RNA Recombination in Brome Mosaic Virus date: 2008-02-28 pages: extension: .txt txt: ./txt/cord-008541-0u2fatbg.txt cache: ./cache/cord-008541-0u2fatbg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-008541-0u2fatbg.txt' === file2bib.sh === id: cord-007689-0vpp3xdl author: Schlee, M. title: Beyond Double-Stranded RNA-Type I IFN Induction by 3pRNA and Other Viral Nucleic Acids date: 2007 pages: extension: .txt txt: ./txt/cord-007689-0vpp3xdl.txt cache: ./cache/cord-007689-0vpp3xdl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007689-0vpp3xdl.txt' === file2bib.sh === id: cord-006826-vnmg0zid author: Rayaprolu, Vamseedhar title: Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles date: 2017-12-06 pages: extension: .txt txt: ./txt/cord-006826-vnmg0zid.txt cache: ./cache/cord-006826-vnmg0zid.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006826-vnmg0zid.txt' === file2bib.sh === id: cord-005060-n901y2d4 author: ZHANG, Feiyun title: Complete Nucleotide Sequence of Ryegrass Mottle Virus : A New Species of the Genus Sobemovirus date: 2001 pages: extension: .txt txt: ./txt/cord-005060-n901y2d4.txt cache: ./cache/cord-005060-n901y2d4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-005060-n901y2d4.txt' === file2bib.sh === id: cord-007181-qpahuqld author: YOGO, Yoshiaki title: Polyadenylate in the Virion RNA of Mouse Hepatitis Virus date: 1977-10-17 pages: extension: .txt txt: ./txt/cord-007181-qpahuqld.txt cache: ./cache/cord-007181-qpahuqld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-007181-qpahuqld.txt' === file2bib.sh === id: cord-010161-bcuec2fz author: Matson, David O. title: IV, 6. Calicivirus RNA recombination date: 2004-09-14 pages: extension: .txt txt: ./txt/cord-010161-bcuec2fz.txt cache: ./cache/cord-010161-bcuec2fz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010161-bcuec2fz.txt' === file2bib.sh === id: cord-009943-fzynh14x author: Ai‐Nakib, W. title: Detection of Human Rhinoviruses and Their Molecular Relationship Using cDNA Probes date: 2005-12-11 pages: extension: .txt txt: ./txt/cord-009943-fzynh14x.txt cache: ./cache/cord-009943-fzynh14x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-009943-fzynh14x.txt' === file2bib.sh === id: cord-011794-ejoufvvj author: Binder, Florian title: Isolation and characterization of new Puumala orthohantavirus strains from Germany date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-011794-ejoufvvj.txt cache: ./cache/cord-011794-ejoufvvj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-011794-ejoufvvj.txt' === file2bib.sh === id: cord-006935-wzz5t3sv author: Gorbalenya, Alexander E. title: Viral cysteine proteinases date: 1996 pages: extension: .txt txt: ./txt/cord-006935-wzz5t3sv.txt cache: ./cache/cord-006935-wzz5t3sv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-006935-wzz5t3sv.txt' === file2bib.sh === id: cord-010120-mqvm9zn4 author: Dinman, Jonathan D. title: Ribosomal frameshifting in yeast viruses date: 2004-01-29 pages: extension: .txt txt: ./txt/cord-010120-mqvm9zn4.txt cache: ./cache/cord-010120-mqvm9zn4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-010120-mqvm9zn4.txt' === file2bib.sh === id: cord-010273-0c56x9f5 author: Simmonds, Peter title: Virology of hepatitis C virus date: 2001-10-10 pages: extension: .txt txt: ./txt/cord-010273-0c56x9f5.txt cache: ./cache/cord-010273-0c56x9f5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010273-0c56x9f5.txt' === file2bib.sh === id: cord-008407-jbp8bxjz author: Derdeyn, Cynthia A. title: Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date: 1995-01-10 pages: extension: .txt txt: ./txt/cord-008407-jbp8bxjz.txt cache: ./cache/cord-008407-jbp8bxjz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-008407-jbp8bxjz.txt' === file2bib.sh === id: cord-012784-c74jr4ga author: Zhang, Le-le title: Identification of nagilactone E as a protein synthesis inhibitor with anticancer activity date: 2020-02-11 pages: extension: .txt txt: ./txt/cord-012784-c74jr4ga.txt cache: ./cache/cord-012784-c74jr4ga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-012784-c74jr4ga.txt' === file2bib.sh === id: cord-008575-bbpmlo3c author: Lawton, Jeffrey A title: Mechanism of genome transcription in segmented dsRNA viruses date: 2004-01-07 pages: extension: .txt txt: ./txt/cord-008575-bbpmlo3c.txt cache: ./cache/cord-008575-bbpmlo3c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-008575-bbpmlo3c.txt' === file2bib.sh === id: cord-011803-9122f1zc author: Zhao, Yang title: The RNA quality control pathway nonsense-mediated mRNA decay targets cellular and viral RNAs to restrict KSHV date: 2020-07-03 pages: extension: .txt txt: ./txt/cord-011803-9122f1zc.txt cache: ./cache/cord-011803-9122f1zc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-011803-9122f1zc.txt' === file2bib.sh === id: cord-010374-z9ygudv6 author: Siddell, S.G. title: Coronaviridae1 date: 2008-07-24 pages: extension: .txt txt: ./txt/cord-010374-z9ygudv6.txt cache: ./cache/cord-010374-z9ygudv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010374-z9ygudv6.txt' === file2bib.sh === id: cord-006068-w3if1hns author: Marshak-Rothstein, Ann title: Toll-like receptors in systemic autoimmune disease date: 2006 pages: extension: .txt txt: ./txt/cord-006068-w3if1hns.txt cache: ./cache/cord-006068-w3if1hns.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-006068-w3if1hns.txt' === file2bib.sh === id: cord-008613-tysyq6o4 author: Thomas, Sheila M. title: Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5 date: 1988-09-09 pages: extension: .txt txt: ./txt/cord-008613-tysyq6o4.txt cache: ./cache/cord-008613-tysyq6o4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-008613-tysyq6o4.txt' === file2bib.sh === id: cord-010045-eqzs01au author: Britton, P. title: Sequence of the nucleoprotein gene from a virulent British field isolate of transmissible gastroenteritis virus and its expression in Saccharomyces cerevisiae date: 2006-10-27 pages: extension: .txt txt: ./txt/cord-010045-eqzs01au.txt cache: ./cache/cord-010045-eqzs01au.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-010045-eqzs01au.txt' === file2bib.sh === id: cord-012032-zolowuhj author: Yu, Peifa title: 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705 date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-012032-zolowuhj.txt cache: ./cache/cord-012032-zolowuhj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-012032-zolowuhj.txt' === file2bib.sh === id: cord-008426-ktn8c0zx author: Othman, Yasmin title: Nucleotide sequence of the bean strain of southern bean mosaic virus() date: 1995-01-10 pages: extension: .txt txt: ./txt/cord-008426-ktn8c0zx.txt cache: ./cache/cord-008426-ktn8c0zx.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-008426-ktn8c0zx.txt' === file2bib.sh === id: cord-007208-wnkjdg6y author: Li, Sheng-Hsiang title: Demonstration of a Glycoprotein Derived From the Ceacam10 Gene in Mouse Seminal Vesicle Secretions(1) date: 2005-09-01 pages: extension: .txt txt: ./txt/cord-007208-wnkjdg6y.txt cache: ./cache/cord-007208-wnkjdg6y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007208-wnkjdg6y.txt' === file2bib.sh === id: cord-008588-4eu9v5d3 author: Chastain, Michael title: Structural Elements in RNA date: 2008-02-29 pages: extension: .txt txt: ./txt/cord-008588-4eu9v5d3.txt cache: ./cache/cord-008588-4eu9v5d3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-008588-4eu9v5d3.txt' === file2bib.sh === id: cord-010762-c01wgg4v author: Wu, Jiqin title: A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-010762-c01wgg4v.txt cache: ./cache/cord-010762-c01wgg4v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010762-c01wgg4v.txt' === file2bib.sh === id: cord-014397-7b88ycv8 author: Gavora, JS title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date: 1996-12-15 pages: extension: .txt txt: ./txt/cord-014397-7b88ycv8.txt cache: ./cache/cord-014397-7b88ycv8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-014397-7b88ycv8.txt' === file2bib.sh === id: cord-010977-fwz7chzf author: Myserlis, Pavlos title: Translational Genomics in Neurocritical Care: a Review date: 2020-02-20 pages: extension: .txt txt: ./txt/cord-010977-fwz7chzf.txt cache: ./cache/cord-010977-fwz7chzf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010977-fwz7chzf.txt' === file2bib.sh === id: cord-012484-c9ajmbw2 author: Wahlund, Martina title: The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia date: 2020-07-26 pages: extension: .txt txt: ./txt/cord-012484-c9ajmbw2.txt cache: ./cache/cord-012484-c9ajmbw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012484-c9ajmbw2.txt' === file2bib.sh === id: cord-007920-mh3tesdc author: Dhar, Arun K. title: Genomic Organization, Biology, and Diagnosis of Taura Syndrome Virus and Yellowhead Virus of Penaeid Shrimp date: 2004-11-11 pages: extension: .txt txt: ./txt/cord-007920-mh3tesdc.txt cache: ./cache/cord-007920-mh3tesdc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-007920-mh3tesdc.txt' === file2bib.sh === id: cord-013243-1hj5clsw author: Brewer, Gary title: Editorial for “Methods to characterize virus small RNAs and RNA structures” date: 2020-10-16 pages: extension: .txt txt: ./txt/cord-013243-1hj5clsw.txt cache: ./cache/cord-013243-1hj5clsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-013243-1hj5clsw.txt' === file2bib.sh === id: cord-010188-884d196k author: Schlesinger, Sondra title: Alphaviruses — vectors for the expression of heterologous genes date: 2004-08-26 pages: extension: .txt txt: ./txt/cord-010188-884d196k.txt cache: ./cache/cord-010188-884d196k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-010188-884d196k.txt' === file2bib.sh === id: cord-010680-lc1onm53 author: Patel, Ami title: In Vivo Delivery of Nucleic Acid-Encoded Monoclonal Antibodies date: 2020-03-10 pages: extension: .txt txt: ./txt/cord-010680-lc1onm53.txt cache: ./cache/cord-010680-lc1onm53.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-010680-lc1onm53.txt' === file2bib.sh === id: cord-012420-llh22iq2 author: Stott, Robert J. title: Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-012420-llh22iq2.txt cache: ./cache/cord-012420-llh22iq2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-012420-llh22iq2.txt' === file2bib.sh === id: cord-013176-6ckuya1w author: Ninfali, Paolino title: Antiviral Properties of Flavonoids and Delivery Strategies date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-013176-6ckuya1w.txt cache: ./cache/cord-013176-6ckuya1w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-013176-6ckuya1w.txt' === file2bib.sh === id: cord-012909-o6t2srim author: Chaudhari, Jayeshbhai title: Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-012909-o6t2srim.txt cache: ./cache/cord-012909-o6t2srim.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012909-o6t2srim.txt' === file2bib.sh === id: cord-013177-whd0znan author: Han, Zhenzhi title: The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-013177-whd0znan.txt cache: ./cache/cord-013177-whd0znan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-013177-whd0znan.txt' === file2bib.sh === id: cord-013280-kczj24se author: Yang, Bo title: Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-013280-kczj24se.txt cache: ./cache/cord-013280-kczj24se.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013280-kczj24se.txt' === file2bib.sh === id: cord-013171-wgn529rc author: Zhong, Yi title: STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-013171-wgn529rc.txt cache: ./cache/cord-013171-wgn529rc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013171-wgn529rc.txt' === file2bib.sh === id: cord-013412-gj443yei author: Lebedeva, Natalya Sh. title: The Application of Porphyrins and Their Analogues for Inactivation of Viruses date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-013412-gj443yei.txt cache: ./cache/cord-013412-gj443yei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013412-gj443yei.txt' === file2bib.sh === id: cord-015642-p46abodr author: Backofen, Rolf title: Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures date: 2013 pages: extension: .txt txt: ./txt/cord-015642-p46abodr.txt cache: ./cache/cord-015642-p46abodr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015642-p46abodr.txt' === file2bib.sh === id: cord-013854-wadpugbj author: Fratter, Carl title: EMQN best practice guidelines for genetic testing in dystrophinopathies date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-013854-wadpugbj.txt cache: ./cache/cord-013854-wadpugbj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-013854-wadpugbj.txt' === file2bib.sh === id: cord-012552-porty653 author: Tan, Kun title: The role of the NMD factor UPF3B in olfactory sensory neurons date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-012552-porty653.txt cache: ./cache/cord-012552-porty653.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-012552-porty653.txt' === file2bib.sh === id: cord-015376-z739ifu5 author: Savarino, Andrea title: Potential therapies for coronaviruses date: 2006-08-31 pages: extension: .txt txt: ./txt/cord-015376-z739ifu5.txt cache: ./cache/cord-015376-z739ifu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015376-z739ifu5.txt' === file2bib.sh === id: cord-005147-mvoq9vln author: nan title: Autorenregister date: 2017-02-23 pages: extension: .txt txt: ./txt/cord-005147-mvoq9vln.txt cache: ./cache/cord-005147-mvoq9vln.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-005147-mvoq9vln.txt' === file2bib.sh === id: cord-015673-rz74sh32 author: Lamers, Anne E. title: RNA Interference Mechanisms and Therapeutic Applications date: 2006 pages: extension: .txt txt: ./txt/cord-015673-rz74sh32.txt cache: ./cache/cord-015673-rz74sh32.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015673-rz74sh32.txt' === file2bib.sh === id: cord-015527-ph576eji author: Mostajo, Nelly F title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-015527-ph576eji.txt cache: ./cache/cord-015527-ph576eji.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015527-ph576eji.txt' === file2bib.sh === id: cord-014908-jys1y0k9 author: Yadav, Rakesh title: Trends and Perspectives of Biosensors for Food and Environmental Virology date: 2010-05-19 pages: extension: .txt txt: ./txt/cord-014908-jys1y0k9.txt cache: ./cache/cord-014908-jys1y0k9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-014908-jys1y0k9.txt' === file2bib.sh === id: cord-016108-jlono0x7 author: Marthaler, Douglas title: Next-Generation Sequencing for Porcine Coronaviruses date: 2015-09-10 pages: extension: .txt txt: ./txt/cord-016108-jlono0x7.txt cache: ./cache/cord-016108-jlono0x7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016108-jlono0x7.txt' === file2bib.sh === id: cord-016144-280kwlev author: Maan, Sushila title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date: 2018-04-26 pages: extension: .txt txt: ./txt/cord-016144-280kwlev.txt cache: ./cache/cord-016144-280kwlev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016144-280kwlev.txt' === file2bib.sh === id: cord-004879-pgyzluwp author: nan title: Programmed cell death date: 1994 pages: extension: .txt txt: ./txt/cord-004879-pgyzluwp.txt cache: ./cache/cord-004879-pgyzluwp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-004879-pgyzluwp.txt' === file2bib.sh === id: cord-014685-ihh30q6f author: nan title: Posters P788 - P999 date: 2005-09-21 pages: extension: .txt txt: ./txt/cord-014685-ihh30q6f.txt cache: ./cache/cord-014685-ihh30q6f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-014685-ihh30q6f.txt' === file2bib.sh === id: cord-013784-zhgjmt2j author: Tang, Min title: Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-013784-zhgjmt2j.txt cache: ./cache/cord-013784-zhgjmt2j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-013784-zhgjmt2j.txt' === file2bib.sh === id: cord-016209-6p9btua0 author: Merl, S. title: Targeting Viral Heart Disease by RNA Interference date: 2008 pages: extension: .txt txt: ./txt/cord-016209-6p9btua0.txt cache: ./cache/cord-016209-6p9btua0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016209-6p9btua0.txt' === file2bib.sh === id: cord-016808-gy8d8285 author: Agol, Vadim I. title: The Origin and Evolution of Viruses date: 2008 pages: extension: .txt txt: ./txt/cord-016808-gy8d8285.txt cache: ./cache/cord-016808-gy8d8285.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016808-gy8d8285.txt' === file2bib.sh === id: cord-015237-8cxfa8wf author: nan title: Structure Watch date: 2005 pages: extension: .txt txt: ./txt/cord-015237-8cxfa8wf.txt cache: ./cache/cord-015237-8cxfa8wf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-015237-8cxfa8wf.txt' === file2bib.sh === id: cord-016261-jms7hrmp author: Liu, Chunmei title: Profiling and Searching for RNA Pseudoknot Structures in Genomes date: 2005 pages: extension: .txt txt: ./txt/cord-016261-jms7hrmp.txt cache: ./cache/cord-016261-jms7hrmp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016261-jms7hrmp.txt' === file2bib.sh === id: cord-016343-wc3i54fc author: Frese, Michael title: Interferon-Induced Effector Proteins and Hepatitis C Virus Replication date: 2008 pages: extension: .txt txt: ./txt/cord-016343-wc3i54fc.txt cache: ./cache/cord-016343-wc3i54fc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016343-wc3i54fc.txt' === file2bib.sh === id: cord-015606-h9bbvpzd author: Highfield, P.E. title: Translation of infectious bronchitis virus RNA date: 2006-03-27 pages: extension: .txt txt: ./txt/cord-015606-h9bbvpzd.txt cache: ./cache/cord-015606-h9bbvpzd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015606-h9bbvpzd.txt' === file2bib.sh === id: cord-016179-4i1n9j4x author: Chen, Yi-Ning title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues date: 2015-09-10 pages: extension: .txt txt: ./txt/cord-016179-4i1n9j4x.txt cache: ./cache/cord-016179-4i1n9j4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016179-4i1n9j4x.txt' === file2bib.sh === id: cord-000083-3p81yr4n author: nan title: Poster Exhibition date: 2009-01-31 pages: extension: .txt txt: ./txt/cord-000083-3p81yr4n.txt cache: ./cache/cord-000083-3p81yr4n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-000083-3p81yr4n.txt' === file2bib.sh === id: cord-016309-6mw8okmt author: Bule, Mohammed title: Antivirals: Past, Present and Future date: 2019-06-06 pages: extension: .txt txt: ./txt/cord-016309-6mw8okmt.txt cache: ./cache/cord-016309-6mw8okmt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016309-6mw8okmt.txt' === file2bib.sh === id: cord-015871-1tuf4zxi author: Ergonul, Onder title: Treatment of Crimean-Congo Hemorrhagic Fever date: 2007 pages: extension: .txt txt: ./txt/cord-015871-1tuf4zxi.txt cache: ./cache/cord-015871-1tuf4zxi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-015871-1tuf4zxi.txt' === file2bib.sh === id: cord-017181-ywz6w2po author: Maus, Carsten title: Component-Based Modelling of RNA Structure Folding date: 2008 pages: extension: .txt txt: ./txt/cord-017181-ywz6w2po.txt cache: ./cache/cord-017181-ywz6w2po.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017181-ywz6w2po.txt' === file2bib.sh === id: cord-017968-17d37a2z author: Lewinski, Martin title: Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana date: 2018-08-30 pages: extension: .txt txt: ./txt/cord-017968-17d37a2z.txt cache: ./cache/cord-017968-17d37a2z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017968-17d37a2z.txt' === file2bib.sh === id: cord-001835-0s7ok4uw author: nan title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 pages: extension: .txt txt: ./txt/cord-001835-0s7ok4uw.txt cache: ./cache/cord-001835-0s7ok4uw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-001835-0s7ok4uw.txt' === file2bib.sh === id: cord-014462-11ggaqf1 author: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 pages: extension: .txt txt: ./txt/cord-014462-11ggaqf1.txt cache: ./cache/cord-014462-11ggaqf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-014462-11ggaqf1.txt' === file2bib.sh === id: cord-016095-jop2rx61 author: Vignais, Pierre V. title: Challenges for Experimentation on Living Beings at the Dawn of the 21(st) Century date: 2010-06-08 pages: extension: .txt txt: ./txt/cord-016095-jop2rx61.txt cache: ./cache/cord-016095-jop2rx61.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016095-jop2rx61.txt' === file2bib.sh === id: cord-015850-ef6svn8f author: Saitou, Naruya title: Eukaryote Genomes date: 2013-08-22 pages: extension: .txt txt: ./txt/cord-015850-ef6svn8f.txt cache: ./cache/cord-015850-ef6svn8f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-015850-ef6svn8f.txt' === file2bib.sh === id: cord-018804-wj35q88f author: Lázaro, Ester title: Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date: 2007 pages: extension: .txt txt: ./txt/cord-018804-wj35q88f.txt cache: ./cache/cord-018804-wj35q88f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018804-wj35q88f.txt' === file2bib.sh === id: cord-017297-q3qtgrfc author: Rajagopal, Vaishnavi title: Viral Helicases date: 2008-11-01 pages: extension: .txt txt: ./txt/cord-017297-q3qtgrfc.txt cache: ./cache/cord-017297-q3qtgrfc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-017297-q3qtgrfc.txt' === file2bib.sh === id: cord-016293-pyb00pt5 author: Newell-McGloughlin, Martina title: The flowering of the age of Biotechnology 1990–2000 date: 2006 pages: extension: .txt txt: ./txt/cord-016293-pyb00pt5.txt cache: ./cache/cord-016293-pyb00pt5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016293-pyb00pt5.txt' === file2bib.sh === id: cord-018944-du42ho11 author: Shin, Jeong Hwan title: Nucleic Acid Extraction and Enrichment date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-018944-du42ho11.txt cache: ./cache/cord-018944-du42ho11.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018944-du42ho11.txt' === file2bib.sh === id: cord-004584-bcw90f5b author: nan title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date: 2011-08-06 pages: extension: .txt txt: ./txt/cord-004584-bcw90f5b.txt cache: ./cache/cord-004584-bcw90f5b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-004584-bcw90f5b.txt' === file2bib.sh === id: cord-015933-x5cq4k4x author: Verbrugh, H.A. title: 1 Micro-organismen, de mens en het ontstaan van infectieziekten: algemene principes date: 2011 pages: extension: .txt txt: ./txt/cord-015933-x5cq4k4x.txt cache: ./cache/cord-015933-x5cq4k4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-015933-x5cq4k4x.txt' === file2bib.sh === id: cord-016499-5iqpl23p author: Mackay, Ian M. title: Rhinoviruses date: 2014-02-27 pages: extension: .txt txt: ./txt/cord-016499-5iqpl23p.txt cache: ./cache/cord-016499-5iqpl23p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016499-5iqpl23p.txt' === file2bib.sh === id: cord-021115-2fkghukw author: Guo, Yun title: Molecular dynamics simulation of RNA pseudoknot unfolding pathway date: 2013-03-12 pages: extension: .txt txt: ./txt/cord-021115-2fkghukw.txt cache: ./cache/cord-021115-2fkghukw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-021115-2fkghukw.txt' === file2bib.sh === id: cord-018164-h5k1zsyg author: Taylor, Milton W. title: What Is a Virus? date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-018164-h5k1zsyg.txt cache: ./cache/cord-018164-h5k1zsyg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018164-h5k1zsyg.txt' === file2bib.sh === id: cord-017167-8cdbcrh7 author: Ahola, Tero title: Functions of Chikungunya Virus Nonstructural Proteins date: 2016-12-03 pages: extension: .txt txt: ./txt/cord-017167-8cdbcrh7.txt cache: ./cache/cord-017167-8cdbcrh7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017167-8cdbcrh7.txt' === file2bib.sh === id: cord-016419-v1f6dx3e author: Gupta, Varsha title: Production of Recombinant Pharmaceutical Proteins date: 2016-10-23 pages: extension: .txt txt: ./txt/cord-016419-v1f6dx3e.txt cache: ./cache/cord-016419-v1f6dx3e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016419-v1f6dx3e.txt' === file2bib.sh === id: cord-016755-ye37z5h9 author: Li, Jiandong title: The Discovery Process of SFTS in China date: 2019-10-12 pages: extension: .txt txt: ./txt/cord-016755-ye37z5h9.txt cache: ./cache/cord-016755-ye37z5h9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016755-ye37z5h9.txt' === file2bib.sh === id: cord-020969-lh2ergpm author: STRAUSS, JAMES H. title: Gene Therapy date: 2012-07-27 pages: extension: .txt txt: ./txt/cord-020969-lh2ergpm.txt cache: ./cache/cord-020969-lh2ergpm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-020969-lh2ergpm.txt' === file2bib.sh === id: cord-016313-n4ewq0pt author: Baranyi, Lajos title: Advances in Lentiviral Vector-based Cell Therapy with Mesenchymal Stem Cells date: 2012-09-27 pages: extension: .txt txt: ./txt/cord-016313-n4ewq0pt.txt cache: ./cache/cord-016313-n4ewq0pt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016313-n4ewq0pt.txt' === file2bib.sh === id: cord-018437-yjvwa1ot author: Mitchell, Michael title: Taxonomy date: 2013-08-26 pages: extension: .txt txt: ./txt/cord-018437-yjvwa1ot.txt cache: ./cache/cord-018437-yjvwa1ot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-018437-yjvwa1ot.txt' === file2bib.sh === id: cord-019076-4qu9j953 author: Ulferts, Rachel title: Expression and Functions of SARS Coronavirus Replicative Proteins date: 2009-07-22 pages: extension: .txt txt: ./txt/cord-019076-4qu9j953.txt cache: ./cache/cord-019076-4qu9j953.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-019076-4qu9j953.txt' === file2bib.sh === id: cord-016652-x8t3lf1x author: Matthews, David title: Viruses and the Nucleolus date: 2011-05-23 pages: extension: .txt txt: ./txt/cord-016652-x8t3lf1x.txt cache: ./cache/cord-016652-x8t3lf1x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-016652-x8t3lf1x.txt' === file2bib.sh === id: cord-021481-tvs1pnib author: Singh, Gatikrushna title: Cellular RNA Helicases Support Early and Late Events in Retroviral Replication date: 2018-08-17 pages: extension: .txt txt: ./txt/cord-021481-tvs1pnib.txt cache: ./cache/cord-021481-tvs1pnib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-021481-tvs1pnib.txt' === file2bib.sh === id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 pages: extension: .txt txt: ./txt/cord-022084-hap7flng.txt cache: ./cache/cord-022084-hap7flng.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022084-hap7flng.txt' === file2bib.sh === id: cord-017732-1pwa6zsk author: Miller, W. Allen title: Ribosomal Frameshifting in Decoding Plant Viral RNAs date: 2009-07-21 pages: extension: .txt txt: ./txt/cord-017732-1pwa6zsk.txt cache: ./cache/cord-017732-1pwa6zsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-017732-1pwa6zsk.txt' === file2bib.sh === id: cord-016538-4og05fuo author: Dolja, V. V. title: Biotechnology Applications of Grapevine Viruses date: 2017-03-30 pages: extension: .txt txt: ./txt/cord-016538-4og05fuo.txt cache: ./cache/cord-016538-4og05fuo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-016538-4og05fuo.txt' === file2bib.sh === id: cord-018724-ss8x2g3b author: Stobbe, Anthony title: Plant Virus Diversity and Evolution date: 2016-06-22 pages: extension: .txt txt: ./txt/cord-018724-ss8x2g3b.txt cache: ./cache/cord-018724-ss8x2g3b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018724-ss8x2g3b.txt' === file2bib.sh === id: cord-022348-w7z97wir author: Sola, Monica title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-022348-w7z97wir.txt cache: ./cache/cord-022348-w7z97wir.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-022348-w7z97wir.txt' === file2bib.sh === id: cord-018798-yzxy9ogf author: Jain, Pradeep Kumar title: RNAi for Resistance Against Biotic Stresses in Crop Plants date: 2018-07-10 pages: extension: .txt txt: ./txt/cord-018798-yzxy9ogf.txt cache: ./cache/cord-018798-yzxy9ogf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-018798-yzxy9ogf.txt' === file2bib.sh === id: cord-023865-6rafp3x3 author: Surjit, Milan title: The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date: 2009-07-22 pages: extension: .txt txt: ./txt/cord-023865-6rafp3x3.txt cache: ./cache/cord-023865-6rafp3x3.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023865-6rafp3x3.txt' === file2bib.sh === id: cord-019051-gtruu1op author: Weber, Olaf title: The role of viruses in the etiology and pathogenesis of common cold date: 2009-11-10 pages: extension: .txt txt: ./txt/cord-019051-gtruu1op.txt cache: ./cache/cord-019051-gtruu1op.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-019051-gtruu1op.txt' === file2bib.sh === id: cord-016796-g4kqqpy1 author: Bramhachari, Pallaval Veera title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 pages: extension: .txt txt: ./txt/cord-016796-g4kqqpy1.txt cache: ./cache/cord-016796-g4kqqpy1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-016796-g4kqqpy1.txt' === file2bib.sh === id: cord-023724-5at0rhqk author: Cann, Alan J. title: Infection date: 2015-07-24 pages: extension: .txt txt: ./txt/cord-023724-5at0rhqk.txt cache: ./cache/cord-023724-5at0rhqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-023724-5at0rhqk.txt' === file2bib.sh === id: cord-018017-c8myq6bi author: Iversen, Patrick L. title: The Threat from Viruses date: 2018-09-30 pages: extension: .txt txt: ./txt/cord-018017-c8myq6bi.txt cache: ./cache/cord-018017-c8myq6bi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018017-c8myq6bi.txt' === file2bib.sh === id: cord-025181-eg108wcd author: Zheng, Zhihang title: Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date: 2020-05-25 pages: extension: .txt txt: ./txt/cord-025181-eg108wcd.txt cache: ./cache/cord-025181-eg108wcd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-025181-eg108wcd.txt' === file2bib.sh === id: cord-021568-tdfn6up8 author: STRAUSS, JAMES H. title: Subviral Agents date: 2012-07-27 pages: extension: .txt txt: ./txt/cord-021568-tdfn6up8.txt cache: ./cache/cord-021568-tdfn6up8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-021568-tdfn6up8.txt' === file2bib.sh === id: cord-022336-zqnczjpp author: Robertson, Hugh D. title: Virus Origins: Conjoined RNA Genomes as Precursors to DNA Genomes date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-022336-zqnczjpp.txt cache: ./cache/cord-022336-zqnczjpp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-022336-zqnczjpp.txt' === file2bib.sh === id: cord-020235-stcrozdw author: nan title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 pages: extension: .txt txt: ./txt/cord-020235-stcrozdw.txt cache: ./cache/cord-020235-stcrozdw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-020235-stcrozdw.txt' === file2bib.sh === id: cord-022262-ck2lhojz author: Gromeier, Matthias title: Genetics, Pathogenesis and Evolution of Picornaviruses date: 2007-09-02 pages: extension: .txt txt: ./txt/cord-022262-ck2lhojz.txt cache: ./cache/cord-022262-ck2lhojz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-022262-ck2lhojz.txt' === file2bib.sh === id: cord-023770-ymxapsv6 author: nan title: Closteroviridae date: 2011-11-23 pages: extension: .txt txt: ./txt/cord-023770-ymxapsv6.txt cache: ./cache/cord-023770-ymxapsv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023770-ymxapsv6.txt' === file2bib.sh === id: cord-023120-jcgf2401 author: nan title: Animal virus genetics date: 2004-06-18 pages: extension: .txt txt: ./txt/cord-023120-jcgf2401.txt cache: ./cache/cord-023120-jcgf2401.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-023120-jcgf2401.txt' === file2bib.sh === id: cord-023726-2fduzqyb author: STRAUSS, JAMES H. title: The Structure of Viruses date: 2012-07-27 pages: extension: .txt txt: ./txt/cord-023726-2fduzqyb.txt cache: ./cache/cord-023726-2fduzqyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023726-2fduzqyb.txt' === file2bib.sh === id: cord-030028-s6sxi8uj author: Rubio, Luis title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-030028-s6sxi8uj.txt cache: ./cache/cord-030028-s6sxi8uj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-030028-s6sxi8uj.txt' === file2bib.sh === id: cord-027975-77544sed author: Tars, Kaspars title: ssRNA Phages: Life Cycle, Structure and Applications date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-027975-77544sed.txt cache: ./cache/cord-027975-77544sed.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027975-77544sed.txt' === file2bib.sh === id: cord-033692-txfuuu7d author: Lim, Byeonghwi title: Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-033692-txfuuu7d.txt cache: ./cache/cord-033692-txfuuu7d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-033692-txfuuu7d.txt' === file2bib.sh === id: cord-035067-ic843wr9 author: de Almeida, Joana Ferro Machado title: COVID-19 and the gastrointestinal tract: what do we already know? date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-035067-ic843wr9.txt cache: ./cache/cord-035067-ic843wr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035067-ic843wr9.txt' === file2bib.sh === id: cord-027865-p1epjn51 author: Sterchi, Diane L. title: Molecular pathology date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-027865-p1epjn51.txt cache: ./cache/cord-027865-p1epjn51.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-027865-p1epjn51.txt' === file2bib.sh === id: cord-017764-h1w9gbxk author: Meanwell, Nicholas A. title: The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date: 2018-06-08 pages: extension: .txt txt: ./txt/cord-017764-h1w9gbxk.txt cache: ./cache/cord-017764-h1w9gbxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-017764-h1w9gbxk.txt' === file2bib.sh === id: cord-024282-t5wl0bih author: Mao, Shunfu title: BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance date: 2020-02-01 pages: extension: .txt txt: ./txt/cord-024282-t5wl0bih.txt cache: ./cache/cord-024282-t5wl0bih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-024282-t5wl0bih.txt' === file2bib.sh === id: cord-023705-3q9yr6np author: FENNER, FRANK title: Viral Replication date: 2014-06-27 pages: extension: .txt txt: ./txt/cord-023705-3q9yr6np.txt cache: ./cache/cord-023705-3q9yr6np.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-023705-3q9yr6np.txt' === file2bib.sh === id: cord-018564-3igg5s57 author: Schomburg, Dietmar title: RNA helicase 3.6.4.13 date: 2013 pages: extension: .txt txt: ./txt/cord-018564-3igg5s57.txt cache: ./cache/cord-018564-3igg5s57.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-018564-3igg5s57.txt' === file2bib.sh === id: cord-023766-qx0qdjmt author: Nirwan, Sonam title: Rhinovirus RNA Polymerase: Structure, Function, and Inhibitors date: 2018-11-02 pages: extension: .txt txt: ./txt/cord-023766-qx0qdjmt.txt cache: ./cache/cord-023766-qx0qdjmt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-023766-qx0qdjmt.txt' === file2bib.sh === id: cord-034648-vfqth54o author: nan title: WITHDRAWN date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-034648-vfqth54o.txt cache: ./cache/cord-034648-vfqth54o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-034648-vfqth54o.txt' === file2bib.sh === id: cord-023608-w2g7v7g1 author: nan title: ISAR News date: 2017-10-20 pages: extension: .txt txt: ./txt/cord-023608-w2g7v7g1.txt cache: ./cache/cord-023608-w2g7v7g1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-023608-w2g7v7g1.txt' === file2bib.sh === id: cord-048204-6lvn10f4 author: Shi, Stephanie T. title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus date: 2000-09-01 pages: extension: .txt txt: ./txt/cord-048204-6lvn10f4.txt cache: ./cache/cord-048204-6lvn10f4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-048204-6lvn10f4.txt' === file2bib.sh === id: cord-022290-p0l1kv6n author: Bergmann, Ernst M. title: Proteolytic Enzymes of the Viruses of the Family Picornaviridae date: 2007-05-09 pages: extension: .txt txt: ./txt/cord-022290-p0l1kv6n.txt cache: ./cache/cord-022290-p0l1kv6n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022290-p0l1kv6n.txt' === file2bib.sh === id: cord-048471-7jszm1nd author: Salim, Omar title: Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus date: 2008-05-14 pages: extension: .txt txt: ./txt/cord-048471-7jszm1nd.txt cache: ./cache/cord-048471-7jszm1nd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048471-7jszm1nd.txt' === file2bib.sh === id: cord-048327-xgwbl8em author: Henderson, Clark M. title: Antisense-induced ribosomal frameshifting date: 2006-08-18 pages: extension: .txt txt: ./txt/cord-048327-xgwbl8em.txt cache: ./cache/cord-048327-xgwbl8em.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-048327-xgwbl8em.txt' === file2bib.sh === id: cord-022196-1tionxun author: FENNER, FRANK title: The Nature and Classification of Animal Viruses date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-022196-1tionxun.txt cache: ./cache/cord-022196-1tionxun.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-022196-1tionxun.txt' === file2bib.sh === id: cord-022128-r8el8nqm author: Domingo, Esteban title: Molecular basis of genetic variation of viruses: error-prone replication date: 2019-11-08 pages: extension: .txt txt: ./txt/cord-022128-r8el8nqm.txt cache: ./cache/cord-022128-r8el8nqm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-022128-r8el8nqm.txt' === file2bib.sh === id: cord-048198-zjufx4fo author: Pasternak, Alexander O. title: Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis date: 2001-12-17 pages: extension: .txt txt: ./txt/cord-048198-zjufx4fo.txt cache: ./cache/cord-048198-zjufx4fo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-048198-zjufx4fo.txt' === file2bib.sh === id: cord-102547-nxut8ov1 author: Grädel, C. title: Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-102547-nxut8ov1.txt cache: ./cache/cord-102547-nxut8ov1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102547-nxut8ov1.txt' === file2bib.sh === id: cord-023017-k6edtg58 author: nan title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 pages: extension: .txt txt: ./txt/cord-023017-k6edtg58.txt cache: ./cache/cord-023017-k6edtg58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-023017-k6edtg58.txt' === file2bib.sh === id: cord-102892-nt1zoktv author: Sweeney, Blake A. title: R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-102892-nt1zoktv.txt cache: ./cache/cord-102892-nt1zoktv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102892-nt1zoktv.txt' === file2bib.sh === id: cord-048222-1pq6dkl5 author: Imbeaud, Sandrine title: Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces date: 2005-03-30 pages: extension: .txt txt: ./txt/cord-048222-1pq6dkl5.txt cache: ./cache/cord-048222-1pq6dkl5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-048222-1pq6dkl5.txt' === file2bib.sh === id: cord-102967-dx0tg077 author: Mahajan, Lakshmi S. title: Mapping RNA dependent RNA polymerase activity and immune gene expression using PRO-seq date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-102967-dx0tg077.txt cache: ./cache/cord-102967-dx0tg077.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-102967-dx0tg077.txt' === file2bib.sh === id: cord-023208-w99gc5nx author: nan title: Poster Presentation Abstracts date: 2006-09-01 pages: extension: .txt txt: ./txt/cord-023208-w99gc5nx.txt cache: ./cache/cord-023208-w99gc5nx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-023208-w99gc5nx.txt' === file2bib.sh === id: cord-030654-8yxa1r1c author: Zhang, Changhui title: Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-030654-8yxa1r1c.txt cache: ./cache/cord-030654-8yxa1r1c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-030654-8yxa1r1c.txt' === file2bib.sh === id: cord-102931-vxkbctiz author: Mao, Kai title: Induction of RNA interference by C. elegans mitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme date: 2020-06-06 pages: extension: .txt txt: ./txt/cord-102931-vxkbctiz.txt cache: ./cache/cord-102931-vxkbctiz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-102931-vxkbctiz.txt' === file2bib.sh === id: cord-035110-5lkzhjfh author: Zhu, Le title: Isolation and characterization of exosomes for cancer research date: 2020-11-10 pages: extension: .txt txt: ./txt/cord-035110-5lkzhjfh.txt cache: ./cache/cord-035110-5lkzhjfh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-035110-5lkzhjfh.txt' === file2bib.sh === id: cord-048485-b8xb1f12 author: Hulst, Marcel title: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date: 2008-06-04 pages: extension: .txt txt: ./txt/cord-048485-b8xb1f12.txt cache: ./cache/cord-048485-b8xb1f12.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048485-b8xb1f12.txt' === file2bib.sh === id: cord-102898-eyyd7ent author: Rizvi, Vaseef A. title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-102898-eyyd7ent.txt cache: ./cache/cord-102898-eyyd7ent.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-102898-eyyd7ent.txt' === file2bib.sh === id: cord-001521-l36f1gp7 author: nan title: Oral and Poster Manuscripts date: 2011-04-08 pages: extension: .txt txt: ./txt/cord-001521-l36f1gp7.txt cache: ./cache/cord-001521-l36f1gp7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-001521-l36f1gp7.txt' === file2bib.sh === id: cord-020010-q58x6xb0 author: nan title: 19th ICAR Abstracts: date: 2006-03-13 pages: extension: .txt txt: ./txt/cord-020010-q58x6xb0.txt cache: ./cache/cord-020010-q58x6xb0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-020010-q58x6xb0.txt' === file2bib.sh === id: cord-102336-ex3zlq38 author: De Wijngaert, Brent title: Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-102336-ex3zlq38.txt cache: ./cache/cord-102336-ex3zlq38.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102336-ex3zlq38.txt' === file2bib.sh === id: cord-048322-5eqdrd52 author: Aigner, Achim title: Delivery Systems for the Direct Application of siRNAs to Induce RNA Interference (RNAi) In Vivo date: 2006-05-18 pages: extension: .txt txt: ./txt/cord-048322-5eqdrd52.txt cache: ./cache/cord-048322-5eqdrd52.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-048322-5eqdrd52.txt' === file2bib.sh === id: cord-102934-7e2mqooe author: Dogra, N. title: exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-102934-7e2mqooe.txt cache: ./cache/cord-102934-7e2mqooe.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-102934-7e2mqooe.txt' === file2bib.sh === id: cord-103511-31njndob author: Broggi, Achille title: Type III interferons disrupt the lung epithelial barrier upon viral recognition date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-103511-31njndob.txt cache: ./cache/cord-103511-31njndob.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103511-31njndob.txt' === file2bib.sh === id: cord-102766-n6mpdhyu author: Alam, Md. Nafis Ul title: Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-102766-n6mpdhyu.txt cache: ./cache/cord-102766-n6mpdhyu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102766-n6mpdhyu.txt' === file2bib.sh === id: cord-048478-ftlb5b95 author: Mroczek, Seweryn title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast date: 2008-04-01 pages: extension: .txt txt: ./txt/cord-048478-ftlb5b95.txt cache: ./cache/cord-048478-ftlb5b95.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-048478-ftlb5b95.txt' === file2bib.sh === id: cord-104162-fe51v2pt author: Zhang, Chiyu title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-104162-fe51v2pt.txt cache: ./cache/cord-104162-fe51v2pt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-104162-fe51v2pt.txt' === file2bib.sh === id: cord-103015-3dxwbmd2 author: Shengjuler, Djoshkun title: The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain date: 2017-08-04 pages: extension: .txt txt: ./txt/cord-103015-3dxwbmd2.txt cache: ./cache/cord-103015-3dxwbmd2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103015-3dxwbmd2.txt' === file2bib.sh === id: cord-029779-9b6zs1sb author: Casey, Sophie title: Temporally Altered miRNA Expression in a Piglet Model of Hypoxic Ischemic Brain Injury date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-029779-9b6zs1sb.txt cache: ./cache/cord-029779-9b6zs1sb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-029779-9b6zs1sb.txt' === file2bib.sh === id: cord-025948-6dsx7pey author: Maitra, Arindam title: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-025948-6dsx7pey.txt cache: ./cache/cord-025948-6dsx7pey.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-025948-6dsx7pey.txt' === file2bib.sh === id: cord-252268-o63ep08b author: Carolan, Louise A. title: TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date: 2014-09-01 pages: extension: .txt txt: ./txt/cord-252268-o63ep08b.txt cache: ./cache/cord-252268-o63ep08b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252268-o63ep08b.txt' === file2bib.sh === id: cord-102412-cnlvyey4 author: Tekman, Mehmet title: A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-102412-cnlvyey4.txt cache: ./cache/cord-102412-cnlvyey4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-102412-cnlvyey4.txt' === file2bib.sh === id: cord-146406-85usg3uh author: Morelli, Marco J. title: Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing date: 2011-01-27 pages: extension: .txt txt: ./txt/cord-146406-85usg3uh.txt cache: ./cache/cord-146406-85usg3uh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-146406-85usg3uh.txt' === file2bib.sh === id: cord-026641-eemp6b5j author: Kabiljo, Julijan title: From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date: 2020-06-11 pages: extension: .txt txt: ./txt/cord-026641-eemp6b5j.txt cache: ./cache/cord-026641-eemp6b5j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-026641-eemp6b5j.txt' === file2bib.sh === id: cord-103914-ppgx7mci author: Maughan, Elizabeth F. title: Cell-intrinsic differences between human airway epithelial cells from children and adults date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-103914-ppgx7mci.txt cache: ./cache/cord-103914-ppgx7mci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103914-ppgx7mci.txt' === file2bib.sh === id: cord-243806-26n22jbx author: Vandelli, Andrea title: Structural analysis of SARS-CoV-2 and prediction of the human interactome date: 2020-03-30 pages: extension: .txt txt: ./txt/cord-243806-26n22jbx.txt cache: ./cache/cord-243806-26n22jbx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-243806-26n22jbx.txt' === file2bib.sh === id: cord-103807-x4hrwhkz author: Prokop, J. W. title: Viral Induced Genetics Revealed by Multi-Dimensional Precision Medicine Transcriptional Workflow date: 2020-04-06 pages: extension: .txt txt: ./txt/cord-103807-x4hrwhkz.txt cache: ./cache/cord-103807-x4hrwhkz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103807-x4hrwhkz.txt' === file2bib.sh === id: cord-102866-40s64455 author: Bhadra, Sanchita title: One enzyme reverse transcription qPCR using Taq DNA polymerase date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-102866-40s64455.txt cache: ./cache/cord-102866-40s64455.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-102866-40s64455.txt' === file2bib.sh === id: cord-103853-ar09nzmw author: Wayment-Steele, Hannah K. title: RNA secondary structure packages ranked and improved by high-throughput experiments date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-103853-ar09nzmw.txt cache: ./cache/cord-103853-ar09nzmw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103853-ar09nzmw.txt' === file2bib.sh === id: cord-254192-86ksgl5t author: Li, Liang title: IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia date: 2019-10-17 pages: extension: .txt txt: ./txt/cord-254192-86ksgl5t.txt cache: ./cache/cord-254192-86ksgl5t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254192-86ksgl5t.txt' === file2bib.sh === id: cord-253282-zwl0safn author: Plant, Ewan P. title: Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date: 2013-01-18 pages: extension: .txt txt: ./txt/cord-253282-zwl0safn.txt cache: ./cache/cord-253282-zwl0safn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253282-zwl0safn.txt' === file2bib.sh === id: cord-253115-ekgdsv4f author: Mehta, Meenu title: Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases date: 2019-08-01 pages: extension: .txt txt: ./txt/cord-253115-ekgdsv4f.txt cache: ./cache/cord-253115-ekgdsv4f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253115-ekgdsv4f.txt' === file2bib.sh === id: cord-254250-l0v602x9 author: Hooper, Chantelle title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-254250-l0v602x9.txt cache: ./cache/cord-254250-l0v602x9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254250-l0v602x9.txt' === file2bib.sh === id: cord-253024-b393ea2u author: Fu, Kaisong title: Evidence for variable rates of recombination in the MHV genome date: 1992-07-31 pages: extension: .txt txt: ./txt/cord-253024-b393ea2u.txt cache: ./cache/cord-253024-b393ea2u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-253024-b393ea2u.txt' === file2bib.sh === id: cord-103638-n5kpvsvg author: Nguyen, Long T. title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-103638-n5kpvsvg.txt cache: ./cache/cord-103638-n5kpvsvg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103638-n5kpvsvg.txt' === file2bib.sh === id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 pages: extension: .txt txt: ./txt/cord-103735-nil1vv6h.txt cache: ./cache/cord-103735-nil1vv6h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103735-nil1vv6h.txt' === file2bib.sh === id: cord-253616-7jyui5ca author: Lai, Zheng-Zong title: Harringtonine Inhibits Zika Virus Infection through Multiple Mechanisms date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-253616-7jyui5ca.txt cache: ./cache/cord-253616-7jyui5ca.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253616-7jyui5ca.txt' === file2bib.sh === id: cord-103377-j1mmx7k7 author: Karasik, Agnes title: Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-103377-j1mmx7k7.txt cache: ./cache/cord-103377-j1mmx7k7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103377-j1mmx7k7.txt' === file2bib.sh === id: cord-103899-6tqm99g1 author: Mirzaei, Rasoul title: The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date: 2020-11-13 pages: extension: .txt txt: ./txt/cord-103899-6tqm99g1.txt cache: ./cache/cord-103899-6tqm99g1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103899-6tqm99g1.txt' === file2bib.sh === id: cord-102968-mhawyect author: Desirò, Daniel title: SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs date: 2018-09-23 pages: extension: .txt txt: ./txt/cord-102968-mhawyect.txt cache: ./cache/cord-102968-mhawyect.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-102968-mhawyect.txt' === file2bib.sh === id: cord-253539-0kcujnfa author: Agranovsky, A. A. title: Principles of Molecular Organization, Expression, and Evolution of Closteroviruses: Over The Barriers date: 1996-12-31 pages: extension: .txt txt: ./txt/cord-253539-0kcujnfa.txt cache: ./cache/cord-253539-0kcujnfa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253539-0kcujnfa.txt' === file2bib.sh === id: cord-122092-gdyt02er author: Fatehi, Farzad title: Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-122092-gdyt02er.txt cache: ./cache/cord-122092-gdyt02er.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-122092-gdyt02er.txt' === file2bib.sh === id: cord-253862-jl1zhg13 author: Khalaf, Khalil title: SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-253862-jl1zhg13.txt cache: ./cache/cord-253862-jl1zhg13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-253862-jl1zhg13.txt' === file2bib.sh === id: cord-103823-3rchp9yy author: Taufer, Michela title: RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology date: 2008-11-30 pages: extension: .txt txt: ./txt/cord-103823-3rchp9yy.txt cache: ./cache/cord-103823-3rchp9yy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-103823-3rchp9yy.txt' === file2bib.sh === id: cord-103163-0rreoh4o author: Smith, Sydni Caet title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date: 2020-10-22 pages: extension: .txt txt: ./txt/cord-103163-0rreoh4o.txt cache: ./cache/cord-103163-0rreoh4o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103163-0rreoh4o.txt' === file2bib.sh === id: cord-004534-jqm1hxps author: nan title: Abstract date: 2009-06-09 pages: extension: .txt txt: ./txt/cord-004534-jqm1hxps.txt cache: ./cache/cord-004534-jqm1hxps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 11 resourceName b'cord-004534-jqm1hxps.txt' === file2bib.sh === id: cord-103787-qhftb6d7 author: Garcia, Elizabeth P. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 pages: extension: .txt txt: ./txt/cord-103787-qhftb6d7.txt cache: ./cache/cord-103787-qhftb6d7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103787-qhftb6d7.txt' === file2bib.sh === id: cord-103430-x6zzuu7v author: Contu, Lara title: Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-103430-x6zzuu7v.txt cache: ./cache/cord-103430-x6zzuu7v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-103430-x6zzuu7v.txt' === file2bib.sh === id: cord-103925-i73ymrov author: Hill, Chris H. title: Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-103925-i73ymrov.txt cache: ./cache/cord-103925-i73ymrov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-103925-i73ymrov.txt' === file2bib.sh === id: cord-252485-cxi3cr15 author: Yoshida, Asuka title: IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date: 2015-08-04 pages: extension: .txt txt: ./txt/cord-252485-cxi3cr15.txt cache: ./cache/cord-252485-cxi3cr15.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252485-cxi3cr15.txt' === file2bib.sh === id: cord-184744-oyc2djxk author: Parvez, Md Sorwer Alam title: Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-184744-oyc2djxk.txt cache: ./cache/cord-184744-oyc2djxk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-184744-oyc2djxk.txt' === file2bib.sh === id: cord-254210-3mi2aop5 author: Haddad, Rodrigo title: Silencing of HTLV-1 gag and env genes by small interfering RNAs in HEK 293 cells date: 2011-01-26 pages: extension: .txt txt: ./txt/cord-254210-3mi2aop5.txt cache: ./cache/cord-254210-3mi2aop5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254210-3mi2aop5.txt' === file2bib.sh === id: cord-252871-qfrpuy3t author: Nasir, Arshan title: Investigating the Concept and Origin of Viruses date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-252871-qfrpuy3t.txt cache: ./cache/cord-252871-qfrpuy3t.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252871-qfrpuy3t.txt' === file2bib.sh === id: cord-103739-mmkrwj8t author: Snijder, Eric J. title: A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-103739-mmkrwj8t.txt cache: ./cache/cord-103739-mmkrwj8t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-103739-mmkrwj8t.txt' === file2bib.sh === id: cord-007890-bie1veti author: nan title: ECC-4 Abstracts date: 2002-04-16 pages: extension: .txt txt: ./txt/cord-007890-bie1veti.txt cache: ./cache/cord-007890-bie1veti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 10 resourceName b'cord-007890-bie1veti.txt' === file2bib.sh === id: cord-252466-usrpodjx author: Yun, Nadezhda E. title: Pathogenesis of Lassa Fever date: 2012-10-09 pages: extension: .txt txt: ./txt/cord-252466-usrpodjx.txt cache: ./cache/cord-252466-usrpodjx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-252466-usrpodjx.txt' === file2bib.sh === id: cord-104186-fyw1xfgi author: Cui, Y title: Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. date: 1996-10-15 pages: extension: .txt txt: ./txt/cord-104186-fyw1xfgi.txt cache: ./cache/cord-104186-fyw1xfgi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-104186-fyw1xfgi.txt' === file2bib.sh === id: cord-254747-vox5xsgd author: Deng, Xufang title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 pages: extension: .txt txt: ./txt/cord-254747-vox5xsgd.txt cache: ./cache/cord-254747-vox5xsgd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254747-vox5xsgd.txt' === file2bib.sh === id: cord-253480-qchrw337 author: Pu, Jieying title: Antiviral activity of Carbenoxolone disodium against dengue virus infection date: 2016-12-23 pages: extension: .txt txt: ./txt/cord-253480-qchrw337.txt cache: ./cache/cord-253480-qchrw337.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253480-qchrw337.txt' === file2bib.sh === id: cord-252433-0e9lonq4 author: Cullen, Bryan R. title: Viral RNAs: Lessons from the Enemy date: 2009-02-20 pages: extension: .txt txt: ./txt/cord-252433-0e9lonq4.txt cache: ./cache/cord-252433-0e9lonq4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-252433-0e9lonq4.txt' === file2bib.sh === id: cord-022889-lv6fy6e6 author: Dávalos, Alberto title: Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date: 2019-08-07 pages: extension: .txt txt: ./txt/cord-022889-lv6fy6e6.txt cache: ./cache/cord-022889-lv6fy6e6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-022889-lv6fy6e6.txt' === file2bib.sh === id: cord-254592-wa5il5go author: Brierley, Liam title: Tissue tropism and transmission ecology predict virulence of human RNA viruses date: 2019-11-26 pages: extension: .txt txt: ./txt/cord-254592-wa5il5go.txt cache: ./cache/cord-254592-wa5il5go.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254592-wa5il5go.txt' === file2bib.sh === id: cord-253501-hkxlq3os author: Anang, Saumya title: Recent Advances Towards the Development of a Potent Antiviral Against the Hepatitis E Virus date: 2018-06-28 pages: extension: .txt txt: ./txt/cord-253501-hkxlq3os.txt cache: ./cache/cord-253501-hkxlq3os.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253501-hkxlq3os.txt' === file2bib.sh === id: cord-253307-4bpdfgau author: Sanz, Miguel A. title: Inhibition of host protein synthesis by Sindbis virus: correlation with viral RNA replication and release of nuclear proteins to the cytoplasm date: 2014-11-19 pages: extension: .txt txt: ./txt/cord-253307-4bpdfgau.txt cache: ./cache/cord-253307-4bpdfgau.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-253307-4bpdfgau.txt' === file2bib.sh === id: cord-254916-y1rw9q11 author: Ogando, Natacha S. title: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date: 2020-06-22 pages: extension: .txt txt: ./txt/cord-254916-y1rw9q11.txt cache: ./cache/cord-254916-y1rw9q11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-254916-y1rw9q11.txt' === file2bib.sh === id: cord-254070-v9gabn1a author: Bordería, Antonio V. title: Fidelity Variants and RNA Quasispecies date: 2015-10-25 pages: extension: .txt txt: ./txt/cord-254070-v9gabn1a.txt cache: ./cache/cord-254070-v9gabn1a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254070-v9gabn1a.txt' === file2bib.sh === id: cord-254713-ghcwfcx2 author: Razanajatovo, Norosoa H title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date: 2015-03-12 pages: extension: .txt txt: ./txt/cord-254713-ghcwfcx2.txt cache: ./cache/cord-254713-ghcwfcx2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254713-ghcwfcx2.txt' === file2bib.sh === id: cord-254100-u6x5zd4i author: Taliansky, M.E. title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date: 2010-10-15 pages: extension: .txt txt: ./txt/cord-254100-u6x5zd4i.txt cache: ./cache/cord-254100-u6x5zd4i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-254100-u6x5zd4i.txt' === file2bib.sh === id: cord-254903-g9ropt9c author: Xu, Xiaofeng title: Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data date: 2020-09-16 pages: extension: .txt txt: ./txt/cord-254903-g9ropt9c.txt cache: ./cache/cord-254903-g9ropt9c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254903-g9ropt9c.txt' === file2bib.sh === id: cord-253466-7gpije5d author: Netherton, Christopher title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date: 2007-08-31 pages: extension: .txt txt: ./txt/cord-253466-7gpije5d.txt cache: ./cache/cord-253466-7gpije5d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-253466-7gpije5d.txt' === file2bib.sh === id: cord-254596-wsmnlnlk author: Grädel, Carole title: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-254596-wsmnlnlk.txt cache: ./cache/cord-254596-wsmnlnlk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254596-wsmnlnlk.txt' === file2bib.sh === id: cord-254963-cnvxlv6h author: Paskey, Adrian C. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 pages: extension: .txt txt: ./txt/cord-254963-cnvxlv6h.txt cache: ./cache/cord-254963-cnvxlv6h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254963-cnvxlv6h.txt' === file2bib.sh === id: cord-255252-md0avnqg author: Tang, Julian W. title: Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date: 2007-07-02 pages: extension: .txt txt: ./txt/cord-255252-md0avnqg.txt cache: ./cache/cord-255252-md0avnqg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255252-md0avnqg.txt' === file2bib.sh === id: cord-255607-dbexsugq author: Wu, Yang title: Porcine Epidemic Diarrhea Virus nsp15 Antagonizes Interferon Signaling by RNA Degradation of TBK1 and IRF3 date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-255607-dbexsugq.txt cache: ./cache/cord-255607-dbexsugq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255607-dbexsugq.txt' === file2bib.sh === id: cord-255576-738khdwv author: Van Duyne, Rachel title: Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery date: 2012-07-10 pages: extension: .txt txt: ./txt/cord-255576-738khdwv.txt cache: ./cache/cord-255576-738khdwv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255576-738khdwv.txt' === file2bib.sh === id: cord-254895-ym0jsir5 author: Eisenächer, Katharina title: The role of viral nucleic acid recognition in dendritic cells for innate and adaptive antiviral immunity date: 2008-01-18 pages: extension: .txt txt: ./txt/cord-254895-ym0jsir5.txt cache: ./cache/cord-254895-ym0jsir5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-254895-ym0jsir5.txt' === file2bib.sh === id: cord-255090-2gpsu1y4 author: Lv, Ke title: Transient inhibition of foot-and-mouth disease virus replication by siRNAs silencing VP1 protein coding region date: 2009-06-30 pages: extension: .txt txt: ./txt/cord-255090-2gpsu1y4.txt cache: ./cache/cord-255090-2gpsu1y4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-255090-2gpsu1y4.txt' === file2bib.sh === id: cord-255619-5h3l6nh6 author: Kuo, Shu-Ming title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date: 2013-03-23 pages: extension: .txt txt: ./txt/cord-255619-5h3l6nh6.txt cache: ./cache/cord-255619-5h3l6nh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255619-5h3l6nh6.txt' === file2bib.sh === id: cord-255499-31xmue1g author: Bujarski, J.J. title: Recombination date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-255499-31xmue1g.txt cache: ./cache/cord-255499-31xmue1g.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255499-31xmue1g.txt' === file2bib.sh === id: cord-256036-gd53s4dv author: Sandmann, Lisa title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 pages: extension: .txt txt: ./txt/cord-256036-gd53s4dv.txt cache: ./cache/cord-256036-gd53s4dv.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-256036-gd53s4dv.txt' === file2bib.sh === id: cord-255545-nycdhdsd author: Schoenike, Barry title: Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date: 1999-03-10 pages: extension: .txt txt: ./txt/cord-255545-nycdhdsd.txt cache: ./cache/cord-255545-nycdhdsd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255545-nycdhdsd.txt' === file2bib.sh === id: cord-255495-xnoppq3y author: Elrashdy, Fatma title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-255495-xnoppq3y.txt cache: ./cache/cord-255495-xnoppq3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255495-xnoppq3y.txt' === file2bib.sh === id: cord-255738-r8zfdsix author: Ge, Feng title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 pages: extension: .txt txt: ./txt/cord-255738-r8zfdsix.txt cache: ./cache/cord-255738-r8zfdsix.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255738-r8zfdsix.txt' === file2bib.sh === id: cord-255795-su7f5ges author: Yelin, Idan title: Evaluation of COVID-19 RT-qPCR test in multi-sample pools date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-255795-su7f5ges.txt cache: ./cache/cord-255795-su7f5ges.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-255795-su7f5ges.txt' === file2bib.sh === id: cord-256325-q70rky3r author: Stewart, Cameron R. title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date: 2017-07-04 pages: extension: .txt txt: ./txt/cord-256325-q70rky3r.txt cache: ./cache/cord-256325-q70rky3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256325-q70rky3r.txt' === file2bib.sh === id: cord-256370-cz88t29n author: Jansen van Vuren, Petrus title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date: 2016-02-29 pages: extension: .txt txt: ./txt/cord-256370-cz88t29n.txt cache: ./cache/cord-256370-cz88t29n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256370-cz88t29n.txt' === file2bib.sh === id: cord-255883-mz6nyisw author: Asif, Muhammad title: COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date: 2020-08-14 pages: extension: .txt txt: ./txt/cord-255883-mz6nyisw.txt cache: ./cache/cord-255883-mz6nyisw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-255883-mz6nyisw.txt' === file2bib.sh === id: cord-256510-orr2roxz author: de Castro, Isabel Fernández title: Virus factories: biogenesis and structural design date: 2012-10-04 pages: extension: .txt txt: ./txt/cord-256510-orr2roxz.txt cache: ./cache/cord-256510-orr2roxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256510-orr2roxz.txt' === file2bib.sh === id: cord-256561-fnh2do4z author: Barik, Sailen title: Therapy of Respiratory Viral Infections with Intranasal siRNAs date: 2014-09-23 pages: extension: .txt txt: ./txt/cord-256561-fnh2do4z.txt cache: ./cache/cord-256561-fnh2do4z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-256561-fnh2do4z.txt' === file2bib.sh === id: cord-256508-ce59ovan author: Asselah, Tarik title: COVID-19: discovery, diagnostics and drug development date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-256508-ce59ovan.txt cache: ./cache/cord-256508-ce59ovan.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256508-ce59ovan.txt' === file2bib.sh === id: cord-256940-yuja99jg author: Wei, Bo title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-256940-yuja99jg.txt cache: ./cache/cord-256940-yuja99jg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256940-yuja99jg.txt' === file2bib.sh === id: cord-256918-mauzesor author: Domingo, Esteban title: Quasispecies and the implications for virus persistence and escape date: 1998-07-15 pages: extension: .txt txt: ./txt/cord-256918-mauzesor.txt cache: ./cache/cord-256918-mauzesor.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-256918-mauzesor.txt' === file2bib.sh === id: cord-257456-15bm9psj author: Arumugam, Arunkumar title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-257456-15bm9psj.txt cache: ./cache/cord-257456-15bm9psj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257456-15bm9psj.txt' === file2bib.sh === id: cord-256615-gvq8uyfk author: Rosenberg, Ronald title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans date: 2014-11-22 pages: extension: .txt txt: ./txt/cord-256615-gvq8uyfk.txt cache: ./cache/cord-256615-gvq8uyfk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256615-gvq8uyfk.txt' === file2bib.sh === id: cord-257652-ndt8f812 author: Zhang, Yong-Zhen title: The diversity, evolution and origins of vertebrate RNA viruses date: 2018-08-13 pages: extension: .txt txt: ./txt/cord-257652-ndt8f812.txt cache: ./cache/cord-257652-ndt8f812.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257652-ndt8f812.txt' === file2bib.sh === id: cord-257693-rnchfjbe author: Wang, Yeming title: Factors Associated With Prolonged Viral Shedding in Patients With Avian Influenza A(H7N9) Virus Infection date: 2018-04-10 pages: extension: .txt txt: ./txt/cord-257693-rnchfjbe.txt cache: ./cache/cord-257693-rnchfjbe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257693-rnchfjbe.txt' === file2bib.sh === id: cord-257569-36qx1sy9 author: Hanada, Kousuke title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date: 2004-06-17 pages: extension: .txt txt: ./txt/cord-257569-36qx1sy9.txt cache: ./cache/cord-257569-36qx1sy9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-257569-36qx1sy9.txt' === file2bib.sh === id: cord-258035-2tk7maqk author: DeFilippis, Victor title: Functional genomics in virology and antiviral drug discovery date: 2003-10-31 pages: extension: .txt txt: ./txt/cord-258035-2tk7maqk.txt cache: ./cache/cord-258035-2tk7maqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258035-2tk7maqk.txt' === file2bib.sh === id: cord-259152-pwvcwlh8 author: Ji, Wei title: Cross‐species transmission of the newly identified coronavirus 2019‐nCoV date: 2020-02-19 pages: extension: .txt txt: ./txt/cord-259152-pwvcwlh8.txt cache: ./cache/cord-259152-pwvcwlh8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-259152-pwvcwlh8.txt' === file2bib.sh === id: cord-258547-47cyyetb author: Asasi, Keramat title: Changes of several acute phase factors in broiler chickens in response to infectious bronchitis virus infection date: 2013-08-01 pages: extension: .txt txt: ./txt/cord-258547-47cyyetb.txt cache: ./cache/cord-258547-47cyyetb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258547-47cyyetb.txt' === file2bib.sh === id: cord-258696-01wj76es author: Decaro, Nicola title: Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia date: 2008-04-30 pages: extension: .txt txt: ./txt/cord-258696-01wj76es.txt cache: ./cache/cord-258696-01wj76es.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258696-01wj76es.txt' === file2bib.sh === id: cord-258286-lodjcj8c author: Zhang, Xuming title: Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date: 1997-07-07 pages: extension: .txt txt: ./txt/cord-258286-lodjcj8c.txt cache: ./cache/cord-258286-lodjcj8c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-258286-lodjcj8c.txt' === file2bib.sh === id: cord-258172-p54j4zzo author: Barker, Harlan title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-258172-p54j4zzo.txt cache: ./cache/cord-258172-p54j4zzo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258172-p54j4zzo.txt' === file2bib.sh === id: cord-259916-gr6v098c author: Wang, Hongliang title: Mechanisms of Cellular Membrane Reorganization to Support Hepatitis C Virus Replication date: 2016-05-20 pages: extension: .txt txt: ./txt/cord-259916-gr6v098c.txt cache: ./cache/cord-259916-gr6v098c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259916-gr6v098c.txt' === file2bib.sh === id: cord-259500-ndjbrtrv author: Satyanarayana, Tatineni title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date: 2003-09-01 pages: extension: .txt txt: ./txt/cord-259500-ndjbrtrv.txt cache: ./cache/cord-259500-ndjbrtrv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259500-ndjbrtrv.txt' === file2bib.sh === id: cord-259710-qrht9tq3 author: Burimuah, Vitus title: Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-259710-qrht9tq3.txt cache: ./cache/cord-259710-qrht9tq3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259710-qrht9tq3.txt' === file2bib.sh === id: cord-258678-0atfsivf author: Liu, Hong Yan title: A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date: 2013-11-07 pages: extension: .txt txt: ./txt/cord-258678-0atfsivf.txt cache: ./cache/cord-258678-0atfsivf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258678-0atfsivf.txt' === file2bib.sh === id: cord-256444-grw5s2pf author: Lai, Michael M.C. title: The Molecular Biology of Coronaviruses date: 1997-12-31 pages: extension: .txt txt: ./txt/cord-256444-grw5s2pf.txt cache: ./cache/cord-256444-grw5s2pf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-256444-grw5s2pf.txt' === file2bib.sh === id: cord-259246-azt5sr9w author: Peng, Qi title: Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-259246-azt5sr9w.txt cache: ./cache/cord-259246-azt5sr9w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259246-azt5sr9w.txt' === file2bib.sh === id: cord-259593-shrd1s7r author: Qin, Zhao-ling title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date: 2007-06-27 pages: extension: .txt txt: ./txt/cord-259593-shrd1s7r.txt cache: ./cache/cord-259593-shrd1s7r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259593-shrd1s7r.txt' === file2bib.sh === id: cord-258595-bk35vxlr author: Westhaus, Sandra title: Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-258595-bk35vxlr.txt cache: ./cache/cord-258595-bk35vxlr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-258595-bk35vxlr.txt' === file2bib.sh === id: cord-261735-03hvi4el author: Rodrigues, R. title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date: 2011-06-14 pages: extension: .txt txt: ./txt/cord-261735-03hvi4el.txt cache: ./cache/cord-261735-03hvi4el.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261735-03hvi4el.txt' === file2bib.sh === id: cord-259927-xh9cw9ao author: Papadopoulos, Nikolaos G. title: Promising approaches for the treatment and prevention of viral respiratory illnesses date: 2017-07-21 pages: extension: .txt txt: ./txt/cord-259927-xh9cw9ao.txt cache: ./cache/cord-259927-xh9cw9ao.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259927-xh9cw9ao.txt' === file2bib.sh === id: cord-259311-ccx61owl author: Kapitula, D. S. title: Performance & Quality Evaluation of Marketed COVID-19 RNA Detection Kits date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-259311-ccx61owl.txt cache: ./cache/cord-259311-ccx61owl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259311-ccx61owl.txt' === file2bib.sh === id: cord-261532-q923xxn2 author: Chen, Huihui title: The essential adaptors of innate immune signaling date: 2012-09-21 pages: extension: .txt txt: ./txt/cord-261532-q923xxn2.txt cache: ./cache/cord-261532-q923xxn2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261532-q923xxn2.txt' === file2bib.sh === id: cord-261417-4pf5nsw2 author: Harwig, Alex title: The Battle of RNA Synthesis: Virus versus Host date: 2017-10-21 pages: extension: .txt txt: ./txt/cord-261417-4pf5nsw2.txt cache: ./cache/cord-261417-4pf5nsw2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261417-4pf5nsw2.txt' === file2bib.sh === id: cord-259603-bh198xgl author: Snijder, E.J. title: The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date: 2016-09-14 pages: extension: .txt txt: ./txt/cord-259603-bh198xgl.txt cache: ./cache/cord-259603-bh198xgl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259603-bh198xgl.txt' === file2bib.sh === id: cord-262592-0rdiosxd author: Cuevas, José M. title: Human norovirus hyper-mutation revealed by ultra-deep sequencing date: 2016-04-17 pages: extension: .txt txt: ./txt/cord-262592-0rdiosxd.txt cache: ./cache/cord-262592-0rdiosxd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262592-0rdiosxd.txt' === file2bib.sh === id: cord-259233-smmhhroe author: de Armas‐Rillo, Laura title: Membrane dynamics associated with viral infection date: 2016-01-28 pages: extension: .txt txt: ./txt/cord-259233-smmhhroe.txt cache: ./cache/cord-259233-smmhhroe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-259233-smmhhroe.txt' === file2bib.sh === id: cord-261160-g92zhv19 author: Rowland, Raymond R.R title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 pages: extension: .txt txt: ./txt/cord-261160-g92zhv19.txt cache: ./cache/cord-261160-g92zhv19.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261160-g92zhv19.txt' === file2bib.sh === id: cord-260225-bc1hr0fr author: Sirpilla, Olivia title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-260225-bc1hr0fr.txt cache: ./cache/cord-260225-bc1hr0fr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260225-bc1hr0fr.txt' === file2bib.sh === id: cord-260042-cs0wp99n author: Khan, Samiullah title: Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date: 2019-04-01 pages: extension: .txt txt: ./txt/cord-260042-cs0wp99n.txt cache: ./cache/cord-260042-cs0wp99n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260042-cs0wp99n.txt' === file2bib.sh === id: cord-260168-rb7j94dh author: Gu, Jiang title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 pages: extension: .txt txt: ./txt/cord-260168-rb7j94dh.txt cache: ./cache/cord-260168-rb7j94dh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260168-rb7j94dh.txt' === file2bib.sh === id: cord-262318-qpztmdnw author: Guo, Jingxu title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors date: 2020-07-16 pages: extension: .txt txt: ./txt/cord-262318-qpztmdnw.txt cache: ./cache/cord-262318-qpztmdnw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262318-qpztmdnw.txt' === file2bib.sh === id: cord-260250-t48y27wg author: Decaro, Nicola title: Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date: 2004-05-07 pages: extension: .txt txt: ./txt/cord-260250-t48y27wg.txt cache: ./cache/cord-260250-t48y27wg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260250-t48y27wg.txt' === file2bib.sh === id: cord-260782-1lm8tzbc author: Giles, Julia title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date: 2018-07-14 pages: extension: .txt txt: ./txt/cord-260782-1lm8tzbc.txt cache: ./cache/cord-260782-1lm8tzbc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260782-1lm8tzbc.txt' === file2bib.sh === id: cord-260452-js4nr4d8 author: Yu, Junyang title: Activation and Role of NACHT, LRR, and PYD Domains-Containing Protein 3 Inflammasome in RNA Viral Infection date: 2017-10-31 pages: extension: .txt txt: ./txt/cord-260452-js4nr4d8.txt cache: ./cache/cord-260452-js4nr4d8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260452-js4nr4d8.txt' === file2bib.sh === id: cord-261110-cnj0e0s9 author: Debarnot, Claire title: Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date: 2011-02-25 pages: extension: .txt txt: ./txt/cord-261110-cnj0e0s9.txt cache: ./cache/cord-261110-cnj0e0s9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261110-cnj0e0s9.txt' === file2bib.sh === id: cord-262841-nr42rs8f author: Li, Lanjuan title: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-262841-nr42rs8f.txt cache: ./cache/cord-262841-nr42rs8f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262841-nr42rs8f.txt' === file2bib.sh === id: cord-262923-kgzbd6w3 author: Koo, Bonhan title: CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases date: 2018-11-10 pages: extension: .txt txt: ./txt/cord-262923-kgzbd6w3.txt cache: ./cache/cord-262923-kgzbd6w3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262923-kgzbd6w3.txt' === file2bib.sh === id: cord-259671-7de21oaq author: Madhugiri, Ramakanth title: RNA structure analysis of alphacoronavirus terminal genome regions date: 2014-12-19 pages: extension: .txt txt: ./txt/cord-259671-7de21oaq.txt cache: ./cache/cord-259671-7de21oaq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-259671-7de21oaq.txt' === file2bib.sh === id: cord-260695-qwepi0we author: Postler, Thomas S. title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date: 2017-11-01 pages: extension: .txt txt: ./txt/cord-260695-qwepi0we.txt cache: ./cache/cord-260695-qwepi0we.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260695-qwepi0we.txt' === file2bib.sh === id: cord-260345-ugd8kkor author: Giles, Ian G. title: A compendium of reviews in biochemistry and molecular biology published in the first half of 1992 date: 1992-12-31 pages: extension: .txt txt: ./txt/cord-260345-ugd8kkor.txt cache: ./cache/cord-260345-ugd8kkor.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260345-ugd8kkor.txt' === file2bib.sh === id: cord-262753-jld1ygxt author: Neidermyer, William J. title: Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date: 2019-06-21 pages: extension: .txt txt: ./txt/cord-262753-jld1ygxt.txt cache: ./cache/cord-262753-jld1ygxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262753-jld1ygxt.txt' === file2bib.sh === id: cord-263033-4790dhc5 author: Laptev, I. G. title: Posttranscriptional modification of messenger RNAs in eukaryotes date: 2015-12-11 pages: extension: .txt txt: ./txt/cord-263033-4790dhc5.txt cache: ./cache/cord-263033-4790dhc5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263033-4790dhc5.txt' === file2bib.sh === id: cord-263699-gosqpg3k author: Martínez, José L. title: Role of the Guanine Nucleotide Exchange Factor GBF1 in the Replication of RNA Viruses date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-263699-gosqpg3k.txt cache: ./cache/cord-263699-gosqpg3k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263699-gosqpg3k.txt' === file2bib.sh === id: cord-261279-6mef38eo author: Chu, Daniel K W title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 pages: extension: .txt txt: ./txt/cord-261279-6mef38eo.txt cache: ./cache/cord-261279-6mef38eo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-261279-6mef38eo.txt' === file2bib.sh === id: cord-262844-qeheeqe3 author: Xia, Xuhua title: Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-262844-qeheeqe3.txt cache: ./cache/cord-262844-qeheeqe3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262844-qeheeqe3.txt' === file2bib.sh === id: cord-263433-oldy0gta author: Barriocanal, Marina title: Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin date: 2015-01-09 pages: extension: .txt txt: ./txt/cord-263433-oldy0gta.txt cache: ./cache/cord-263433-oldy0gta.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263433-oldy0gta.txt' === file2bib.sh === id: cord-262776-6k7tcgfs author: Burnouf, Thierry title: Assessment of the viral safety of antivenoms fractionated from equine plasma date: 2004-09-30 pages: extension: .txt txt: ./txt/cord-262776-6k7tcgfs.txt cache: ./cache/cord-262776-6k7tcgfs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262776-6k7tcgfs.txt' === file2bib.sh === id: cord-263239-andje0wu author: Dorobantu, Cristina M. title: Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus date: 2015-09-25 pages: extension: .txt txt: ./txt/cord-263239-andje0wu.txt cache: ./cache/cord-263239-andje0wu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263239-andje0wu.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 92325 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-262282-9xh51cd1 author: Serwer, Philip title: Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-262282-9xh51cd1.txt cache: ./cache/cord-262282-9xh51cd1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262282-9xh51cd1.txt' === file2bib.sh === id: cord-260647-7bjhobg7 author: Coudray-Meunier, Coralie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 pages: extension: .txt txt: ./txt/cord-260647-7bjhobg7.txt cache: ./cache/cord-260647-7bjhobg7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260647-7bjhobg7.txt' === file2bib.sh === id: cord-263468-996kl9jz author: Cattaneo, Roberto title: Biased hypermutation and other genetic changes in defective measles viruses in human brain infections date: 1988-10-21 pages: extension: .txt txt: ./txt/cord-263468-996kl9jz.txt cache: ./cache/cord-263468-996kl9jz.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263468-996kl9jz.txt' === file2bib.sh === id: cord-266585-jfjrk9gy author: Fang, Shouguo title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 pages: extension: .txt txt: ./txt/cord-266585-jfjrk9gy.txt cache: ./cache/cord-266585-jfjrk9gy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266585-jfjrk9gy.txt' === file2bib.sh === id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 pages: extension: .txt txt: ./txt/cord-263315-g7os15m1.txt cache: ./cache/cord-263315-g7os15m1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263315-g7os15m1.txt' === file2bib.sh === id: cord-260705-huyyw5z6 author: Moshe, Adi title: Virus-Induced Aggregates in Infected Cells date: 2012-10-17 pages: extension: .txt txt: ./txt/cord-260705-huyyw5z6.txt cache: ./cache/cord-260705-huyyw5z6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-260705-huyyw5z6.txt' === file2bib.sh === id: cord-260422-z22t57ju author: Godet, Julien title: Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1 date: 2012-06-26 pages: extension: .txt txt: ./txt/cord-260422-z22t57ju.txt cache: ./cache/cord-260422-z22t57ju.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260422-z22t57ju.txt' === file2bib.sh === id: cord-260708-l9w5jhsw author: Lasecka, Lidia title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 pages: extension: .txt txt: ./txt/cord-260708-l9w5jhsw.txt cache: ./cache/cord-260708-l9w5jhsw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-260708-l9w5jhsw.txt' === file2bib.sh === id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023354-f2ciho6o.txt cache: ./cache/cord-023354-f2ciho6o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-023354-f2ciho6o.txt' === file2bib.sh === id: cord-262347-ejhz9rra author: Kappes, Matthew A. title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity date: 2015-03-07 pages: extension: .txt txt: ./txt/cord-262347-ejhz9rra.txt cache: ./cache/cord-262347-ejhz9rra.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-262347-ejhz9rra.txt' === file2bib.sh === id: cord-264159-e9071tyv author: Lin, Weikang Nicholas title: The Role of Single-Cell Technology in the Study and Control of Infectious Diseases date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-264159-e9071tyv.txt cache: ./cache/cord-264159-e9071tyv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264159-e9071tyv.txt' === file2bib.sh === id: cord-263334-wwkdum94 author: Li, Chen title: Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date: 2014-01-20 pages: extension: .txt txt: ./txt/cord-263334-wwkdum94.txt cache: ./cache/cord-263334-wwkdum94.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263334-wwkdum94.txt' === file2bib.sh === id: cord-264884-ydkigome author: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 pages: extension: .txt txt: ./txt/cord-264884-ydkigome.txt cache: ./cache/cord-264884-ydkigome.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264884-ydkigome.txt' === file2bib.sh === id: cord-265855-zf52vl11 author: Mayor-Ibarguren, Ander title: A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-265855-zf52vl11.txt cache: ./cache/cord-265855-zf52vl11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265855-zf52vl11.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 45878 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-264944-7xj27r98 author: Koopmans, Marion title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date: 1993-07-31 pages: extension: .txt txt: ./txt/cord-264944-7xj27r98.txt cache: ./cache/cord-264944-7xj27r98.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264944-7xj27r98.txt' === file2bib.sh === id: cord-264678-wt0lvhfl author: Wu, Tzong-Yuan title: IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico date: 2009-05-27 pages: extension: .txt txt: ./txt/cord-264678-wt0lvhfl.txt cache: ./cache/cord-264678-wt0lvhfl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-264678-wt0lvhfl.txt' === file2bib.sh === id: cord-263157-8jin6oru author: Martínez, Miguel Angel title: Progress in the Therapeutic Applications of siRNAs Against HIV-1 date: 2008-10-13 pages: extension: .txt txt: ./txt/cord-263157-8jin6oru.txt cache: ./cache/cord-263157-8jin6oru.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263157-8jin6oru.txt' === file2bib.sh === id: cord-265895-ck7eto16 author: Baric, Ralph S. title: Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date: 1987-02-28 pages: extension: .txt txt: ./txt/cord-265895-ck7eto16.txt cache: ./cache/cord-265895-ck7eto16.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265895-ck7eto16.txt' === file2bib.sh === id: cord-263987-ff6kor0c author: Holmes, Ian H. title: Solving the master equation for Indels date: 2017-05-12 pages: extension: .txt txt: ./txt/cord-263987-ff6kor0c.txt cache: ./cache/cord-263987-ff6kor0c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-263987-ff6kor0c.txt' === file2bib.sh === id: cord-266921-x9q7dwc4 author: Worrall, Jonathan AR title: Information available at cut rates: structure and mechanism of ribonucleases date: 2006-12-26 pages: extension: .txt txt: ./txt/cord-266921-x9q7dwc4.txt cache: ./cache/cord-266921-x9q7dwc4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-266921-x9q7dwc4.txt' === file2bib.sh === id: cord-266521-vovas81d author: Yokobayashi, Yohei title: Aptamer-based and aptazyme-based riboswitches in mammalian cells date: 2019-06-22 pages: extension: .txt txt: ./txt/cord-266521-vovas81d.txt cache: ./cache/cord-266521-vovas81d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266521-vovas81d.txt' === file2bib.sh === id: cord-262076-b5u5hp2r author: Liu, Ying Poi title: Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron date: 2008-03-16 pages: extension: .txt txt: ./txt/cord-262076-b5u5hp2r.txt cache: ./cache/cord-262076-b5u5hp2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262076-b5u5hp2r.txt' === file2bib.sh === id: cord-267115-6jqdi417 author: Giobbe, Giovanni Giuseppe title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-267115-6jqdi417.txt cache: ./cache/cord-267115-6jqdi417.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267115-6jqdi417.txt' === file2bib.sh === id: cord-262511-96xp1v0r author: Khabar, Khalid S. A. title: Rapid transit in the immune cells: the role of mRNA turnover regulation date: 2007-03-30 pages: extension: .txt txt: ./txt/cord-262511-96xp1v0r.txt cache: ./cache/cord-262511-96xp1v0r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-262511-96xp1v0r.txt' === file2bib.sh === id: cord-267588-ruuzr6l1 author: Garnett, Lauren title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date: 2020-08-08 pages: extension: .txt txt: ./txt/cord-267588-ruuzr6l1.txt cache: ./cache/cord-267588-ruuzr6l1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267588-ruuzr6l1.txt' === file2bib.sh === id: cord-266960-kyx6xhvj author: Temple, Mark D. title: Real-time audio and visual display of the Coronavirus genome date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-266960-kyx6xhvj.txt cache: ./cache/cord-266960-kyx6xhvj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266960-kyx6xhvj.txt' === file2bib.sh === id: cord-266520-n439dwcx author: Levanova, Alesia A. title: Enzymatically synthesized 2'-fluoro-modified Dicer-substrate siRNA swarms against herpes simplex virus demonstrate enhanced antiviral efficacy and low cytotoxicity date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-266520-n439dwcx.txt cache: ./cache/cord-266520-n439dwcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266520-n439dwcx.txt' === file2bib.sh === id: cord-262609-cssgzvus author: Sivakumaran, K title: RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis date: 1999-12-03 pages: extension: .txt txt: ./txt/cord-262609-cssgzvus.txt cache: ./cache/cord-262609-cssgzvus.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-262609-cssgzvus.txt' === file2bib.sh === id: cord-266464-wuf3s8m0 author: Kim, So Yeon title: Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection date: 2016-10-17 pages: extension: .txt txt: ./txt/cord-266464-wuf3s8m0.txt cache: ./cache/cord-266464-wuf3s8m0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266464-wuf3s8m0.txt' === file2bib.sh === id: cord-267027-diwm1940 author: Le, Shu-Yun title: Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses date: 1992-12-31 pages: extension: .txt txt: ./txt/cord-267027-diwm1940.txt cache: ./cache/cord-267027-diwm1940.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-267027-diwm1940.txt' === file2bib.sh === id: cord-265381-ppjohov8 author: Pillai-Nair, Neeta title: Cis-acting Regulatory Elements in the Potato Virus X 3′ Non-translated Region Differentially Affect Minus-strand and Plus-strand RNA Accumulation date: 2003-02-21 pages: extension: .txt txt: ./txt/cord-265381-ppjohov8.txt cache: ./cache/cord-265381-ppjohov8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-265381-ppjohov8.txt' === file2bib.sh === id: cord-263645-wupre5uj author: Morgan, Brittany S title: Insights into the development of chemical probes for RNA date: 2018-09-19 pages: extension: .txt txt: ./txt/cord-263645-wupre5uj.txt cache: ./cache/cord-263645-wupre5uj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263645-wupre5uj.txt' === file2bib.sh === id: cord-267036-llngs3v5 author: Lai, Ming‐Chih title: Functional interplay between viral and cellular SR proteins in control of post‐transcriptional gene regulation date: 2009-02-10 pages: extension: .txt txt: ./txt/cord-267036-llngs3v5.txt cache: ./cache/cord-267036-llngs3v5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267036-llngs3v5.txt' === file2bib.sh === id: cord-265173-70wyecwj author: Trujillo-Uscanga, Adrian title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-265173-70wyecwj.txt cache: ./cache/cord-265173-70wyecwj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265173-70wyecwj.txt' === file2bib.sh === id: cord-267326-355q6k6k author: Gu, Xiaoqiong title: Geospatial distribution of viromes in tropical freshwater ecosystems date: 2018-06-15 pages: extension: .txt txt: ./txt/cord-267326-355q6k6k.txt cache: ./cache/cord-267326-355q6k6k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267326-355q6k6k.txt' === file2bib.sh === id: cord-267867-q52nvn0n author: Chevalier, Christophe title: Inhibition of Hepatitis C Virus Infection in Cell Culture by Small Interfering RNAs date: 2016-12-14 pages: extension: .txt txt: ./txt/cord-267867-q52nvn0n.txt cache: ./cache/cord-267867-q52nvn0n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267867-q52nvn0n.txt' === file2bib.sh === id: cord-267377-wyhsxj6g author: Edwards, Michael C. title: Coat protein expression strategy of oat blue dwarf virus() date: 2014-01-14 pages: extension: .txt txt: ./txt/cord-267377-wyhsxj6g.txt cache: ./cache/cord-267377-wyhsxj6g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-267377-wyhsxj6g.txt' === file2bib.sh === id: cord-265508-t1nfyzf5 author: Boursnell, M.E.G. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date: 1984-08-31 pages: extension: .txt txt: ./txt/cord-265508-t1nfyzf5.txt cache: ./cache/cord-265508-t1nfyzf5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265508-t1nfyzf5.txt' === file2bib.sh === id: cord-263357-krvei97r author: Holmes, Kathryn V. title: The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia date: 2013-01-08 pages: extension: .txt txt: ./txt/cord-263357-krvei97r.txt cache: ./cache/cord-263357-krvei97r.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-263357-krvei97r.txt' === file2bib.sh === id: cord-265139-x7g3jcjm author: Zaiou, Mohamed title: The Emerging Role and Promise of Circular RNAs in Obesity and Related Metabolic Disorders date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-265139-x7g3jcjm.txt cache: ./cache/cord-265139-x7g3jcjm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-265139-x7g3jcjm.txt' === file2bib.sh === id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023346-8sqbqjm1.txt cache: ./cache/cord-023346-8sqbqjm1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-023346-8sqbqjm1.txt' === file2bib.sh === id: cord-263302-z5uhrta5 author: Zhang, Xuming title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 pages: extension: .txt txt: ./txt/cord-263302-z5uhrta5.txt cache: ./cache/cord-263302-z5uhrta5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-263302-z5uhrta5.txt' === file2bib.sh === id: cord-263580-zxnmylkw author: Pyle, Anna Marie title: RNA helicases and remodeling proteins date: 2011-08-20 pages: extension: .txt txt: ./txt/cord-263580-zxnmylkw.txt cache: ./cache/cord-263580-zxnmylkw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-263580-zxnmylkw.txt' === file2bib.sh === id: cord-264746-gfn312aa author: Muse, Spencer title: GENOMICS AND BIOINFORMATICS date: 2012-03-29 pages: extension: .txt txt: ./txt/cord-264746-gfn312aa.txt cache: ./cache/cord-264746-gfn312aa.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264746-gfn312aa.txt' === file2bib.sh === id: cord-266127-phv08xe2 author: Mukhopadhyay, Urbi title: Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date: 2019-08-26 pages: extension: .txt txt: ./txt/cord-266127-phv08xe2.txt cache: ./cache/cord-266127-phv08xe2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-266127-phv08xe2.txt' === file2bib.sh === id: cord-267533-nmgtan4e author: Hu, Zhigang title: Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-267533-nmgtan4e.txt cache: ./cache/cord-267533-nmgtan4e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267533-nmgtan4e.txt' === file2bib.sh === id: cord-266634-bww62vx8 author: Gopinath, M. title: Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus date: 2015-10-07 pages: extension: .txt txt: ./txt/cord-266634-bww62vx8.txt cache: ./cache/cord-266634-bww62vx8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266634-bww62vx8.txt' === file2bib.sh === id: cord-268071-ow2aijmj author: Pachetti, Maria title: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-268071-ow2aijmj.txt cache: ./cache/cord-268071-ow2aijmj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268071-ow2aijmj.txt' === file2bib.sh === id: cord-265461-hj2b1wc4 author: Decroly, Etienne title: Biochemical principles and inhibitors to interfere with viral capping pathways date: 2017-05-18 pages: extension: .txt txt: ./txt/cord-265461-hj2b1wc4.txt cache: ./cache/cord-265461-hj2b1wc4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265461-hj2b1wc4.txt' === file2bib.sh === id: cord-267124-8efdzlc0 author: Wichmann, Dominic title: Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-267124-8efdzlc0.txt cache: ./cache/cord-267124-8efdzlc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267124-8efdzlc0.txt' === file2bib.sh === id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 pages: extension: .txt txt: ./txt/cord-023364-ut56gczm.txt cache: ./cache/cord-023364-ut56gczm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-023364-ut56gczm.txt' === file2bib.sh === id: cord-264488-989t9ld1 author: Park, Il-Hyun title: Inhibition of hepatitis B virus replication by ligand-mediated activation of RNase L date: 2014-02-06 pages: extension: .txt txt: ./txt/cord-264488-989t9ld1.txt cache: ./cache/cord-264488-989t9ld1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-264488-989t9ld1.txt' === file2bib.sh === id: cord-266985-9qwttt2y author: Gale, P. title: Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date: 2014-11-04 pages: extension: .txt txt: ./txt/cord-266985-9qwttt2y.txt cache: ./cache/cord-266985-9qwttt2y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-266985-9qwttt2y.txt' === file2bib.sh === id: cord-268337-o6lo55o8 author: Lloyd, Richard E. title: Translational control by viral proteinases date: 2005-11-21 pages: extension: .txt txt: ./txt/cord-268337-o6lo55o8.txt cache: ./cache/cord-268337-o6lo55o8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268337-o6lo55o8.txt' === file2bib.sh === id: cord-265410-khwzdi79 author: Bartlett, Stuart title: Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars date: 2020-04-16 pages: extension: .txt txt: ./txt/cord-265410-khwzdi79.txt cache: ./cache/cord-265410-khwzdi79.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-265410-khwzdi79.txt' === file2bib.sh === id: cord-269496-tnw7sxlh author: Sen Gupta, Parth Sarthi title: Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date: 2020-10-28 pages: extension: .txt txt: ./txt/cord-269496-tnw7sxlh.txt cache: ./cache/cord-269496-tnw7sxlh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269496-tnw7sxlh.txt' === file2bib.sh === id: cord-268206-ino9srb6 author: Hamed, Manal A. title: An overview on COVID-19: reality and expectation date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-268206-ino9srb6.txt cache: ./cache/cord-268206-ino9srb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-268206-ino9srb6.txt' === file2bib.sh === id: cord-269193-a647hwu9 author: Lin, Debby A. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 pages: extension: .txt txt: ./txt/cord-269193-a647hwu9.txt cache: ./cache/cord-269193-a647hwu9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269193-a647hwu9.txt' === file2bib.sh === id: cord-267532-5rnqd9mb author: Zhang, Xuming title: Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date: 1998-03-01 pages: extension: .txt txt: ./txt/cord-267532-5rnqd9mb.txt cache: ./cache/cord-267532-5rnqd9mb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267532-5rnqd9mb.txt' === file2bib.sh === id: cord-268763-s16n7f17 author: Williams, J. G. title: Identification of Three Endotypes in Pediatric Acute Respiratory Distress Syndrome by Nasal Transcriptomic Profiling date: 2020-05-02 pages: extension: .txt txt: ./txt/cord-268763-s16n7f17.txt cache: ./cache/cord-268763-s16n7f17.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268763-s16n7f17.txt' === file2bib.sh === id: cord-269726-z0frgm7s author: Gidari, Anna title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-269726-z0frgm7s.txt cache: ./cache/cord-269726-z0frgm7s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269726-z0frgm7s.txt' === file2bib.sh === id: cord-268565-2sg1tlrg author: Clarke, David K. title: Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector date: 2006-09-15 pages: extension: .txt txt: ./txt/cord-268565-2sg1tlrg.txt cache: ./cache/cord-268565-2sg1tlrg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268565-2sg1tlrg.txt' === file2bib.sh === id: cord-268718-tt07cwrf author: Tan, Heng Wee title: Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-268718-tt07cwrf.txt cache: ./cache/cord-268718-tt07cwrf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268718-tt07cwrf.txt' === file2bib.sh === id: cord-267475-6f4h3cck author: Kozak, Marilyn title: Pushing the limits of the scanning mechanism for initiation of translation date: 2002-10-16 pages: extension: .txt txt: ./txt/cord-267475-6f4h3cck.txt cache: ./cache/cord-267475-6f4h3cck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-267475-6f4h3cck.txt' === file2bib.sh === id: cord-268139-tgpsu4qz author: Brockway, Sarah M. title: Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication date: 2005-09-30 pages: extension: .txt txt: ./txt/cord-268139-tgpsu4qz.txt cache: ./cache/cord-268139-tgpsu4qz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268139-tgpsu4qz.txt' === file2bib.sh === id: cord-269771-hffxb7bm author: Cheung, Ka Shing title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-269771-hffxb7bm.txt cache: ./cache/cord-269771-hffxb7bm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269771-hffxb7bm.txt' === file2bib.sh === id: cord-268970-uz7q6z2f author: Ott, Isabel M. title: Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date: 2020-08-04 pages: extension: .txt txt: ./txt/cord-268970-uz7q6z2f.txt cache: ./cache/cord-268970-uz7q6z2f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268970-uz7q6z2f.txt' === file2bib.sh === id: cord-268467-btfz6ye8 author: Schreiber, Steven S. title: Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E date: 1989-03-31 pages: extension: .txt txt: ./txt/cord-268467-btfz6ye8.txt cache: ./cache/cord-268467-btfz6ye8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-268467-btfz6ye8.txt' === file2bib.sh === id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 pages: extension: .txt txt: ./txt/cord-269194-b1wlr3t7.txt cache: ./cache/cord-269194-b1wlr3t7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269194-b1wlr3t7.txt' === file2bib.sh === id: cord-269150-d1sgnxc0 author: Tan, Yong Wah title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 pages: extension: .txt txt: ./txt/cord-269150-d1sgnxc0.txt cache: ./cache/cord-269150-d1sgnxc0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269150-d1sgnxc0.txt' === file2bib.sh === id: cord-268122-74nj66vb author: Xie, Na title: NAD(+) metabolism: pathophysiologic mechanisms and therapeutic potential date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-268122-74nj66vb.txt cache: ./cache/cord-268122-74nj66vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-268122-74nj66vb.txt' === file2bib.sh === id: cord-269011-230p8rsf author: de Haan, Cornelis A.M. title: Molecular Interactions in the Assembly of Coronaviruses date: 2005-08-31 pages: extension: .txt txt: ./txt/cord-269011-230p8rsf.txt cache: ./cache/cord-269011-230p8rsf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-269011-230p8rsf.txt' === file2bib.sh === id: cord-269466-9hnal9ad author: Agbeci, Maxime title: Contribution of Host Intracellular Transport Machineries to Intercellular Movement of Turnip Mosaic Virus date: 2013-10-03 pages: extension: .txt txt: ./txt/cord-269466-9hnal9ad.txt cache: ./cache/cord-269466-9hnal9ad.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269466-9hnal9ad.txt' === file2bib.sh === id: cord-270550-if748w2n author: Bailey, Adam L. title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-270550-if748w2n.txt cache: ./cache/cord-270550-if748w2n.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270550-if748w2n.txt' === file2bib.sh === id: cord-270143-muxrxvyo author: Markotter, Wanda title: Paramyxo- and Coronaviruses in Rwandan Bats date: 2019-07-02 pages: extension: .txt txt: ./txt/cord-270143-muxrxvyo.txt cache: ./cache/cord-270143-muxrxvyo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270143-muxrxvyo.txt' === file2bib.sh === id: cord-269294-vx7xr80t author: Kwong, Ann D. title: Viral and cellular RNA helicases as antiviral targets date: 2005-09-23 pages: extension: .txt txt: ./txt/cord-269294-vx7xr80t.txt cache: ./cache/cord-269294-vx7xr80t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269294-vx7xr80t.txt' === file2bib.sh === id: cord-270243-moxleyjg author: Cholleti, Harindranath title: Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date: 2018-05-28 pages: extension: .txt txt: ./txt/cord-270243-moxleyjg.txt cache: ./cache/cord-270243-moxleyjg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-270243-moxleyjg.txt' === file2bib.sh === id: cord-269766-arjoemla author: Dutescu, R. Michael title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date: 2020-09-08 pages: extension: .txt txt: ./txt/cord-269766-arjoemla.txt cache: ./cache/cord-269766-arjoemla.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269766-arjoemla.txt' === file2bib.sh === id: cord-270594-62xotol3 author: He, Lei title: Identification and characterization of vp7 gene in Bombyx mori cytoplasmic polyhedrosis virus date: 2017-09-05 pages: extension: .txt txt: ./txt/cord-270594-62xotol3.txt cache: ./cache/cord-270594-62xotol3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270594-62xotol3.txt' === file2bib.sh === id: cord-269720-o81j3d1j author: Page, Kevin W. title: Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus date: 1990 pages: extension: .txt txt: ./txt/cord-269720-o81j3d1j.txt cache: ./cache/cord-269720-o81j3d1j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-269720-o81j3d1j.txt' === file2bib.sh === id: cord-271648-m2c5bvuj author: Ashour, Hossam M. title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date: 2020-03-04 pages: extension: .txt txt: ./txt/cord-271648-m2c5bvuj.txt cache: ./cache/cord-271648-m2c5bvuj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271648-m2c5bvuj.txt' === file2bib.sh === id: cord-270604-u62437dh author: Cuthill, Jennifer Hoyal title: A SIMPLE MODEL EXPLAINS THE DYNAMICS OF PREFERENTIAL HOST SWITCHING AMONG MAMMAL RNA VIRUSES date: 2013-02-19 pages: extension: .txt txt: ./txt/cord-270604-u62437dh.txt cache: ./cache/cord-270604-u62437dh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270604-u62437dh.txt' === file2bib.sh === id: cord-272378-umvi0veu author: Subramanian, Subbaya title: Special Issue: MicroRNA Regulation in Health and Disease date: 2019-06-15 pages: extension: .txt txt: ./txt/cord-272378-umvi0veu.txt cache: ./cache/cord-272378-umvi0veu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272378-umvi0veu.txt' === file2bib.sh === id: cord-270940-acwkh6ed author: Kallio-Kokko, Hannimari title: Viral zoonoses in Europe date: 2005-06-29 pages: extension: .txt txt: ./txt/cord-270940-acwkh6ed.txt cache: ./cache/cord-270940-acwkh6ed.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270940-acwkh6ed.txt' === file2bib.sh === id: cord-270473-5tok4mqk author: Nanda, S. K. title: Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome date: 2003-09-19 pages: extension: .txt txt: ./txt/cord-270473-5tok4mqk.txt cache: ./cache/cord-270473-5tok4mqk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270473-5tok4mqk.txt' === file2bib.sh === id: cord-270670-cubh9jxc author: Domingo, E. title: Viruses as Quasispecies: Biological Implications date: 2006 pages: extension: .txt txt: ./txt/cord-270670-cubh9jxc.txt cache: ./cache/cord-270670-cubh9jxc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-270670-cubh9jxc.txt' === file2bib.sh === id: cord-271972-qhr6iir6 author: Gaglia, Marta Maria title: Viruses and the cellular RNA decay machinery date: 2010-05-06 pages: extension: .txt txt: ./txt/cord-271972-qhr6iir6.txt cache: ./cache/cord-271972-qhr6iir6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271972-qhr6iir6.txt' === file2bib.sh === id: cord-269975-1ebmq7t8 author: Duplantier, Allen J. title: Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-269975-1ebmq7t8.txt cache: ./cache/cord-269975-1ebmq7t8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-269975-1ebmq7t8.txt' === file2bib.sh === id: cord-271091-ffn59sgf author: Galao, Rui P title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology date: 2007-10-10 pages: extension: .txt txt: ./txt/cord-271091-ffn59sgf.txt cache: ./cache/cord-271091-ffn59sgf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271091-ffn59sgf.txt' === file2bib.sh === id: cord-269866-3tpyj04y author: Liu, D. X. title: Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus date: 1992-01-31 pages: extension: .txt txt: ./txt/cord-269866-3tpyj04y.txt cache: ./cache/cord-269866-3tpyj04y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-269866-3tpyj04y.txt' === file2bib.sh === id: cord-271526-14nfqusv author: Molenkamp, Richard title: Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal date: 1997-12-08 pages: extension: .txt txt: ./txt/cord-271526-14nfqusv.txt cache: ./cache/cord-271526-14nfqusv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271526-14nfqusv.txt' === file2bib.sh === id: cord-271127-l9bxqtqs author: Renault, Sylvaine title: Commensal and mutualistic relationships of reoviruses with their parasitoid wasp hosts date: 2005-02-28 pages: extension: .txt txt: ./txt/cord-271127-l9bxqtqs.txt cache: ./cache/cord-271127-l9bxqtqs.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271127-l9bxqtqs.txt' === file2bib.sh === id: cord-272050-0u62j7nj author: Okamoto, Kimiyuki title: cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1 date: 2008-05-25 pages: extension: .txt txt: ./txt/cord-272050-0u62j7nj.txt cache: ./cache/cord-272050-0u62j7nj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272050-0u62j7nj.txt' === file2bib.sh === id: cord-271130-6s79q1c1 author: Filoni, Claudia title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date: 2017-11-17 pages: extension: .txt txt: ./txt/cord-271130-6s79q1c1.txt cache: ./cache/cord-271130-6s79q1c1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271130-6s79q1c1.txt' === file2bib.sh === id: cord-274110-nyyunoha author: Orlinger, Klaus K. title: An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system date: 2010-04-26 pages: extension: .txt txt: ./txt/cord-274110-nyyunoha.txt cache: ./cache/cord-274110-nyyunoha.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274110-nyyunoha.txt' === file2bib.sh === id: cord-271701-tx0lqgff author: te Velthuis, Aartjan J.W. title: The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date: 2011-10-29 pages: extension: .txt txt: ./txt/cord-271701-tx0lqgff.txt cache: ./cache/cord-271701-tx0lqgff.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271701-tx0lqgff.txt' === file2bib.sh === id: cord-271504-t3y1w9ef author: Luo, Zichao title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-271504-t3y1w9ef.txt cache: ./cache/cord-271504-t3y1w9ef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271504-t3y1w9ef.txt' === file2bib.sh === id: cord-273487-nfgjz6f9 author: Xu, Zaikun title: The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles date: 2012-11-10 pages: extension: .txt txt: ./txt/cord-273487-nfgjz6f9.txt cache: ./cache/cord-273487-nfgjz6f9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273487-nfgjz6f9.txt' === file2bib.sh === id: cord-271434-30nh2gc7 author: Tian, Fei title: A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-271434-30nh2gc7.txt cache: ./cache/cord-271434-30nh2gc7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-271434-30nh2gc7.txt' === file2bib.sh === id: cord-271781-cfv0ta10 author: Patel, Kishan P. title: Transmission of SARS-CoV-2: an update of current literature date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-271781-cfv0ta10.txt cache: ./cache/cord-271781-cfv0ta10.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271781-cfv0ta10.txt' === file2bib.sh === id: cord-271188-ewlxy5po author: Liu, Wei title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 pages: extension: .txt txt: ./txt/cord-271188-ewlxy5po.txt cache: ./cache/cord-271188-ewlxy5po.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271188-ewlxy5po.txt' === file2bib.sh === id: cord-272871-gu9ptt9y author: White, K.Andrew title: Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products date: 1991-08-31 pages: extension: .txt txt: ./txt/cord-272871-gu9ptt9y.txt cache: ./cache/cord-272871-gu9ptt9y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272871-gu9ptt9y.txt' === file2bib.sh === id: cord-274049-3gw65kpu author: Zhang, Han title: CRISPR Editing in Biological and Biomedical Investigation date: 2017-05-31 pages: extension: .txt txt: ./txt/cord-274049-3gw65kpu.txt cache: ./cache/cord-274049-3gw65kpu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274049-3gw65kpu.txt' === file2bib.sh === id: cord-273326-gmw8gl2r author: Saiz, Juan-Carlos title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 pages: extension: .txt txt: ./txt/cord-273326-gmw8gl2r.txt cache: ./cache/cord-273326-gmw8gl2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273326-gmw8gl2r.txt' === file2bib.sh === id: cord-274353-tzlcpx7q author: McDermott, Amy title: Inner Workings: Molecular biologists offer “wartime service” in the effort to test for COVID-19 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-274353-tzlcpx7q.txt cache: ./cache/cord-274353-tzlcpx7q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274353-tzlcpx7q.txt' === file2bib.sh === id: cord-271241-w1q46y63 author: Ruggiero, Emanuela title: Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-271241-w1q46y63.txt cache: ./cache/cord-271241-w1q46y63.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-271241-w1q46y63.txt' === file2bib.sh === id: cord-272579-aenuyht0 author: Emmett, Stevan R. title: The Cell Cycle and Virus Infection date: 2005 pages: extension: .txt txt: ./txt/cord-272579-aenuyht0.txt cache: ./cache/cord-272579-aenuyht0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272579-aenuyht0.txt' === file2bib.sh === id: cord-270892-ycc3csyh author: Rollinger, Judith M. title: The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date: 2010-12-13 pages: extension: .txt txt: ./txt/cord-270892-ycc3csyh.txt cache: ./cache/cord-270892-ycc3csyh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-270892-ycc3csyh.txt' === file2bib.sh === id: cord-272268-8vrcwwll author: Kedersha, Nancy title: Chapter 4 Regulation of Translation by Stress Granules and Processing Bodies date: 2009-10-27 pages: extension: .txt txt: ./txt/cord-272268-8vrcwwll.txt cache: ./cache/cord-272268-8vrcwwll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272268-8vrcwwll.txt' === file2bib.sh === id: cord-272573-wxqly479 author: Maia Chagas, Andre title: Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-272573-wxqly479.txt cache: ./cache/cord-272573-wxqly479.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272573-wxqly479.txt' === file2bib.sh === id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 pages: extension: .txt txt: ./txt/cord-274080-884x48on.txt cache: ./cache/cord-274080-884x48on.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274080-884x48on.txt' === file2bib.sh === id: cord-275720-kf9m4zho author: Cho, Won Kyong title: Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date: 2012-05-06 pages: extension: .txt txt: ./txt/cord-275720-kf9m4zho.txt cache: ./cache/cord-275720-kf9m4zho.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275720-kf9m4zho.txt' === file2bib.sh === id: cord-273609-whm2ce4u author: Li, Qingdi Quentin title: Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment date: 2012-06-29 pages: extension: .txt txt: ./txt/cord-273609-whm2ce4u.txt cache: ./cache/cord-273609-whm2ce4u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273609-whm2ce4u.txt' === file2bib.sh === id: cord-274536-fv7mltj7 author: Tong, Yongqing title: Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-274536-fv7mltj7.txt cache: ./cache/cord-274536-fv7mltj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-274536-fv7mltj7.txt' === file2bib.sh === id: cord-271419-v6dfel3l author: Adachi, Shun title: Commentary: Origin and evolution of pathogenic coronaviruses date: 2020-04-21 pages: extension: .txt txt: ./txt/cord-271419-v6dfel3l.txt cache: ./cache/cord-271419-v6dfel3l.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-271419-v6dfel3l.txt' === file2bib.sh === id: cord-275225-fvq8hezk author: Hornyák, Ákos title: Detection of subgenomic mRNA of feline coronavirus by real-time polymerase chain reaction based on primer-probe energy transfer (P-sg-QPCR) date: 2012-02-18 pages: extension: .txt txt: ./txt/cord-275225-fvq8hezk.txt cache: ./cache/cord-275225-fvq8hezk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275225-fvq8hezk.txt' === file2bib.sh === id: cord-274401-pjyvg53w author: Hrkach, Jeff title: From micro to nano: evolution and impact of drug delivery in treating disease date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-274401-pjyvg53w.txt cache: ./cache/cord-274401-pjyvg53w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-274401-pjyvg53w.txt' === file2bib.sh === id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 pages: extension: .txt txt: ./txt/cord-273019-hbpfz8rt.txt cache: ./cache/cord-273019-hbpfz8rt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273019-hbpfz8rt.txt' === file2bib.sh === id: cord-275683-1qj9ri18 author: Roux, Simon title: Metagenomics in Virology date: 2019-06-12 pages: extension: .txt txt: ./txt/cord-275683-1qj9ri18.txt cache: ./cache/cord-275683-1qj9ri18.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275683-1qj9ri18.txt' === file2bib.sh === id: cord-275602-cog4nma0 author: Watkins, Kevin title: Emerging Infectious Diseases: a Review date: 2018-06-22 pages: extension: .txt txt: ./txt/cord-275602-cog4nma0.txt cache: ./cache/cord-275602-cog4nma0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275602-cog4nma0.txt' === file2bib.sh === id: cord-274569-jh0dyyz7 author: Alenquer, Marta title: Exosome Biogenesis, Regulation, and Function in Viral Infection date: 2015-09-17 pages: extension: .txt txt: ./txt/cord-274569-jh0dyyz7.txt cache: ./cache/cord-274569-jh0dyyz7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274569-jh0dyyz7.txt' === file2bib.sh === id: cord-273379-w8vy5rl8 author: Mizutani, Tetsuya title: Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA date: 2000-09-30 pages: extension: .txt txt: ./txt/cord-273379-w8vy5rl8.txt cache: ./cache/cord-273379-w8vy5rl8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273379-w8vy5rl8.txt' === file2bib.sh === id: cord-276988-bvsz5q6d author: Neu, Carolin T. title: Post-Transcriptional Expression Control in Platelet Biogenesis and Function date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-276988-bvsz5q6d.txt cache: ./cache/cord-276988-bvsz5q6d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276988-bvsz5q6d.txt' === file2bib.sh === id: cord-275252-4e3cn50u author: Rad SM, Ali Hosseini title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date: 2020-05-16 pages: extension: .txt txt: ./txt/cord-275252-4e3cn50u.txt cache: ./cache/cord-275252-4e3cn50u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275252-4e3cn50u.txt' === file2bib.sh === id: cord-275403-g4rohhtt author: Bautista, Elida M. title: Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus date: 2002-07-05 pages: extension: .txt txt: ./txt/cord-275403-g4rohhtt.txt cache: ./cache/cord-275403-g4rohhtt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-275403-g4rohhtt.txt' === file2bib.sh === id: cord-272702-7uc4ozjy author: Graham, T. G. W. title: Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-272702-7uc4ozjy.txt cache: ./cache/cord-272702-7uc4ozjy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272702-7uc4ozjy.txt' === file2bib.sh === id: cord-272729-nbgdmavr author: Kim, Youngnam title: Ribavirin efficiently suppresses porcine nidovirus replication date: 2012-10-27 pages: extension: .txt txt: ./txt/cord-272729-nbgdmavr.txt cache: ./cache/cord-272729-nbgdmavr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272729-nbgdmavr.txt' === file2bib.sh === id: cord-277355-si3g5dih author: He, Yu title: The role of capsid in the flaviviral life cycle and perspectives for vaccine development date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-277355-si3g5dih.txt cache: ./cache/cord-277355-si3g5dih.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277355-si3g5dih.txt' === file2bib.sh === id: cord-275859-ix8du1er author: Mouzakis, Kathryn D. title: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date: 2012-12-15 pages: extension: .txt txt: ./txt/cord-275859-ix8du1er.txt cache: ./cache/cord-275859-ix8du1er.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275859-ix8du1er.txt' === file2bib.sh === id: cord-273910-fna7s9te author: Bochud, Pierre-Yves title: Innate immunogenetics: a tool for exploring new frontiers of host defence date: 2007-07-20 pages: extension: .txt txt: ./txt/cord-273910-fna7s9te.txt cache: ./cache/cord-273910-fna7s9te.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273910-fna7s9te.txt' === file2bib.sh === id: cord-276739-84vf5bts author: Sakurai, Akira title: Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date: 2011-08-22 pages: extension: .txt txt: ./txt/cord-276739-84vf5bts.txt cache: ./cache/cord-276739-84vf5bts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276739-84vf5bts.txt' === file2bib.sh === id: cord-273723-srfypn7j author: Omar, Sarah title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-273723-srfypn7j.txt cache: ./cache/cord-273723-srfypn7j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273723-srfypn7j.txt' === file2bib.sh === id: cord-274773-3jhka8wl author: Zhang, Jialin title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-274773-3jhka8wl.txt cache: ./cache/cord-274773-3jhka8wl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274773-3jhka8wl.txt' === file2bib.sh === id: cord-275565-xerr4vki author: Kumar, Manish title: Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date: 2020-09-15 pages: extension: .txt txt: ./txt/cord-275565-xerr4vki.txt cache: ./cache/cord-275565-xerr4vki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275565-xerr4vki.txt' === file2bib.sh === id: cord-272576-ez731lif author: Wada, Yoshiko title: Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count date: 2016-11-03 pages: extension: .txt txt: ./txt/cord-272576-ez731lif.txt cache: ./cache/cord-272576-ez731lif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-272576-ez731lif.txt' === file2bib.sh === id: cord-272666-3uidpr79 author: Doyle, Nicole title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date: 2018-09-06 pages: extension: .txt txt: ./txt/cord-272666-3uidpr79.txt cache: ./cache/cord-272666-3uidpr79.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-272666-3uidpr79.txt' === file2bib.sh === id: cord-273711-bxijla09 author: Zhao, Zhixun title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells date: 2012-02-17 pages: extension: .txt txt: ./txt/cord-273711-bxijla09.txt cache: ./cache/cord-273711-bxijla09.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-273711-bxijla09.txt' === file2bib.sh === id: cord-276185-ysspkbj7 author: Milewska, Aleksandra title: APOBEC3-mediated restriction of RNA virus replication date: 2018-04-13 pages: extension: .txt txt: ./txt/cord-276185-ysspkbj7.txt cache: ./cache/cord-276185-ysspkbj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276185-ysspkbj7.txt' === file2bib.sh === id: cord-274463-0nvw2egm author: Sánchez-Navarro, Jesús A. title: Plant tissue distribution and chemical inactivation of six carnation viruses date: 2006-12-11 pages: extension: .txt txt: ./txt/cord-274463-0nvw2egm.txt cache: ./cache/cord-274463-0nvw2egm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274463-0nvw2egm.txt' === file2bib.sh === id: cord-275307-d7htyfcl author: Gaglia, Marta Maria title: Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date: 2015-12-08 pages: extension: .txt txt: ./txt/cord-275307-d7htyfcl.txt cache: ./cache/cord-275307-d7htyfcl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-275307-d7htyfcl.txt' === file2bib.sh === id: cord-276908-9jthjf24 author: Gupta, Akanksha title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 pages: extension: .txt txt: ./txt/cord-276908-9jthjf24.txt cache: ./cache/cord-276908-9jthjf24.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276908-9jthjf24.txt' === file2bib.sh === id: cord-273367-gl266pvt author: Gunawardana, M. title: Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-273367-gl266pvt.txt cache: ./cache/cord-273367-gl266pvt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-273367-gl266pvt.txt' === file2bib.sh === id: cord-273366-xd84f8ct author: Brownsword, Matthew J. title: Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-273366-xd84f8ct.txt cache: ./cache/cord-273366-xd84f8ct.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-273366-xd84f8ct.txt' === file2bib.sh === id: cord-274663-zyzgk2z3 author: Chang, Stewart T. title: Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line date: 2011-09-20 pages: extension: .txt txt: ./txt/cord-274663-zyzgk2z3.txt cache: ./cache/cord-274663-zyzgk2z3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274663-zyzgk2z3.txt' === file2bib.sh === id: cord-274097-11hvriqy author: Katz, Louis M. title: Is SARS‐CoV‐2 transfusion transmitted? date: 2020-06-16 pages: extension: .txt txt: ./txt/cord-274097-11hvriqy.txt cache: ./cache/cord-274097-11hvriqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274097-11hvriqy.txt' === file2bib.sh === id: cord-274567-xd37wxxf author: Monpoeho, S. title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date: 2002-07-13 pages: extension: .txt txt: ./txt/cord-274567-xd37wxxf.txt cache: ./cache/cord-274567-xd37wxxf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-274567-xd37wxxf.txt' === file2bib.sh === id: cord-276997-hbovh7s9 author: Alsved, Malin title: Aerosolization and recovery of viable murine norovirus in an experimental setup date: 2020-09-29 pages: extension: .txt txt: ./txt/cord-276997-hbovh7s9.txt cache: ./cache/cord-276997-hbovh7s9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276997-hbovh7s9.txt' === file2bib.sh === id: cord-278099-ypov9ha3 author: Kumar, Surender title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants date: 2017-08-03 pages: extension: .txt txt: ./txt/cord-278099-ypov9ha3.txt cache: ./cache/cord-278099-ypov9ha3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278099-ypov9ha3.txt' === file2bib.sh === id: cord-276364-zyw5aukk author: Wong, Ho Him title: Manipulation of autophagy by (+) RNA viruses date: 2019-08-08 pages: extension: .txt txt: ./txt/cord-276364-zyw5aukk.txt cache: ./cache/cord-276364-zyw5aukk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276364-zyw5aukk.txt' === file2bib.sh === id: cord-274785-9jgg8ukr author: Zhang, Qiang title: Viral Regulation of RNA Granules in Infected Cells date: 2019-04-29 pages: extension: .txt txt: ./txt/cord-274785-9jgg8ukr.txt cache: ./cache/cord-274785-9jgg8ukr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-274785-9jgg8ukr.txt' === file2bib.sh === id: cord-277841-7sp8ftbc author: Kumari, Pratibha title: Potential diagnostics and therapeutic approaches in COVID-19 date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-277841-7sp8ftbc.txt cache: ./cache/cord-277841-7sp8ftbc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277841-7sp8ftbc.txt' === file2bib.sh === id: cord-276493-hoaxv5e0 author: Jeong, Gi Uk title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-276493-hoaxv5e0.txt cache: ./cache/cord-276493-hoaxv5e0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-276493-hoaxv5e0.txt' === file2bib.sh === id: cord-277318-cwuls6xs author: Visscher, Koen title: −1 Programmed Ribosomal Frameshifting as a Force-Dependent Process date: 2016-02-02 pages: extension: .txt txt: ./txt/cord-277318-cwuls6xs.txt cache: ./cache/cord-277318-cwuls6xs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-277318-cwuls6xs.txt' === file2bib.sh === id: cord-277687-u3q36o3e author: Shean, Ryan C. title: VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank date: 2019-01-23 pages: extension: .txt txt: ./txt/cord-277687-u3q36o3e.txt cache: ./cache/cord-277687-u3q36o3e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-277687-u3q36o3e.txt' === file2bib.sh === id: cord-276198-psjua913 author: V’kovski, Philip title: New insights on the role of paired membrane structures in coronavirus replication date: 2015-04-16 pages: extension: .txt txt: ./txt/cord-276198-psjua913.txt cache: ./cache/cord-276198-psjua913.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276198-psjua913.txt' === file2bib.sh === id: cord-279070-cy049zbi author: Hewson, I. title: Description of viral assemblages associated with the Gorgonia ventalina holobiont date: 2011-12-29 pages: extension: .txt txt: ./txt/cord-279070-cy049zbi.txt cache: ./cache/cord-279070-cy049zbi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279070-cy049zbi.txt' === file2bib.sh === id: cord-276541-u9ebql5a author: Lan, Yungang title: Inhibition of porcine hemagglutinating encephalomyelitis virus replication by short hairpin RNAs targeting of the nucleocapsid gene in a porcine kidney cell line date: 2011-11-25 pages: extension: .txt txt: ./txt/cord-276541-u9ebql5a.txt cache: ./cache/cord-276541-u9ebql5a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-276541-u9ebql5a.txt' === file2bib.sh === id: cord-277306-r8jki3x4 author: Osborne, Christina title: Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans date: 2011-05-12 pages: extension: .txt txt: ./txt/cord-277306-r8jki3x4.txt cache: ./cache/cord-277306-r8jki3x4.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277306-r8jki3x4.txt' === file2bib.sh === id: cord-276575-jfug80yu author: Aigner, Achim title: Applications of RNA interference: current state and prospects for siRNA-based strategies in vivo date: 2007-04-25 pages: extension: .txt txt: ./txt/cord-276575-jfug80yu.txt cache: ./cache/cord-276575-jfug80yu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276575-jfug80yu.txt' === file2bib.sh === id: cord-279841-oq25o4qr author: Ahlquist, Paul title: Viral and host determinants of RNA virus vector replication and expression date: 2005-03-07 pages: extension: .txt txt: ./txt/cord-279841-oq25o4qr.txt cache: ./cache/cord-279841-oq25o4qr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279841-oq25o4qr.txt' === file2bib.sh === id: cord-278123-mq56em3z author: Hasan, Mohammad Rubayet title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-278123-mq56em3z.txt cache: ./cache/cord-278123-mq56em3z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278123-mq56em3z.txt' === file2bib.sh === id: cord-277566-j3ehiwn9 author: Verheije, Monique H. title: Mouse Hepatitis Coronavirus RNA Replication Depends on GBF1-Mediated ARF1 Activation date: 2008-06-13 pages: extension: .txt txt: ./txt/cord-277566-j3ehiwn9.txt cache: ./cache/cord-277566-j3ehiwn9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277566-j3ehiwn9.txt' === file2bib.sh === id: cord-278436-job4854r author: Xie, Mao-Hua title: A phage RNA-binding protein binds to a non-cognate structured RNA and stabilizes its core structure date: 2009-01-09 pages: extension: .txt txt: ./txt/cord-278436-job4854r.txt cache: ./cache/cord-278436-job4854r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278436-job4854r.txt' === file2bib.sh === id: cord-278482-j5zlismf author: Taylor, Raymond title: BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date: 2016-06-30 pages: extension: .txt txt: ./txt/cord-278482-j5zlismf.txt cache: ./cache/cord-278482-j5zlismf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278482-j5zlismf.txt' === file2bib.sh === id: cord-276006-mjjnkqv6 author: Jarach, Natanel title: Polymers in the Medical Antiviral Front-Line date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-276006-mjjnkqv6.txt cache: ./cache/cord-276006-mjjnkqv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276006-mjjnkqv6.txt' === file2bib.sh === id: cord-280272-mn596x1p author: Akhrymuk, Ivan title: Magnetic Nanotrap Particles Preserve the Stability of Venezuelan Equine Encephalitis Virus in Blood for Laboratory Detection date: 2020-01-28 pages: extension: .txt txt: ./txt/cord-280272-mn596x1p.txt cache: ./cache/cord-280272-mn596x1p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280272-mn596x1p.txt' === file2bib.sh === id: cord-275795-ee7qyw5h author: Monette, Anne title: T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-275795-ee7qyw5h.txt cache: ./cache/cord-275795-ee7qyw5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-275795-ee7qyw5h.txt' === file2bib.sh === id: cord-279418-3r1ijafm author: Nevers, Quentin title: Negri bodies and other virus membrane-less replication compartments() date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-279418-3r1ijafm.txt cache: ./cache/cord-279418-3r1ijafm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279418-3r1ijafm.txt' === file2bib.sh === id: cord-279404-u0fs6xcj author: Carrington, Christine V.F. title: Detection and Phylogenetic Analysis of Group 1 Coronaviruses in South American Bats date: 2008-12-17 pages: extension: .txt txt: ./txt/cord-279404-u0fs6xcj.txt cache: ./cache/cord-279404-u0fs6xcj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279404-u0fs6xcj.txt' === file2bib.sh === id: cord-280795-wtrt13ij author: Han, Yu-Tsung title: Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus date: 2007-10-10 pages: extension: .txt txt: ./txt/cord-280795-wtrt13ij.txt cache: ./cache/cord-280795-wtrt13ij.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280795-wtrt13ij.txt' === file2bib.sh === id: cord-280003-ndpuezpo author: Lou, Bin title: Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date: 2020-03-27 pages: extension: .txt txt: ./txt/cord-280003-ndpuezpo.txt cache: ./cache/cord-280003-ndpuezpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280003-ndpuezpo.txt' === file2bib.sh === id: cord-278684-txlvla0j author: Gonzalez–Dunia, Daniel title: Borna Disease Virus and the Brain date: 1998-01-30 pages: extension: .txt txt: ./txt/cord-278684-txlvla0j.txt cache: ./cache/cord-278684-txlvla0j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278684-txlvla0j.txt' === file2bib.sh === id: cord-277547-2vim1wno author: Zandi, Keivan title: Antiviral activity of four types of bioflavonoid against dengue virus type-2 date: 2011-12-28 pages: extension: .txt txt: ./txt/cord-277547-2vim1wno.txt cache: ./cache/cord-277547-2vim1wno.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277547-2vim1wno.txt' === file2bib.sh === id: cord-281020-g1muealp author: Belov, George A title: (+)RNA viruses rewire cellular pathways to build replication organelles date: 2012-10-01 pages: extension: .txt txt: ./txt/cord-281020-g1muealp.txt cache: ./cache/cord-281020-g1muealp.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281020-g1muealp.txt' === file2bib.sh === id: cord-276914-44ji0g78 author: Chen, Weilie title: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity date: 2020-02-26 pages: extension: .txt txt: ./txt/cord-276914-44ji0g78.txt cache: ./cache/cord-276914-44ji0g78.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-276914-44ji0g78.txt' === file2bib.sh === id: cord-280048-b4dz1lnn author: Domingo, Esteban title: Viral quasispecies date: 2019-10-17 pages: extension: .txt txt: ./txt/cord-280048-b4dz1lnn.txt cache: ./cache/cord-280048-b4dz1lnn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280048-b4dz1lnn.txt' === file2bib.sh === id: cord-279985-de0b27nq author: Anraku, Itaru title: Kunjin replicon-based simian immunodeficiency virus gag vaccines date: 2008-06-19 pages: extension: .txt txt: ./txt/cord-279985-de0b27nq.txt cache: ./cache/cord-279985-de0b27nq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-279985-de0b27nq.txt' === file2bib.sh === id: cord-280001-y7pvj2l1 author: Patel, Robin title: Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date: 2020-03-26 pages: extension: .txt txt: ./txt/cord-280001-y7pvj2l1.txt cache: ./cache/cord-280001-y7pvj2l1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280001-y7pvj2l1.txt' === file2bib.sh === id: cord-277874-cr53ycrm author: Neault, N. title: SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date: 2020-09-03 pages: extension: .txt txt: ./txt/cord-277874-cr53ycrm.txt cache: ./cache/cord-277874-cr53ycrm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277874-cr53ycrm.txt' === file2bib.sh === id: cord-280130-ewqe9edq author: Weber, Friedemann title: Viral suppression of the interferon system date: 2007-01-27 pages: extension: .txt txt: ./txt/cord-280130-ewqe9edq.txt cache: ./cache/cord-280130-ewqe9edq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280130-ewqe9edq.txt' === file2bib.sh === id: cord-279623-ezax8c1u author: Huang, Yong title: Regulatory long non-coding RNA and its functions date: 2012-04-26 pages: extension: .txt txt: ./txt/cord-279623-ezax8c1u.txt cache: ./cache/cord-279623-ezax8c1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-279623-ezax8c1u.txt' === file2bib.sh === id: cord-281124-4nhy35xn author: Soowannayan, Chumporn title: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date: 2011-08-03 pages: extension: .txt txt: ./txt/cord-281124-4nhy35xn.txt cache: ./cache/cord-281124-4nhy35xn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281124-4nhy35xn.txt' === file2bib.sh === id: cord-278635-vwdxr1bl author: Świętoń, Edyta title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-278635-vwdxr1bl.txt cache: ./cache/cord-278635-vwdxr1bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278635-vwdxr1bl.txt' === file2bib.sh === id: cord-281174-3c1vue0y author: Greene, Shermalyn R title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 pages: extension: .txt txt: ./txt/cord-281174-3c1vue0y.txt cache: ./cache/cord-281174-3c1vue0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-281174-3c1vue0y.txt' === file2bib.sh === id: cord-280941-ds6x0yym author: Kim, Young-Seok title: Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date: 2018-05-17 pages: extension: .txt txt: ./txt/cord-280941-ds6x0yym.txt cache: ./cache/cord-280941-ds6x0yym.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280941-ds6x0yym.txt' === file2bib.sh === id: cord-282372-nmii30mc author: Youk, Jeonghwan title: Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-282372-nmii30mc.txt cache: ./cache/cord-282372-nmii30mc.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-282372-nmii30mc.txt' === file2bib.sh === id: cord-277830-6fsz9iy7 author: Saikatendu, Kumar Singh title: Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date: 2005-11-08 pages: extension: .txt txt: ./txt/cord-277830-6fsz9iy7.txt cache: ./cache/cord-277830-6fsz9iy7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-277830-6fsz9iy7.txt' === file2bib.sh === id: cord-278186-t3izmz6n author: Le Naour, Julie title: Trial watch: TLR3 agonists in cancer therapy date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-278186-t3izmz6n.txt cache: ./cache/cord-278186-t3izmz6n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278186-t3izmz6n.txt' === file2bib.sh === id: cord-278081-tk7vn1v1 author: Brooks, Wesley H. title: Viral Impact in Autoimmune Diseases: Expanding the “X Chromosome–Nucleolus Nexus” Hypothesis date: 2017-11-28 pages: extension: .txt txt: ./txt/cord-278081-tk7vn1v1.txt cache: ./cache/cord-278081-tk7vn1v1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278081-tk7vn1v1.txt' === file2bib.sh === id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 pages: extension: .txt txt: ./txt/cord-022888-dnsdg04n.txt cache: ./cache/cord-022888-dnsdg04n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 14 resourceName b'cord-022888-dnsdg04n.txt' === file2bib.sh === id: cord-279691-v5kpmk0b author: Hagemeijer, Marne C. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 pages: extension: .txt txt: ./txt/cord-279691-v5kpmk0b.txt cache: ./cache/cord-279691-v5kpmk0b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279691-v5kpmk0b.txt' === file2bib.sh === id: cord-278647-krh63hqp author: Carter, Robert W title: A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918 date: 2012-10-12 pages: extension: .txt txt: ./txt/cord-278647-krh63hqp.txt cache: ./cache/cord-278647-krh63hqp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-278647-krh63hqp.txt' === file2bib.sh === id: cord-278250-dwok857k author: Li, Heng title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date: 2019-08-19 pages: extension: .txt txt: ./txt/cord-278250-dwok857k.txt cache: ./cache/cord-278250-dwok857k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-278250-dwok857k.txt' === file2bib.sh === id: cord-279346-7del8d2p author: Callendret, Benoît title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date: 2007-07-05 pages: extension: .txt txt: ./txt/cord-279346-7del8d2p.txt cache: ./cache/cord-279346-7del8d2p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-279346-7del8d2p.txt' === file2bib.sh === id: cord-278055-v2ed3tei author: Sia, Sin Fun title: Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-278055-v2ed3tei.txt cache: ./cache/cord-278055-v2ed3tei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-278055-v2ed3tei.txt' === file2bib.sh === id: cord-280994-w8dtfjel author: Peng, Qi title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-280994-w8dtfjel.txt cache: ./cache/cord-280994-w8dtfjel.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-280994-w8dtfjel.txt' === file2bib.sh === id: cord-281385-oxohdfpu author: Noble, Christian G. title: Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine date: 2014-09-19 pages: extension: .txt txt: ./txt/cord-281385-oxohdfpu.txt cache: ./cache/cord-281385-oxohdfpu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281385-oxohdfpu.txt' === file2bib.sh === id: cord-286332-cdg4im5h author: van Beurden, Steven J. title: A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination date: 2017-06-12 pages: extension: .txt txt: ./txt/cord-286332-cdg4im5h.txt cache: ./cache/cord-286332-cdg4im5h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286332-cdg4im5h.txt' === file2bib.sh === id: cord-281717-kzd9vvci author: Digard, Paul title: Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-281717-kzd9vvci.txt cache: ./cache/cord-281717-kzd9vvci.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281717-kzd9vvci.txt' === file2bib.sh === id: cord-283132-rfw8njpo author: Olsen, Christopher W. title: A review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination date: 1993-07-31 pages: extension: .txt txt: ./txt/cord-283132-rfw8njpo.txt cache: ./cache/cord-283132-rfw8njpo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283132-rfw8njpo.txt' === file2bib.sh === id: cord-282764-d9x1wii6 author: Chang, Chia-Yin title: Influence of intron and exon splicing enhancers on mammalian cell expression of a truncated spike protein of SARS-CoV and its implication for subunit vaccine development date: 2006-02-20 pages: extension: .txt txt: ./txt/cord-282764-d9x1wii6.txt cache: ./cache/cord-282764-d9x1wii6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282764-d9x1wii6.txt' === file2bib.sh === id: cord-280616-9mwr6a4x author: Yang, Ying title: Small non-coding RNAs-based bone regulation and targeting therapeutic strategies date: 2017-11-15 pages: extension: .txt txt: ./txt/cord-280616-9mwr6a4x.txt cache: ./cache/cord-280616-9mwr6a4x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-280616-9mwr6a4x.txt' === file2bib.sh === id: cord-280427-smqc23vr author: Singla, Rubal title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 pages: extension: .txt txt: ./txt/cord-280427-smqc23vr.txt cache: ./cache/cord-280427-smqc23vr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-280427-smqc23vr.txt' === file2bib.sh === id: cord-285290-l7mnq4yb author: Warner, Katherine Deigan title: Principles for targeting RNA with drug-like small molecules date: 2018-07-06 pages: extension: .txt txt: ./txt/cord-285290-l7mnq4yb.txt cache: ./cache/cord-285290-l7mnq4yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285290-l7mnq4yb.txt' === file2bib.sh === id: cord-284549-edliu3it author: Zhou, Hui title: Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells date: 2019-11-27 pages: extension: .txt txt: ./txt/cord-284549-edliu3it.txt cache: ./cache/cord-284549-edliu3it.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284549-edliu3it.txt' === file2bib.sh === id: cord-281254-x7ivjvti author: Chang, Zhijie title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date: 2012-08-16 pages: extension: .txt txt: ./txt/cord-281254-x7ivjvti.txt cache: ./cache/cord-281254-x7ivjvti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281254-x7ivjvti.txt' === file2bib.sh === id: cord-286298-pn9nwl64 author: Helmy, Yosra A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 pages: extension: .txt txt: ./txt/cord-286298-pn9nwl64.txt cache: ./cache/cord-286298-pn9nwl64.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286298-pn9nwl64.txt' === file2bib.sh === id: cord-281285-5g1rw202 author: Simonis, Alexander title: A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-281285-5g1rw202.txt cache: ./cache/cord-281285-5g1rw202.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-281285-5g1rw202.txt' === file2bib.sh === id: cord-284941-wfn0pnev author: Samal, S.K. title: Paramyxoviruses of Animals date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-284941-wfn0pnev.txt cache: ./cache/cord-284941-wfn0pnev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284941-wfn0pnev.txt' === file2bib.sh === id: cord-286352-uftl1mx5 author: Baril, Martin title: The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot date: 2003-08-15 pages: extension: .txt txt: ./txt/cord-286352-uftl1mx5.txt cache: ./cache/cord-286352-uftl1mx5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286352-uftl1mx5.txt' === file2bib.sh === id: cord-285935-5rsk6g7l author: Kinast, Volker title: Hepatitis E Virus Drug Development date: 2019-05-28 pages: extension: .txt txt: ./txt/cord-285935-5rsk6g7l.txt cache: ./cache/cord-285935-5rsk6g7l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285935-5rsk6g7l.txt' === file2bib.sh === id: cord-286232-jo24ia4s author: Hasebe, Rie title: Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways date: 2009-10-25 pages: extension: .txt txt: ./txt/cord-286232-jo24ia4s.txt cache: ./cache/cord-286232-jo24ia4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286232-jo24ia4s.txt' === file2bib.sh === id: cord-284076-087oltss author: Patel, Deendayal title: Peptide-conjugated morpholino oligomers inhibit porcine reproductive and respiratory syndrome virus replication date: 2007-10-04 pages: extension: .txt txt: ./txt/cord-284076-087oltss.txt cache: ./cache/cord-284076-087oltss.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284076-087oltss.txt' === file2bib.sh === id: cord-285159-gytebbua author: Eydoux, Cecilia title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date: 2020-07-07 pages: extension: .txt txt: ./txt/cord-285159-gytebbua.txt cache: ./cache/cord-285159-gytebbua.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285159-gytebbua.txt' === file2bib.sh === id: cord-286149-awhnjwyc author: Hoon‐Hanks, L.L. title: Metagenomic Investigation of Idiopathic Meningoencephalomyelitis in Dogs date: 2017-12-02 pages: extension: .txt txt: ./txt/cord-286149-awhnjwyc.txt cache: ./cache/cord-286149-awhnjwyc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286149-awhnjwyc.txt' === file2bib.sh === id: cord-283168-kl1hoa1x author: Farkas, Tibor title: Molecular detection of novel picornaviruses in chickens and turkeys date: 2011-12-13 pages: extension: .txt txt: ./txt/cord-283168-kl1hoa1x.txt cache: ./cache/cord-283168-kl1hoa1x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283168-kl1hoa1x.txt' === file2bib.sh === id: cord-283439-hqdq2qrh author: Rahman, Mohammad Tariqur title: Can Zn Be a Critical Element in COVID-19 Treatment? date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-283439-hqdq2qrh.txt cache: ./cache/cord-283439-hqdq2qrh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283439-hqdq2qrh.txt' === file2bib.sh === id: cord-287093-9mertwj7 author: Netherton, Christopher L title: Virus factories, double membrane vesicles and viroplasm generated in animal cells date: 2011-10-12 pages: extension: .txt txt: ./txt/cord-287093-9mertwj7.txt cache: ./cache/cord-287093-9mertwj7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287093-9mertwj7.txt' === file2bib.sh === id: cord-283895-1p5uog38 author: Trottier, J. title: Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-283895-1p5uog38.txt cache: ./cache/cord-283895-1p5uog38.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-283895-1p5uog38.txt' === file2bib.sh === id: cord-287501-7it4kh0e author: Roh, Changhyun title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date: 2012-05-03 pages: extension: .txt txt: ./txt/cord-287501-7it4kh0e.txt cache: ./cache/cord-287501-7it4kh0e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287501-7it4kh0e.txt' === file2bib.sh === id: cord-283097-rlf5nv5q author: Ganar, Ketan title: Newcastle disease virus: Current status and our understanding date: 2014-05-12 pages: extension: .txt txt: ./txt/cord-283097-rlf5nv5q.txt cache: ./cache/cord-283097-rlf5nv5q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283097-rlf5nv5q.txt' === file2bib.sh === id: cord-286416-8eu6wp9b author: Valiente-Echeverría, Fernando title: Viral modulation of stress granules date: 2012-06-14 pages: extension: .txt txt: ./txt/cord-286416-8eu6wp9b.txt cache: ./cache/cord-286416-8eu6wp9b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-286416-8eu6wp9b.txt' === file2bib.sh === id: cord-281565-v8s2ski3 author: Belmonte-Reche, Efres title: Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2 date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-281565-v8s2ski3.txt cache: ./cache/cord-281565-v8s2ski3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-281565-v8s2ski3.txt' === file2bib.sh === id: cord-287228-0qm939ve author: Hong, Ke title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-287228-0qm939ve.txt cache: ./cache/cord-287228-0qm939ve.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287228-0qm939ve.txt' === file2bib.sh === id: cord-282618-tjvjlyn9 author: Luke, J M title: Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers date: 2010-11-25 pages: extension: .txt txt: ./txt/cord-282618-tjvjlyn9.txt cache: ./cache/cord-282618-tjvjlyn9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-282618-tjvjlyn9.txt' === file2bib.sh === id: cord-281281-knelqmzx author: Villas-Boas, Gustavo R. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 pages: extension: .txt txt: ./txt/cord-281281-knelqmzx.txt cache: ./cache/cord-281281-knelqmzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-281281-knelqmzx.txt' === file2bib.sh === id: cord-287153-jbuuph6w author: Lund, Morten title: Experimental Piscine orthoreovirus infection mediates protection against pancreas disease in Atlantic salmon (Salmo salar) date: 2016-10-21 pages: extension: .txt txt: ./txt/cord-287153-jbuuph6w.txt cache: ./cache/cord-287153-jbuuph6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287153-jbuuph6w.txt' === file2bib.sh === id: cord-287275-vwyny1vt author: Zhang, Meng-Jia title: Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China date: 2018-10-30 pages: extension: .txt txt: ./txt/cord-287275-vwyny1vt.txt cache: ./cache/cord-287275-vwyny1vt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287275-vwyny1vt.txt' === file2bib.sh === id: cord-287396-18p171nr author: Schroyen, Martine title: Current transcriptomics in pig immunity research date: 2014-11-15 pages: extension: .txt txt: ./txt/cord-287396-18p171nr.txt cache: ./cache/cord-287396-18p171nr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287396-18p171nr.txt' === file2bib.sh === id: cord-287324-ecpicv5v author: Qiu, Yuan title: Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods date: 2017-06-02 pages: extension: .txt txt: ./txt/cord-287324-ecpicv5v.txt cache: ./cache/cord-287324-ecpicv5v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287324-ecpicv5v.txt' === file2bib.sh === id: cord-282742-eyukbot7 author: Diosa-Toro, Mayra title: Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date: 2013-02-20 pages: extension: .txt txt: ./txt/cord-282742-eyukbot7.txt cache: ./cache/cord-282742-eyukbot7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-282742-eyukbot7.txt' === file2bib.sh === id: cord-287372-ya5uvoki author: Böszörményi, Kinga P. title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date: 2020-11-05 pages: extension: .txt txt: ./txt/cord-287372-ya5uvoki.txt cache: ./cache/cord-287372-ya5uvoki.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287372-ya5uvoki.txt' === file2bib.sh === id: cord-287488-h102xn29 author: Araujo, Danielle Bastos title: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date: 2020-10-23 pages: extension: .txt txt: ./txt/cord-287488-h102xn29.txt cache: ./cache/cord-287488-h102xn29.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287488-h102xn29.txt' === file2bib.sh === id: cord-286877-0h5vgi5c author: Dahiya, Shyam S. title: Immunogenicity of a DNA-launched replicon-based canine parvovirus DNA vaccine expressing VP2 antigen in dogs date: 2012-10-31 pages: extension: .txt txt: ./txt/cord-286877-0h5vgi5c.txt cache: ./cache/cord-286877-0h5vgi5c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286877-0h5vgi5c.txt' === file2bib.sh === id: cord-284609-1q75zw6b author: King, Andrew M.Q. title: Recombination in RNA date: 1982-07-31 pages: extension: .txt txt: ./txt/cord-284609-1q75zw6b.txt cache: ./cache/cord-284609-1q75zw6b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-284609-1q75zw6b.txt' === file2bib.sh === id: cord-284933-flbibrcm author: Kim, Jong-Oh title: Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection date: 2017-01-13 pages: extension: .txt txt: ./txt/cord-284933-flbibrcm.txt cache: ./cache/cord-284933-flbibrcm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284933-flbibrcm.txt' === file2bib.sh === id: cord-287487-qeltdch7 author: Graepel, Kevin W. title: Proofreading-Deficient Coronaviruses Adapt for Increased Fitness over Long-Term Passage without Reversion of Exoribonuclease-Inactivating Mutations date: 2017-11-07 pages: extension: .txt txt: ./txt/cord-287487-qeltdch7.txt cache: ./cache/cord-287487-qeltdch7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-287487-qeltdch7.txt' === file2bib.sh === id: cord-287349-1zcq7kzx author: Chen, James title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-287349-1zcq7kzx.txt cache: ./cache/cord-287349-1zcq7kzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287349-1zcq7kzx.txt' === file2bib.sh === id: cord-283411-40ojqv1y author: Ben-Shmuel, Amir title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-283411-40ojqv1y.txt cache: ./cache/cord-283411-40ojqv1y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-283411-40ojqv1y.txt' === file2bib.sh === id: cord-288167-976qxja2 author: Park, Wan Beom title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date: 2018-05-09 pages: extension: .txt txt: ./txt/cord-288167-976qxja2.txt cache: ./cache/cord-288167-976qxja2.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288167-976qxja2.txt' === file2bib.sh === id: cord-284118-z8zwjvbu author: Baczko, Knut title: Measles virus gene expression in subacute sclerosing panencephalitis date: 1984-10-31 pages: extension: .txt txt: ./txt/cord-284118-z8zwjvbu.txt cache: ./cache/cord-284118-z8zwjvbu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284118-z8zwjvbu.txt' === file2bib.sh === id: cord-288962-jgtoehcr author: Andréoletti, Laurent title: Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date: 2000-06-06 pages: extension: .txt txt: ./txt/cord-288962-jgtoehcr.txt cache: ./cache/cord-288962-jgtoehcr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288962-jgtoehcr.txt' === file2bib.sh === id: cord-287466-ag5y781z author: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-287466-ag5y781z.txt cache: ./cache/cord-287466-ag5y781z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287466-ag5y781z.txt' === file2bib.sh === id: cord-283880-lrrkuist author: Kumar, Arvind title: Evolution of selective-sequencing approaches for virus discovery and virome analysis date: 2017-07-15 pages: extension: .txt txt: ./txt/cord-283880-lrrkuist.txt cache: ./cache/cord-283880-lrrkuist.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283880-lrrkuist.txt' === file2bib.sh === id: cord-283998-whwksoxt author: Tannock, Gregory A. title: The RNA of human coronavirus OC-43 date: 1977-12-31 pages: extension: .txt txt: ./txt/cord-283998-whwksoxt.txt cache: ./cache/cord-283998-whwksoxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-283998-whwksoxt.txt' === file2bib.sh === id: cord-286243-ddpemgqt author: Whitaker, Amy M. title: APE1: A skilled nucleic acid surgeon date: 2018-11-30 pages: extension: .txt txt: ./txt/cord-286243-ddpemgqt.txt cache: ./cache/cord-286243-ddpemgqt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286243-ddpemgqt.txt' === file2bib.sh === id: cord-288093-012ipcdr author: Bouvette, Jonathan title: High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date: 2018-12-06 pages: extension: .txt txt: ./txt/cord-288093-012ipcdr.txt cache: ./cache/cord-288093-012ipcdr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288093-012ipcdr.txt' === file2bib.sh === id: cord-283590-xvnv17zy author: Chen, Dabiao title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 pages: extension: .txt txt: ./txt/cord-283590-xvnv17zy.txt cache: ./cache/cord-283590-xvnv17zy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-283590-xvnv17zy.txt' === file2bib.sh === id: cord-283346-0v4b6do2 author: Ansari, Abdul Wahid title: Host chemokine (C-C motif) ligand-2 (CCL2) is differentially regulated in HIV type 1 (HIV-1)-infected individuals date: 2006-08-17 pages: extension: .txt txt: ./txt/cord-283346-0v4b6do2.txt cache: ./cache/cord-283346-0v4b6do2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-283346-0v4b6do2.txt' === file2bib.sh === id: cord-288390-p1q3v1ie author: Habjan, Matthias title: Cytoplasmic sensing of viral nucleic acids date: 2015-02-07 pages: extension: .txt txt: ./txt/cord-288390-p1q3v1ie.txt cache: ./cache/cord-288390-p1q3v1ie.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288390-p1q3v1ie.txt' === file2bib.sh === id: cord-289038-15yp9uqy author: Chow, Jonathan Tak-Sum title: Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date: 2020-08-26 pages: extension: .txt txt: ./txt/cord-289038-15yp9uqy.txt cache: ./cache/cord-289038-15yp9uqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-289038-15yp9uqy.txt' === file2bib.sh === id: cord-285330-td4vr0zv author: Mohammadi, Ali title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date: 2015-11-12 pages: extension: .txt txt: ./txt/cord-285330-td4vr0zv.txt cache: ./cache/cord-285330-td4vr0zv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285330-td4vr0zv.txt' === file2bib.sh === id: cord-285868-fz5utxss author: Jheng, Jia-Rong title: ER stress, autophagy, and RNA viruses date: 2014-08-05 pages: extension: .txt txt: ./txt/cord-285868-fz5utxss.txt cache: ./cache/cord-285868-fz5utxss.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285868-fz5utxss.txt' === file2bib.sh === id: cord-288701-nx9fg4yn author: Mari, Viviana title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 pages: extension: .txt txt: ./txt/cord-288701-nx9fg4yn.txt cache: ./cache/cord-288701-nx9fg4yn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288701-nx9fg4yn.txt' === file2bib.sh === id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-031907-ilhr3iu5.txt cache: ./cache/cord-031907-ilhr3iu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 18 resourceName b'cord-031907-ilhr3iu5.txt' === file2bib.sh === id: cord-289192-1ecr16a3 author: Fujita, Motomichi title: Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA date: 2019-02-01 pages: extension: .txt txt: ./txt/cord-289192-1ecr16a3.txt cache: ./cache/cord-289192-1ecr16a3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-289192-1ecr16a3.txt' === file2bib.sh === id: cord-288651-bgo8istm author: SHI, Yi title: Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date: 2005-03-17 pages: extension: .txt txt: ./txt/cord-288651-bgo8istm.txt cache: ./cache/cord-288651-bgo8istm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-288651-bgo8istm.txt' === file2bib.sh === id: cord-289093-si8btsab author: Beard, Philippa M. title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 pages: extension: .txt txt: ./txt/cord-289093-si8btsab.txt cache: ./cache/cord-289093-si8btsab.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-289093-si8btsab.txt' === file2bib.sh === id: cord-286711-nr6vnl9h author: nan title: Other viruses causing gastroenteritis date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-286711-nr6vnl9h.txt cache: ./cache/cord-286711-nr6vnl9h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286711-nr6vnl9h.txt' === file2bib.sh === id: cord-289321-ahl46ql9 author: van Buuren, Nicholas title: Transmission genetics of drug-resistant hepatitis C virus date: 2018-03-28 pages: extension: .txt txt: ./txt/cord-289321-ahl46ql9.txt cache: ./cache/cord-289321-ahl46ql9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289321-ahl46ql9.txt' === file2bib.sh === id: cord-285262-690kpupt author: Imre, Gergely title: The involvement of regulated cell death forms in modulating the bacterial and viral pathogenesis date: 2020-01-27 pages: extension: .txt txt: ./txt/cord-285262-690kpupt.txt cache: ./cache/cord-285262-690kpupt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285262-690kpupt.txt' === file2bib.sh === id: cord-284707-72vx11aq author: Leibowitz, Julian L. title: Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells date: 1988-09-30 pages: extension: .txt txt: ./txt/cord-284707-72vx11aq.txt cache: ./cache/cord-284707-72vx11aq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-284707-72vx11aq.txt' === file2bib.sh === id: cord-288960-v6l6o5va author: Li, Yang title: Regulating STING in health and disease date: 2017-06-07 pages: extension: .txt txt: ./txt/cord-288960-v6l6o5va.txt cache: ./cache/cord-288960-v6l6o5va.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288960-v6l6o5va.txt' === file2bib.sh === id: cord-288879-rj03dsib author: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 pages: extension: .txt txt: ./txt/cord-288879-rj03dsib.txt cache: ./cache/cord-288879-rj03dsib.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-288879-rj03dsib.txt' === file2bib.sh === id: cord-289407-8fje16z1 author: Moore, G. title: Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date: 2020-09-25 pages: extension: .txt txt: ./txt/cord-289407-8fje16z1.txt cache: ./cache/cord-289407-8fje16z1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289407-8fje16z1.txt' === file2bib.sh === id: cord-284156-btb4oodz author: Liu, Yiliu title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date: 2017-01-03 pages: extension: .txt txt: ./txt/cord-284156-btb4oodz.txt cache: ./cache/cord-284156-btb4oodz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-284156-btb4oodz.txt' === file2bib.sh === id: cord-286103-cgky6ar6 author: Otaki, Momoko title: Inhibition of measles virus and subacute sclerosing panencephalitis virus by RNA interference date: 2006-02-13 pages: extension: .txt txt: ./txt/cord-286103-cgky6ar6.txt cache: ./cache/cord-286103-cgky6ar6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286103-cgky6ar6.txt' === file2bib.sh === id: cord-290481-i2ppvsh5 author: Dolja, Valerian V. title: Comparative and functional genomics of closteroviruses date: 2006-03-09 pages: extension: .txt txt: ./txt/cord-290481-i2ppvsh5.txt cache: ./cache/cord-290481-i2ppvsh5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290481-i2ppvsh5.txt' === file2bib.sh === id: cord-285505-8norumv6 author: Vere Hodge, R. Anthony title: Meeting report: 27th International conference on antiviral research, in Raleigh, NC, USA date: 2014-09-16 pages: extension: .txt txt: ./txt/cord-285505-8norumv6.txt cache: ./cache/cord-285505-8norumv6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285505-8norumv6.txt' === file2bib.sh === id: cord-291026-99cit4ig author: Lung, O. title: Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date: 2015-01-27 pages: extension: .txt txt: ./txt/cord-291026-99cit4ig.txt cache: ./cache/cord-291026-99cit4ig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291026-99cit4ig.txt' === file2bib.sh === id: cord-285676-4kgy20o9 author: de Vries, Antoine A.F. title: The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses date: 1997-02-28 pages: extension: .txt txt: ./txt/cord-285676-4kgy20o9.txt cache: ./cache/cord-285676-4kgy20o9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-285676-4kgy20o9.txt' === file2bib.sh === id: cord-290472-w77cmljm author: Sharon, Donald title: Systems Biology Approaches to Disease Marker Discovery date: 2010-06-09 pages: extension: .txt txt: ./txt/cord-290472-w77cmljm.txt cache: ./cache/cord-290472-w77cmljm.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290472-w77cmljm.txt' === file2bib.sh === id: cord-290550-u8x9drva author: Radford, Alan D. title: Application of next-generation sequencing technologies in virology date: 2012-09-17 pages: extension: .txt txt: ./txt/cord-290550-u8x9drva.txt cache: ./cache/cord-290550-u8x9drva.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290550-u8x9drva.txt' === file2bib.sh === id: cord-291765-97lk5qfo author: Eckerle, Lance D. title: Effects of Mutagenesis of Murine Hepatitis Virus NSP1 and NSP14 on Replication in Culture date: 2006 pages: extension: .txt txt: ./txt/cord-291765-97lk5qfo.txt cache: ./cache/cord-291765-97lk5qfo.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291765-97lk5qfo.txt' === file2bib.sh === id: cord-291029-oldket3n author: Sefers, Susan E. title: QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date: 2005-07-21 pages: extension: .txt txt: ./txt/cord-291029-oldket3n.txt cache: ./cache/cord-291029-oldket3n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291029-oldket3n.txt' === file2bib.sh === id: cord-286343-s8n1ldol author: Martin, Javier title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 pages: extension: .txt txt: ./txt/cord-286343-s8n1ldol.txt cache: ./cache/cord-286343-s8n1ldol.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286343-s8n1ldol.txt' === file2bib.sh === id: cord-290744-m0vpizuh author: Kindler, E. title: Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date: 2016-09-09 pages: extension: .txt txt: ./txt/cord-290744-m0vpizuh.txt cache: ./cache/cord-290744-m0vpizuh.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-290744-m0vpizuh.txt' === file2bib.sh === id: cord-285785-29ohzeug author: Chen, Xiaolan title: Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-285785-29ohzeug.txt cache: ./cache/cord-285785-29ohzeug.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-285785-29ohzeug.txt' === file2bib.sh === id: cord-291749-revhbd0q author: Mongan, Arthur Elia title: Portable sequencer in the fight against infectious disease date: 2019-10-03 pages: extension: .txt txt: ./txt/cord-291749-revhbd0q.txt cache: ./cache/cord-291749-revhbd0q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291749-revhbd0q.txt' === file2bib.sh === id: cord-291063-de7v4e5s author: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 pages: extension: .txt txt: ./txt/cord-291063-de7v4e5s.txt cache: ./cache/cord-291063-de7v4e5s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291063-de7v4e5s.txt' === file2bib.sh === id: cord-287658-c2lljdi7 author: Lopez-Rincon, Alejandro title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-287658-c2lljdi7.txt cache: ./cache/cord-287658-c2lljdi7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287658-c2lljdi7.txt' === file2bib.sh === id: cord-290801-dv6aak01 author: Ivanyi-Nagy, Roland title: Reprint of: Core protein-mediated 5′–3′ annealing of the West Nile virus genomic RNA in vitro() date: 2012-09-27 pages: extension: .txt txt: ./txt/cord-290801-dv6aak01.txt cache: ./cache/cord-290801-dv6aak01.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290801-dv6aak01.txt' === file2bib.sh === id: cord-286719-1xjmlwqr author: Draz, Mohamed Shehata title: Applications of gold nanoparticles in virus detection date: 2018-02-15 pages: extension: .txt txt: ./txt/cord-286719-1xjmlwqr.txt cache: ./cache/cord-286719-1xjmlwqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-286719-1xjmlwqr.txt' === file2bib.sh === id: cord-290254-m9l8ntur author: Rodriguez-Manzano, J. title: A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-290254-m9l8ntur.txt cache: ./cache/cord-290254-m9l8ntur.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290254-m9l8ntur.txt' === file2bib.sh === id: cord-291513-vpehn6nx author: Minich, Jeremiah title: Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-291513-vpehn6nx.txt cache: ./cache/cord-291513-vpehn6nx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291513-vpehn6nx.txt' === file2bib.sh === id: cord-290813-6ylwj5je author: Ng, Enders K. O. title: Molecular Diagnosis of Severe Acute Respiratory Syndrome date: 2006 pages: extension: .txt txt: ./txt/cord-290813-6ylwj5je.txt cache: ./cache/cord-290813-6ylwj5je.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-290813-6ylwj5je.txt' === file2bib.sh === id: cord-291677-zcbyhsf1 author: Wilamowski, M. title: Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-291677-zcbyhsf1.txt cache: ./cache/cord-291677-zcbyhsf1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291677-zcbyhsf1.txt' === file2bib.sh === id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 pages: extension: .txt txt: ./txt/cord-291860-dw1sfzqx.txt cache: ./cache/cord-291860-dw1sfzqx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291860-dw1sfzqx.txt' === file2bib.sh === id: cord-286842-04cuk2cn author: Plyusnina, Angelina title: Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture date: 2005-02-22 pages: extension: .txt txt: ./txt/cord-286842-04cuk2cn.txt cache: ./cache/cord-286842-04cuk2cn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-286842-04cuk2cn.txt' === file2bib.sh === id: cord-287018-g4y5kjju author: Konstantinova, P title: Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA date: 2006-05-18 pages: extension: .txt txt: ./txt/cord-287018-g4y5kjju.txt cache: ./cache/cord-287018-g4y5kjju.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287018-g4y5kjju.txt' === file2bib.sh === id: cord-287931-cxqzac4a author: Huang, Weiwei title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date: 2013-09-20 pages: extension: .txt txt: ./txt/cord-287931-cxqzac4a.txt cache: ./cache/cord-287931-cxqzac4a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-287931-cxqzac4a.txt' === file2bib.sh === id: cord-291962-rp172ugk author: Jing, Huiyuan title: Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 date: 2019-07-15 pages: extension: .txt txt: ./txt/cord-291962-rp172ugk.txt cache: ./cache/cord-291962-rp172ugk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291962-rp172ugk.txt' === file2bib.sh === id: cord-286603-4p3t0vre author: Duan, Zhiqiang title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-286603-4p3t0vre.txt cache: ./cache/cord-286603-4p3t0vre.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-286603-4p3t0vre.txt' === file2bib.sh === id: cord-289965-qcezqpze author: Lehmann, Kathleen C. title: Arterivirus nsp12 versus the coronavirus nsp16 2′-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins date: 2015-09-01 pages: extension: .txt txt: ./txt/cord-289965-qcezqpze.txt cache: ./cache/cord-289965-qcezqpze.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289965-qcezqpze.txt' === file2bib.sh === id: cord-294138-h7sfd1wa author: McIver, David J. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-294138-h7sfd1wa.txt cache: ./cache/cord-294138-h7sfd1wa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294138-h7sfd1wa.txt' === file2bib.sh === id: cord-293215-6flf5ig0 author: Eriksson, Klara Kristin title: Generation of Recombinant Coronaviruses Using Vaccinia Virus as the Cloning Vector and Stable Cell Lines Containing Coronaviral Replicon RNAs date: 2007-11-28 pages: extension: .txt txt: ./txt/cord-293215-6flf5ig0.txt cache: ./cache/cord-293215-6flf5ig0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-293215-6flf5ig0.txt' === file2bib.sh === id: cord-287748-co9j3uig author: Kobayashi, Tomoya title: Detection of bat hepatitis E virus RNA in microbats in Japan date: 2018-05-29 pages: extension: .txt txt: ./txt/cord-287748-co9j3uig.txt cache: ./cache/cord-287748-co9j3uig.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287748-co9j3uig.txt' === file2bib.sh === id: cord-291727-4wfhuvww author: Ketteler, Robin title: On programmed ribosomal frameshifting: the alternative proteomes date: 2012-11-19 pages: extension: .txt txt: ./txt/cord-291727-4wfhuvww.txt cache: ./cache/cord-291727-4wfhuvww.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-291727-4wfhuvww.txt' === file2bib.sh === id: cord-291754-1zxztadu author: Zhao, Ye title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 pages: extension: .txt txt: ./txt/cord-291754-1zxztadu.txt cache: ./cache/cord-291754-1zxztadu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291754-1zxztadu.txt' === file2bib.sh === id: cord-290948-cuu78cvl author: Imbert, Isabelle title: The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date: 2008-02-05 pages: extension: .txt txt: ./txt/cord-290948-cuu78cvl.txt cache: ./cache/cord-290948-cuu78cvl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290948-cuu78cvl.txt' === file2bib.sh === id: cord-291965-9r9ll83m author: Pfefferle, Susanne title: Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date: 2009-09-17 pages: extension: .txt txt: ./txt/cord-291965-9r9ll83m.txt cache: ./cache/cord-291965-9r9ll83m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291965-9r9ll83m.txt' === file2bib.sh === id: cord-294056-7e477y1x author: La Monica, Nicola title: Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences date: 1992-05-31 pages: extension: .txt txt: ./txt/cord-294056-7e477y1x.txt cache: ./cache/cord-294056-7e477y1x.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294056-7e477y1x.txt' === file2bib.sh === id: cord-295733-f3rt1fyk author: Ge, Tianxiang title: Evaluation of disinfection procedures in a designated hospital for COVID-19 date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-295733-f3rt1fyk.txt cache: ./cache/cord-295733-f3rt1fyk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295733-f3rt1fyk.txt' === file2bib.sh === id: cord-292045-pnid9dmq author: Kumar, Manish title: First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-292045-pnid9dmq.txt cache: ./cache/cord-292045-pnid9dmq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292045-pnid9dmq.txt' === file2bib.sh === id: cord-293747-ds8rhbkv author: Lani, Rafidah title: Antiviral activity of silymarin against chikungunya virus date: 2015-06-16 pages: extension: .txt txt: ./txt/cord-293747-ds8rhbkv.txt cache: ./cache/cord-293747-ds8rhbkv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293747-ds8rhbkv.txt' === file2bib.sh === id: cord-293038-pjjvfdnq author: Fontana, Juan title: The unique architecture of Bunyamwera virus factories around the Golgi complex date: 2008-06-10 pages: extension: .txt txt: ./txt/cord-293038-pjjvfdnq.txt cache: ./cache/cord-293038-pjjvfdnq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293038-pjjvfdnq.txt' === file2bib.sh === id: cord-293988-f5gvwjyh author: Musso, Nicolò title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date: 2020-09-11 pages: extension: .txt txt: ./txt/cord-293988-f5gvwjyh.txt cache: ./cache/cord-293988-f5gvwjyh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-293988-f5gvwjyh.txt' === file2bib.sh === id: cord-292353-z86rjwle author: Hussein, Islam T.M. title: Recent Advances in Hantavirus Molecular Biology and Disease date: 2011-04-01 pages: extension: .txt txt: ./txt/cord-292353-z86rjwle.txt cache: ./cache/cord-292353-z86rjwle.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292353-z86rjwle.txt' === file2bib.sh === id: cord-287758-da11ypiy author: Mônica Vitalino de Almeida, Sinara title: COVID-19 therapy: what weapons do we bring into battle? date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-287758-da11ypiy.txt cache: ./cache/cord-287758-da11ypiy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-287758-da11ypiy.txt' === file2bib.sh === id: cord-290218-dvyeg5fk author: Jiang, Yi title: RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-290218-dvyeg5fk.txt cache: ./cache/cord-290218-dvyeg5fk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290218-dvyeg5fk.txt' === file2bib.sh === id: cord-296847-r752bcsu author: Campanini, Giulia title: Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants date: 2007-04-23 pages: extension: .txt txt: ./txt/cord-296847-r752bcsu.txt cache: ./cache/cord-296847-r752bcsu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296847-r752bcsu.txt' === file2bib.sh === id: cord-296309-i1mpov7k author: Houldcroft, Charlotte J. title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 pages: extension: .txt txt: ./txt/cord-296309-i1mpov7k.txt cache: ./cache/cord-296309-i1mpov7k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-296309-i1mpov7k.txt' === file2bib.sh === id: cord-293375-qcy56ui7 author: Strauss, Ellen G. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 pages: extension: .txt txt: ./txt/cord-293375-qcy56ui7.txt cache: ./cache/cord-293375-qcy56ui7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-293375-qcy56ui7.txt' === file2bib.sh === id: cord-289612-4x5t4c5u author: Alsuliman, Tamim title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-289612-4x5t4c5u.txt cache: ./cache/cord-289612-4x5t4c5u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289612-4x5t4c5u.txt' === file2bib.sh === id: cord-288669-46tkedw7 author: Lee, Changhee title: The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties date: 2006-11-10 pages: extension: .txt txt: ./txt/cord-288669-46tkedw7.txt cache: ./cache/cord-288669-46tkedw7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-288669-46tkedw7.txt' === file2bib.sh === id: cord-293766-vpfda3pd author: Ji, Jingjing title: Glucocorticoid therapy does not delay viral clearance in COVID-19 patients date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-293766-vpfda3pd.txt cache: ./cache/cord-293766-vpfda3pd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293766-vpfda3pd.txt' === file2bib.sh === id: cord-293646-d4qcckh1 author: Meanwell, Nicholas A. title: Chapter 22. Non-HIV antiviral agents date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-293646-d4qcckh1.txt cache: ./cache/cord-293646-d4qcckh1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-293646-d4qcckh1.txt' === file2bib.sh === id: cord-292673-00s3wgem author: Buonaguro, Luigi title: SARS-CoV-2 RNA polymerase as target for antiviral therapy date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-292673-00s3wgem.txt cache: ./cache/cord-292673-00s3wgem.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-292673-00s3wgem.txt' === file2bib.sh === id: cord-294483-mozabpcs author: Choudhary, Manohar Lal title: Development of in vitro transcribed RNA as positive control for laboratory diagnosis of SARS-CoV-2 in India date: 2020-04-28 pages: extension: .txt txt: ./txt/cord-294483-mozabpcs.txt cache: ./cache/cord-294483-mozabpcs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294483-mozabpcs.txt' === file2bib.sh === id: cord-294890-93ldjyi5 author: Chen, Yan title: Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour date: 2018-11-06 pages: extension: .txt txt: ./txt/cord-294890-93ldjyi5.txt cache: ./cache/cord-294890-93ldjyi5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294890-93ldjyi5.txt' === file2bib.sh === id: cord-293481-bmfj50fb author: Malin, Jakob J. title: Remdesivir against COVID-19 and Other Viral Diseases date: 2020-10-14 pages: extension: .txt txt: ./txt/cord-293481-bmfj50fb.txt cache: ./cache/cord-293481-bmfj50fb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293481-bmfj50fb.txt' === file2bib.sh === id: cord-293852-r72c6584 author: Greco, S. title: Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date: 2020-10-31 pages: extension: .txt txt: ./txt/cord-293852-r72c6584.txt cache: ./cache/cord-293852-r72c6584.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293852-r72c6584.txt' === file2bib.sh === id: cord-294800-akr4f5p8 author: Kabir, Md. Tanvir title: nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-294800-akr4f5p8.txt cache: ./cache/cord-294800-akr4f5p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294800-akr4f5p8.txt' === file2bib.sh === id: cord-289926-y1rjgbui author: Veretnik, S. title: RNA binding domain of HDV antigen is homologous to the HMG box of SRY date: 2014-05-18 pages: extension: .txt txt: ./txt/cord-289926-y1rjgbui.txt cache: ./cache/cord-289926-y1rjgbui.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289926-y1rjgbui.txt' === file2bib.sh === id: cord-292643-n6xp5mlz author: Hall, Richard J. title: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date: 2013-09-13 pages: extension: .txt txt: ./txt/cord-292643-n6xp5mlz.txt cache: ./cache/cord-292643-n6xp5mlz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292643-n6xp5mlz.txt' === file2bib.sh === id: cord-289248-6mx4o0eb author: Wang, Yilong title: Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-289248-6mx4o0eb.txt cache: ./cache/cord-289248-6mx4o0eb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289248-6mx4o0eb.txt' === file2bib.sh === id: cord-291590-24psoaer author: Ogando, Natacha S. title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-291590-24psoaer.txt cache: ./cache/cord-291590-24psoaer.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291590-24psoaer.txt' === file2bib.sh === id: cord-297078-pxggjaby author: Poole, Anthony M. title: Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome? date: 2005-03-16 pages: extension: .txt txt: ./txt/cord-297078-pxggjaby.txt cache: ./cache/cord-297078-pxggjaby.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297078-pxggjaby.txt' === file2bib.sh === id: cord-297323-l3f12hg4 author: Amor, Sandra title: Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date: 2020-09-26 pages: extension: .txt txt: ./txt/cord-297323-l3f12hg4.txt cache: ./cache/cord-297323-l3f12hg4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297323-l3f12hg4.txt' === file2bib.sh === id: cord-293355-0v71xwqy author: Aguiar, Eric Roberto Guimarães Rocha title: Virus‐derived small RNAs: molecular footprints of host–pathogen interactions date: 2016-05-12 pages: extension: .txt txt: ./txt/cord-293355-0v71xwqy.txt cache: ./cache/cord-293355-0v71xwqy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293355-0v71xwqy.txt' === file2bib.sh === id: cord-298847-szezd2vb author: Jacomy, Hélène title: Vacuolating encephalitis in mice infected by human coronavirus OC43 date: 2003-10-10 pages: extension: .txt txt: ./txt/cord-298847-szezd2vb.txt cache: ./cache/cord-298847-szezd2vb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298847-szezd2vb.txt' === file2bib.sh === id: cord-291916-5yqc3zcx author: Hozhabri, Hossein title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-291916-5yqc3zcx.txt cache: ./cache/cord-291916-5yqc3zcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-291916-5yqc3zcx.txt' === file2bib.sh === id: cord-290802-761wqgbe author: Zhao, Zheng title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-290802-761wqgbe.txt cache: ./cache/cord-290802-761wqgbe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-290802-761wqgbe.txt' === file2bib.sh === id: cord-292831-oihcay6w author: Choudhary, Manohar L. title: Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR date: 2013-01-08 pages: extension: .txt txt: ./txt/cord-292831-oihcay6w.txt cache: ./cache/cord-292831-oihcay6w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292831-oihcay6w.txt' === file2bib.sh === id: cord-293913-frkb8iso author: Gao, Hong-Qiang title: Identification of the polymerase polyprotein products p72 and p65 of the murine coronavirus MHV-JHM date: 1996-12-31 pages: extension: .txt txt: ./txt/cord-293913-frkb8iso.txt cache: ./cache/cord-293913-frkb8iso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293913-frkb8iso.txt' === file2bib.sh === id: cord-294363-bv6xa8v8 author: Zhou, Hong title: Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-294363-bv6xa8v8.txt cache: ./cache/cord-294363-bv6xa8v8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294363-bv6xa8v8.txt' === file2bib.sh === id: cord-294764-v28wbrqp author: Deval, Jerome title: Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses date: 2017-04-15 pages: extension: .txt txt: ./txt/cord-294764-v28wbrqp.txt cache: ./cache/cord-294764-v28wbrqp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294764-v28wbrqp.txt' === file2bib.sh === id: cord-289535-srrfr1es author: Tregoning, J. S. title: Vaccines for COVID‐19 date: 2020-10-18 pages: extension: .txt txt: ./txt/cord-289535-srrfr1es.txt cache: ./cache/cord-289535-srrfr1es.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-289535-srrfr1es.txt' === file2bib.sh === id: cord-293417-oqusfhei author: Ma, Yanlin title: Structures of the N- and C-terminal domains of MHV-A59 nucleocapsid protein corroborate a conserved RNA-protein binding mechanism in coronavirus date: 2010-07-01 pages: extension: .txt txt: ./txt/cord-293417-oqusfhei.txt cache: ./cache/cord-293417-oqusfhei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293417-oqusfhei.txt' === file2bib.sh === id: cord-298036-2zurc60t author: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-298036-2zurc60t.txt cache: ./cache/cord-298036-2zurc60t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-298036-2zurc60t.txt' === file2bib.sh === id: cord-293163-udcw1mx5 author: Lu, Patrick Y. title: Modulation of angiogenesis with siRNA inhibitors for novel therapeutics date: 2005-02-04 pages: extension: .txt txt: ./txt/cord-293163-udcw1mx5.txt cache: ./cache/cord-293163-udcw1mx5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293163-udcw1mx5.txt' === file2bib.sh === id: cord-298032-3zlu8g8y author: Nan, Yuchen title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-298032-3zlu8g8y.txt cache: ./cache/cord-298032-3zlu8g8y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298032-3zlu8g8y.txt' === file2bib.sh === id: cord-295351-0zr2e8lh author: Mohd Ropidi, Muhammad Izzuddin title: Endoplasmic reticulum: a focal point of Zika virus infection date: 2020-01-20 pages: extension: .txt txt: ./txt/cord-295351-0zr2e8lh.txt cache: ./cache/cord-295351-0zr2e8lh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295351-0zr2e8lh.txt' === file2bib.sh === id: cord-297974-sduz0j35 author: Bokelmann, L. title: Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-297974-sduz0j35.txt cache: ./cache/cord-297974-sduz0j35.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297974-sduz0j35.txt' === file2bib.sh === id: cord-299509-7xjdryoq author: Scholte, Florine E. M. title: Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates date: 2013-08-01 pages: extension: .txt txt: ./txt/cord-299509-7xjdryoq.txt cache: ./cache/cord-299509-7xjdryoq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299509-7xjdryoq.txt' === file2bib.sh === id: cord-293790-7hyelm88 author: Guévin, Carl title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection date: 2010-09-01 pages: extension: .txt txt: ./txt/cord-293790-7hyelm88.txt cache: ./cache/cord-293790-7hyelm88.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-293790-7hyelm88.txt' === file2bib.sh === id: cord-297834-me1ajoyb author: Schountz, Tony title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 pages: extension: .txt txt: ./txt/cord-297834-me1ajoyb.txt cache: ./cache/cord-297834-me1ajoyb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297834-me1ajoyb.txt' === file2bib.sh === id: cord-291225-75ys908n author: Martins, Nelson title: A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells date: 2018-12-12 pages: extension: .txt txt: ./txt/cord-291225-75ys908n.txt cache: ./cache/cord-291225-75ys908n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-291225-75ys908n.txt' === file2bib.sh === id: cord-294842-aesiff1f author: Romero-Brey, Inés title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-294842-aesiff1f.txt cache: ./cache/cord-294842-aesiff1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-294842-aesiff1f.txt' === file2bib.sh === id: cord-293651-96cmduez author: Callison, Scott A. title: Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens date: 2006-08-28 pages: extension: .txt txt: ./txt/cord-293651-96cmduez.txt cache: ./cache/cord-293651-96cmduez.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-293651-96cmduez.txt' === file2bib.sh === id: cord-294718-n3gx862b author: Tam, Patrick C K title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-294718-n3gx862b.txt cache: ./cache/cord-294718-n3gx862b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-294718-n3gx862b.txt' === file2bib.sh === id: cord-294108-uvnh0s9r author: Dube, Taru title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 pages: extension: .txt txt: ./txt/cord-294108-uvnh0s9r.txt cache: ./cache/cord-294108-uvnh0s9r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294108-uvnh0s9r.txt' === file2bib.sh === id: cord-300884-rqfxe0x1 author: Zhang, Jianqiang title: Genomic characterization of equine coronavirus date: 2007-12-05 pages: extension: .txt txt: ./txt/cord-300884-rqfxe0x1.txt cache: ./cache/cord-300884-rqfxe0x1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300884-rqfxe0x1.txt' === file2bib.sh === id: cord-299943-wzkh04dv author: Santhanam, Manikandan title: DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment date: 2020-08-18 pages: extension: .txt txt: ./txt/cord-299943-wzkh04dv.txt cache: ./cache/cord-299943-wzkh04dv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299943-wzkh04dv.txt' === file2bib.sh === id: cord-295217-z2erqkr9 author: Seow, Justine Jia Wen title: Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-295217-z2erqkr9.txt cache: ./cache/cord-295217-z2erqkr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-295217-z2erqkr9.txt' === file2bib.sh === id: cord-292751-tk1oggi9 author: Hosseini, Elahe Seyed title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date: 2020-09-24 pages: extension: .txt txt: ./txt/cord-292751-tk1oggi9.txt cache: ./cache/cord-292751-tk1oggi9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-292751-tk1oggi9.txt' === file2bib.sh === id: cord-292112-dejrksum author: Wang, Jinglu title: Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells date: 2020-08-03 pages: extension: .txt txt: ./txt/cord-292112-dejrksum.txt cache: ./cache/cord-292112-dejrksum.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292112-dejrksum.txt' === file2bib.sh === id: cord-292983-msuluuuu author: Ballesteros-Briones, María Cristina title: A new generation of vaccines based on alphavirus self-amplifying RNA date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-292983-msuluuuu.txt cache: ./cache/cord-292983-msuluuuu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-292983-msuluuuu.txt' === file2bib.sh === id: cord-297790-tpjxt0w5 author: Mandl, Judith N. title: Going to Bat(s) for Studies of Disease Tolerance date: 2018-09-20 pages: extension: .txt txt: ./txt/cord-297790-tpjxt0w5.txt cache: ./cache/cord-297790-tpjxt0w5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297790-tpjxt0w5.txt' === file2bib.sh === id: cord-295019-8tf8ah6g author: Weber, Wilfried title: Emerging biomedical applications of synthetic biology date: 2011-11-29 pages: extension: .txt txt: ./txt/cord-295019-8tf8ah6g.txt cache: ./cache/cord-295019-8tf8ah6g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295019-8tf8ah6g.txt' === file2bib.sh === id: cord-294592-zwvr57a0 author: Mukherjee, Moumita title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-294592-zwvr57a0.txt cache: ./cache/cord-294592-zwvr57a0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-294592-zwvr57a0.txt' === file2bib.sh === id: cord-300685-bcjnujlj author: Poon, Leo L M title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 pages: extension: .txt txt: ./txt/cord-300685-bcjnujlj.txt cache: ./cache/cord-300685-bcjnujlj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300685-bcjnujlj.txt' === file2bib.sh === id: cord-295130-e7j7kac0 author: Moreno-Contreras, Joaquín title: Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-295130-e7j7kac0.txt cache: ./cache/cord-295130-e7j7kac0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-295130-e7j7kac0.txt' === file2bib.sh === id: cord-299754-tgexahwd author: van Tol, Sarah title: The TRIMendous Role of TRIMs in Virus–Host Interactions date: 2017-08-22 pages: extension: .txt txt: ./txt/cord-299754-tgexahwd.txt cache: ./cache/cord-299754-tgexahwd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-299754-tgexahwd.txt' === file2bib.sh === id: cord-292416-3hhi4wps author: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-292416-3hhi4wps.txt cache: ./cache/cord-292416-3hhi4wps.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292416-3hhi4wps.txt' === file2bib.sh === id: cord-299848-fft1brwz author: Claridge, Jolyon K. title: A picornaviral loop-to-loop replication complex date: 2009-03-04 pages: extension: .txt txt: ./txt/cord-299848-fft1brwz.txt cache: ./cache/cord-299848-fft1brwz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-299848-fft1brwz.txt' === file2bib.sh === id: cord-297092-oq14cwka author: Tan, Shaoyuan title: Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-297092-oq14cwka.txt cache: ./cache/cord-297092-oq14cwka.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297092-oq14cwka.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 3185 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 4162 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 1878 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-293525-c7nwygl1 author: Saldanha, I. F. title: Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date: 2019-04-03 pages: extension: .txt txt: ./txt/cord-293525-c7nwygl1.txt cache: ./cache/cord-293525-c7nwygl1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-293525-c7nwygl1.txt' === file2bib.sh === id: cord-301226-hmc2wmst author: Randazzo, Walter title: Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-301226-hmc2wmst.txt cache: ./cache/cord-301226-hmc2wmst.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301226-hmc2wmst.txt' === file2bib.sh === id: cord-299747-qovrstak author: Deval, Jerome title: Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus date: 2014-09-17 pages: extension: .txt txt: ./txt/cord-299747-qovrstak.txt cache: ./cache/cord-299747-qovrstak.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-299747-qovrstak.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 17003 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-292347-d7xq7x5g author: Carter, Linda J. title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 pages: extension: .txt txt: ./txt/cord-292347-d7xq7x5g.txt cache: ./cache/cord-292347-d7xq7x5g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-292347-d7xq7x5g.txt' === file2bib.sh === id: cord-300963-1n1f8mf2 author: Gajendran, Mahesh title: Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-300963-1n1f8mf2.txt cache: ./cache/cord-300963-1n1f8mf2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-300963-1n1f8mf2.txt' === file2bib.sh === id: cord-297579-ohpm5ys0 author: Netzler, Natalie E. title: Norovirus antivirals: Where are we now? date: 2018-12-25 pages: extension: .txt txt: ./txt/cord-297579-ohpm5ys0.txt cache: ./cache/cord-297579-ohpm5ys0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297579-ohpm5ys0.txt' === file2bib.sh === id: cord-297880-jlnv90vn author: Stewart, Hazel title: Transcriptional and Translational Landscape of Equine Torovirus date: 2018-08-16 pages: extension: .txt txt: ./txt/cord-297880-jlnv90vn.txt cache: ./cache/cord-297880-jlnv90vn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297880-jlnv90vn.txt' === file2bib.sh === id: cord-298078-uqrwq5qk author: Kwak, Hoyun title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date: 2011-08-30 pages: extension: .txt txt: ./txt/cord-298078-uqrwq5qk.txt cache: ./cache/cord-298078-uqrwq5qk.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298078-uqrwq5qk.txt' === file2bib.sh === id: cord-298938-xemarhlv author: Goswami, Biswendu B. title: Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase date: 2004-04-07 pages: extension: .txt txt: ./txt/cord-298938-xemarhlv.txt cache: ./cache/cord-298938-xemarhlv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298938-xemarhlv.txt' === file2bib.sh === id: cord-301233-nenw0f81 author: Naydenova, Katerina title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-301233-nenw0f81.txt cache: ./cache/cord-301233-nenw0f81.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301233-nenw0f81.txt' === file2bib.sh === id: cord-297760-uzzuoy9v author: Naito, Yuki title: siVirus: web-based antiviral siRNA design software for highly divergent viral sequences date: 2006-07-01 pages: extension: .txt txt: ./txt/cord-297760-uzzuoy9v.txt cache: ./cache/cord-297760-uzzuoy9v.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-297760-uzzuoy9v.txt' === file2bib.sh === id: cord-298905-c2uuvfm5 author: Horzinek, M. C. title: Molecular pathogenesis of virus infections date: 1987 pages: extension: .txt txt: ./txt/cord-298905-c2uuvfm5.txt cache: ./cache/cord-298905-c2uuvfm5.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298905-c2uuvfm5.txt' === file2bib.sh === id: cord-297039-vfuem6bk author: Beltrán-García, Jesús title: Circular RNAs in Sepsis: Biogenesis, Function, and Clinical Significance date: 2020-06-25 pages: extension: .txt txt: ./txt/cord-297039-vfuem6bk.txt cache: ./cache/cord-297039-vfuem6bk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-297039-vfuem6bk.txt' === file2bib.sh === id: cord-296977-yzhsdz9c author: Soares, R. R. G. title: Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-296977-yzhsdz9c.txt cache: ./cache/cord-296977-yzhsdz9c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-296977-yzhsdz9c.txt' === file2bib.sh === id: cord-297776-k38jssr0 author: Volk, Aaron title: Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages date: 2020-05-18 pages: extension: .txt txt: ./txt/cord-297776-k38jssr0.txt cache: ./cache/cord-297776-k38jssr0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-297776-k38jssr0.txt' === file2bib.sh === id: cord-298820-nogoqyxl author: Zhang, Qi title: Transcriptome altered by latent human cytomegalovirus infection on THP-1 cells using RNA-seq date: 2016-12-05 pages: extension: .txt txt: ./txt/cord-298820-nogoqyxl.txt cache: ./cache/cord-298820-nogoqyxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298820-nogoqyxl.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 33828 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 38828 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 39414 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42182 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-298281-wkje5jyt author: Chan, Vinson Wai-Shun title: A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-298281-wkje5jyt.txt cache: ./cache/cord-298281-wkje5jyt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-298281-wkje5jyt.txt' === file2bib.sh === id: cord-298779-0mjizsoo author: Narendrula, Rashmi title: RNA disruption is associated with response to multiple classes of chemotherapy drugs in tumor cell lines date: 2016-02-24 pages: extension: .txt txt: ./txt/cord-298779-0mjizsoo.txt cache: ./cache/cord-298779-0mjizsoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-298779-0mjizsoo.txt' === file2bib.sh === id: cord-301115-sedfbjlw author: Han, Mingfeng title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date: 2020-08-28 pages: extension: .txt txt: ./txt/cord-301115-sedfbjlw.txt cache: ./cache/cord-301115-sedfbjlw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301115-sedfbjlw.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-301904-mjfbvl5n author: Schultz-Cherry, S. title: Astroviruses date: 2014-11-28 pages: extension: .txt txt: ./txt/cord-301904-mjfbvl5n.txt cache: ./cache/cord-301904-mjfbvl5n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301904-mjfbvl5n.txt' === file2bib.sh === id: cord-302425-aaxvlktp author: Cortey, Martí title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date: 2019-12-05 pages: extension: .txt txt: ./txt/cord-302425-aaxvlktp.txt cache: ./cache/cord-302425-aaxvlktp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302425-aaxvlktp.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-295467-9fnis6ci author: Botella, Leticia title: The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history date: 2014-12-12 pages: extension: .txt txt: ./txt/cord-295467-9fnis6ci.txt cache: ./cache/cord-295467-9fnis6ci.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-295467-9fnis6ci.txt' === file2bib.sh === id: cord-302355-3se1wp8o author: Chen, Yi-Shiuan title: The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-302355-3se1wp8o.txt cache: ./cache/cord-302355-3se1wp8o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302355-3se1wp8o.txt' === file2bib.sh === id: cord-301285-p83ondy8 author: Kautz, Tiffany F title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 pages: extension: .txt txt: ./txt/cord-301285-p83ondy8.txt cache: ./cache/cord-301285-p83ondy8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-301285-p83ondy8.txt' === file2bib.sh === /data-disk/reader-compute/reader-cord/bin/file2bib.sh: fork: retry: No child processes id: cord-294260-g410mavp author: Sztuba-Solińska, Joanna title: Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle date: 2011-04-10 pages: extension: .txt txt: ./txt/cord-294260-g410mavp.txt cache: ./cache/cord-294260-g410mavp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-294260-g410mavp.txt' === file2bib.sh === id: cord-302195-25gjbyi1 author: Al Huraimel, Khalid title: SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-302195-25gjbyi1.txt cache: ./cache/cord-302195-25gjbyi1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302195-25gjbyi1.txt' === file2bib.sh === id: cord-301997-63160t7f author: Schwer, Beate title: Discontinuous transcription or RNA processing of vaccinia virus late messengers results in a 5′ poly(A) leader date: 1987-07-17 pages: extension: .txt txt: ./txt/cord-301997-63160t7f.txt cache: ./cache/cord-301997-63160t7f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-301997-63160t7f.txt' === file2bib.sh === id: cord-302020-ypsh3rjv author: Kim, Dongwan title: The Architecture of SARS-CoV-2 Transcriptome date: 2020-04-23 pages: extension: .txt txt: ./txt/cord-302020-ypsh3rjv.txt cache: ./cache/cord-302020-ypsh3rjv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302020-ypsh3rjv.txt' === file2bib.sh === id: cord-301535-eui41zyg author: Chandler-Brown, Devon title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date: 2020-04-10 pages: extension: .txt txt: ./txt/cord-301535-eui41zyg.txt cache: ./cache/cord-301535-eui41zyg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301535-eui41zyg.txt' === file2bib.sh === id: cord-303111-iv4lzpev author: Almazán, Fernando title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date: 2014-12-19 pages: extension: .txt txt: ./txt/cord-303111-iv4lzpev.txt cache: ./cache/cord-303111-iv4lzpev.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303111-iv4lzpev.txt' === file2bib.sh === id: cord-302316-raf5rlkq author: Brüssow, Harald title: COVID‐19: From pathogenesis models to the first drug trials date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-302316-raf5rlkq.txt cache: ./cache/cord-302316-raf5rlkq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302316-raf5rlkq.txt' === file2bib.sh === id: cord-302085-xyru2q9o author: Shepard, Samuel S. title: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler date: 2016-09-05 pages: extension: .txt txt: ./txt/cord-302085-xyru2q9o.txt cache: ./cache/cord-302085-xyru2q9o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302085-xyru2q9o.txt' === file2bib.sh === id: cord-302980-2jlz4c58 author: Crucière, C. title: Sequence and analysis of bovine enteritic coronavirus (F15) genome I.—Sequence of the gene coding for the nucleocapsid protein; analysis of the predicted protein date: 1988-03-31 pages: extension: .txt txt: ./txt/cord-302980-2jlz4c58.txt cache: ./cache/cord-302980-2jlz4c58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302980-2jlz4c58.txt' === file2bib.sh === id: cord-302368-uhhtvdif author: Longhini, Andrew P. title: Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations date: 2016-04-07 pages: extension: .txt txt: ./txt/cord-302368-uhhtvdif.txt cache: ./cache/cord-302368-uhhtvdif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302368-uhhtvdif.txt' === file2bib.sh === id: cord-302409-40ktyt5q author: Wang, Jie title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 pages: extension: .txt txt: ./txt/cord-302409-40ktyt5q.txt cache: ./cache/cord-302409-40ktyt5q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-302409-40ktyt5q.txt' === file2bib.sh === id: cord-303153-z7bdiuvx author: Ulasli, Mustafa title: Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus date: 2010-01-20 pages: extension: .txt txt: ./txt/cord-303153-z7bdiuvx.txt cache: ./cache/cord-303153-z7bdiuvx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303153-z7bdiuvx.txt' === file2bib.sh === id: cord-304306-rxjahqwh author: Vlachakis, Dimitrios title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-304306-rxjahqwh.txt cache: ./cache/cord-304306-rxjahqwh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304306-rxjahqwh.txt' === file2bib.sh === id: cord-303265-v6ci69n0 author: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 pages: extension: .txt txt: ./txt/cord-303265-v6ci69n0.txt cache: ./cache/cord-303265-v6ci69n0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303265-v6ci69n0.txt' === file2bib.sh === id: cord-303408-coesfldm author: Konstantinova, Pavlina title: Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome date: 2007-03-01 pages: extension: .txt txt: ./txt/cord-303408-coesfldm.txt cache: ./cache/cord-303408-coesfldm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303408-coesfldm.txt' === file2bib.sh === id: cord-301362-f3lp10lm author: Delgui, Laura R. title: A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases date: 2017-01-20 pages: extension: .txt txt: ./txt/cord-301362-f3lp10lm.txt cache: ./cache/cord-301362-f3lp10lm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-301362-f3lp10lm.txt' === file2bib.sh === id: cord-304044-i1ikf96b author: Wu, Yue title: Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date: 2007-10-03 pages: extension: .txt txt: ./txt/cord-304044-i1ikf96b.txt cache: ./cache/cord-304044-i1ikf96b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304044-i1ikf96b.txt' === file2bib.sh === id: cord-304356-jyp9gjh9 author: Grant, Rogan A. title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date: 2020-08-05 pages: extension: .txt txt: ./txt/cord-304356-jyp9gjh9.txt cache: ./cache/cord-304356-jyp9gjh9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304356-jyp9gjh9.txt' === file2bib.sh === id: cord-302047-vv5gpldi author: Willemsen, Anouk title: On the stability of sequences inserted into viral genomes date: 2019-11-14 pages: extension: .txt txt: ./txt/cord-302047-vv5gpldi.txt cache: ./cache/cord-302047-vv5gpldi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302047-vv5gpldi.txt' === file2bib.sh === id: cord-303319-v3iyur78 author: Abe, Takayuki title: Cytosolic DNA‐sensing immune response and viral infection date: 2019-02-26 pages: extension: .txt txt: ./txt/cord-303319-v3iyur78.txt cache: ./cache/cord-303319-v3iyur78.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303319-v3iyur78.txt' === file2bib.sh === id: cord-303377-lkewcf8a author: Dimke, H. title: Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-303377-lkewcf8a.txt cache: ./cache/cord-303377-lkewcf8a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-303377-lkewcf8a.txt' === file2bib.sh === id: cord-302895-471zei5o author: Deng, Zengqin title: Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase date: 2013-12-24 pages: extension: .txt txt: ./txt/cord-302895-471zei5o.txt cache: ./cache/cord-302895-471zei5o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-302895-471zei5o.txt' === file2bib.sh === id: cord-304058-i8cywew0 author: Pfefferle, Susanne title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 pages: extension: .txt txt: ./txt/cord-304058-i8cywew0.txt cache: ./cache/cord-304058-i8cywew0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-304058-i8cywew0.txt' === file2bib.sh === id: cord-306948-wkisfz1m author: Han, Mingyuan title: Engineering the PRRS virus genome: Updates and perspectives date: 2014-12-05 pages: extension: .txt txt: ./txt/cord-306948-wkisfz1m.txt cache: ./cache/cord-306948-wkisfz1m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306948-wkisfz1m.txt' === file2bib.sh === id: cord-305811-987dhnf7 author: Cho, Che-Pei title: Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date: 2013-04-29 pages: extension: .txt txt: ./txt/cord-305811-987dhnf7.txt cache: ./cache/cord-305811-987dhnf7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305811-987dhnf7.txt' === file2bib.sh === id: cord-304553-gbwb7fqi author: Christopher, Mary E. title: Broad-Spectrum Drugs Against Viral Agents date: 2008-09-01 pages: extension: .txt txt: ./txt/cord-304553-gbwb7fqi.txt cache: ./cache/cord-304553-gbwb7fqi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304553-gbwb7fqi.txt' === file2bib.sh === id: cord-302830-5psqxxc8 author: Ávila‐Pérez, Ginés title: Ultrastructural characterization of membranous torovirus replication factories date: 2016-07-05 pages: extension: .txt txt: ./txt/cord-302830-5psqxxc8.txt cache: ./cache/cord-302830-5psqxxc8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-302830-5psqxxc8.txt' === file2bib.sh === id: cord-308216-s6rd8p41 author: Duan, Fang title: Small interfering RNA targeting for infected‐cell polypeptide 4 inhibits herpes simplex virus type 1 replication in retinal pigment epithelial cells date: 2011-10-20 pages: extension: .txt txt: ./txt/cord-308216-s6rd8p41.txt cache: ./cache/cord-308216-s6rd8p41.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308216-s6rd8p41.txt' === file2bib.sh === id: cord-303189-ktl4jw8v author: Coccia, Eliana M. title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 pages: extension: .txt txt: ./txt/cord-303189-ktl4jw8v.txt cache: ./cache/cord-303189-ktl4jw8v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303189-ktl4jw8v.txt' === file2bib.sh === id: cord-304876-txaoz7oh author: Jordan, Paul C title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 pages: extension: .txt txt: ./txt/cord-304876-txaoz7oh.txt cache: ./cache/cord-304876-txaoz7oh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304876-txaoz7oh.txt' === file2bib.sh === id: cord-308835-999kewdw author: Leibowitz, Julian L. title: The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM date: 1981-10-15 pages: extension: .txt txt: ./txt/cord-308835-999kewdw.txt cache: ./cache/cord-308835-999kewdw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-308835-999kewdw.txt' === file2bib.sh === id: cord-305859-vt8vwo3y author: Jung, Kwonil title: Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus date: 2017-04-03 pages: extension: .txt txt: ./txt/cord-305859-vt8vwo3y.txt cache: ./cache/cord-305859-vt8vwo3y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305859-vt8vwo3y.txt' === file2bib.sh === id: cord-305591-ir3wz6nr author: Ji, Danyang title: Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-305591-ir3wz6nr.txt cache: ./cache/cord-305591-ir3wz6nr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305591-ir3wz6nr.txt' === file2bib.sh === id: cord-304014-k62mtr9j author: Ma, Xuelian title: Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection date: 2019-11-04 pages: extension: .txt txt: ./txt/cord-304014-k62mtr9j.txt cache: ./cache/cord-304014-k62mtr9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304014-k62mtr9j.txt' === file2bib.sh === id: cord-304873-ppb9k3zu author: Kang, Hunseung title: Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1 date: 1998-04-01 pages: extension: .txt txt: ./txt/cord-304873-ppb9k3zu.txt cache: ./cache/cord-304873-ppb9k3zu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304873-ppb9k3zu.txt' === file2bib.sh === id: cord-303403-9th2jiq6 author: Qing, Jie title: Cyclophilin A Associates with Enterovirus-71 Virus Capsid and Plays an Essential Role in Viral Infection as an Uncoating Regulator date: 2014-10-02 pages: extension: .txt txt: ./txt/cord-303403-9th2jiq6.txt cache: ./cache/cord-303403-9th2jiq6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303403-9th2jiq6.txt' === file2bib.sh === id: cord-303915-14yfs4pa author: Almazán, Fernando title: Engineering a Replication-Competent, Propagation-Defective Middle East Respiratory Syndrome Coronavirus as a Vaccine Candidate date: 2013-09-10 pages: extension: .txt txt: ./txt/cord-303915-14yfs4pa.txt cache: ./cache/cord-303915-14yfs4pa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-303915-14yfs4pa.txt' === file2bib.sh === id: cord-310141-2jofy8fo author: Qureshi, Abid title: A review on current status of antiviral siRNA date: 2018-04-15 pages: extension: .txt txt: ./txt/cord-310141-2jofy8fo.txt cache: ./cache/cord-310141-2jofy8fo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310141-2jofy8fo.txt' === file2bib.sh === id: cord-310748-ao29zx1u author: Banner, Lisa R. title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 pages: extension: .txt txt: ./txt/cord-310748-ao29zx1u.txt cache: ./cache/cord-310748-ao29zx1u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310748-ao29zx1u.txt' === file2bib.sh === id: cord-305290-xnjwv0d7 author: Atkins, John F. title: Ribosome gymnastics—Degree of difficulty 9.5, style 10.0 date: 1990-08-10 pages: extension: .txt txt: ./txt/cord-305290-xnjwv0d7.txt cache: ./cache/cord-305290-xnjwv0d7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-305290-xnjwv0d7.txt' === file2bib.sh === id: cord-307860-iqk1yiw4 author: Ionescu, Mihaela Ileana title: An Overview of the Crystallized Structures of the SARS-CoV-2 date: 2020-10-24 pages: extension: .txt txt: ./txt/cord-307860-iqk1yiw4.txt cache: ./cache/cord-307860-iqk1yiw4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307860-iqk1yiw4.txt' === file2bib.sh === id: cord-015394-uj7fe5y6 author: nan title: Scientific Abstracts date: 2008-12-23 pages: extension: .txt txt: ./txt/cord-015394-uj7fe5y6.txt cache: ./cache/cord-015394-uj7fe5y6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 15 resourceName b'cord-015394-uj7fe5y6.txt' === file2bib.sh === id: cord-308034-9b219k0v author: Murray, James L. title: A Role for H/ACA and C/D Small Nucleolar RNAs in Viral Replication date: 2014-01-30 pages: extension: .txt txt: ./txt/cord-308034-9b219k0v.txt cache: ./cache/cord-308034-9b219k0v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-308034-9b219k0v.txt' === file2bib.sh === id: cord-307893-mvl0wrsj author: Goulter-Thorsen, R.M. title: Disciplines Associated with Food Safety: Food Virology date: 2014-01-13 pages: extension: .txt txt: ./txt/cord-307893-mvl0wrsj.txt cache: ./cache/cord-307893-mvl0wrsj.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307893-mvl0wrsj.txt' === file2bib.sh === id: cord-306076-ygfnkgqp author: Fujita, Yu title: RNAi Therapeutic Platforms for Lung Diseases date: 2013-02-06 pages: extension: .txt txt: ./txt/cord-306076-ygfnkgqp.txt cache: ./cache/cord-306076-ygfnkgqp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306076-ygfnkgqp.txt' === file2bib.sh === id: cord-310192-8x37nx4s author: Zhang, Huaqun title: Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date: 2019-04-25 pages: extension: .txt txt: ./txt/cord-310192-8x37nx4s.txt cache: ./cache/cord-310192-8x37nx4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310192-8x37nx4s.txt' === file2bib.sh === id: cord-305393-96mrxt8a author: Lai, Yvonne title: Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3 date: 2011-10-10 pages: extension: .txt txt: ./txt/cord-305393-96mrxt8a.txt cache: ./cache/cord-305393-96mrxt8a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305393-96mrxt8a.txt' === file2bib.sh === id: cord-307934-84zfabti author: Lai, Chao-Kuen title: Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport date: 2014-06-06 pages: extension: .txt txt: ./txt/cord-307934-84zfabti.txt cache: ./cache/cord-307934-84zfabti.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-307934-84zfabti.txt' === file2bib.sh === id: cord-307354-dkwcheu0 author: Abernathy, Emma title: Emerging roles for RNA degradation in viral replication and antiviral defense date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-307354-dkwcheu0.txt cache: ./cache/cord-307354-dkwcheu0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307354-dkwcheu0.txt' === file2bib.sh === id: cord-310086-9e4txeck author: Fu, Wei title: Letter to the Editor: Three cases of re‐detectable positive SARS‐CoV‐2 RNA in recovered COVID‐19 patients with antibodies date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-310086-9e4txeck.txt cache: ./cache/cord-310086-9e4txeck.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310086-9e4txeck.txt' === file2bib.sh === id: cord-312544-vip4jtlv author: Ng, Lisa FP title: Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay date: 2006-03-02 pages: extension: .txt txt: ./txt/cord-312544-vip4jtlv.txt cache: ./cache/cord-312544-vip4jtlv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312544-vip4jtlv.txt' === file2bib.sh === id: cord-304283-nv4ret1f author: Hung, Chuan-Fu title: A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells date: 2006-08-04 pages: extension: .txt txt: ./txt/cord-304283-nv4ret1f.txt cache: ./cache/cord-304283-nv4ret1f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304283-nv4ret1f.txt' === file2bib.sh === id: cord-304498-ty41xob0 author: Denison, Mark R title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 pages: extension: .txt txt: ./txt/cord-304498-ty41xob0.txt cache: ./cache/cord-304498-ty41xob0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-304498-ty41xob0.txt' === file2bib.sh === id: cord-306535-j26eqmxt author: Robertson, Matthew J. title: Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-306535-j26eqmxt.txt cache: ./cache/cord-306535-j26eqmxt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306535-j26eqmxt.txt' === file2bib.sh === id: cord-310771-tnwfp1je author: Revilla-Fernández, Sandra title: The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date: 2005-02-23 pages: extension: .txt txt: ./txt/cord-310771-tnwfp1je.txt cache: ./cache/cord-310771-tnwfp1je.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310771-tnwfp1je.txt' === file2bib.sh === id: cord-311982-wkg56xeq author: Dye, Charlotte title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 pages: extension: .txt txt: ./txt/cord-311982-wkg56xeq.txt cache: ./cache/cord-311982-wkg56xeq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311982-wkg56xeq.txt' === file2bib.sh === id: cord-306921-3afgpunj author: Owino, Collins Oduor title: Recent advances on the role of host factors during non-poliovirus enteroviral infections date: 2019-06-19 pages: extension: .txt txt: ./txt/cord-306921-3afgpunj.txt cache: ./cache/cord-306921-3afgpunj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306921-3afgpunj.txt' === file2bib.sh === id: cord-304794-z2kx314h author: Métifiot, Mathieu title: G-quadruplexes in viruses: function and potential therapeutic applications date: 2014-11-10 pages: extension: .txt txt: ./txt/cord-304794-z2kx314h.txt cache: ./cache/cord-304794-z2kx314h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-304794-z2kx314h.txt' === file2bib.sh === id: cord-306688-po4p1466 author: Wang, X. title: Brome Mosaic Virus date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-306688-po4p1466.txt cache: ./cache/cord-306688-po4p1466.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306688-po4p1466.txt' === file2bib.sh === id: cord-306288-w43wec48 author: Jang, Sungho title: RNA-based dynamic genetic controllers: development strategies and applications date: 2017-11-10 pages: extension: .txt txt: ./txt/cord-306288-w43wec48.txt cache: ./cache/cord-306288-w43wec48.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306288-w43wec48.txt' === file2bib.sh === id: cord-305336-wxiazglk author: Li, Ji Lian title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 pages: extension: .txt txt: ./txt/cord-305336-wxiazglk.txt cache: ./cache/cord-305336-wxiazglk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305336-wxiazglk.txt' === file2bib.sh === id: cord-304424-048xo7jn author: Greninger, Alexander L. title: A decade of RNA virus metagenomics is (not) enough date: 2018-01-15 pages: extension: .txt txt: ./txt/cord-304424-048xo7jn.txt cache: ./cache/cord-304424-048xo7jn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-304424-048xo7jn.txt' === file2bib.sh === id: cord-305737-bnzd7b25 author: Rehwinkel, Jan title: Targeting the viral Achilles’ heel: recognition of 5′-triphosphate RNA in innate anti-viral defence date: 2013-05-23 pages: extension: .txt txt: ./txt/cord-305737-bnzd7b25.txt cache: ./cache/cord-305737-bnzd7b25.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-305737-bnzd7b25.txt' === file2bib.sh === id: cord-305871-w1quh4fx author: Hindawi, Salwa I. title: Inactivation of Middle East respiratory syndrome‐coronavirus in human plasma using amotosalen and ultraviolet A light date: 2017-12-14 pages: extension: .txt txt: ./txt/cord-305871-w1quh4fx.txt cache: ./cache/cord-305871-w1quh4fx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-305871-w1quh4fx.txt' === file2bib.sh === id: cord-310371-pylrg91h author: Bishop, R.F. title: Enteric Viruses date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-310371-pylrg91h.txt cache: ./cache/cord-310371-pylrg91h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-310371-pylrg91h.txt' === file2bib.sh === id: cord-307603-uqr6r14u author: Kauppinen, S. title: Locked Nucleic Acid: High-Affinity Targeting of Complementary RNA for RNomics date: 2006 pages: extension: .txt txt: ./txt/cord-307603-uqr6r14u.txt cache: ./cache/cord-307603-uqr6r14u.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307603-uqr6r14u.txt' === file2bib.sh === id: cord-306934-29ljbl7g author: Tonelli, Michele title: Antiviral and cytotoxic activities of aminoarylazo compounds and aryltriazene derivatives date: 2009-07-01 pages: extension: .txt txt: ./txt/cord-306934-29ljbl7g.txt cache: ./cache/cord-306934-29ljbl7g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306934-29ljbl7g.txt' === file2bib.sh === id: cord-312431-de7zhswl author: Ganesh, Atheesha title: Detecting Virus‐Like Particles from the Umgeni River, South Africa date: 2013-08-30 pages: extension: .txt txt: ./txt/cord-312431-de7zhswl.txt cache: ./cache/cord-312431-de7zhswl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312431-de7zhswl.txt' === file2bib.sh === id: cord-310605-r63sg73c author: Dorward, D. A. title: Tissue-specific tolerance in fatal Covid-19 date: 2020-07-04 pages: extension: .txt txt: ./txt/cord-310605-r63sg73c.txt cache: ./cache/cord-310605-r63sg73c.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310605-r63sg73c.txt' === file2bib.sh === id: cord-311625-d7iycdyh author: Choong, Oi Kuan title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication date: 2014-02-20 pages: extension: .txt txt: ./txt/cord-311625-d7iycdyh.txt cache: ./cache/cord-311625-d7iycdyh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-311625-d7iycdyh.txt' === file2bib.sh === id: cord-307904-lnagg1uw author: Johnson, Jennifer A title: Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo date: 2003-08-15 pages: extension: .txt txt: ./txt/cord-307904-lnagg1uw.txt cache: ./cache/cord-307904-lnagg1uw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307904-lnagg1uw.txt' === file2bib.sh === id: cord-311628-ep795pil author: Fu, Yu title: A novel delivery platform based on Bacteriophage MS2 virus-like particles date: 2016-01-04 pages: extension: .txt txt: ./txt/cord-311628-ep795pil.txt cache: ./cache/cord-311628-ep795pil.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311628-ep795pil.txt' === file2bib.sh === id: cord-309048-emmtplv3 author: Lomonossoff, George P. title: TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date: 2018-07-26 pages: extension: .txt txt: ./txt/cord-309048-emmtplv3.txt cache: ./cache/cord-309048-emmtplv3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309048-emmtplv3.txt' === file2bib.sh === id: cord-308331-55ge7kmr author: Routh, Andrew title: Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data date: 2013-10-09 pages: extension: .txt txt: ./txt/cord-308331-55ge7kmr.txt cache: ./cache/cord-308331-55ge7kmr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308331-55ge7kmr.txt' === file2bib.sh === id: cord-311007-0i1abjfa author: Schwarz, Megan C. title: Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone date: 2016-09-28 pages: extension: .txt txt: ./txt/cord-311007-0i1abjfa.txt cache: ./cache/cord-311007-0i1abjfa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-311007-0i1abjfa.txt' === file2bib.sh === id: cord-310268-8q4tk6fd author: Zhu, Qinchang title: DNA Aptamers in the Diagnosis and Treatment of Human Diseases date: 2015-11-25 pages: extension: .txt txt: ./txt/cord-310268-8q4tk6fd.txt cache: ./cache/cord-310268-8q4tk6fd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310268-8q4tk6fd.txt' === file2bib.sh === id: cord-308884-erofmh39 author: Yang, Seung Won title: Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date: 2018-01-08 pages: extension: .txt txt: ./txt/cord-308884-erofmh39.txt cache: ./cache/cord-308884-erofmh39.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-308884-erofmh39.txt' === file2bib.sh === id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 pages: extension: .txt txt: ./txt/cord-312332-rwmuucsp.txt cache: ./cache/cord-312332-rwmuucsp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312332-rwmuucsp.txt' === file2bib.sh === id: cord-307817-2vy28i4m author: Lou, Zhiyong title: Current progress in antiviral strategies date: 2014-01-14 pages: extension: .txt txt: ./txt/cord-307817-2vy28i4m.txt cache: ./cache/cord-307817-2vy28i4m.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307817-2vy28i4m.txt' === file2bib.sh === id: cord-306424-gf0bglm0 author: Scutigliani, Enzo Maxim title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 pages: extension: .txt txt: ./txt/cord-306424-gf0bglm0.txt cache: ./cache/cord-306424-gf0bglm0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-306424-gf0bglm0.txt' === file2bib.sh === id: cord-309043-dlmx12vt author: von Brunn, Albrecht title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 pages: extension: .txt txt: ./txt/cord-309043-dlmx12vt.txt cache: ./cache/cord-309043-dlmx12vt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309043-dlmx12vt.txt' === file2bib.sh === id: cord-306754-qohrnpgq author: Lee, Justin S. title: Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species date: 2017-05-23 pages: extension: .txt txt: ./txt/cord-306754-qohrnpgq.txt cache: ./cache/cord-306754-qohrnpgq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-306754-qohrnpgq.txt' === file2bib.sh === id: cord-312240-0k8y86pf author: Schlaberg, Robert title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date: 2017-05-01 pages: extension: .txt txt: ./txt/cord-312240-0k8y86pf.txt cache: ./cache/cord-312240-0k8y86pf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312240-0k8y86pf.txt' === file2bib.sh === id: cord-310920-itqwhi6a author: Haddad, Christina title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-310920-itqwhi6a.txt cache: ./cache/cord-310920-itqwhi6a.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310920-itqwhi6a.txt' === file2bib.sh === id: cord-309469-2naxn580 author: An, Hongliu title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date: 2019-01-05 pages: extension: .txt txt: ./txt/cord-309469-2naxn580.txt cache: ./cache/cord-309469-2naxn580.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-309469-2naxn580.txt' === file2bib.sh === id: cord-309722-04pp3lv0 author: Qiu, Yingshan title: Delivery of RNAi Therapeutics to the Airways—From Bench to Bedside date: 2016-09-20 pages: extension: .txt txt: ./txt/cord-309722-04pp3lv0.txt cache: ./cache/cord-309722-04pp3lv0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-309722-04pp3lv0.txt' === file2bib.sh === id: cord-314254-9ye8tfvz author: Pfaender, Stephanie title: Natural reservoirs for homologs of hepatitis C virus date: 2014-03-26 pages: extension: .txt txt: ./txt/cord-314254-9ye8tfvz.txt cache: ./cache/cord-314254-9ye8tfvz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314254-9ye8tfvz.txt' === file2bib.sh === id: cord-314369-o4nis91y author: Lopez-Lopes, G. I. S. title: Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date: 2020-08-01 pages: extension: .txt txt: ./txt/cord-314369-o4nis91y.txt cache: ./cache/cord-314369-o4nis91y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314369-o4nis91y.txt' === file2bib.sh === id: cord-313161-07iwwsfz author: Lundstrom, Kenneth title: Alphavirus-Based Vaccines date: 2014-06-16 pages: extension: .txt txt: ./txt/cord-313161-07iwwsfz.txt cache: ./cache/cord-313161-07iwwsfz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313161-07iwwsfz.txt' === file2bib.sh === id: cord-310947-aqau2n7q author: Pan, Ji'An title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 pages: extension: .txt txt: ./txt/cord-310947-aqau2n7q.txt cache: ./cache/cord-310947-aqau2n7q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310947-aqau2n7q.txt' === file2bib.sh === id: cord-313138-y485ev30 author: Magor, Katharine E. title: Defense genes missing from the flight division date: 2013-04-24 pages: extension: .txt txt: ./txt/cord-313138-y485ev30.txt cache: ./cache/cord-313138-y485ev30.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-313138-y485ev30.txt' === file2bib.sh === id: cord-314753-xflhxb13 author: Manso, Carmen F. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 pages: extension: .txt txt: ./txt/cord-314753-xflhxb13.txt cache: ./cache/cord-314753-xflhxb13.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314753-xflhxb13.txt' === file2bib.sh === id: cord-314560-rswa5zdn author: Manjunath, N. title: Interfering antiviral immunity: application, subversion, hope? date: 2006-06-06 pages: extension: .txt txt: ./txt/cord-314560-rswa5zdn.txt cache: ./cache/cord-314560-rswa5zdn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314560-rswa5zdn.txt' === file2bib.sh === id: cord-310967-15mv5yx7 author: Morris, Vincent L. title: Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease date: 1989-03-31 pages: extension: .txt txt: ./txt/cord-310967-15mv5yx7.txt cache: ./cache/cord-310967-15mv5yx7.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-310967-15mv5yx7.txt' === file2bib.sh === id: cord-313439-cadyykks author: Felten, Sandra title: Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date: 2019-11-15 pages: extension: .txt txt: ./txt/cord-313439-cadyykks.txt cache: ./cache/cord-313439-cadyykks.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313439-cadyykks.txt' === file2bib.sh === id: cord-307914-lgprrwee author: Bartok, Eva title: Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-307914-lgprrwee.txt cache: ./cache/cord-307914-lgprrwee.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307914-lgprrwee.txt' === file2bib.sh === id: cord-312392-8zxl48af author: Buonavoglia, Canio title: Canine Coronavirus Highly Pathogenic for Dogs date: 2006-03-17 pages: extension: .txt txt: ./txt/cord-312392-8zxl48af.txt cache: ./cache/cord-312392-8zxl48af.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312392-8zxl48af.txt' === file2bib.sh === id: cord-310861-9kb0b6rq author: Koo, Bonhan title: An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections date: 2017-04-15 pages: extension: .txt txt: ./txt/cord-310861-9kb0b6rq.txt cache: ./cache/cord-310861-9kb0b6rq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-310861-9kb0b6rq.txt' === file2bib.sh === id: cord-307598-p54p7enk author: Schlee, Martin title: Master sensors of pathogenic RNA – RIG-I like receptors date: 2013-07-01 pages: extension: .txt txt: ./txt/cord-307598-p54p7enk.txt cache: ./cache/cord-307598-p54p7enk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-307598-p54p7enk.txt' === file2bib.sh === id: cord-315909-vwugf0wp author: Letko, Michael title: Studying Evolutionary Adaptation of MERS-CoV date: 2019-09-14 pages: extension: .txt txt: ./txt/cord-315909-vwugf0wp.txt cache: ./cache/cord-315909-vwugf0wp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-315909-vwugf0wp.txt' === file2bib.sh === id: cord-315069-xo4mbxei author: Knorr, D. A. title: De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage date: 1991-03-31 pages: extension: .txt txt: ./txt/cord-315069-xo4mbxei.txt cache: ./cache/cord-315069-xo4mbxei.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-315069-xo4mbxei.txt' === file2bib.sh === id: cord-312741-0au4nctt author: Lin, Panpan title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 pages: extension: .txt txt: ./txt/cord-312741-0au4nctt.txt cache: ./cache/cord-312741-0au4nctt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312741-0au4nctt.txt' === file2bib.sh === id: cord-314572-1pou702r author: Lin, Ya-Hui title: Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date: 2016-10-14 pages: extension: .txt txt: ./txt/cord-314572-1pou702r.txt cache: ./cache/cord-314572-1pou702r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314572-1pou702r.txt' === file2bib.sh === id: cord-314891-brgtwxhe author: Fumian, Tulio M. title: Potential Therapeutic Agents for Feline Calicivirus Infection date: 2018-08-16 pages: extension: .txt txt: ./txt/cord-314891-brgtwxhe.txt cache: ./cache/cord-314891-brgtwxhe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314891-brgtwxhe.txt' === file2bib.sh === id: cord-312223-qgwzgazd author: Shafagati, Nazly title: The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date: 2013-07-04 pages: extension: .txt txt: ./txt/cord-312223-qgwzgazd.txt cache: ./cache/cord-312223-qgwzgazd.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312223-qgwzgazd.txt' === file2bib.sh === id: cord-317244-4su5on6s author: Maganga, Gael D. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 pages: extension: .txt txt: ./txt/cord-317244-4su5on6s.txt cache: ./cache/cord-317244-4su5on6s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317244-4su5on6s.txt' === file2bib.sh === id: cord-315072-b28yikvj author: Giotis, Efstathios S. title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) date: 2016-08-05 pages: extension: .txt txt: ./txt/cord-315072-b28yikvj.txt cache: ./cache/cord-315072-b28yikvj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315072-b28yikvj.txt' === file2bib.sh === id: cord-312517-b24zlaqt author: Kim, Denny title: The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-312517-b24zlaqt.txt cache: ./cache/cord-312517-b24zlaqt.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-312517-b24zlaqt.txt' === file2bib.sh === id: cord-313684-61hkogdh author: Samaddar, Arghadip title: Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-313684-61hkogdh.txt cache: ./cache/cord-313684-61hkogdh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313684-61hkogdh.txt' === file2bib.sh === id: cord-316134-lkd2mj27 author: Sungsuwan, Suttipun title: Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication date: 2020-01-15 pages: extension: .txt txt: ./txt/cord-316134-lkd2mj27.txt cache: ./cache/cord-316134-lkd2mj27.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-316134-lkd2mj27.txt' === file2bib.sh === id: cord-303533-6s01qplg author: Neuman, Benjamin W. title: Does form meet function in the coronavirus replicative organelle? date: 2014-07-15 pages: extension: .txt txt: ./txt/cord-303533-6s01qplg.txt cache: ./cache/cord-303533-6s01qplg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-303533-6s01qplg.txt' === file2bib.sh === id: cord-314877-db7tze8j author: Chkuaseli, Tamari title: Activation of viral transcription by stepwise largescale folding of an RNA virus genome date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-314877-db7tze8j.txt cache: ./cache/cord-314877-db7tze8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314877-db7tze8j.txt' === file2bib.sh === id: cord-315483-l6dm82pp author: Santhakumar, Diwakar title: Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses date: 2018-05-01 pages: extension: .txt txt: ./txt/cord-315483-l6dm82pp.txt cache: ./cache/cord-315483-l6dm82pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-315483-l6dm82pp.txt' === file2bib.sh === id: cord-313301-7mkadtp9 author: Duffy, Siobain title: EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date: 2007-08-23 pages: extension: .txt txt: ./txt/cord-313301-7mkadtp9.txt cache: ./cache/cord-313301-7mkadtp9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-313301-7mkadtp9.txt' === file2bib.sh === id: cord-315611-xbj41ekc author: Ahmad, Mohammed title: Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date: 2020-07-14 pages: extension: .txt txt: ./txt/cord-315611-xbj41ekc.txt cache: ./cache/cord-315611-xbj41ekc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-315611-xbj41ekc.txt' === file2bib.sh === id: cord-317591-qa6oxy4j author: Fukushima, Akiko title: Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date: 2009-05-07 pages: extension: .txt txt: ./txt/cord-317591-qa6oxy4j.txt cache: ./cache/cord-317591-qa6oxy4j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317591-qa6oxy4j.txt' === file2bib.sh === id: cord-316503-wtmmewiz author: Warren, Travis K. title: Advanced morpholino oligomers: A novel approach to antiviral therapy date: 2012-02-14 pages: extension: .txt txt: ./txt/cord-316503-wtmmewiz.txt cache: ./cache/cord-316503-wtmmewiz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-316503-wtmmewiz.txt' === file2bib.sh === id: cord-316179-kmdxltie author: Fozouni, P. title: Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-316179-kmdxltie.txt cache: ./cache/cord-316179-kmdxltie.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-316179-kmdxltie.txt' === file2bib.sh === id: cord-315384-eqiokrub author: van der Hoek, Lia title: Croup Is Associated with the Novel Coronavirus NL63 date: 2005-08-23 pages: extension: .txt txt: ./txt/cord-315384-eqiokrub.txt cache: ./cache/cord-315384-eqiokrub.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315384-eqiokrub.txt' === file2bib.sh === id: cord-312461-5qzpo6l1 author: Adalja, Amesh A. title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date: 2019-08-30 pages: extension: .txt txt: ./txt/cord-312461-5qzpo6l1.txt cache: ./cache/cord-312461-5qzpo6l1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312461-5qzpo6l1.txt' === file2bib.sh === id: cord-312688-12san3m7 author: Martin, Baptiste title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date: 2016-09-14 pages: extension: .txt txt: ./txt/cord-312688-12san3m7.txt cache: ./cache/cord-312688-12san3m7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312688-12san3m7.txt' === file2bib.sh === id: cord-313541-fpqwzf9k author: Ulloa, S. title: A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date: 2020-08-22 pages: extension: .txt txt: ./txt/cord-313541-fpqwzf9k.txt cache: ./cache/cord-313541-fpqwzf9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-313541-fpqwzf9k.txt' === file2bib.sh === id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 pages: extension: .txt txt: ./txt/cord-010092-uftc8inx.txt cache: ./cache/cord-010092-uftc8inx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 17 resourceName b'cord-010092-uftc8inx.txt' === file2bib.sh === id: cord-317851-lj07947c author: Elena, S F title: Experimental evolution of plant RNA viruses date: 2008-02-06 pages: extension: .txt txt: ./txt/cord-317851-lj07947c.txt cache: ./cache/cord-317851-lj07947c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317851-lj07947c.txt' === file2bib.sh === id: cord-318359-41h90h05 author: Irigoyen, Nerea title: Ribosome profiling of the retrovirus murine leukemia virus date: 2018-01-22 pages: extension: .txt txt: ./txt/cord-318359-41h90h05.txt cache: ./cache/cord-318359-41h90h05.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318359-41h90h05.txt' === file2bib.sh === id: cord-317037-1qydcc5e author: Kumar, Asit title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-317037-1qydcc5e.txt cache: ./cache/cord-317037-1qydcc5e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317037-1qydcc5e.txt' === file2bib.sh === id: cord-312001-8p7scli8 author: Majzoub, Karim title: The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans date: 2019-08-16 pages: extension: .txt txt: ./txt/cord-312001-8p7scli8.txt cache: ./cache/cord-312001-8p7scli8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-312001-8p7scli8.txt' === file2bib.sh === id: cord-312886-o3ipzn05 author: Onomoto, Koji title: Antiviral innate immunity and stress granule responses date: 2014-08-19 pages: extension: .txt txt: ./txt/cord-312886-o3ipzn05.txt cache: ./cache/cord-312886-o3ipzn05.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-312886-o3ipzn05.txt' === file2bib.sh === id: cord-319664-gyktrd36 author: Mancini, Fabiola title: Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-319664-gyktrd36.txt cache: ./cache/cord-319664-gyktrd36.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319664-gyktrd36.txt' === file2bib.sh === id: cord-314019-8n0jafsk author: Feng, Qian title: Induction and suppression of innate antiviral responses by picornaviruses date: 2014-07-18 pages: extension: .txt txt: ./txt/cord-314019-8n0jafsk.txt cache: ./cache/cord-314019-8n0jafsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314019-8n0jafsk.txt' === file2bib.sh === id: cord-315616-pvt0amth author: Poole, Anthony title: Methyl-RNA: an evolutionary bridge between RNA and DNA? date: 2004-06-17 pages: extension: .txt txt: ./txt/cord-315616-pvt0amth.txt cache: ./cache/cord-315616-pvt0amth.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315616-pvt0amth.txt' === file2bib.sh === id: cord-314567-purplsjn author: Fernández-Ponce, Cecilia title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 pages: extension: .txt txt: ./txt/cord-314567-purplsjn.txt cache: ./cache/cord-314567-purplsjn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314567-purplsjn.txt' === file2bib.sh === id: cord-319100-3gdawhfn author: Kirkland, P.D. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-319100-3gdawhfn.txt cache: ./cache/cord-319100-3gdawhfn.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-319100-3gdawhfn.txt' === file2bib.sh === id: cord-314833-6fue84x6 author: Chang, Chung-ke title: The SARS coronavirus nucleocapsid protein – Forms and functions date: 2014-01-11 pages: extension: .txt txt: ./txt/cord-314833-6fue84x6.txt cache: ./cache/cord-314833-6fue84x6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-314833-6fue84x6.txt' === file2bib.sh === id: cord-318853-mxyxwkhx author: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 pages: extension: .txt txt: ./txt/cord-318853-mxyxwkhx.txt cache: ./cache/cord-318853-mxyxwkhx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318853-mxyxwkhx.txt' === file2bib.sh === id: cord-318576-dc5n6ni4 author: Jitobaom, Kunlakanya title: Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation date: 2020-05-08 pages: extension: .txt txt: ./txt/cord-318576-dc5n6ni4.txt cache: ./cache/cord-318576-dc5n6ni4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318576-dc5n6ni4.txt' === file2bib.sh === id: cord-317720-gbi11oxx author: Lefferts, Joel A. title: Implementation of an Emergency Use Authorization Test During an Impending National Crisis date: 2020-05-14 pages: extension: .txt txt: ./txt/cord-317720-gbi11oxx.txt cache: ./cache/cord-317720-gbi11oxx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317720-gbi11oxx.txt' === file2bib.sh === id: cord-318164-6rqi17oz author: Paoli, D. title: Sperm cryopreservation during the SARS-CoV-2 pandemic date: 2020-10-10 pages: extension: .txt txt: ./txt/cord-318164-6rqi17oz.txt cache: ./cache/cord-318164-6rqi17oz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318164-6rqi17oz.txt' === file2bib.sh === id: cord-319842-4mnaicki author: Jackson, William T title: Subversion of Cellular Autophagosomal Machinery by RNA Viruses date: 2005-04-26 pages: extension: .txt txt: ./txt/cord-319842-4mnaicki.txt cache: ./cache/cord-319842-4mnaicki.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319842-4mnaicki.txt' === file2bib.sh === id: cord-315054-kji2kfek author: Chakraborty, Nabarun title: Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration date: 2020-07-22 pages: extension: .txt txt: ./txt/cord-315054-kji2kfek.txt cache: ./cache/cord-315054-kji2kfek.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315054-kji2kfek.txt' === file2bib.sh === id: cord-318551-c1qr27lg author: Boguszewska‐Chachulska, Anna M. title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 pages: extension: .txt txt: ./txt/cord-318551-c1qr27lg.txt cache: ./cache/cord-318551-c1qr27lg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318551-c1qr27lg.txt' === file2bib.sh === id: cord-319501-a2x1hvkk author: Wong, Lok-Yin Roy title: A molecular arms race between host innate antiviral response and emerging human coronaviruses date: 2016-01-15 pages: extension: .txt txt: ./txt/cord-319501-a2x1hvkk.txt cache: ./cache/cord-319501-a2x1hvkk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319501-a2x1hvkk.txt' === file2bib.sh === id: cord-319179-gqaxf7mz author: Denison, M. title: Identification of putative polymerase gene product in cells infected with murine coronavirus A59 date: 1987-04-30 pages: extension: .txt txt: ./txt/cord-319179-gqaxf7mz.txt cache: ./cache/cord-319179-gqaxf7mz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319179-gqaxf7mz.txt' === file2bib.sh === id: cord-314316-hsspggp8 author: Sirinarumitr, Theerapol title: Rapid in situ hybridization technique for the detection of ribonucleic acids in tissues using radiolabelled and fluorescein-labelled riboprobes date: 1997-08-31 pages: extension: .txt txt: ./txt/cord-314316-hsspggp8.txt cache: ./cache/cord-314316-hsspggp8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-314316-hsspggp8.txt' === file2bib.sh === id: cord-318749-k91oku7h author: Dong, Hui-Jun title: Selective regulation in ribosome biogenesis and protein production for efficient viral translation date: 2020-10-29 pages: extension: .txt txt: ./txt/cord-318749-k91oku7h.txt cache: ./cache/cord-318749-k91oku7h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318749-k91oku7h.txt' === file2bib.sh === id: cord-312892-p72zwmtb author: Chen, Nanhua title: RNA sensors of the innate immune system and their detection of pathogens date: 2017-04-04 pages: extension: .txt txt: ./txt/cord-312892-p72zwmtb.txt cache: ./cache/cord-312892-p72zwmtb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-312892-p72zwmtb.txt' === file2bib.sh === id: cord-317455-6qx0v28w author: Brown, Paul A. title: Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date: 2018-09-10 pages: extension: .txt txt: ./txt/cord-317455-6qx0v28w.txt cache: ./cache/cord-317455-6qx0v28w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317455-6qx0v28w.txt' === file2bib.sh === id: cord-318495-1w74wf02 author: Vignuzzi, Marco title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 pages: extension: .txt txt: ./txt/cord-318495-1w74wf02.txt cache: ./cache/cord-318495-1w74wf02.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318495-1w74wf02.txt' === file2bib.sh === id: cord-319729-6lzjhn8j author: Tian, Bin title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway date: 2018-01-19 pages: extension: .txt txt: ./txt/cord-319729-6lzjhn8j.txt cache: ./cache/cord-319729-6lzjhn8j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319729-6lzjhn8j.txt' === file2bib.sh === id: cord-315085-rucfowvv author: Sekulic, Miroslav title: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-315085-rucfowvv.txt cache: ./cache/cord-315085-rucfowvv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-315085-rucfowvv.txt' === file2bib.sh === id: cord-320169-dtv7to3l author: Liu, Yen-Chin title: COVID-19: the First Documented Coronavirus Pandemic in History date: 2020-05-05 pages: extension: .txt txt: ./txt/cord-320169-dtv7to3l.txt cache: ./cache/cord-320169-dtv7to3l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-320169-dtv7to3l.txt' === file2bib.sh === id: cord-318478-fn0gcxbb author: Ziv, Omer title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-318478-fn0gcxbb.txt cache: ./cache/cord-318478-fn0gcxbb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318478-fn0gcxbb.txt' === file2bib.sh === id: cord-319116-2ts6zpdb author: Ruggiero, Emanuela title: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy date: 2018-04-20 pages: extension: .txt txt: ./txt/cord-319116-2ts6zpdb.txt cache: ./cache/cord-319116-2ts6zpdb.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319116-2ts6zpdb.txt' === file2bib.sh === id: cord-319681-kjet3e50 author: Lin, Zhaoru title: Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U(6)A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting date: 2012-06-28 pages: extension: .txt txt: ./txt/cord-319681-kjet3e50.txt cache: ./cache/cord-319681-kjet3e50.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319681-kjet3e50.txt' === file2bib.sh === id: cord-317715-xtsi663k author: Ortiz-Riaño, Emilio title: D471G Mutation in LCMV-NP Affects its Ability to Self-associate and Results in a Dominant Negative Effect in Viral RNA Synthesis date: 2012-10-16 pages: extension: .txt txt: ./txt/cord-317715-xtsi663k.txt cache: ./cache/cord-317715-xtsi663k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317715-xtsi663k.txt' === file2bib.sh === id: cord-317537-wgu5cd0y author: Lu, Hsiang-Chia title: Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant date: 2009-05-25 pages: extension: .txt txt: ./txt/cord-317537-wgu5cd0y.txt cache: ./cache/cord-317537-wgu5cd0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-317537-wgu5cd0y.txt' === file2bib.sh === id: cord-319780-rfj9t99r author: Alexander, S.P.H. title: A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-319780-rfj9t99r.txt cache: ./cache/cord-319780-rfj9t99r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319780-rfj9t99r.txt' === file2bib.sh === id: cord-320501-xqgqq55q author: Theobald, Nigel title: Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine date: 2020-06-24 pages: extension: .txt txt: ./txt/cord-320501-xqgqq55q.txt cache: ./cache/cord-320501-xqgqq55q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320501-xqgqq55q.txt' === file2bib.sh === id: cord-317773-jdq1d98i author: Meng, Qing-Wen title: Enhanced inhibition of Avian leukosis virus subgroup J replication by multi-target miRNAs date: 2011-12-22 pages: extension: .txt txt: ./txt/cord-317773-jdq1d98i.txt cache: ./cache/cord-317773-jdq1d98i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-317773-jdq1d98i.txt' === file2bib.sh === id: cord-321053-lgae22f8 author: Gerold, Gisa title: Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date: 2013-10-04 pages: extension: .txt txt: ./txt/cord-321053-lgae22f8.txt cache: ./cache/cord-321053-lgae22f8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321053-lgae22f8.txt' === file2bib.sh === id: cord-321505-m40s6uw9 author: Sakamoto, Naoya title: Inhibition of hepatitis C virus infection and expression in vitro and in vivo by recombinant adenovirus expressing short hairpin RNA date: 2007-08-07 pages: extension: .txt txt: ./txt/cord-321505-m40s6uw9.txt cache: ./cache/cord-321505-m40s6uw9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321505-m40s6uw9.txt' === file2bib.sh === id: cord-319906-s7kzp795 author: Zemla, Adam T title: StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase date: 2011-06-02 pages: extension: .txt txt: ./txt/cord-319906-s7kzp795.txt cache: ./cache/cord-319906-s7kzp795.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319906-s7kzp795.txt' === file2bib.sh === id: cord-319635-kh99n7q2 author: Chiang, Wei-Wei title: Cell Type-Dependent RNA Recombination Frequency in the Japanese Encephalitis Virus date: 2014-07-22 pages: extension: .txt txt: ./txt/cord-319635-kh99n7q2.txt cache: ./cache/cord-319635-kh99n7q2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319635-kh99n7q2.txt' === file2bib.sh === id: cord-318751-4v2tl0gi author: Arias, Armando title: Progress towards the prevention and treatment of norovirus infections date: 2013-11-17 pages: extension: .txt txt: ./txt/cord-318751-4v2tl0gi.txt cache: ./cache/cord-318751-4v2tl0gi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-318751-4v2tl0gi.txt' === file2bib.sh === id: cord-320921-eumuid3r author: Widagdo, W. title: Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits date: 2019-04-24 pages: extension: .txt txt: ./txt/cord-320921-eumuid3r.txt cache: ./cache/cord-320921-eumuid3r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320921-eumuid3r.txt' === file2bib.sh === id: cord-319781-6thdg2up author: Payne, Kelly title: Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date: 2020-07-24 pages: extension: .txt txt: ./txt/cord-319781-6thdg2up.txt cache: ./cache/cord-319781-6thdg2up.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319781-6thdg2up.txt' === file2bib.sh === id: cord-319821-ij34t1ae author: Bauer, Lisa title: Direct-acting antivirals and host-targeting strategies to combat enterovirus infections date: 2017-04-12 pages: extension: .txt txt: ./txt/cord-319821-ij34t1ae.txt cache: ./cache/cord-319821-ij34t1ae.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319821-ij34t1ae.txt' === file2bib.sh === id: cord-320935-3n157yl4 author: Kumar, Manish title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 pages: extension: .txt txt: ./txt/cord-320935-3n157yl4.txt cache: ./cache/cord-320935-3n157yl4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320935-3n157yl4.txt' === file2bib.sh === id: cord-320709-2pnqpljt author: Munster, Vincent J. title: Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis) date: 2016-02-22 pages: extension: .txt txt: ./txt/cord-320709-2pnqpljt.txt cache: ./cache/cord-320709-2pnqpljt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320709-2pnqpljt.txt' === file2bib.sh === id: cord-319194-ukuia48s author: Liò, Pietro title: Phylogenomics and bioinformatics of SARS-CoV date: 2004-02-04 pages: extension: .txt txt: ./txt/cord-319194-ukuia48s.txt cache: ./cache/cord-319194-ukuia48s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-319194-ukuia48s.txt' === file2bib.sh === id: cord-318276-so5jooj0 author: Bertholet, Christine title: Vaccinia virus produces late mRNAs by discontinuous synthesis date: 1987-07-17 pages: extension: .txt txt: ./txt/cord-318276-so5jooj0.txt cache: ./cache/cord-318276-so5jooj0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-318276-so5jooj0.txt' === file2bib.sh === id: cord-320325-sjab8zsk author: Mendez, Aaron S title: Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX date: 2018-12-14 pages: extension: .txt txt: ./txt/cord-320325-sjab8zsk.txt cache: ./cache/cord-320325-sjab8zsk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320325-sjab8zsk.txt' === file2bib.sh === id: cord-319649-d6dqr03e author: Yang, Jie title: A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing date: 2013-12-05 pages: extension: .txt txt: ./txt/cord-319649-d6dqr03e.txt cache: ./cache/cord-319649-d6dqr03e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-319649-d6dqr03e.txt' === file2bib.sh === id: cord-322240-z8zkl2xh author: Maeda, Ken title: Isolation of Novel Adenovirus from Fruit Bat (Pteropus dasymallus yayeyamae) date: 2008-02-17 pages: extension: .txt txt: ./txt/cord-322240-z8zkl2xh.txt cache: ./cache/cord-322240-z8zkl2xh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-322240-z8zkl2xh.txt' === file2bib.sh === id: cord-320212-fw51w4nm author: Friedman, Stephanie D. title: Genomic Sequences of two Novel Levivirus Single-Stranded RNA Coliphages (Family Leviviridae): Evidence for Recombinationin Environmental Strains date: 2012-09-13 pages: extension: .txt txt: ./txt/cord-320212-fw51w4nm.txt cache: ./cache/cord-320212-fw51w4nm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320212-fw51w4nm.txt' === file2bib.sh === id: cord-321957-ybtk9cp1 author: Carey, Brian D. title: Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation date: 2020-03-09 pages: extension: .txt txt: ./txt/cord-321957-ybtk9cp1.txt cache: ./cache/cord-321957-ybtk9cp1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321957-ybtk9cp1.txt' === file2bib.sh === id: cord-321938-pda4a5n7 author: Weisshoff, Hardy title: Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-321938-pda4a5n7.txt cache: ./cache/cord-321938-pda4a5n7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321938-pda4a5n7.txt' === file2bib.sh === id: cord-320351-47d0nby0 author: Li, Zhouxiao title: The emerging landscape of circular RNAs in immunity: breakthroughs and challenges date: 2020-07-10 pages: extension: .txt txt: ./txt/cord-320351-47d0nby0.txt cache: ./cache/cord-320351-47d0nby0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-320351-47d0nby0.txt' === file2bib.sh === id: cord-322084-gkg1059v author: JEONG, YONG SEOK title: Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence date: 1996-03-01 pages: extension: .txt txt: ./txt/cord-322084-gkg1059v.txt cache: ./cache/cord-322084-gkg1059v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322084-gkg1059v.txt' === file2bib.sh === id: cord-321155-dty18esg author: Zhang, Rongxin title: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date: 2020-06-05 pages: extension: .txt txt: ./txt/cord-321155-dty18esg.txt cache: ./cache/cord-321155-dty18esg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321155-dty18esg.txt' === file2bib.sh === id: cord-321013-8pkrg0mx author: McBride, Ruth title: The Coronavirus Nucleocapsid Is a Multifunctional Protein date: 2014-08-07 pages: extension: .txt txt: ./txt/cord-321013-8pkrg0mx.txt cache: ./cache/cord-321013-8pkrg0mx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-321013-8pkrg0mx.txt' === file2bib.sh === id: cord-320713-b37c8aye author: Roberts, Lisa O. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 pages: extension: .txt txt: ./txt/cord-320713-b37c8aye.txt cache: ./cache/cord-320713-b37c8aye.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-320713-b37c8aye.txt' === file2bib.sh === id: cord-322062-nnefbeo6 author: Tam, Albert W. title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome date: 1991-11-30 pages: extension: .txt txt: ./txt/cord-322062-nnefbeo6.txt cache: ./cache/cord-322062-nnefbeo6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-322062-nnefbeo6.txt' === file2bib.sh === id: cord-321773-5fw9abzl author: Cheng, Wenyu title: DDX5 RNA Helicases: Emerging Roles in Viral Infection date: 2018-04-09 pages: extension: .txt txt: ./txt/cord-321773-5fw9abzl.txt cache: ./cache/cord-321773-5fw9abzl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-321773-5fw9abzl.txt' === file2bib.sh === id: cord-321607-3r736dnk author: Ezelle, Heather J. title: The Roles of RNase-L in Antimicrobial Immunity and the Cytoskeleton-Associated Innate Response date: 2016-01-08 pages: extension: .txt txt: ./txt/cord-321607-3r736dnk.txt cache: ./cache/cord-321607-3r736dnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-321607-3r736dnk.txt' === file2bib.sh === id: cord-322234-1zyy536y author: Lorusso, Alessio title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 pages: extension: .txt txt: ./txt/cord-322234-1zyy536y.txt cache: ./cache/cord-322234-1zyy536y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322234-1zyy536y.txt' === file2bib.sh === id: cord-322206-roxa3ix6 author: I. Sardi, Silvia title: High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-322206-roxa3ix6.txt cache: ./cache/cord-322206-roxa3ix6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322206-roxa3ix6.txt' === file2bib.sh === id: cord-323585-iv2dcpqj author: Li, Su title: eEF1A Interacts with the NS5A Protein and Inhibits the Growth of Classical Swine Fever Virus date: 2015-08-10 pages: extension: .txt txt: ./txt/cord-323585-iv2dcpqj.txt cache: ./cache/cord-323585-iv2dcpqj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323585-iv2dcpqj.txt' === file2bib.sh === id: cord-322410-k23engcx author: Naguib, Mahmoud M. title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses date: 2017-03-21 pages: extension: .txt txt: ./txt/cord-322410-k23engcx.txt cache: ./cache/cord-322410-k23engcx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-322410-k23engcx.txt' === file2bib.sh === id: cord-322756-ouvn71r9 author: Chow, Michael Y.T. title: Inhaled RNA Therapy: From Promise to Reality date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-322756-ouvn71r9.txt cache: ./cache/cord-322756-ouvn71r9.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-322756-ouvn71r9.txt' === file2bib.sh === id: cord-323668-evzzfu04 author: Yin, Zhixin title: lncRNA expression signatures in response to enterovirus 71 infection date: 2013-01-11 pages: extension: .txt txt: ./txt/cord-323668-evzzfu04.txt cache: ./cache/cord-323668-evzzfu04.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323668-evzzfu04.txt' === file2bib.sh === id: cord-323737-6ajqy0ch author: Jiang, Yuanyuan title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus date: 2020-10-04 pages: extension: .txt txt: ./txt/cord-323737-6ajqy0ch.txt cache: ./cache/cord-323737-6ajqy0ch.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323737-6ajqy0ch.txt' === file2bib.sh === id: cord-323691-5s5almd2 author: Mishin, Vasiliy P title: A ‘minimal’ approach in design of flavivirus infectious DNA date: 2001-12-04 pages: extension: .txt txt: ./txt/cord-323691-5s5almd2.txt cache: ./cache/cord-323691-5s5almd2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323691-5s5almd2.txt' === file2bib.sh === id: cord-323845-s78t5qxj author: Soliman, H. title: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) date: 2006-05-31 pages: extension: .txt txt: ./txt/cord-323845-s78t5qxj.txt cache: ./cache/cord-323845-s78t5qxj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323845-s78t5qxj.txt' === file2bib.sh === id: cord-323756-atnrw9ew author: Vabret, Nicolas title: Sensing Microbial RNA in the Cytosol date: 2013-12-25 pages: extension: .txt txt: ./txt/cord-323756-atnrw9ew.txt cache: ./cache/cord-323756-atnrw9ew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323756-atnrw9ew.txt' === file2bib.sh === id: cord-324137-nau83mjv author: Saranathan, Nandhini title: G-Quadruplexes: More Than Just a Kink in Microbial Genomes date: 2018-09-14 pages: extension: .txt txt: ./txt/cord-324137-nau83mjv.txt cache: ./cache/cord-324137-nau83mjv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324137-nau83mjv.txt' === file2bib.sh === id: cord-324212-aqp73hi9 author: Wyszko, Eliza title: Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum date: 2006-10-09 pages: extension: .txt txt: ./txt/cord-324212-aqp73hi9.txt cache: ./cache/cord-324212-aqp73hi9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324212-aqp73hi9.txt' === file2bib.sh === id: cord-323973-wszo9s3d author: Zhu, Hanliang title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-323973-wszo9s3d.txt cache: ./cache/cord-323973-wszo9s3d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323973-wszo9s3d.txt' === file2bib.sh === id: cord-324638-gwd8qin6 author: Chiu, Rossa WK title: Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date: 2006-02-09 pages: extension: .txt txt: ./txt/cord-324638-gwd8qin6.txt cache: ./cache/cord-324638-gwd8qin6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324638-gwd8qin6.txt' === file2bib.sh === id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 pages: extension: .txt txt: ./txt/cord-323987-gh1m05gi.txt cache: ./cache/cord-323987-gh1m05gi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-323987-gh1m05gi.txt' === file2bib.sh === id: cord-324495-0pee1i3o author: Kang, Hyeonjeong title: Sasa quelpaertensis Nakai extract suppresses porcine reproductive and respiratory syndrome virus replication and modulates virus-induced cytokine production date: 2015-06-06 pages: extension: .txt txt: ./txt/cord-324495-0pee1i3o.txt cache: ./cache/cord-324495-0pee1i3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324495-0pee1i3o.txt' === file2bib.sh === id: cord-324324-8ybfiz8f author: Decaro, Nicola title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 pages: extension: .txt txt: ./txt/cord-324324-8ybfiz8f.txt cache: ./cache/cord-324324-8ybfiz8f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324324-8ybfiz8f.txt' === file2bib.sh === id: cord-323029-7hqp8xuq author: Bognár, Zsófia title: Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-323029-7hqp8xuq.txt cache: ./cache/cord-323029-7hqp8xuq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-323029-7hqp8xuq.txt' === file2bib.sh === id: cord-325043-vqjhiv7p author: Gorbalenya, Alexander E. title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication date: 1989 pages: extension: .txt txt: ./txt/cord-325043-vqjhiv7p.txt cache: ./cache/cord-325043-vqjhiv7p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325043-vqjhiv7p.txt' === file2bib.sh === id: cord-324697-c0dv1zmi author: Rodriguez, William title: Fated for decay: RNA elements targeted by viral endonucleases date: 2020-06-07 pages: extension: .txt txt: ./txt/cord-324697-c0dv1zmi.txt cache: ./cache/cord-324697-c0dv1zmi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324697-c0dv1zmi.txt' === file2bib.sh === id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-325113-sou8xyld.txt cache: ./cache/cord-325113-sou8xyld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325113-sou8xyld.txt' === file2bib.sh === id: cord-324928-cpryxa6p author: Lello, Laura Sandra title: Cross-utilisation of template RNAs by alphavirus replicases date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-324928-cpryxa6p.txt cache: ./cache/cord-324928-cpryxa6p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-324928-cpryxa6p.txt' === file2bib.sh === id: cord-324640-2zhaknbi author: Munday, Diane C. title: Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus date: 2010-07-20 pages: extension: .txt txt: ./txt/cord-324640-2zhaknbi.txt cache: ./cache/cord-324640-2zhaknbi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324640-2zhaknbi.txt' === file2bib.sh === id: cord-325197-j1uo8qmf author: Crimi, Ettore title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-325197-j1uo8qmf.txt cache: ./cache/cord-325197-j1uo8qmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325197-j1uo8qmf.txt' === file2bib.sh === id: cord-325137-6c6er06a author: Moser, Lindsey A. title: A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date: 2016-06-07 pages: extension: .txt txt: ./txt/cord-325137-6c6er06a.txt cache: ./cache/cord-325137-6c6er06a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325137-6c6er06a.txt' === file2bib.sh === id: cord-325529-pid58g2r author: Ben-Ami, Roni title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 pages: extension: .txt txt: ./txt/cord-325529-pid58g2r.txt cache: ./cache/cord-325529-pid58g2r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-325529-pid58g2r.txt' === file2bib.sh === id: cord-324984-ojrpsdt9 author: Ji, Xingyue title: Medicinal chemistry strategies toward host targeting antiviral agents date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-324984-ojrpsdt9.txt cache: ./cache/cord-324984-ojrpsdt9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-324984-ojrpsdt9.txt' === file2bib.sh === id: cord-325280-4whzcmqv author: Takizawa, Naoki title: Current landscape and future prospects of antiviral drugs derived from microbial products date: 2017-10-11 pages: extension: .txt txt: ./txt/cord-325280-4whzcmqv.txt cache: ./cache/cord-325280-4whzcmqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325280-4whzcmqv.txt' === file2bib.sh === id: cord-325326-2bbqz4o7 author: Beitzel, Brett F. title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date: 2010-10-14 pages: extension: .txt txt: ./txt/cord-325326-2bbqz4o7.txt cache: ./cache/cord-325326-2bbqz4o7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325326-2bbqz4o7.txt' === file2bib.sh === id: cord-325230-3kg4oe4g author: Agol, Vadim I. title: Viral security proteins: counteracting host defences date: 2010-11-09 pages: extension: .txt txt: ./txt/cord-325230-3kg4oe4g.txt cache: ./cache/cord-325230-3kg4oe4g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325230-3kg4oe4g.txt' === file2bib.sh === id: cord-325479-2r4oomdp author: Torii, Shotaro title: Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-325479-2r4oomdp.txt cache: ./cache/cord-325479-2r4oomdp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325479-2r4oomdp.txt' === file2bib.sh === id: cord-325328-3l3jznkj author: Holbrook, Stephen R title: RNA structure: the long and the short of it date: 2005-05-16 pages: extension: .txt txt: ./txt/cord-325328-3l3jznkj.txt cache: ./cache/cord-325328-3l3jznkj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325328-3l3jznkj.txt' === file2bib.sh === id: cord-325736-gs9d8y55 author: Marin, J title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date: 2000-07-31 pages: extension: .txt txt: ./txt/cord-325736-gs9d8y55.txt cache: ./cache/cord-325736-gs9d8y55.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325736-gs9d8y55.txt' === file2bib.sh === id: cord-325954-rhrkr97h author: Han, Mi Seon title: Viral RNA Load in Mildly Symptomatic and Asymptomatic Children with COVID-19, Seoul, South Korea date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-325954-rhrkr97h.txt cache: ./cache/cord-325954-rhrkr97h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325954-rhrkr97h.txt' === file2bib.sh === id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 pages: extension: .txt txt: ./txt/cord-324944-ixh3ykrc.txt cache: ./cache/cord-324944-ixh3ykrc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-324944-ixh3ykrc.txt' === file2bib.sh === id: cord-325958-1v1pg2z0 author: Lange, Clemens title: Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date: 2020-05-06 pages: extension: .txt txt: ./txt/cord-325958-1v1pg2z0.txt cache: ./cache/cord-325958-1v1pg2z0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325958-1v1pg2z0.txt' === file2bib.sh === id: cord-325925-010xj69x author: Mordecai, Gideon J title: Endangered wild salmon infected by newly discovered viruses date: 2019-09-03 pages: extension: .txt txt: ./txt/cord-325925-010xj69x.txt cache: ./cache/cord-325925-010xj69x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325925-010xj69x.txt' === file2bib.sh === id: cord-325624-6anybxnk author: Ireland, Derek D. C. title: RNase L Mediated Protection from Virus Induced Demyelination date: 2009-10-02 pages: extension: .txt txt: ./txt/cord-325624-6anybxnk.txt cache: ./cache/cord-325624-6anybxnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-325624-6anybxnk.txt' === file2bib.sh === id: cord-325820-tnyzmrm8 author: Kovacikova, Kristina title: 6′-β-Fluoro-Homoaristeromycin and 6′-Fluoro-Homoneplanocin A Are Potent Inhibitors of Chikungunya Virus Replication through Their Direct Effect on Viral Nonstructural Protein 1 date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-325820-tnyzmrm8.txt cache: ./cache/cord-325820-tnyzmrm8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-325820-tnyzmrm8.txt' === file2bib.sh === id: cord-326225-crtpzad7 author: Neill, John D. title: Simultaneous rapid sequencing of multiple RNA virus genomes date: 2014-06-01 pages: extension: .txt txt: ./txt/cord-326225-crtpzad7.txt cache: ./cache/cord-326225-crtpzad7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326225-crtpzad7.txt' === file2bib.sh === id: cord-325966-0g7a9s5z author: Shih, Hsin-I. title: Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date: 2020-05-30 pages: extension: .txt txt: ./txt/cord-325966-0g7a9s5z.txt cache: ./cache/cord-325966-0g7a9s5z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-325966-0g7a9s5z.txt' === file2bib.sh === id: cord-326257-rcv8sh22 author: Simmonds, P. title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date: 2020-05-01 pages: extension: .txt txt: ./txt/cord-326257-rcv8sh22.txt cache: ./cache/cord-326257-rcv8sh22.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326257-rcv8sh22.txt' === file2bib.sh === id: cord-326217-ji0njeha author: Saleh, Maged title: Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-326217-ji0njeha.txt cache: ./cache/cord-326217-ji0njeha.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326217-ji0njeha.txt' === file2bib.sh === id: cord-326911-va3x6au2 author: Ramos-Mandujano, G. title: A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-326911-va3x6au2.txt cache: ./cache/cord-326911-va3x6au2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-326911-va3x6au2.txt' === file2bib.sh === id: cord-326719-p1ma4akz author: Enjuanes, Luis title: Virus-based vectors for gene expression in mammalian cells: Coronavirus date: 2003-12-31 pages: extension: .txt txt: ./txt/cord-326719-p1ma4akz.txt cache: ./cache/cord-326719-p1ma4akz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326719-p1ma4akz.txt' === file2bib.sh === id: cord-327259-7o7fs4yb author: Correa, I. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 pages: extension: .txt txt: ./txt/cord-327259-7o7fs4yb.txt cache: ./cache/cord-327259-7o7fs4yb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327259-7o7fs4yb.txt' === file2bib.sh === id: cord-327024-1k5jucae author: Zhang, Qingshui title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date: 2018-04-19 pages: extension: .txt txt: ./txt/cord-327024-1k5jucae.txt cache: ./cache/cord-327024-1k5jucae.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327024-1k5jucae.txt' === file2bib.sh === id: cord-327272-fspxett8 author: Buonaguro, Luigi title: Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date: 2020-05-12 pages: extension: .txt txt: ./txt/cord-327272-fspxett8.txt cache: ./cache/cord-327272-fspxett8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327272-fspxett8.txt' === file2bib.sh === id: cord-022940-atbjwpo5 author: nan title: Poster Sessions date: 2016-09-07 pages: extension: .txt txt: ./txt/cord-022940-atbjwpo5.txt cache: ./cache/cord-022940-atbjwpo5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 15 resourceName b'cord-022940-atbjwpo5.txt' === file2bib.sh === id: cord-326017-qw4qynqv author: Laskar, Partha title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-326017-qw4qynqv.txt cache: ./cache/cord-326017-qw4qynqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-326017-qw4qynqv.txt' === file2bib.sh === id: cord-327855-txryqil7 author: Kulka, M. title: The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date: 2003 pages: extension: .txt txt: ./txt/cord-327855-txryqil7.txt cache: ./cache/cord-327855-txryqil7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327855-txryqil7.txt' === file2bib.sh === id: cord-328300-zehltghv author: Lin, Shing-Yen title: Structural Basis for the Identification of the N-Terminal Domain of Coronavirus Nucleocapsid Protein as an Antiviral Target date: 2014-02-24 pages: extension: .txt txt: ./txt/cord-328300-zehltghv.txt cache: ./cache/cord-328300-zehltghv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328300-zehltghv.txt' === file2bib.sh === id: cord-327518-yilv9z2m author: nan title: Coronaviridae date: 2011-11-23 pages: extension: .txt txt: ./txt/cord-327518-yilv9z2m.txt cache: ./cache/cord-327518-yilv9z2m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-327518-yilv9z2m.txt' === file2bib.sh === id: cord-327000-oyg3oyx1 author: Li, Shasha title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-327000-oyg3oyx1.txt cache: ./cache/cord-327000-oyg3oyx1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327000-oyg3oyx1.txt' === file2bib.sh === id: cord-327660-p1b07b4t author: Wolf, Yuri I. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 pages: extension: .txt txt: ./txt/cord-327660-p1b07b4t.txt cache: ./cache/cord-327660-p1b07b4t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327660-p1b07b4t.txt' === file2bib.sh === id: cord-327997-noqbcxua author: Wu, Kevin E. title: RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-327997-noqbcxua.txt cache: ./cache/cord-327997-noqbcxua.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-327997-noqbcxua.txt' === file2bib.sh === id: cord-328042-e1is656g author: Klein, Steffen title: SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date: 2020-08-07 pages: extension: .txt txt: ./txt/cord-328042-e1is656g.txt cache: ./cache/cord-328042-e1is656g.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328042-e1is656g.txt' === file2bib.sh === id: cord-328085-7wp18qb6 author: Barage, Sagar title: Identification and characterization of novel RdRp and Nsp15 inhibitors for SARS-COV2 using computational approach date: 2020-11-06 pages: extension: .txt txt: ./txt/cord-328085-7wp18qb6.txt cache: ./cache/cord-328085-7wp18qb6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328085-7wp18qb6.txt' === file2bib.sh === id: cord-328471-oz99upzz author: Ahmad, Jamshaid title: SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-328471-oz99upzz.txt cache: ./cache/cord-328471-oz99upzz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-328471-oz99upzz.txt' === file2bib.sh === id: cord-328259-3g4klpyg author: Guajardo-Leiva, Sergio title: Metagenomic Insights into the Sewage RNA Virosphere of a Large City date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-328259-3g4klpyg.txt cache: ./cache/cord-328259-3g4klpyg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328259-3g4klpyg.txt' === file2bib.sh === id: cord-328686-5ik5em5a author: Zhao, L. title: First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date: 2020-08-21 pages: extension: .txt txt: ./txt/cord-328686-5ik5em5a.txt cache: ./cache/cord-328686-5ik5em5a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328686-5ik5em5a.txt' === file2bib.sh === id: cord-328737-6mcefqn5 author: Lee, Eun Yeong title: A novel nucleic acid amplification system based on nano-gap embedded active disk resonators date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-328737-6mcefqn5.txt cache: ./cache/cord-328737-6mcefqn5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328737-6mcefqn5.txt' === file2bib.sh === id: cord-328659-miujzgtd author: Mishra, Akhilesh title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date: 2020-07-27 pages: extension: .txt txt: ./txt/cord-328659-miujzgtd.txt cache: ./cache/cord-328659-miujzgtd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328659-miujzgtd.txt' === file2bib.sh === id: cord-328960-46zui1sl author: Hillen, Hauke S. title: Structure of replicating SARS-CoV-2 polymerase date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-328960-46zui1sl.txt cache: ./cache/cord-328960-46zui1sl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328960-46zui1sl.txt' === file2bib.sh === id: cord-328768-2qk884x2 author: Sabatier, Marina title: Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-328768-2qk884x2.txt cache: ./cache/cord-328768-2qk884x2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328768-2qk884x2.txt' === file2bib.sh === id: cord-329041-coryaz2s author: Brown, Ariane J. title: Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date: 2019-09-30 pages: extension: .txt txt: ./txt/cord-329041-coryaz2s.txt cache: ./cache/cord-329041-coryaz2s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329041-coryaz2s.txt' === file2bib.sh === id: cord-328633-c31xsyeo author: Moser, Michael J. title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date: 2012-06-04 pages: extension: .txt txt: ./txt/cord-328633-c31xsyeo.txt cache: ./cache/cord-328633-c31xsyeo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328633-c31xsyeo.txt' === file2bib.sh === id: cord-328252-dk54w8z9 author: Kikkert, Marjolein title: Innate Immune Evasion by Human Respiratory RNA Viruses date: 2019-10-14 pages: extension: .txt txt: ./txt/cord-328252-dk54w8z9.txt cache: ./cache/cord-328252-dk54w8z9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328252-dk54w8z9.txt' === file2bib.sh === id: cord-328460-thx9zh11 author: Zanoli, Laura Maria title: Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices date: 2012-12-27 pages: extension: .txt txt: ./txt/cord-328460-thx9zh11.txt cache: ./cache/cord-328460-thx9zh11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-328460-thx9zh11.txt' === file2bib.sh === id: cord-328947-3l9ydspz author: Webb, L. G. title: Chikungunya virus antagonizes cGAS-STING mediated type-I interferon responses by degrading cGAS date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-328947-3l9ydspz.txt cache: ./cache/cord-328947-3l9ydspz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-328947-3l9ydspz.txt' === file2bib.sh === id: cord-329107-43e2lkht author: Pawlicka, Kamila title: Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics date: 2020-03-24 pages: extension: .txt txt: ./txt/cord-329107-43e2lkht.txt cache: ./cache/cord-329107-43e2lkht.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329107-43e2lkht.txt' === file2bib.sh === id: cord-329311-p68kr4ga author: Prebensen, Christian title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-329311-p68kr4ga.txt cache: ./cache/cord-329311-p68kr4ga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329311-p68kr4ga.txt' === file2bib.sh === id: cord-329361-0mpbau1b author: Bennasser, Yamina title: RNAi Therapy for HIV Infection: Principles and Practicalities date: 2012-08-16 pages: extension: .txt txt: ./txt/cord-329361-0mpbau1b.txt cache: ./cache/cord-329361-0mpbau1b.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329361-0mpbau1b.txt' === file2bib.sh === id: cord-329504-91te3nu8 author: Croll, Tristan title: Making the invisible enemy visible date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-329504-91te3nu8.txt cache: ./cache/cord-329504-91te3nu8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329504-91te3nu8.txt' === file2bib.sh === id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 pages: extension: .txt txt: ./txt/cord-329429-ur8g68vp.txt cache: ./cache/cord-329429-ur8g68vp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-329429-ur8g68vp.txt' === file2bib.sh === id: cord-329493-ueqlhgn0 author: Stadler, Konrad title: SARS — beginning to understand a new virus date: 2003 pages: extension: .txt txt: ./txt/cord-329493-ueqlhgn0.txt cache: ./cache/cord-329493-ueqlhgn0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329493-ueqlhgn0.txt' === file2bib.sh === id: cord-329102-2y49kcwu author: Lan, Tammy C. T. title: Structure of the full SARS-CoV-2 RNA genome in infected cells date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-329102-2y49kcwu.txt cache: ./cache/cord-329102-2y49kcwu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-329102-2y49kcwu.txt' === file2bib.sh === id: cord-329687-vhi4tbnc author: Verdugo, C. title: A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing. date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-329687-vhi4tbnc.txt cache: ./cache/cord-329687-vhi4tbnc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329687-vhi4tbnc.txt' === file2bib.sh === id: cord-329494-cdn52epy author: Artuso, María C. title: Inhibition of Junín virus replication by small interfering RNAs date: 2009-07-08 pages: extension: .txt txt: ./txt/cord-329494-cdn52epy.txt cache: ./cache/cord-329494-cdn52epy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329494-cdn52epy.txt' === file2bib.sh === id: cord-329366-xuszdrsa author: Hackbart, Matthew title: Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors date: 2020-04-07 pages: extension: .txt txt: ./txt/cord-329366-xuszdrsa.txt cache: ./cache/cord-329366-xuszdrsa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329366-xuszdrsa.txt' === file2bib.sh === id: cord-329707-89zyu8bl author: Zhang, Xue title: Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date: 2006-11-30 pages: extension: .txt txt: ./txt/cord-329707-89zyu8bl.txt cache: ./cache/cord-329707-89zyu8bl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329707-89zyu8bl.txt' === file2bib.sh === id: cord-330045-4gj9d181 author: Sun, Jiufeng title: Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date: 2020-08-17 pages: extension: .txt txt: ./txt/cord-330045-4gj9d181.txt cache: ./cache/cord-330045-4gj9d181.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330045-4gj9d181.txt' === file2bib.sh === id: cord-329710-vqorb6j7 author: Kumar, Krishna title: Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date: 2020-05-27 pages: extension: .txt txt: ./txt/cord-329710-vqorb6j7.txt cache: ./cache/cord-329710-vqorb6j7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329710-vqorb6j7.txt' === file2bib.sh === id: cord-329618-kywhulpc author: Xu, Cheng title: A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells date: 2016-05-23 pages: extension: .txt txt: ./txt/cord-329618-kywhulpc.txt cache: ./cache/cord-329618-kywhulpc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329618-kywhulpc.txt' === file2bib.sh === id: cord-330200-l6bnxi40 author: Huang, Jianping title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-330200-l6bnxi40.txt cache: ./cache/cord-330200-l6bnxi40.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330200-l6bnxi40.txt' === file2bib.sh === id: cord-329866-io9fvy58 author: Lorusso, Eleonora title: Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis date: 2019-08-31 pages: extension: .txt txt: ./txt/cord-329866-io9fvy58.txt cache: ./cache/cord-329866-io9fvy58.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-329866-io9fvy58.txt' === file2bib.sh === id: cord-330213-reb9vo7x author: Miladi, Milad title: The landscape of SARS-CoV-2 RNA modifications date: 2020-07-18 pages: extension: .txt txt: ./txt/cord-330213-reb9vo7x.txt cache: ./cache/cord-330213-reb9vo7x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330213-reb9vo7x.txt' === file2bib.sh === id: cord-330131-yfhrmbvx author: Danchin, Antoine title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 pages: extension: .txt txt: ./txt/cord-330131-yfhrmbvx.txt cache: ./cache/cord-330131-yfhrmbvx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330131-yfhrmbvx.txt' === file2bib.sh === id: cord-329527-0rlotyz3 author: Bohmwald, Karen title: Neurologic Alterations Due to Respiratory Virus Infections date: 2018-10-26 pages: extension: .txt txt: ./txt/cord-329527-0rlotyz3.txt cache: ./cache/cord-329527-0rlotyz3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329527-0rlotyz3.txt' === file2bib.sh === id: cord-331066-ediowz4s author: Chechetkin, Vladimir R. title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-331066-ediowz4s.txt cache: ./cache/cord-331066-ediowz4s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331066-ediowz4s.txt' === file2bib.sh === id: cord-331076-ak481qew author: Eskier, Doğa title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-10-12 pages: extension: .txt txt: ./txt/cord-331076-ak481qew.txt cache: ./cache/cord-331076-ak481qew.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331076-ak481qew.txt' === file2bib.sh === id: cord-330847-a84pcc9z author: Edwards, M. C. title: RNA recombination in the genome of Barley stripe mosaic virus date: 1992-07-31 pages: extension: .txt txt: ./txt/cord-330847-a84pcc9z.txt cache: ./cache/cord-330847-a84pcc9z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-330847-a84pcc9z.txt' === file2bib.sh === id: cord-330954-ft14aa2n author: Liu, B. M. title: Epidemiological characteristics of COVID-19 patients in convalescence period date: 2020-06-03 pages: extension: .txt txt: ./txt/cord-330954-ft14aa2n.txt cache: ./cache/cord-330954-ft14aa2n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-330954-ft14aa2n.txt' === file2bib.sh === id: cord-329794-msxrdhb3 author: Lu, Aili title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date: 2004-06-20 pages: extension: .txt txt: ./txt/cord-329794-msxrdhb3.txt cache: ./cache/cord-329794-msxrdhb3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-329794-msxrdhb3.txt' === file2bib.sh === id: cord-331414-i0oxm5mr author: Kautz, Tiffany F. title: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-331414-i0oxm5mr.txt cache: ./cache/cord-331414-i0oxm5mr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331414-i0oxm5mr.txt' === file2bib.sh === id: cord-331509-p19dg1jw author: Bigault, Lionel title: Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR date: 2020-05-31 pages: extension: .txt txt: ./txt/cord-331509-p19dg1jw.txt cache: ./cache/cord-331509-p19dg1jw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331509-p19dg1jw.txt' === file2bib.sh === id: cord-331680-qlzhtxs0 author: Goryachev, A.N. title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date: 2020-11-03 pages: extension: .txt txt: ./txt/cord-331680-qlzhtxs0.txt cache: ./cache/cord-331680-qlzhtxs0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331680-qlzhtxs0.txt' === file2bib.sh === id: cord-331916-n744pymd author: Liu, Jue title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference date: 2006-04-10 pages: extension: .txt txt: ./txt/cord-331916-n744pymd.txt cache: ./cache/cord-331916-n744pymd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331916-n744pymd.txt' === file2bib.sh === id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 pages: extension: .txt txt: ./txt/cord-330800-s91zfzfi.txt cache: ./cache/cord-330800-s91zfzfi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-330800-s91zfzfi.txt' === file2bib.sh === id: cord-332270-fusfdkjw author: Lukiw, Walter J. title: Biomarkers for Alzheimer’s Disease (AD) and the Application of Precision Medicine date: 2020-09-21 pages: extension: .txt txt: ./txt/cord-332270-fusfdkjw.txt cache: ./cache/cord-332270-fusfdkjw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332270-fusfdkjw.txt' === file2bib.sh === id: cord-331607-2h56vb0n author: Jin, Xuejiao title: Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication date: 2018-01-30 pages: extension: .txt txt: ./txt/cord-331607-2h56vb0n.txt cache: ./cache/cord-331607-2h56vb0n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-331607-2h56vb0n.txt' === file2bib.sh === id: cord-332024-jk983q4p author: Briese, Thomas title: Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date: 2005-02-17 pages: extension: .txt txt: ./txt/cord-332024-jk983q4p.txt cache: ./cache/cord-332024-jk983q4p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332024-jk983q4p.txt' === file2bib.sh === id: cord-331802-wo462anq author: Xia, Hongjie title: Human Enterovirus Nonstructural Protein 2C(ATPase) Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone date: 2015-07-28 pages: extension: .txt txt: ./txt/cord-331802-wo462anq.txt cache: ./cache/cord-331802-wo462anq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-331802-wo462anq.txt' === file2bib.sh === id: cord-332006-if46jycd author: Whitehead, Kathryn A. title: Knocking down barriers: advances in siRNA delivery date: 2009 pages: extension: .txt txt: ./txt/cord-332006-if46jycd.txt cache: ./cache/cord-332006-if46jycd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332006-if46jycd.txt' === file2bib.sh === id: cord-333261-knj2rrut author: Albright, Catherine J. title: An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date: 2011-11-11 pages: extension: .txt txt: ./txt/cord-333261-knj2rrut.txt cache: ./cache/cord-333261-knj2rrut.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333261-knj2rrut.txt' === file2bib.sh === id: cord-332356-au7s3dmp author: Strandin, Tomas title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date: 2011-09-15 pages: extension: .txt txt: ./txt/cord-332356-au7s3dmp.txt cache: ./cache/cord-332356-au7s3dmp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332356-au7s3dmp.txt' === file2bib.sh === id: cord-332003-67e9fchy author: Boisguérin, Prisca title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 pages: extension: .txt txt: ./txt/cord-332003-67e9fchy.txt cache: ./cache/cord-332003-67e9fchy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-332003-67e9fchy.txt' === file2bib.sh === id: cord-333429-bq7kfpby author: Shi, Ding title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-333429-bq7kfpby.txt cache: ./cache/cord-333429-bq7kfpby.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333429-bq7kfpby.txt' === file2bib.sh === id: cord-332632-u2ud0vmq author: Lussi, Carmela title: What can pestiviral endonucleases teach us about innate immunotolerance? date: 2016-03-17 pages: extension: .txt txt: ./txt/cord-332632-u2ud0vmq.txt cache: ./cache/cord-332632-u2ud0vmq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332632-u2ud0vmq.txt' === file2bib.sh === id: cord-333547-88dkh6xd author: Hasan, Shadi W. title: Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date: 2020-10-19 pages: extension: .txt txt: ./txt/cord-333547-88dkh6xd.txt cache: ./cache/cord-333547-88dkh6xd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333547-88dkh6xd.txt' === file2bib.sh === id: cord-333636-h2sg6shp author: Kochan, G. title: Characterization of the RNA-binding activity of VP3, a major structural protein of Infectious bursal disease virus date: 2003 pages: extension: .txt txt: ./txt/cord-333636-h2sg6shp.txt cache: ./cache/cord-333636-h2sg6shp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333636-h2sg6shp.txt' === file2bib.sh === id: cord-333979-bx2xspbe author: Kalikiri, Mahesh K R title: High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads date: 2020-04-11 pages: extension: .txt txt: ./txt/cord-333979-bx2xspbe.txt cache: ./cache/cord-333979-bx2xspbe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333979-bx2xspbe.txt' === file2bib.sh === id: cord-332992-8rmqg4rf author: de Vries, A. A. F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 pages: extension: .txt txt: ./txt/cord-332992-8rmqg4rf.txt cache: ./cache/cord-332992-8rmqg4rf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332992-8rmqg4rf.txt' === file2bib.sh === id: cord-334082-fyxn0g3v author: O’Carroll, I.P. title: Viral Nucleic Acids date: 2015-08-20 pages: extension: .txt txt: ./txt/cord-334082-fyxn0g3v.txt cache: ./cache/cord-334082-fyxn0g3v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-334082-fyxn0g3v.txt' === file2bib.sh === id: cord-333515-llqpfhwg author: Zhao, Juanjuan title: Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date: 2020-03-03 pages: extension: .txt txt: ./txt/cord-333515-llqpfhwg.txt cache: ./cache/cord-333515-llqpfhwg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333515-llqpfhwg.txt' === file2bib.sh === id: cord-333524-a6p6ma8r author: Khan, Pavana title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-333524-a6p6ma8r.txt cache: ./cache/cord-333524-a6p6ma8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333524-a6p6ma8r.txt' === file2bib.sh === id: cord-334123-wb45ww7f author: Schimmel, Paul title: RNA pseudoknots that interact with components of the translation apparatus date: 1989-07-14 pages: extension: .txt txt: ./txt/cord-334123-wb45ww7f.txt cache: ./cache/cord-334123-wb45ww7f.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334123-wb45ww7f.txt' === file2bib.sh === id: cord-332747-u46xryoo author: Mingorance, Lidia title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date: 2018-09-18 pages: extension: .txt txt: ./txt/cord-332747-u46xryoo.txt cache: ./cache/cord-332747-u46xryoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-332747-u46xryoo.txt' === file2bib.sh === id: cord-333473-c1lykari author: Irigoyen, Nerea title: High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling date: 2016-02-26 pages: extension: .txt txt: ./txt/cord-333473-c1lykari.txt cache: ./cache/cord-333473-c1lykari.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-333473-c1lykari.txt' === file2bib.sh === id: cord-333080-qytwbsne author: Alahari, Suresh K. title: SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-333080-qytwbsne.txt cache: ./cache/cord-333080-qytwbsne.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-333080-qytwbsne.txt' === file2bib.sh === id: cord-334771-uy3s6443 author: Rao, BL title: A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date: 2004-09-09 pages: extension: .txt txt: ./txt/cord-334771-uy3s6443.txt cache: ./cache/cord-334771-uy3s6443.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334771-uy3s6443.txt' === file2bib.sh === id: cord-335482-nx7odchj author: Makino, Shinji title: Defective interfering particles of mouse hepatitis virus date: 1984-02-29 pages: extension: .txt txt: ./txt/cord-335482-nx7odchj.txt cache: ./cache/cord-335482-nx7odchj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335482-nx7odchj.txt' === file2bib.sh === id: cord-332710-2s14knw6 author: Lai, Michael M.C. title: Recombination in large RNA viruses: Coronaviruses date: 1996-12-31 pages: extension: .txt txt: ./txt/cord-332710-2s14knw6.txt cache: ./cache/cord-332710-2s14knw6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332710-2s14knw6.txt' === file2bib.sh === id: cord-332484-qy8vj6uu author: Pierini, Roberto title: Modulation of membrane traffic between endoplasmic reticulum, ERGIC and Golgi to generate compartments for the replication of bacteria and viruses date: 2009-04-01 pages: extension: .txt txt: ./txt/cord-332484-qy8vj6uu.txt cache: ./cache/cord-332484-qy8vj6uu.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-332484-qy8vj6uu.txt' === file2bib.sh === id: cord-332844-2se4d1yp author: Yun, Sang-Im title: Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses date: 2015-12-29 pages: extension: .txt txt: ./txt/cord-332844-2se4d1yp.txt cache: ./cache/cord-332844-2se4d1yp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-332844-2se4d1yp.txt' === file2bib.sh === id: cord-335443-iv2gs3kg author: Kim, Youngchang title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date: 2020-06-28 pages: extension: .txt txt: ./txt/cord-335443-iv2gs3kg.txt cache: ./cache/cord-335443-iv2gs3kg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335443-iv2gs3kg.txt' === file2bib.sh === id: cord-335614-qh98622y author: Xu, Puzhi title: A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date: 2019-11-16 pages: extension: .txt txt: ./txt/cord-335614-qh98622y.txt cache: ./cache/cord-335614-qh98622y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335614-qh98622y.txt' === file2bib.sh === id: cord-335040-1qa6pe4v author: Rogstam, Annika title: Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-10-06 pages: extension: .txt txt: ./txt/cord-335040-1qa6pe4v.txt cache: ./cache/cord-335040-1qa6pe4v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-335040-1qa6pe4v.txt' === file2bib.sh === id: cord-334299-0zn1z7rc author: Ahmed, Warish title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date: 2020-09-30 pages: extension: .txt txt: ./txt/cord-334299-0zn1z7rc.txt cache: ./cache/cord-334299-0zn1z7rc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-334299-0zn1z7rc.txt' === file2bib.sh === id: cord-335067-tg66h99q author: Woolhouse, Mark E.J. title: Ecological and taxonomic variation among human RNA viruses date: 2013-03-19 pages: extension: .txt txt: ./txt/cord-335067-tg66h99q.txt cache: ./cache/cord-335067-tg66h99q.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335067-tg66h99q.txt' === file2bib.sh === id: cord-334463-nvu5tqxb author: Kim, Chonsaeng title: Echovirus 7 Entry into Polarized Intestinal Epithelial Cells Requires Clathrin and Rab7 date: 2012-04-10 pages: extension: .txt txt: ./txt/cord-334463-nvu5tqxb.txt cache: ./cache/cord-334463-nvu5tqxb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334463-nvu5tqxb.txt' === file2bib.sh === id: cord-334315-ymkrgj0h author: Moon, Stephanie L. title: Cytoplasmic Viruses: Rage against the (Cellular RNA Decay) Machine date: 2013-12-05 pages: extension: .txt txt: ./txt/cord-334315-ymkrgj0h.txt cache: ./cache/cord-334315-ymkrgj0h.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334315-ymkrgj0h.txt' === file2bib.sh === id: cord-336560-m5u6ryy9 author: Boudewijns, Robbert title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date: 2020-07-02 pages: extension: .txt txt: ./txt/cord-336560-m5u6ryy9.txt cache: ./cache/cord-336560-m5u6ryy9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336560-m5u6ryy9.txt' === file2bib.sh === id: cord-336012-8klkojpo author: Harilal, Divinlal title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date: 2020-06-18 pages: extension: .txt txt: ./txt/cord-336012-8klkojpo.txt cache: ./cache/cord-336012-8klkojpo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336012-8klkojpo.txt' === file2bib.sh === id: cord-335864-392xmrq0 author: Sun, Yu-Meng title: Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-335864-392xmrq0.txt cache: ./cache/cord-335864-392xmrq0.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335864-392xmrq0.txt' === file2bib.sh === id: cord-336093-ic6q6ke8 author: Sun, Ying title: Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date: 2014-02-11 pages: extension: .txt txt: ./txt/cord-336093-ic6q6ke8.txt cache: ./cache/cord-336093-ic6q6ke8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336093-ic6q6ke8.txt' === file2bib.sh === id: cord-336319-8068s9a3 author: Graci, Jason D. title: Mechanisms of action of ribavirin against distinct viruses date: 2005-11-15 pages: extension: .txt txt: ./txt/cord-336319-8068s9a3.txt cache: ./cache/cord-336319-8068s9a3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336319-8068s9a3.txt' === file2bib.sh === id: cord-334394-qgyzk7th author: Edgar, Robert C. title: Petabase-scale sequence alignment catalyses viral discovery date: 2020-08-10 pages: extension: .txt txt: ./txt/cord-334394-qgyzk7th.txt cache: ./cache/cord-334394-qgyzk7th.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334394-qgyzk7th.txt' === file2bib.sh === id: cord-335377-zrbn637z author: Ishimaru, Daniella title: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date: 2012-12-26 pages: extension: .txt txt: ./txt/cord-335377-zrbn637z.txt cache: ./cache/cord-335377-zrbn637z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335377-zrbn637z.txt' === file2bib.sh === id: cord-335441-bj3me7p8 author: Jourdain, Elsa title: Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data date: 2010-01-28 pages: extension: .txt txt: ./txt/cord-335441-bj3me7p8.txt cache: ./cache/cord-335441-bj3me7p8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335441-bj3me7p8.txt' === file2bib.sh === id: cord-337339-0vkigjv2 author: Osterrieder, Nikolaus title: Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date: 2020-07-20 pages: extension: .txt txt: ./txt/cord-337339-0vkigjv2.txt cache: ./cache/cord-337339-0vkigjv2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337339-0vkigjv2.txt' === file2bib.sh === id: cord-337026-osgi06o4 author: Panoutsopoulos, Alexios A. title: Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-337026-osgi06o4.txt cache: ./cache/cord-337026-osgi06o4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337026-osgi06o4.txt' === file2bib.sh === id: cord-337673-1nau263l author: Wu, Chang-Jer title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 pages: extension: .txt txt: ./txt/cord-337673-1nau263l.txt cache: ./cache/cord-337673-1nau263l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337673-1nau263l.txt' === file2bib.sh === id: cord-337879-liqhbqxl author: Kriesel, John D. title: Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain date: 2012-03-08 pages: extension: .txt txt: ./txt/cord-337879-liqhbqxl.txt cache: ./cache/cord-337879-liqhbqxl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337879-liqhbqxl.txt' === file2bib.sh === id: cord-336447-hpnkou41 author: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 pages: extension: .txt txt: ./txt/cord-336447-hpnkou41.txt cache: ./cache/cord-336447-hpnkou41.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336447-hpnkou41.txt' === file2bib.sh === id: cord-336775-d4hi9myk author: Kirtipal, Nikhil title: From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-336775-d4hi9myk.txt cache: ./cache/cord-336775-d4hi9myk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-336775-d4hi9myk.txt' === file2bib.sh === id: cord-334947-pa0p5dif author: Rozen-Gagnon, Kathryn title: Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date: 2014-01-16 pages: extension: .txt txt: ./txt/cord-334947-pa0p5dif.txt cache: ./cache/cord-334947-pa0p5dif.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-334947-pa0p5dif.txt' === file2bib.sh === id: cord-337508-nfzaw8gg author: Kirkland, P.D. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-337508-nfzaw8gg.txt cache: ./cache/cord-337508-nfzaw8gg.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337508-nfzaw8gg.txt' === file2bib.sh === id: cord-336554-n8n5ii5k author: Singh, Thakur Uttam title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 pages: extension: .txt txt: ./txt/cord-336554-n8n5ii5k.txt cache: ./cache/cord-336554-n8n5ii5k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-336554-n8n5ii5k.txt' === file2bib.sh === id: cord-337976-c2auspti author: Weiss, Susan R. title: Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date: 1983-04-30 pages: extension: .txt txt: ./txt/cord-337976-c2auspti.txt cache: ./cache/cord-337976-c2auspti.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337976-c2auspti.txt' === file2bib.sh === id: cord-334891-4jgtxg07 author: Choudhury, Abhigyan title: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date: 2020-11-11 pages: extension: .txt txt: ./txt/cord-334891-4jgtxg07.txt cache: ./cache/cord-334891-4jgtxg07.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-334891-4jgtxg07.txt' === file2bib.sh === id: cord-337361-salby0fu author: Bujarski, Jozef J. title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date: 2013-03-26 pages: extension: .txt txt: ./txt/cord-337361-salby0fu.txt cache: ./cache/cord-337361-salby0fu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337361-salby0fu.txt' === file2bib.sh === id: cord-337998-08tknscm author: Sztuba-Solinska, Joanna title: A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8 date: 2016-11-16 pages: extension: .txt txt: ./txt/cord-337998-08tknscm.txt cache: ./cache/cord-337998-08tknscm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337998-08tknscm.txt' === file2bib.sh === id: cord-336986-rmxin1da author: De Clercq, Erik title: New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date: 2019-08-07 pages: extension: .txt txt: ./txt/cord-336986-rmxin1da.txt cache: ./cache/cord-336986-rmxin1da.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-336986-rmxin1da.txt' === file2bib.sh === id: cord-338083-77re4l0w author: Bolin, Steven R. title: Origination and consequences of bovine viral diarrhea virus diversity date: 2005-03-04 pages: extension: .txt txt: ./txt/cord-338083-77re4l0w.txt cache: ./cache/cord-338083-77re4l0w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338083-77re4l0w.txt' === file2bib.sh === id: cord-337199-mbv8kd1k author: Ballarín-González, Borja title: Clinical translation of RNAi-based treatments for respiratory diseases date: 2012-09-07 pages: extension: .txt txt: ./txt/cord-337199-mbv8kd1k.txt cache: ./cache/cord-337199-mbv8kd1k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337199-mbv8kd1k.txt' === file2bib.sh === id: cord-338345-mr1orklo author: Adedeji, Adeyemi O. title: Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase date: 2016-09-07 pages: extension: .txt txt: ./txt/cord-338345-mr1orklo.txt cache: ./cache/cord-338345-mr1orklo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338345-mr1orklo.txt' === file2bib.sh === id: cord-335231-617e5dcy author: Pettersson, Lisa title: Hantavirus RNA in Saliva from Patients with Hemorrhagic Fever with Renal Syndrome date: 2008-03-17 pages: extension: .txt txt: ./txt/cord-335231-617e5dcy.txt cache: ./cache/cord-335231-617e5dcy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-335231-617e5dcy.txt' === file2bib.sh === id: cord-337285-t6qr41wc author: Ikeda, Masanori title: Modulation of host metabolism as a target of new antivirals() date: 2007-10-10 pages: extension: .txt txt: ./txt/cord-337285-t6qr41wc.txt cache: ./cache/cord-337285-t6qr41wc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-337285-t6qr41wc.txt' === file2bib.sh === id: cord-338680-wwlttymp author: Khonyongwa, K. title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-07-30 pages: extension: .txt txt: ./txt/cord-338680-wwlttymp.txt cache: ./cache/cord-338680-wwlttymp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338680-wwlttymp.txt' === file2bib.sh === id: cord-337899-w5zh40gv author: Bissoyi, Akalabya title: Alphavirus Nonstructural Proteases and Their Inhibitors date: 2017-07-14 pages: extension: .txt txt: ./txt/cord-337899-w5zh40gv.txt cache: ./cache/cord-337899-w5zh40gv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-337899-w5zh40gv.txt' === file2bib.sh === id: cord-338727-1kodz527 author: Ilinskaya, O. N. title: Ribonucleases as antiviral agents date: 2014-10-11 pages: extension: .txt txt: ./txt/cord-338727-1kodz527.txt cache: ./cache/cord-338727-1kodz527.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338727-1kodz527.txt' === file2bib.sh === id: cord-338358-ppjxo2di author: Whitworth, Kristin M. title: Zygote injection of CRISPR/Cas9 RNA successfully modifies the target gene without delaying blastocyst development or altering the sex ratio in pigs date: 2016-10-15 pages: extension: .txt txt: ./txt/cord-338358-ppjxo2di.txt cache: ./cache/cord-338358-ppjxo2di.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338358-ppjxo2di.txt' === file2bib.sh === id: cord-338901-1kzy7rts author: Li, Heng title: Overview of therapeutic drug research for COVID-19 in China date: 2020-06-17 pages: extension: .txt txt: ./txt/cord-338901-1kzy7rts.txt cache: ./cache/cord-338901-1kzy7rts.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-338901-1kzy7rts.txt' === file2bib.sh === id: cord-339782-rybjc58j author: Carmo, Anália title: Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-339782-rybjc58j.txt cache: ./cache/cord-339782-rybjc58j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339782-rybjc58j.txt' === file2bib.sh === id: cord-339456-82iks0xf author: Mikel, P. title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date: 2015-02-25 pages: extension: .txt txt: ./txt/cord-339456-82iks0xf.txt cache: ./cache/cord-339456-82iks0xf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-339456-82iks0xf.txt' === file2bib.sh === id: cord-339288-y8woqsii author: Tews, Birke Andrea title: Self-Replicating RNA date: 2016-06-11 pages: extension: .txt txt: ./txt/cord-339288-y8woqsii.txt cache: ./cache/cord-339288-y8woqsii.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339288-y8woqsii.txt' === file2bib.sh === id: cord-339431-kyr5lv15 author: Saçar Demirci, Müşerref Duygu title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date: 2020-03-17 pages: extension: .txt txt: ./txt/cord-339431-kyr5lv15.txt cache: ./cache/cord-339431-kyr5lv15.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-339431-kyr5lv15.txt' === file2bib.sh === id: cord-339976-tg2jkss7 author: Wang, Haibin title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 pages: extension: .txt txt: ./txt/cord-339976-tg2jkss7.txt cache: ./cache/cord-339976-tg2jkss7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-339976-tg2jkss7.txt' === file2bib.sh === id: cord-338582-o976nab9 author: Dahlhausen, Bob title: Future Veterinary Diagnostics date: 2010-09-19 pages: extension: .txt txt: ./txt/cord-338582-o976nab9.txt cache: ./cache/cord-338582-o976nab9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338582-o976nab9.txt' === file2bib.sh === id: cord-340189-jo38hjqa author: Bar-On, Yinon M title: SARS-CoV-2 (COVID-19) by the numbers date: 2020-04-02 pages: extension: .txt txt: ./txt/cord-340189-jo38hjqa.txt cache: ./cache/cord-340189-jo38hjqa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340189-jo38hjqa.txt' === file2bib.sh === id: cord-336628-0evl3wnd author: Neufeldt, Christopher J. title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date: 2020-07-21 pages: extension: .txt txt: ./txt/cord-336628-0evl3wnd.txt cache: ./cache/cord-336628-0evl3wnd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-336628-0evl3wnd.txt' === file2bib.sh === id: cord-338812-q24jycgk author: Zakaryan, H. title: Nuclear remodelling during viral infections date: 2011-04-28 pages: extension: .txt txt: ./txt/cord-338812-q24jycgk.txt cache: ./cache/cord-338812-q24jycgk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-338812-q24jycgk.txt' === file2bib.sh === id: cord-339209-oe8onyr9 author: Vasilakis, Nikos title: Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date: 2014-05-20 pages: extension: .txt txt: ./txt/cord-339209-oe8onyr9.txt cache: ./cache/cord-339209-oe8onyr9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-339209-oe8onyr9.txt' === file2bib.sh === id: cord-338307-vfutmwxq author: Sturman, Lawrence S. title: The Molecular Biology of Coronaviruses date: 1983-12-31 pages: extension: .txt txt: ./txt/cord-338307-vfutmwxq.txt cache: ./cache/cord-338307-vfutmwxq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-338307-vfutmwxq.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8402 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 8117 Aborted $FILE2BIB "$FILE" > "$OUTPUT" parallel: Warning: No more processes: Decreasing number of running jobs to 9. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 11746 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 10516 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 9557 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-340046-kgbvld0y author: Houspie, Lieselot title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 pages: extension: .txt txt: ./txt/cord-340046-kgbvld0y.txt cache: ./cache/cord-340046-kgbvld0y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 6 resourceName b'cord-340046-kgbvld0y.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 13336 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 17985 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 20235 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 20610 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-339172-210dwhgj author: Knoops, Kèvin title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 pages: extension: .txt txt: ./txt/cord-339172-210dwhgj.txt cache: ./cache/cord-339172-210dwhgj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-339172-210dwhgj.txt' === file2bib.sh === id: cord-341541-3l6tjf3t author: Hajijafari Anaraki, Mozafar title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-341541-3l6tjf3t.txt cache: ./cache/cord-341541-3l6tjf3t.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341541-3l6tjf3t.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 23835 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-341342-kyavg4vu author: Masters, P. S. title: Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date: 1992 pages: extension: .txt txt: ./txt/cord-341342-kyavg4vu.txt cache: ./cache/cord-341342-kyavg4vu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341342-kyavg4vu.txt' === file2bib.sh === id: cord-340422-8f5xe4zc author: Rowland, R. R. R. title: Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine date: 2001 pages: extension: .txt txt: ./txt/cord-340422-8f5xe4zc.txt cache: ./cache/cord-340422-8f5xe4zc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-340422-8f5xe4zc.txt' === file2bib.sh === id: cord-341034-2oigu75k author: Moser, Theresa S. title: AMP-Activated Kinase Restricts Rift Valley Fever Virus Infection by Inhibiting Fatty Acid Synthesis date: 2012-04-19 pages: extension: .txt txt: ./txt/cord-341034-2oigu75k.txt cache: ./cache/cord-341034-2oigu75k.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-341034-2oigu75k.txt' === file2bib.sh === id: cord-342117-r2chpw7y author: Wu, Xinwei title: Inhibitory effect of small interfering RNA on dengue virus replication in mosquito cells date: 2010-10-14 pages: extension: .txt txt: ./txt/cord-342117-r2chpw7y.txt cache: ./cache/cord-342117-r2chpw7y.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 9 resourceName b'cord-342117-r2chpw7y.txt' === file2bib.sh === id: cord-340475-h0q1m3ed author: Carnero, Elena title: Type I Interferon Regulates the Expression of Long Non-Coding RNAs date: 2014-11-06 pages: extension: .txt txt: ./txt/cord-340475-h0q1m3ed.txt cache: ./cache/cord-340475-h0q1m3ed.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-340475-h0q1m3ed.txt' === file2bib.sh === id: cord-341502-jlzufa28 author: Lee, Sungyul title: The SARS-CoV-2 RNA interactome date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-341502-jlzufa28.txt cache: ./cache/cord-341502-jlzufa28.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341502-jlzufa28.txt' === file2bib.sh === id: cord-341324-f9g9gitn author: Rojas, José M. title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date: 2020-10-21 pages: extension: .txt txt: ./txt/cord-341324-f9g9gitn.txt cache: ./cache/cord-341324-f9g9gitn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-341324-f9g9gitn.txt' === file2bib.sh === id: cord-341804-rnj3wtg4 author: Jin, Zhe title: Drug treatment of coronavirus disease 2019 (COVID-19) in China. date: 2020-06-27 pages: extension: .txt txt: ./txt/cord-341804-rnj3wtg4.txt cache: ./cache/cord-341804-rnj3wtg4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341804-rnj3wtg4.txt' === file2bib.sh === id: cord-342456-5gp3cry0 author: Hoagland, Daisy A. title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-342456-5gp3cry0.txt cache: ./cache/cord-342456-5gp3cry0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342456-5gp3cry0.txt' === file2bib.sh === id: cord-342344-jjnf4yje author: Mello, C. J. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-342344-jjnf4yje.txt cache: ./cache/cord-342344-jjnf4yje.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-342344-jjnf4yje.txt' === file2bib.sh === id: cord-342189-ya05m58o author: Banerjee, Abhik K. title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 pages: extension: .txt txt: ./txt/cord-342189-ya05m58o.txt cache: ./cache/cord-342189-ya05m58o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-342189-ya05m58o.txt' === file2bib.sh === id: cord-342412-azkamnpa author: Ecker, David J title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date: 2005-04-25 pages: extension: .txt txt: ./txt/cord-342412-azkamnpa.txt cache: ./cache/cord-342412-azkamnpa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342412-azkamnpa.txt' === file2bib.sh === id: cord-342676-ykog278j author: Stewart, H. title: Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging date: 2016-03-14 pages: extension: .txt txt: ./txt/cord-342676-ykog278j.txt cache: ./cache/cord-342676-ykog278j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342676-ykog278j.txt' === file2bib.sh === id: cord-343470-w215pzdc author: Tsai, Kevin title: Epigenetic and epitranscriptomic regulation of viral replication date: 2020-06-12 pages: extension: .txt txt: ./txt/cord-343470-w215pzdc.txt cache: ./cache/cord-343470-w215pzdc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343470-w215pzdc.txt' === file2bib.sh === id: cord-342681-pqzcy9wu author: Pongpirul, Wannarat A. title: Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date: 2020-07-17 pages: extension: .txt txt: ./txt/cord-342681-pqzcy9wu.txt cache: ./cache/cord-342681-pqzcy9wu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342681-pqzcy9wu.txt' === file2bib.sh === id: cord-342649-ysossker author: Scagnolari, Carolina title: Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus date: 2012-03-10 pages: extension: .txt txt: ./txt/cord-342649-ysossker.txt cache: ./cache/cord-342649-ysossker.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342649-ysossker.txt' === file2bib.sh === id: cord-343448-xhm97wy2 author: Rinaldi, Andrea title: RNA to the rescue: RNA is one of the most promising targets for drug development given its wide variety of uses date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-343448-xhm97wy2.txt cache: ./cache/cord-343448-xhm97wy2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343448-xhm97wy2.txt' === file2bib.sh === id: cord-342145-cq6xe5r7 author: Dao Thi, Viet Loan title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date: 2020-08-12 pages: extension: .txt txt: ./txt/cord-342145-cq6xe5r7.txt cache: ./cache/cord-342145-cq6xe5r7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342145-cq6xe5r7.txt' === file2bib.sh === id: cord-342902-y1v8wzxq author: Yuan, Shuofeng title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date: 2020-10-07 pages: extension: .txt txt: ./txt/cord-342902-y1v8wzxq.txt cache: ./cache/cord-342902-y1v8wzxq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342902-y1v8wzxq.txt' === file2bib.sh === id: cord-343350-04e6wvov author: Liu, Haipeng title: Antiviral immunity in crustaceans date: 2009-02-15 pages: extension: .txt txt: ./txt/cord-343350-04e6wvov.txt cache: ./cache/cord-343350-04e6wvov.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343350-04e6wvov.txt' === file2bib.sh === id: cord-343221-e29of29o author: Kindler, Eveline title: Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication date: 2017-02-03 pages: extension: .txt txt: ./txt/cord-343221-e29of29o.txt cache: ./cache/cord-343221-e29of29o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-343221-e29of29o.txt' === file2bib.sh === id: cord-344714-0cam9ipf author: Russo, Maria title: Roles of flavonoids against coronavirus infection date: 2020-07-28 pages: extension: .txt txt: ./txt/cord-344714-0cam9ipf.txt cache: ./cache/cord-344714-0cam9ipf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344714-0cam9ipf.txt' === file2bib.sh === id: cord-344006-0iq9s94n author: Atzrodt, Cassandra L. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 pages: extension: .txt txt: ./txt/cord-344006-0iq9s94n.txt cache: ./cache/cord-344006-0iq9s94n.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344006-0iq9s94n.txt' === file2bib.sh === id: cord-342653-bpyc2gbl author: Wang, Hai-Tao title: Substrate recognition by TRIM and TRIM-like proteins in innate immunity date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-342653-bpyc2gbl.txt cache: ./cache/cord-342653-bpyc2gbl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-342653-bpyc2gbl.txt' === file2bib.sh === id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 pages: extension: .txt txt: ./txt/cord-340489-yo3cp5vs.txt cache: ./cache/cord-340489-yo3cp5vs.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-340489-yo3cp5vs.txt' === file2bib.sh === id: cord-343632-cv3qgno3 author: Zhang, Yinhua title: Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP date: 2020-02-29 pages: extension: .txt txt: ./txt/cord-343632-cv3qgno3.txt cache: ./cache/cord-343632-cv3qgno3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343632-cv3qgno3.txt' === file2bib.sh === id: cord-343963-99rd3o79 author: Wong, Mun-Teng title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 pages: extension: .txt txt: ./txt/cord-343963-99rd3o79.txt cache: ./cache/cord-343963-99rd3o79.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343963-99rd3o79.txt' === file2bib.sh === id: cord-344464-if6js43s author: Cowley, J. A. title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date: 2002 pages: extension: .txt txt: ./txt/cord-344464-if6js43s.txt cache: ./cache/cord-344464-if6js43s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344464-if6js43s.txt' === file2bib.sh === id: cord-342901-ca2xxkb2 author: Lloyd, Richard E. title: Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses date: 2015-05-31 pages: extension: .txt txt: ./txt/cord-342901-ca2xxkb2.txt cache: ./cache/cord-342901-ca2xxkb2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342901-ca2xxkb2.txt' === file2bib.sh === id: cord-343604-v986m9jd author: Vijayakumar, Balaji Gowrivel title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-343604-v986m9jd.txt cache: ./cache/cord-343604-v986m9jd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-343604-v986m9jd.txt' === file2bib.sh === id: cord-344410-yo9libo0 author: Zhou, Yan title: Mutational analysis of the SDD sequence motif of a PRRSV RNA-dependent RNA polymerase date: 2011-09-16 pages: extension: .txt txt: ./txt/cord-344410-yo9libo0.txt cache: ./cache/cord-344410-yo9libo0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344410-yo9libo0.txt' === file2bib.sh === id: cord-341513-e6p3lrlf author: Li, Yunchuan title: Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection date: 2017-09-29 pages: extension: .txt txt: ./txt/cord-341513-e6p3lrlf.txt cache: ./cache/cord-341513-e6p3lrlf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-341513-e6p3lrlf.txt' === file2bib.sh === id: cord-344636-go5cw92q author: Huang, Wei E. title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date: 2020-04-25 pages: extension: .txt txt: ./txt/cord-344636-go5cw92q.txt cache: ./cache/cord-344636-go5cw92q.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344636-go5cw92q.txt' === file2bib.sh === id: cord-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 pages: extension: .txt txt: ./txt/cord-344782-ond1ziu5.txt cache: ./cache/cord-344782-ond1ziu5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-344782-ond1ziu5.txt' === file2bib.sh === id: cord-345204-ch0e6lzl author: Scarlata, S. title: Design Of A Rapid And Reversible Fluorescence Assay To Detect COVID-19 And Other Pathogens date: 2020-10-05 pages: extension: .txt txt: ./txt/cord-345204-ch0e6lzl.txt cache: ./cache/cord-345204-ch0e6lzl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345204-ch0e6lzl.txt' === file2bib.sh === id: cord-344749-omzhhr0k author: Kaya, Sariye Irem title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 pages: extension: .txt txt: ./txt/cord-344749-omzhhr0k.txt cache: ./cache/cord-344749-omzhhr0k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-344749-omzhhr0k.txt' === file2bib.sh === id: cord-345647-h3imwhss author: Gao, Wen-Hua title: Newly identified viral genomes in pangolins with fatal disease date: 2020-04-12 pages: extension: .txt txt: ./txt/cord-345647-h3imwhss.txt cache: ./cache/cord-345647-h3imwhss.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345647-h3imwhss.txt' === file2bib.sh === id: cord-345157-fhmhpobi author: Qi, Dan title: Virus infection-induced host mRNA degradation and potential application of live cell imaging date: 2018-12-12 pages: extension: .txt txt: ./txt/cord-345157-fhmhpobi.txt cache: ./cache/cord-345157-fhmhpobi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-345157-fhmhpobi.txt' === file2bib.sh === id: cord-342756-rgm9ffpk author: Senger, Mario Roberto title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date: 2020-10-02 pages: extension: .txt txt: ./txt/cord-342756-rgm9ffpk.txt cache: ./cache/cord-342756-rgm9ffpk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-342756-rgm9ffpk.txt' === file2bib.sh === id: cord-345863-j01l71dh author: Drechsler, Yvonne title: Host Gene Expression of Macrophages in Response to Feline Coronavirus Infection date: 2020-06-09 pages: extension: .txt txt: ./txt/cord-345863-j01l71dh.txt cache: ./cache/cord-345863-j01l71dh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-345863-j01l71dh.txt' === file2bib.sh === id: cord-345302-wbkfjz8r author: Devaney, Ryan title: A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date: 2016-10-04 pages: extension: .txt txt: ./txt/cord-345302-wbkfjz8r.txt cache: ./cache/cord-345302-wbkfjz8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-345302-wbkfjz8r.txt' === file2bib.sh === id: cord-342800-62jklwiy author: Xu, Shuqin title: mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection date: 2020-09-09 pages: extension: .txt txt: ./txt/cord-342800-62jklwiy.txt cache: ./cache/cord-342800-62jklwiy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342800-62jklwiy.txt' === file2bib.sh === id: cord-343662-scn7b4c6 author: Delli Ponti, Riccardo title: A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs date: 2018-12-03 pages: extension: .txt txt: ./txt/cord-343662-scn7b4c6.txt cache: ./cache/cord-343662-scn7b4c6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-343662-scn7b4c6.txt' === file2bib.sh === id: cord-345898-a6vt8kso author: Ren, Linzhu title: Live Cell Reporter Systems for Positive-Sense Single Strand RNA Viruses date: 2016-01-04 pages: extension: .txt txt: ./txt/cord-345898-a6vt8kso.txt cache: ./cache/cord-345898-a6vt8kso.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345898-a6vt8kso.txt' === file2bib.sh === id: cord-343918-5yk1j4ms author: Gorbalenya, A.E. title: Phylogeny of Viruses date: 2008-07-30 pages: extension: .txt txt: ./txt/cord-343918-5yk1j4ms.txt cache: ./cache/cord-343918-5yk1j4ms.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-343918-5yk1j4ms.txt' === file2bib.sh === id: cord-342634-4ouhdjsr author: Semrad, Katharina title: Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding date: 2010-12-26 pages: extension: .txt txt: ./txt/cord-342634-4ouhdjsr.txt cache: ./cache/cord-342634-4ouhdjsr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-342634-4ouhdjsr.txt' === file2bib.sh === id: cord-345654-vyz6f3he author: Dennehy, John J. title: Evolutionary ecology of virus emergence date: 2016-12-30 pages: extension: .txt txt: ./txt/cord-345654-vyz6f3he.txt cache: ./cache/cord-345654-vyz6f3he.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345654-vyz6f3he.txt' === file2bib.sh === id: cord-345957-wuk2arf9 author: Mohamed, Fakry F. title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt date: 2018-02-08 pages: extension: .txt txt: ./txt/cord-345957-wuk2arf9.txt cache: ./cache/cord-345957-wuk2arf9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-345957-wuk2arf9.txt' === file2bib.sh === id: cord-344321-fjer281d author: Ning, Yi title: Aptamers used for biosensors and targeted therapy date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-344321-fjer281d.txt cache: ./cache/cord-344321-fjer281d.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-344321-fjer281d.txt' === file2bib.sh === id: cord-346544-kk7qyn4w author: Andersson, M. title: SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date: 2020-05-26 pages: extension: .txt txt: ./txt/cord-346544-kk7qyn4w.txt cache: ./cache/cord-346544-kk7qyn4w.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-346544-kk7qyn4w.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42048 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42144 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 43447 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 42598 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-345630-bam3pa70 author: Lee, Han-Jung title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 pages: extension: .txt txt: ./txt/cord-345630-bam3pa70.txt cache: ./cache/cord-345630-bam3pa70.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345630-bam3pa70.txt' === file2bib.sh === id: cord-346267-l08ld2cy author: Wertheim, Joel O. title: Purifying Selection Can Obscure the Ancient Age of Viral Lineages date: 2011-06-24 pages: extension: .txt txt: ./txt/cord-346267-l08ld2cy.txt cache: ./cache/cord-346267-l08ld2cy.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346267-l08ld2cy.txt' === file2bib.sh === id: cord-345413-bsd32j8r author: Terada, Yutaka title: Establishment of a Virulent Full-Length cDNA Clone for Type I Feline Coronavirus Strain C3663 date: 2019-08-02 pages: extension: .txt txt: ./txt/cord-345413-bsd32j8r.txt cache: ./cache/cord-345413-bsd32j8r.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-345413-bsd32j8r.txt' === file2bib.sh === id: cord-344421-rmnck42f author: Theuns, Sebastiaan title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus date: 2018-06-29 pages: extension: .txt txt: ./txt/cord-344421-rmnck42f.txt cache: ./cache/cord-344421-rmnck42f.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-344421-rmnck42f.txt' === file2bib.sh === id: cord-346930-gl573ip9 author: Hussain, Azhar title: Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date: 2020-05-24 pages: extension: .txt txt: ./txt/cord-346930-gl573ip9.txt cache: ./cache/cord-346930-gl573ip9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346930-gl573ip9.txt' === file2bib.sh === id: cord-346138-ip42zcld author: Zhurakivska, Khrystyna title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-346138-ip42zcld.txt cache: ./cache/cord-346138-ip42zcld.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-346138-ip42zcld.txt' === file2bib.sh === id: cord-346514-vyo8l14p author: Chen, I-Hsuan title: Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date: 2013-06-13 pages: extension: .txt txt: ./txt/cord-346514-vyo8l14p.txt cache: ./cache/cord-346514-vyo8l14p.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346514-vyo8l14p.txt' === file2bib.sh === id: cord-347302-ylnb6qfl author: van der Schaar, Hilde M. title: Fat(al) attraction: Picornaviruses Usurp Lipid Transfer at Membrane Contact Sites to Create Replication Organelles date: 2016-03-22 pages: extension: .txt txt: ./txt/cord-347302-ylnb6qfl.txt cache: ./cache/cord-347302-ylnb6qfl.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347302-ylnb6qfl.txt' === file2bib.sh === id: cord-348204-365z3qxz author: Harun, Mohammad Syamsul Reza title: Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats date: 2013-11-09 pages: extension: .txt txt: ./txt/cord-348204-365z3qxz.txt cache: ./cache/cord-348204-365z3qxz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348204-365z3qxz.txt' === file2bib.sh === id: cord-348669-mizygp4j author: Beall, Anne title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date: 2016-01-05 pages: extension: .txt txt: ./txt/cord-348669-mizygp4j.txt cache: ./cache/cord-348669-mizygp4j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348669-mizygp4j.txt' === file2bib.sh === id: cord-347221-g98q9cga author: Piyush, Ravikant title: Nucleic acid-based therapy for coronavirus disease 2019 date: 2020-09-19 pages: extension: .txt txt: ./txt/cord-347221-g98q9cga.txt cache: ./cache/cord-347221-g98q9cga.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347221-g98q9cga.txt' === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 59386 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 60196 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 62439 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 62747 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === OMP: Error #34: System unable to allocate necessary resources for OMP thread: OMP: System error #11: Resource temporarily unavailable OMP: Hint Try decreasing the value of OMP_NUM_THREADS. /data-disk/reader-compute/reader-cord/bin/file2bib.sh: line 39: 65072 Aborted $FILE2BIB "$FILE" > "$OUTPUT" === file2bib.sh === id: cord-347532-n51qv9pp author: Wacharapluesadee, Supaporn title: Group C Betacoronavirus in Bat Guano Fertilizer, Thailand date: 2013-08-17 pages: extension: .txt txt: ./txt/cord-347532-n51qv9pp.txt cache: ./cache/cord-347532-n51qv9pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347532-n51qv9pp.txt' === file2bib.sh === id: cord-345371-pjbviagq author: Lisi, Lucia title: Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date: 2020-07-23 pages: extension: .txt txt: ./txt/cord-345371-pjbviagq.txt cache: ./cache/cord-345371-pjbviagq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-345371-pjbviagq.txt' === file2bib.sh === id: cord-348243-e5tdb08v author: Schermer, Bernhard title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 pages: extension: .txt txt: ./txt/cord-348243-e5tdb08v.txt cache: ./cache/cord-348243-e5tdb08v.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348243-e5tdb08v.txt' === file2bib.sh === id: cord-349839-s32d3di2 author: Westhof, Eric title: RNA pseudoknots date: 1992-06-30 pages: extension: .txt txt: ./txt/cord-349839-s32d3di2.txt cache: ./cache/cord-349839-s32d3di2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349839-s32d3di2.txt' === file2bib.sh === id: cord-349684-2tioh80m author: Pezzotti, Giuseppe title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-349684-2tioh80m.txt cache: ./cache/cord-349684-2tioh80m.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349684-2tioh80m.txt' === file2bib.sh === id: cord-349042-u9svz7pf author: Li, Jifen title: The successes and future prospects of the linear antisense RNA amplification methodology date: 2018-03-29 pages: extension: .txt txt: ./txt/cord-349042-u9svz7pf.txt cache: ./cache/cord-349042-u9svz7pf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349042-u9svz7pf.txt' === file2bib.sh === id: cord-350342-j4p8235a author: Brocato, Rebecca L. title: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date: 2020-10-27 pages: extension: .txt txt: ./txt/cord-350342-j4p8235a.txt cache: ./cache/cord-350342-j4p8235a.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350342-j4p8235a.txt' === file2bib.sh === id: cord-349341-ap5n6ijl author: Kopek, Benjamin G title: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle date: 2007-08-14 pages: extension: .txt txt: ./txt/cord-349341-ap5n6ijl.txt cache: ./cache/cord-349341-ap5n6ijl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-349341-ap5n6ijl.txt' === file2bib.sh === id: cord-348799-qu4zin3o author: Wu, Nannan title: The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation date: 2019-10-10 pages: extension: .txt txt: ./txt/cord-348799-qu4zin3o.txt cache: ./cache/cord-348799-qu4zin3o.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 5 resourceName b'cord-348799-qu4zin3o.txt' === file2bib.sh === id: cord-348147-leni23pa author: Müller, B. title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice date: 2007-05-29 pages: extension: .txt txt: ./txt/cord-348147-leni23pa.txt cache: ./cache/cord-348147-leni23pa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-348147-leni23pa.txt' === file2bib.sh === id: cord-347128-6lyoz8nn author: Kim, Cheorl-Ho title: SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-347128-6lyoz8nn.txt cache: ./cache/cord-347128-6lyoz8nn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-347128-6lyoz8nn.txt' === file2bib.sh === id: cord-350906-ew04zzh6 author: Khambhati, Khushal title: Current progress in CRISPR‐based diagnostic platforms date: 2018-10-26 pages: extension: .txt txt: ./txt/cord-350906-ew04zzh6.txt cache: ./cache/cord-350906-ew04zzh6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350906-ew04zzh6.txt' === file2bib.sh === id: cord-350189-2su7oqbz author: Elmén, Joacim title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date: 2005-01-14 pages: extension: .txt txt: ./txt/cord-350189-2su7oqbz.txt cache: ./cache/cord-350189-2su7oqbz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350189-2su7oqbz.txt' === file2bib.sh === id: cord-348860-zaimorg0 author: Ratra, Ruchi title: Functional genomics as a tool in virus research date: 2008-06-01 pages: extension: .txt txt: ./txt/cord-348860-zaimorg0.txt cache: ./cache/cord-348860-zaimorg0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348860-zaimorg0.txt' === file2bib.sh === id: cord-349623-dw5o9i59 author: Miranda, José P. title: Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-349623-dw5o9i59.txt cache: ./cache/cord-349623-dw5o9i59.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349623-dw5o9i59.txt' === file2bib.sh === id: cord-351864-zozrj7w5 author: Chappleboim, A. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 pages: extension: .txt txt: ./txt/cord-351864-zozrj7w5.txt cache: ./cache/cord-351864-zozrj7w5.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351864-zozrj7w5.txt' === file2bib.sh === id: cord-347472-n6811ens author: Rosebrock, Adam P. title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date: 2020-05-15 pages: extension: .txt txt: ./txt/cord-347472-n6811ens.txt cache: ./cache/cord-347472-n6811ens.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-347472-n6811ens.txt' === file2bib.sh === id: cord-350040-e8q7wq0h author: Aronin, N title: Target selectivity in mRNA silencing date: 2006-02-16 pages: extension: .txt txt: ./txt/cord-350040-e8q7wq0h.txt cache: ./cache/cord-350040-e8q7wq0h.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350040-e8q7wq0h.txt' === file2bib.sh === id: cord-350747-5t5xthk6 author: Gmyl, A. P. title: Diverse Mechanisms of RNA Recombination date: 2005 pages: extension: .txt txt: ./txt/cord-350747-5t5xthk6.txt cache: ./cache/cord-350747-5t5xthk6.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350747-5t5xthk6.txt' === file2bib.sh === id: cord-347351-emdj66vj author: Kampf, Günter title: Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date: 2020-09-18 pages: extension: .txt txt: ./txt/cord-347351-emdj66vj.txt cache: ./cache/cord-347351-emdj66vj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-347351-emdj66vj.txt' === file2bib.sh === id: cord-346916-jj4l9ydl author: Girardi, Erika title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 pages: extension: .txt txt: ./txt/cord-346916-jj4l9ydl.txt cache: ./cache/cord-346916-jj4l9ydl.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-346916-jj4l9ydl.txt' === file2bib.sh === id: cord-348815-lthz75oc author: Kurreck, Jens title: RNA Interference: From Basic Research to Therapeutic Applications date: 2009-01-19 pages: extension: .txt txt: ./txt/cord-348815-lthz75oc.txt cache: ./cache/cord-348815-lthz75oc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348815-lthz75oc.txt' === file2bib.sh === id: cord-348777-pk9y6vfp author: Ding, Cheng title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-348777-pk9y6vfp.txt cache: ./cache/cord-348777-pk9y6vfp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-348777-pk9y6vfp.txt' === file2bib.sh === id: cord-350019-4nlbu54e author: Robinson, Elektra K. title: The how and why of lncRNA function: An innate immune perspective() date: 2019-09-02 pages: extension: .txt txt: ./txt/cord-350019-4nlbu54e.txt cache: ./cache/cord-350019-4nlbu54e.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350019-4nlbu54e.txt' === file2bib.sh === id: cord-350600-73q8mve4 author: Myint, S. title: Detection of human coronavirus 229E in nasal washings using RNA:RNA hybridization date: 2005-12-09 pages: extension: .txt txt: ./txt/cord-350600-73q8mve4.txt cache: ./cache/cord-350600-73q8mve4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-350600-73q8mve4.txt' === file2bib.sh === id: cord-350533-fp1ctpax author: Tchesnokov, Egor P. title: Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein date: 2020-06-04 pages: extension: .txt txt: ./txt/cord-350533-fp1ctpax.txt cache: ./cache/cord-350533-fp1ctpax.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350533-fp1ctpax.txt' === file2bib.sh === id: cord-350697-u032yk0z author: Roy, Anupam title: Can concomitant use of zinc and curcumin with other immunity‐boosting nutraceuticals be the arsenal against COVID‐19? date: 2020-06-02 pages: extension: .txt txt: ./txt/cord-350697-u032yk0z.txt cache: ./cache/cord-350697-u032yk0z.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-350697-u032yk0z.txt' === file2bib.sh === id: cord-349417-vn7q8wc4 author: Ziebuhr, John title: The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date: 2006 pages: extension: .txt txt: ./txt/cord-349417-vn7q8wc4.txt cache: ./cache/cord-349417-vn7q8wc4.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349417-vn7q8wc4.txt' === file2bib.sh === id: cord-349762-f5no10eq author: Nagura-Ikeda, Mayu title: Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date: 2020-08-24 pages: extension: .txt txt: ./txt/cord-349762-f5no10eq.txt cache: ./cache/cord-349762-f5no10eq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349762-f5no10eq.txt' === file2bib.sh === id: cord-350762-rh4zbehk author: Hutcheson, Jessica M. title: Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date: 2015-06-04 pages: extension: .txt txt: ./txt/cord-350762-rh4zbehk.txt cache: ./cache/cord-350762-rh4zbehk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350762-rh4zbehk.txt' === file2bib.sh === id: cord-350640-sz6xj5o3 author: Menzel, Nicolas title: MAP-Kinase Regulated Cytosolic Phospholipase A2 Activity Is Essential for Production of Infectious Hepatitis C Virus Particles date: 2012-07-26 pages: extension: .txt txt: ./txt/cord-350640-sz6xj5o3.txt cache: ./cache/cord-350640-sz6xj5o3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-350640-sz6xj5o3.txt' === file2bib.sh === id: cord-351377-xorj8tnz author: Kao, Chi-Fei title: The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date: 2018-10-04 pages: extension: .txt txt: ./txt/cord-351377-xorj8tnz.txt cache: ./cache/cord-351377-xorj8tnz.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351377-xorj8tnz.txt' === file2bib.sh === id: cord-351489-tzmev77c author: Yuan, Shuofeng title: Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date: 2020-06-10 pages: extension: .txt txt: ./txt/cord-351489-tzmev77c.txt cache: ./cache/cord-351489-tzmev77c.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351489-tzmev77c.txt' === file2bib.sh === id: cord-347710-ff64y6ef author: Wan, Qianya title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 pages: extension: .txt txt: ./txt/cord-347710-ff64y6ef.txt cache: ./cache/cord-347710-ff64y6ef.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 7 resourceName b'cord-347710-ff64y6ef.txt' === file2bib.sh === id: cord-350083-kldu8q8x author: Oany, Arafat Rahman title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date: 2015-08-08 pages: extension: .txt txt: ./txt/cord-350083-kldu8q8x.txt cache: ./cache/cord-350083-kldu8q8x.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350083-kldu8q8x.txt' === file2bib.sh === id: cord-350836-1enteev7 author: Brisse, Morgan title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date: 2019-07-17 pages: extension: .txt txt: ./txt/cord-350836-1enteev7.txt cache: ./cache/cord-350836-1enteev7.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-350836-1enteev7.txt' === file2bib.sh === id: cord-349358-leicos9j author: Ketzinel‐Gilad, Mali title: RNA interference for antiviral therapy date: 2006-06-16 pages: extension: .txt txt: ./txt/cord-349358-leicos9j.txt cache: ./cache/cord-349358-leicos9j.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-349358-leicos9j.txt' === file2bib.sh === id: cord-351482-hzh5tyoo author: Peng, Xinxia title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 pages: extension: .txt txt: ./txt/cord-351482-hzh5tyoo.txt cache: ./cache/cord-351482-hzh5tyoo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-351482-hzh5tyoo.txt' === file2bib.sh === id: cord-351837-vasuu70k author: Shannon, Ashleigh title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date: 2020-09-17 pages: extension: .txt txt: ./txt/cord-351837-vasuu70k.txt cache: ./cache/cord-351837-vasuu70k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351837-vasuu70k.txt' === file2bib.sh === id: cord-351115-dy81dtnk author: Wang, Chen title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date: 2020-10-20 pages: extension: .txt txt: ./txt/cord-351115-dy81dtnk.txt cache: ./cache/cord-351115-dy81dtnk.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351115-dy81dtnk.txt' === file2bib.sh === id: cord-352088-9k01ej6l author: Saiz, Juan-Carlos title: Vaccines against RNA Viruses date: 2020-08-27 pages: extension: .txt txt: ./txt/cord-352088-9k01ej6l.txt cache: ./cache/cord-352088-9k01ej6l.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352088-9k01ej6l.txt' === file2bib.sh === id: cord-349672-2kt7xw8i author: Dasgupta, Tumpa title: Mechanism of Type IA Topoisomerases date: 2020-10-17 pages: extension: .txt txt: ./txt/cord-349672-2kt7xw8i.txt cache: ./cache/cord-349672-2kt7xw8i.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-349672-2kt7xw8i.txt' === file2bib.sh === id: cord-352361-jh31omg2 author: Nobach, Daniel title: No evidence for European bats serving as reservoir for Borna disease virus 1 or other known mammalian orthobornaviruses date: 2020-01-30 pages: extension: .txt txt: ./txt/cord-352361-jh31omg2.txt cache: ./cache/cord-352361-jh31omg2.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352361-jh31omg2.txt' === file2bib.sh === id: cord-352178-irjhmxsg author: Saxton-Shaw, Kali D. title: O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date: 2013-01-24 pages: extension: .txt txt: ./txt/cord-352178-irjhmxsg.txt cache: ./cache/cord-352178-irjhmxsg.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352178-irjhmxsg.txt' === file2bib.sh === id: cord-351559-az4pgi9k author: Turjya, Rafeed Rahman title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 pages: extension: .txt txt: ./txt/cord-351559-az4pgi9k.txt cache: ./cache/cord-351559-az4pgi9k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351559-az4pgi9k.txt' === file2bib.sh === id: cord-351520-c5fi2uoh author: Zhong, Bo title: Regulation of virus-triggered type I interferon signaling by cellular and viral proteins date: 2010-02-01 pages: extension: .txt txt: ./txt/cord-351520-c5fi2uoh.txt cache: ./cache/cord-351520-c5fi2uoh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351520-c5fi2uoh.txt' === file2bib.sh === id: cord-353640-giznbcpd author: Barza, Ruby title: Use of a Simplified Sample Processing step without RNA Extraction for direct SARS-CoV-2 RT-PCR Detection date: 2020-08-11 pages: extension: .txt txt: ./txt/cord-353640-giznbcpd.txt cache: ./cache/cord-353640-giznbcpd.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-353640-giznbcpd.txt' === file2bib.sh === id: cord-351854-5s03f0pp author: Ben-Ami, Roni title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 pages: extension: .txt txt: ./txt/cord-351854-5s03f0pp.txt cache: ./cache/cord-351854-5s03f0pp.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-351854-5s03f0pp.txt' === file2bib.sh === id: cord-351920-igmb2yfe author: Oma, Veslemøy Sunniva title: Bovine coronavirus in naturally and experimentally exposed calves; viral shedding and the potential for transmission date: 2016-06-13 pages: extension: .txt txt: ./txt/cord-351920-igmb2yfe.txt cache: ./cache/cord-351920-igmb2yfe.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-351920-igmb2yfe.txt' === file2bib.sh === id: cord-352768-16vgnq14 author: Tang, Qingquan title: Application of siRNA Against SARS in the Rhesus Macaque Model date: 2008 pages: extension: .txt txt: ./txt/cord-352768-16vgnq14.txt cache: ./cache/cord-352768-16vgnq14.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352768-16vgnq14.txt' === file2bib.sh === id: cord-351365-dc9t3vh3 author: Todt, Daniel title: Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date: 2016-10-13 pages: extension: .txt txt: ./txt/cord-351365-dc9t3vh3.txt cache: ./cache/cord-351365-dc9t3vh3.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351365-dc9t3vh3.txt' === file2bib.sh === id: cord-352891-ljmkqdzx author: Parang, Keykavous title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date: 2020-05-17 pages: extension: .txt txt: ./txt/cord-352891-ljmkqdzx.txt cache: ./cache/cord-352891-ljmkqdzx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352891-ljmkqdzx.txt' === file2bib.sh === id: cord-351548-jvl63652 author: Juranic Lisnic, Vanda title: Dual Analysis of the Murine Cytomegalovirus and Host Cell Transcriptomes Reveal New Aspects of the Virus-Host Cell Interface date: 2013-09-26 pages: extension: .txt txt: ./txt/cord-351548-jvl63652.txt cache: ./cache/cord-351548-jvl63652.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-351548-jvl63652.txt' === file2bib.sh === id: cord-354536-c9v9kbw8 author: Han, Yan-Jie title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 pages: extension: .txt txt: ./txt/cord-354536-c9v9kbw8.txt cache: ./cache/cord-354536-c9v9kbw8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354536-c9v9kbw8.txt' === file2bib.sh === id: cord-352664-heoj8ji8 author: Hubbard, Amelia title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date: 2015-02-25 pages: extension: .txt txt: ./txt/cord-352664-heoj8ji8.txt cache: ./cache/cord-352664-heoj8ji8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352664-heoj8ji8.txt' === file2bib.sh === id: cord-354394-zojhdnlu author: Wang, Wei-Kung title: Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date: 2004-07-17 pages: extension: .txt txt: ./txt/cord-354394-zojhdnlu.txt cache: ./cache/cord-354394-zojhdnlu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354394-zojhdnlu.txt' === file2bib.sh === id: cord-352814-fcl2g5wr author: Balboni, Andrea title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 pages: extension: .txt txt: ./txt/cord-352814-fcl2g5wr.txt cache: ./cache/cord-352814-fcl2g5wr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352814-fcl2g5wr.txt' === file2bib.sh === id: cord-350286-n7ylgqfu author: Giri, Rajanish title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 pages: extension: .txt txt: ./txt/cord-350286-n7ylgqfu.txt cache: ./cache/cord-350286-n7ylgqfu.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-350286-n7ylgqfu.txt' === file2bib.sh === id: cord-353524-3w970ycx author: Dömling, Alexander title: Chemistry and Biology of SARS-CoV-2 date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-353524-3w970ycx.txt cache: ./cache/cord-353524-3w970ycx.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353524-3w970ycx.txt' === file2bib.sh === id: cord-352465-n746e8qt author: Wang, Fei title: Targeting stress granules: A novel therapeutic strategy for human diseases date: 2020-08-16 pages: extension: .txt txt: ./txt/cord-352465-n746e8qt.txt cache: ./cache/cord-352465-n746e8qt.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352465-n746e8qt.txt' === file2bib.sh === id: cord-354465-5nqrrnqr author: Haslinger, Christian title: RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties date: 1999 pages: extension: .txt txt: ./txt/cord-354465-5nqrrnqr.txt cache: ./cache/cord-354465-5nqrrnqr.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354465-5nqrrnqr.txt' === file2bib.sh === id: cord-354510-jlg5je0s author: de Carvalho, A. F. title: THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date: 2020-06-20 pages: extension: .txt txt: ./txt/cord-354510-jlg5je0s.txt cache: ./cache/cord-354510-jlg5je0s.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354510-jlg5je0s.txt' === file2bib.sh === id: cord-354051-ro3o27pv author: Peccia, J. title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date: 2020-05-22 pages: extension: .txt txt: ./txt/cord-354051-ro3o27pv.txt cache: ./cache/cord-354051-ro3o27pv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354051-ro3o27pv.txt' === file2bib.sh === id: cord-355676-2y8vowbi author: Liu, Pinghua title: A Previously Unrecognized Unr Stem-Loop Structure in the Coronavirus 5’ Untranslated Region Plays a Functional role in Replication date: 2006 pages: extension: .txt txt: ./txt/cord-355676-2y8vowbi.txt cache: ./cache/cord-355676-2y8vowbi.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-355676-2y8vowbi.txt' === file2bib.sh === id: cord-353576-f29kmtot author: Maricic, T. title: A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date: 2020-06-26 pages: extension: .txt txt: ./txt/cord-353576-f29kmtot.txt cache: ./cache/cord-353576-f29kmtot.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353576-f29kmtot.txt' === file2bib.sh === id: cord-352379-q5inrxcm author: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 pages: extension: .txt txt: ./txt/cord-352379-q5inrxcm.txt cache: ./cache/cord-352379-q5inrxcm.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352379-q5inrxcm.txt' === file2bib.sh === id: cord-356013-pl3tmky8 author: Brian, D. A. title: Coronavirus Genome Structure and Replication date: 2005 pages: extension: .txt txt: ./txt/cord-356013-pl3tmky8.txt cache: ./cache/cord-356013-pl3tmky8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356013-pl3tmky8.txt' === file2bib.sh === id: cord-354824-7fdcu2f0 author: Wu, Renyi title: An Update on Current Therapeutic Drugs Treating COVID-19 date: 2020-05-11 pages: extension: .txt txt: ./txt/cord-354824-7fdcu2f0.txt cache: ./cache/cord-354824-7fdcu2f0.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354824-7fdcu2f0.txt' === file2bib.sh === id: cord-355743-vjiecd4k author: Ghosh, Sabyasachi title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date: 2020-04-29 pages: extension: .txt txt: ./txt/cord-355743-vjiecd4k.txt cache: ./cache/cord-355743-vjiecd4k.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 1 resourceName b'cord-355743-vjiecd4k.txt' === file2bib.sh === id: cord-353274-wozwpvpq author: Borremans, B. title: Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date: 2020-05-20 pages: extension: .txt txt: ./txt/cord-353274-wozwpvpq.txt cache: ./cache/cord-353274-wozwpvpq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353274-wozwpvpq.txt' === file2bib.sh === id: cord-355499-5vj3oasa author: Song, Xiangjun title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date: 2015-06-07 pages: extension: .txt txt: ./txt/cord-355499-5vj3oasa.txt cache: ./cache/cord-355499-5vj3oasa.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355499-5vj3oasa.txt' === file2bib.sh === id: cord-354096-x2skguz8 author: Ray, Pradipta R. title: A pharmacological interactome between COVID-19 patient samples and human sensory neurons reveals potential drivers of neurogenic pulmonary dysfunction date: 2020-06-01 pages: extension: .txt txt: ./txt/cord-354096-x2skguz8.txt cache: ./cache/cord-354096-x2skguz8.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354096-x2skguz8.txt' === file2bib.sh === id: cord-354733-qxivrhj8 author: Gniazdowski, V. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 pages: extension: .txt txt: ./txt/cord-354733-qxivrhj8.txt cache: ./cache/cord-354733-qxivrhj8.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354733-qxivrhj8.txt' === file2bib.sh === id: cord-353475-dtn7h1gj author: Haddad, Hazem title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date: 2020-08-20 pages: extension: .txt txt: ./txt/cord-353475-dtn7h1gj.txt cache: ./cache/cord-353475-dtn7h1gj.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353475-dtn7h1gj.txt' === file2bib.sh === id: cord-353810-mf753ae9 author: Tan, Cedric Chih Shen title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 pages: extension: .txt txt: ./txt/cord-353810-mf753ae9.txt cache: ./cache/cord-353810-mf753ae9.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353810-mf753ae9.txt' === file2bib.sh === id: cord-354829-god79qzw author: Mao, Kaimin title: Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets date: 2020-09-23 pages: extension: .txt txt: ./txt/cord-354829-god79qzw.txt cache: ./cache/cord-354829-god79qzw.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354829-god79qzw.txt' === file2bib.sh === id: cord-355758-tk7eturq author: Berrio, Alejandro title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date: 2020-09-22 pages: extension: .txt txt: ./txt/cord-355758-tk7eturq.txt cache: ./cache/cord-355758-tk7eturq.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355758-tk7eturq.txt' === file2bib.sh === id: cord-355179-wmfwl2bh author: Jung, Eunhye title: Neutralization of Acidic Intracellular Vesicles by Niclosamide Inhibits Multiple Steps of the Dengue Virus Life Cycle In Vitro date: 2019-06-18 pages: extension: .txt txt: ./txt/cord-355179-wmfwl2bh.txt cache: ./cache/cord-355179-wmfwl2bh.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-355179-wmfwl2bh.txt' === file2bib.sh === id: cord-353484-q7d0ysbo author: Liu, Xue title: COVID-19: Progress in diagnostics, therapy and vaccination date: 2020-06-19 pages: extension: .txt txt: ./txt/cord-353484-q7d0ysbo.txt cache: ./cache/cord-353484-q7d0ysbo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353484-q7d0ysbo.txt' === file2bib.sh === id: cord-355397-y69bk5jc author: Caruso, Ícaro P. title: Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism date: 2020-09-06 pages: extension: .txt txt: ./txt/cord-355397-y69bk5jc.txt cache: ./cache/cord-355397-y69bk5jc.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355397-y69bk5jc.txt' === file2bib.sh === id: cord-355477-7xd93aqv author: SATIJA, NAMITA title: The Molecular Biology of SARS Coronavirus date: 2007-04-23 pages: extension: .txt txt: ./txt/cord-355477-7xd93aqv.txt cache: ./cache/cord-355477-7xd93aqv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355477-7xd93aqv.txt' === file2bib.sh === id: cord-356009-emn2w8if author: Roshandel, M. R. title: What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date: 2020-10-13 pages: extension: .txt txt: ./txt/cord-356009-emn2w8if.txt cache: ./cache/cord-356009-emn2w8if.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356009-emn2w8if.txt' === file2bib.sh === id: cord-355075-ieb35upi author: Papenfuss, Anthony T title: The immune gene repertoire of an important viral reservoir, the Australian black flying fox date: 2012-06-20 pages: extension: .txt txt: ./txt/cord-355075-ieb35upi.txt cache: ./cache/cord-355075-ieb35upi.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355075-ieb35upi.txt' === file2bib.sh === id: cord-354529-k8p2u7iq author: Wu, Yongran title: Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date: 2020-08-31 pages: extension: .txt txt: ./txt/cord-354529-k8p2u7iq.txt cache: ./cache/cord-354529-k8p2u7iq.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354529-k8p2u7iq.txt' === file2bib.sh === id: cord-355357-b6aklh44 author: Stapleford, Kenneth A. title: Viral Polymerase-Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion date: 2015-08-26 pages: extension: .txt txt: ./txt/cord-355357-b6aklh44.txt cache: ./cache/cord-355357-b6aklh44.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355357-b6aklh44.txt' === file2bib.sh === id: cord-354003-ko45l1qv author: Scarpin, M Regina title: Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation date: 2020-10-15 pages: extension: .txt txt: ./txt/cord-354003-ko45l1qv.txt cache: ./cache/cord-354003-ko45l1qv.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 4 resourceName b'cord-354003-ko45l1qv.txt' === file2bib.sh === id: cord-356115-vblgotjn author: Sawicki, Stanley G title: Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins date: 2005-12-09 pages: extension: .txt txt: ./txt/cord-356115-vblgotjn.txt cache: ./cache/cord-356115-vblgotjn.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-356115-vblgotjn.txt' === file2bib.sh === id: cord-352200-i05h8csb author: Xu, Yi title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 pages: extension: .txt txt: ./txt/cord-352200-i05h8csb.txt cache: ./cache/cord-352200-i05h8csb.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-352200-i05h8csb.txt' === file2bib.sh === id: cord-353342-2n6kqyeo author: Corman, Victor M. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 pages: extension: .txt txt: ./txt/cord-353342-2n6kqyeo.txt cache: ./cache/cord-353342-2n6kqyeo.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-353342-2n6kqyeo.txt' === file2bib.sh === id: cord-353703-u86ggw11 author: Gao, Peng title: Reprogramming the unfolded protein response for replication by porcine reproductive and respiratory syndrome virus date: 2019-11-18 pages: extension: .txt txt: ./txt/cord-353703-u86ggw11.txt cache: ./cache/cord-353703-u86ggw11.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353703-u86ggw11.txt' === file2bib.sh === id: cord-354398-f3cg8gi1 author: Al-Saud, Haya title: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date: 2020-09-20 pages: extension: .txt txt: ./txt/cord-354398-f3cg8gi1.txt cache: ./cache/cord-354398-f3cg8gi1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354398-f3cg8gi1.txt' === file2bib.sh === id: cord-354407-zzxjv666 author: Campanacci, Valérie title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date: 2004-06-07 pages: extension: .txt txt: ./txt/cord-354407-zzxjv666.txt cache: ./cache/cord-354407-zzxjv666.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-354407-zzxjv666.txt' === file2bib.sh === id: cord-352991-duqkpkll author: Waghmare, Alpana title: Respiratory Syncytial Virus Lower Respiratory Disease in Hematopoietic Cell Transplant Recipients: Viral RNA Detection in Blood, Antiviral Treatment, and Clinical Outcomes date: 2013-09-24 pages: extension: .txt txt: ./txt/cord-352991-duqkpkll.txt cache: ./cache/cord-352991-duqkpkll.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-352991-duqkpkll.txt' === file2bib.sh === id: cord-353290-1wi1dhv6 author: Kustin, Talia title: Biased mutation and selection in RNA viruses date: 2020-09-28 pages: extension: .txt txt: ./txt/cord-353290-1wi1dhv6.txt cache: ./cache/cord-353290-1wi1dhv6.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-353290-1wi1dhv6.txt' === file2bib.sh === id: cord-355913-fhvt1ht1 author: Burrell, Christopher J. title: Virus Replication date: 2016-11-11 pages: extension: .txt txt: ./txt/cord-355913-fhvt1ht1.txt cache: ./cache/cord-355913-fhvt1ht1.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 2 resourceName b'cord-355913-fhvt1ht1.txt' === file2bib.sh === id: cord-354114-frdsct44 author: Vogel, Liesbeth title: Pathogenic characteristics of persistent feline enteric coronavirus infection in cats date: 2010-07-23 pages: extension: .txt txt: ./txt/cord-354114-frdsct44.txt cache: ./cache/cord-354114-frdsct44.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354114-frdsct44.txt' === file2bib.sh === id: cord-354582-fniymnmf author: Ma, Zhiqian title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 pages: extension: .txt txt: ./txt/cord-354582-fniymnmf.txt cache: ./cache/cord-354582-fniymnmf.txt Content-Encoding UTF-8 Content-Type text/plain; charset=UTF-8 X-Parsed-By ['org.apache.tika.parser.DefaultParser', 'org.apache.tika.parser.csv.TextAndCSVParser'] X-TIKA:content_handler ToTextContentHandler X-TIKA:embedded_depth 0 X-TIKA:parse_time_millis 3 resourceName b'cord-354582-fniymnmf.txt' Que is empty; done keyword-rna-cord === reduce.pl bib === id = cord-000269-v4jochbe author = Wittekindt, Nicola E. title = Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics date = 2010-10-18 pages = extension = .txt mime = text/plain words = 5886 sentences = 314 flesch = 44 summary = cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. The microbial community of mule deer lymph nodes Detection of protein-coding and ribosomal RNA transcripts provides strong support for the presence of viable and replicating microorganisms. As an alternative approach to identifying bacterial microorganisms present in lymph node tissue, we utilized amplicon DNA library sequencing technology. cache = ./cache/cord-000269-v4jochbe.txt txt = ./txt/cord-000269-v4jochbe.txt === reduce.pl bib === id = cord-000322-8ctsa9sd author = Ninove, Laetitia title = RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date = 2011-02-09 pages = extension = .txt mime = text/plain words = 2892 sentences = 130 flesch = 46 summary = Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids. Monitoring rt-PCR and rt-RT-PCR assays and validation of the results rely on the use of relevant external or internal controls (ECs or ICs) [1, 2] and commercial kits including such control systems are being increasingly improved for the molecular diagnosis of a number of pathogens such as HIV, hepatitis viruses, influenza viruses etc.. cache = ./cache/cord-000322-8ctsa9sd.txt txt = ./txt/cord-000322-8ctsa9sd.txt === reduce.pl bib === id = cord-000295-ft5wl70x author = Tomankova, Tereza title = Involvement of microRNAs in physiological and pathological processes in the lung date = 2010-11-23 pages = extension = .txt mime = text/plain words = 4778 sentences = 318 flesch = 46 summary = These short, single-stranded RNA molecules originate from larger precursor molecules that fold to produce hairpin structures, which are subsequently processed by ribonucleases Drosha/Pasha and Dicer to form mature miRNAs. MiRNAs play role in the posttranscriptional regulation of about one third of human genes, mainly via degradation of target mRNAs. Whereas the target mRNAs are often involved in the regulation of diverse physiological processes ranging from developmental timing to apoptosis, miRNAs have a strong potential to regulate fundamental biological processes also in the lung compartment. Small non-coding RNAs (miRNAs) play pivotal role in the posttranscriptional regulation of numerous human genes, mainly via degradation of target mRNAs. There is evidence that the lung has a very specific miRNA expression profile undergoing changes during the lung development. cache = ./cache/cord-000295-ft5wl70x.txt txt = ./txt/cord-000295-ft5wl70x.txt === reduce.pl bib === id = cord-000113-d0eur1hq author = Fooks, Anthony R. title = Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date = 2009-09-29 pages = extension = .txt mime = text/plain words = 6937 sentences = 319 flesch = 38 summary = The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. cache = ./cache/cord-000113-d0eur1hq.txt txt = ./txt/cord-000113-d0eur1hq.txt === reduce.pl bib === id = cord-000088-1xgjdhkx author = Faria, Nuno R title = Rooting human parechovirus evolution in time date = 2009-07-15 pages = extension = .txt mime = text/plain words = 4011 sentences = 214 flesch = 51 summary = Using both strict and relaxed clock Bayesian phylogenetics we investigated 1) the substitutions rates of the structural P1 and capsid VP1 regions and 2) evolutionary timescale of currently circulating HPeV lineages. Their evolutionary history and population dynamics can be reconstructed by means of genealogy-based coalescent approaches using nucleotide sequences sampled over an epidemiological time frame in order to estimate timed viral ancestry as well as the rates of genetic change [27, 29] . We first identified the best-fitting substitution model for the HPeV sequences using the Modelgenerator package (GTR + Γ) [35] , and tested whether the evolution of the P1 and VP1 genetic regions was better described by a strict or relaxed lognormal molecular clock. The Bayesian analysis presented here first indicates that the structural P1 and the capsid VP1 region of this viral species evolve at a high rate of evolutionary change (~10 -3 substitutions per site per year). cache = ./cache/cord-000088-1xgjdhkx.txt txt = ./txt/cord-000088-1xgjdhkx.txt === reduce.pl bib === id = cord-000159-8y8ho2x5 author = Bekaert, Michaël title = Recode-2: new design, new search tools, and many more genes date = 2009-09-25 pages = extension = .txt mime = text/plain words = 2625 sentences = 138 flesch = 42 summary = 'Recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. The term 'translational recoding' describes the utilization of non-standard decoding during protein synthesis and encompasses such processes as ribosomal frameshifting, codon redefinition, translational bypassing and StopGo (1) (2) (3) (4) (5) (6) (7) . To facilitate further development of computational tools for the prediction of recoded genes in the ever faster growing body of sequence data, as well as to provide bench researchers with upto-date information on recoding, an efficient means of Recode database population and annotation are now required. RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression cache = ./cache/cord-000159-8y8ho2x5.txt txt = ./txt/cord-000159-8y8ho2x5.txt === reduce.pl bib === id = cord-000715-zl1s82yi author = Shulman, Lester M. title = Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date = 2012-07-16 pages = extension = .txt mime = text/plain words = 4786 sentences = 248 flesch = 50 summary = These samples were selected from among archived stool samples previously tested for enterovirus and MS2 after extraction by QIAamp Viral RNA Mini Kit. A sufficient number of samples with high, intermediate, and low levels of inhibitors were chosen for re-analysis to enable comparison between extraction procedures at each of these levels of inhibition. Analysis of variance ( Fig. 3 , part 2), indicated that there was no significant difference (paired t-test, P.0.05) between the inhibition of rRT-PCR of the MS2 external control and the added enterovirus (P.0.05) for protocols A, C, and D. Stool suspensions (N = 185) prepared for routine analysis of clinical stool samples sent to the Central Virology Laboratory (CVL) at Chaim Sheba Medical Center in Israel were used to evaluate the efficiency of four different RNA extraction systems in excluding inhibitors of rRT-PCR. cache = ./cache/cord-000715-zl1s82yi.txt txt = ./txt/cord-000715-zl1s82yi.txt === reduce.pl bib === id = cord-000265-llilwq1u author = Gao, Rongbao title = A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date = 2010-10-12 pages = extension = .txt mime = text/plain words = 4896 sentences = 253 flesch = 46 summary = Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Although H5N1 virus infection of humans is primarily one of the lower respiratory tract, more recent reports suggested that influenza A H5N1 may in rare, severe cases, disseminate beyond the lungs and infect brain [26, 27] , intestines [20, 27] and lymphoid tissues [27] , and result in extra-pulmonary clinical manifestations including encephalopathy or encephalitis [15, 28] . To better understand the pathogenesis of human H5N1 virus infection, and investigate the route of virus dissemination in vivo, we report on the use of different techniques to detect virus distribution and infection of 5 organ systems in a laboratory confirmed fatal human H5N1 virus infection, and analyze the relationship between viral load in tissues and host response. cache = ./cache/cord-000265-llilwq1u.txt txt = ./txt/cord-000265-llilwq1u.txt === reduce.pl bib === id = cord-000482-wifs97yy author = Yu, Chien-Hung title = Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting date = 2011-07-29 pages = extension = .txt mime = text/plain words = 4774 sentences = 223 flesch = 55 summary = −1 Programmed ribosomal frameshifting (PRF) in synthesizing the gag-pro precursor polyprotein of Simian retrovirus type-1 (SRV-1) is stimulated by a classical H-type pseudoknot which forms an extended triple helix involving base–base and base–sugar interactions between loop and stem nucleotides. In short, pDUAL-HIV(0) was digested by KpnI and BamHI, followed by insertion of complementary oligonucleotides to clone the SRV-1 gag-pro pseudoknot, various hairpins as shown in Figures 2C and 5, and a negative control (NC) which formed no apparent secondary structure downstream of the slippery sequence. These data support the notion that downstream structures serve as barriers to stall translating ribosomes to stimulate frameshifting, and demonstrate that there is a correlation between the thermodynamic stability of a hairpin and its frameshift inducing capacity. In the present study, a 12 bp hairpin derivative of the SRV-1 gag-pro pseudoknot with a calculated stability of À26.9 kcal/mol was capable of inducing 22% of frameshifting, which is only 1.4-fold . cache = ./cache/cord-000482-wifs97yy.txt txt = ./txt/cord-000482-wifs97yy.txt === reduce.pl bib === id = cord-000435-2u49b7xo author = Firth, Andrew E. title = Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element date = 2011-04-27 pages = extension = .txt mime = text/plain words = 7256 sentences = 324 flesch = 50 summary = With respect to the non-structural polyprotein, SINV and Aura virus (AURAV) form a separate clade from VEEV, WEEV and EEEV but, again, the conservation analysis revealed striking tandem conservation peaks 3 0 of the RT site ( Figure 1B ) and, again, the conservation peaks corresponded to sequences with the potential to base pair to form an RNA structure-this time comprising an 11 bp stem with a 1 nt asymmetric 3 0 bulge, a 12 nt 'spacer' from the RT stop codon, and a 154 nt 'loop' region ( Figure 2 ). The potential to form an extended stemloop structure 3 0 -adjacent to a RT stop codon-phylogenetically conserved and supported by a pair of peaks in synonymous site conservation-was also found in a number of plant virus RT cases, for example, in the replicase gene in the genera (Figures 3 and 4) . cache = ./cache/cord-000435-2u49b7xo.txt txt = ./txt/cord-000435-2u49b7xo.txt === reduce.pl bib === id = cord-000248-zueoyesj author = Berretta, Regina title = Cancer Biomarker Discovery: The Entropic Hallmark date = 2010-08-18 pages = extension = .txt mime = text/plain words = 33594 sentences = 1678 flesch = 43 summary = These authors cite, for example, ''mitochondrial dysfunction'' [5, 6] (including, but not limited to ''glucose avidity'' [7] and ''a shift in glucosemetabolism from oxidative phosphorylation to glycolysis'' [6, 8] , ''altered glycolysis'' [9] , ''altered bioenergetic function of mitochondria'' [10] ), ''dysregulation of cell cycle and defective genome-integrity checkpoints'' [11] , ''aberrant DNA methylation'' [12] (''promoter hypermethylation of hallmark cancer genes'' [13] and ''CpG island hypermethylation and global genomic hypomethylation'' [14] ), ''shift in cellular metabolism'' [15, 16, 17] , ''regional hypoxia'' [18] , ''microenviroment acidosis'' [19] , ''abnormal microRNA regulation'' [20, 21] , ''aneuploidy'' and ''chromosome aberrations'' [22, 23, 24, 25, 26] , ''disruption of cellular junctions'' [27] , ''avoidance of the immune response'' [28] , ''pre-existing chronic inflammatory conditions'' [29, 30] , ''cancerrelated inflammation'' [29] , ''disabled autophagy'' [28] , ''impaired cellular senescence'' [31] , ''altered NF-kappaB signalling'' [32] , ''altered growth patterns, not altered growth per se'' [33] , ''disregulated DNA methylation and histone modifications'' [34] , ''tissue dedifferentiation'' [35, 36] , and ''somatically heritable molecular alterations'' [37] . cache = ./cache/cord-000248-zueoyesj.txt txt = ./txt/cord-000248-zueoyesj.txt === reduce.pl bib === id = cord-002045-m44fic4g author = Horie, Masayuki title = An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus date = 2016-05-13 pages = extension = .txt mime = text/plain words = 4805 sentences = 312 flesch = 59 summary = Endogenous bornavirus-like L (EBLL) elements are inheritable sequences derived from ancient bornavirus L genes that encode a viral RNA-dependent RNA polymerase (RdRp) in many eukaryotic genomes. Furthermore, we showed that the EBLLs evolved under purifying selection and still possess functional motifs conserved among the Mononegavirales RdRps. These results strongly suggest that the EBLL elements encode functional proteins that may be RdRps. ORF screening for these elements in several mammalian species and found an EBLL element in the bat species Eptesicus fuscus (designated efEBLL-1; accession number ALEH01013293). Notably, this element (eEBLL-1) contains a 1,718-amino acid ORF that was conserved for more than 11.8 MY and included almost all of the sequence motifs essential for the enzymatic activity of a RNA virus RdRp. To the best of our knowledge, eEBLL-1 is the first example of an RNA virus-derived RdRp encoded by the mammalian genome. cache = ./cache/cord-002045-m44fic4g.txt txt = ./txt/cord-002045-m44fic4g.txt === reduce.pl bib === id = cord-000143-2xvd5ogf author = Napthine, Sawsan title = Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy date = 2009-12-22 pages = extension = .txt mime = text/plain words = 6886 sentences = 300 flesch = 50 summary = In this process, following translation of an upstream open reading frame (ORF) and termination at the stop codon, a proportion of 40S subunits remain associated with the mRNA and reinitiate at the AUG of a downstream ORF, which is typically in close proximity. Recent studies of termination-reinitiation in the expression of the orthomyxovirus influenza BM2 protein have revealed a requirement for a shorter stretch of mRNA (45 nt) upstream of the stop-start window, but nevertheless, the RNA contains a similar TURBS Motif 1 [19] . Whilst in principle, reinitiation of translation of the MNV 49.7 VP2fluc ORF, following termination, could occur at the next available AUG, this is located 54 amino acids from the natural stop-start signal and initiation here would produce a substantially shorter product that would have been detectable by SDS-PAGE. cache = ./cache/cord-000143-2xvd5ogf.txt txt = ./txt/cord-000143-2xvd5ogf.txt === reduce.pl bib === id = cord-000660-tsvzg0ax author = Fensterl, Volker title = Interferon-Induced Ifit2/ISG54 Protects Mice from Lethal VSV Neuropathogenesis date = 2012-05-17 pages = extension = .txt mime = text/plain words = 8283 sentences = 446 flesch = 55 summary = Interferon protects mice from vesicular stomatitis virus (VSV) infection and pathogenesis; however, it is not known which of the numerous interferon-stimulated genes (ISG) mediate the antiviral effect. In contrast, in acute infection by viruses that cause severe pathogenesis and death within a few days after infection, protection is primarily provided by the intrinsic antiviral actions of IFN-induced proteins encoded by the hundreds of IFN-stimulated genes (ISGs) [10] [11] [12] , several of which often contribute to the overall effect of IFN against a given virus. From the above observations, we conclude that after intranasal infection by VSV, Ifit2 protects mice from neuropathogenesis by suppressing replication or spread of the virus in brain neurons. In the complete absence of type I IFN action in the IFNAR 2/2 mice, intranasally infected VSV replicated vigorously not only in brains, but also in livers and lungs ( Figure 7A-C) . cache = ./cache/cord-000660-tsvzg0ax.txt txt = ./txt/cord-000660-tsvzg0ax.txt === reduce.pl bib === id = cord-001985-iwfidoer author = Urayama, Syun-ichi title = FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date = 2016-02-13 pages = extension = .txt mime = text/plain words = 5007 sentences = 281 flesch = 50 summary = This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. We herein established a novel strategy to obtain full-length RNA virus sequences with extremely high efficiency by applying a short dsRNA full-length cloning method (8) for physically fragmented dsRNAs. The improved method, named FLDS (fragmented and loop primer ligated dsRNA sequencing), was applied to a diatom colony in a tide pool and revealed previously unidentified RNA viruses. These results indicated that FLDS effectively enriched dsRNA reads, thereby allowing the retrieval of complete genome sequences including terminal regions without the requirement for the additional rapid amplification of cDNA ends (RACE). A phylogenetic analysis of RdRp in DCASSRV-2 suggested that the RNA virus was classified into the genus Mitovirus, which has a non-segmented ssRNA genome, infects the mitochondria of fungi, and lacks viral particles (Fig. S4E) . cache = ./cache/cord-001985-iwfidoer.txt txt = ./txt/cord-001985-iwfidoer.txt === reduce.pl bib === id = cord-000532-e18licyc author = Tholstrup, Jesper title = mRNA pseudoknot structures can act as ribosomal roadblocks date = 2011-09-08 pages = extension = .txt mime = text/plain words = 5809 sentences = 270 flesch = 57 summary = The results shown in Figure 2 revealed that a 1D SDS-PAGE assay could not firmly identify polypeptides originating from a À1 frameshifted ribosome stalled in the pseudoknot from the non-frameshifted product in a 'Downstream Stop' construct. In order to quantify the amount of À1 frameshifted ribosomes stalled inside the pseudoknot, we performed a 2D SDS-PAGE separation of the radioactively labelled proteins originating from the 'Upstream Stop' construct (Supplementary Figures S4 and S5) , which is the type of construct most commonly used throughout literature. In the 'Upstream Stop' construct the non-frameshifting ribosomes will translate gene10 and terminate at a UAA stop codon in the spacer sequence and produce a 28 kDa polypeptide. In the following subsections 'Identification of transcripts from the T7gene10-PK-lacZ gene fusions', 'Messenger RNA stability' and 'Coupling between translation and transcription is required for full-length transcripts', we will show that the observed proteins did indeed originate from stalled ribosomes and that they were not caused by other effects. cache = ./cache/cord-000532-e18licyc.txt txt = ./txt/cord-000532-e18licyc.txt === reduce.pl bib === id = cord-001397-nrq4ncdf author = Mlera, Luwanika title = The role of viral persistence in flavivirus biology date = 2014-05-12 pages = extension = .txt mime = text/plain words = 15593 sentences = 812 flesch = 46 summary = Avenues for additional studies include determining if the multifunctional flavivirus protein NS5 has a role in viral persistence, the development of relevant animal models of viral persistence as well as investigating the host responses that allow vector borne flavivirus replication without detrimental effects on infected cells. The SL1 structure is essential for viral replication and acts as a promoter which is targeted initially by NS5 and then delivered to the 3 0 end via cyclization (Filomatori et al., 2006; Zhang et al., 2008; Lodeiro et al., 2009) Although there is low nucleotide conservation between flaviviruses and different CS homology (Hahn et al., 1987) , the 5 0 UTRs of TBFVs share the same genomic organization as the MBFVs (Kofler et al., 2006) Structural proteins Capsid (C) 11 kDa, 114 aa Cytosol/nucleus The capsid protein is a dimeric alpha-helical (Jones et al., 2003) protein and assembles into an icosahedral structure, measuring 30 nm in diameter, which initiates encapsidation of the associated genomic RNA in virus-induced membrane invaginations of the ER (Welsch et al., 2009 ). cache = ./cache/cord-001397-nrq4ncdf.txt txt = ./txt/cord-001397-nrq4ncdf.txt === reduce.pl bib === id = cord-000128-t74b5j2j author = Laufer, S.D title = Peptide-Mediated Cellular Delivery of Oligonucleotide-Based Therapeutics In Vitro: Quantitative Evaluation of Overall Efficacy Employing Easy to Handle Reporter Systems date = 2008-12-17 pages = extension = .txt mime = text/plain words = 11947 sentences = 681 flesch = 41 summary = In this review, we will concentrate on peptide-mediated delivery of siRNAs and steric block oligonucleotides and discuss different methods for quantitative assessment of the amount of cargo taken up and how to correlate those numbers with biological effects by applying easy to handle reporter systems. The focus of this article is recent progress in the field of peptide-mediated cellular delivery of siRNA and steric block oligonucleotides in cell tissue culture as a starting point for further developments illustrated by own experimental data. In contrast to many noncovalent CPP-mediated siRNA delivery approaches, efficient splice correction was only achieved with conjugates of peptide and steric block oligonucleotide. As outlined above, our quantitative studies along with microscopic analyses of siRNAs and steric block oligonucleotides using either a peptide or a commercially availably cationic lipid as carrier clearly show that less than 0.1% -5% of molecules taken up are involved in a biological response, i.e. RNAimediated down regulation or splice correction-mediated up regulation of reporter gene activity. cache = ./cache/cord-000128-t74b5j2j.txt txt = ./txt/cord-000128-t74b5j2j.txt === reduce.pl bib === id = cord-001090-qg2r691d author = Twin, Jimmy title = The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis date = 2013-09-27 pages = extension = .txt mime = text/plain words = 3944 sentences = 201 flesch = 44 summary = BACKGROUND: The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex. An amplicon-based metagenomic library was generated from the extracted DNA using the universal bacterial PCR primers 27F and 338R that target the V1-V2 hypervariable regions of the 16S rRNA gene as previously described [15] . Comparison of cDNA to DNA from Nugent 10 patient All of the predominant bacteria with .1% total abundance identified in the cDNA library were also detected using the 16S rRNA gene amplicon-based approach on extracted DNA. cache = ./cache/cord-001090-qg2r691d.txt txt = ./txt/cord-001090-qg2r691d.txt === reduce.pl bib === id = cord-000895-z5rdf0mi author = Belalov, Ilya S. title = Causes and Implications of Codon Usage Bias in RNA Viruses date = 2013-02-25 pages = extension = .txt mime = text/plain words = 5449 sentences = 272 flesch = 45 summary = A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. A general rationale for analyzing impact of (di)nucleotide bias on ENC is randomizing or shuffling synonymous codons in the original genome sequence whilst preserving the factor under study [37] . Unfortunately, common statistical tests were poorly applicable to this approach, because all factors that affect codon preference (e.g. structural RNA elements) could not be accounted for, and therefore even a negligible difference in ENC between the original and generated sequences (e.g. 0.2 SD) passed a formal significance test upon increasing the number of replicates. Overall, dN 23 and dN 231 shuffling produced ENC values that differed from the original sequence by less than one in 25 of 29 viruses, indicating that we explored almost all types of pressure that affect overall codon usage. cache = ./cache/cord-000895-z5rdf0mi.txt txt = ./txt/cord-000895-z5rdf0mi.txt === reduce.pl bib === id = cord-002015-s3tdllby author = Burton, Aaron S. title = The elusive quest for RNA knots date = 2016-02-01 pages = extension = .txt mime = text/plain words = 3536 sentences = 187 flesch = 53 summary = 2, 3 It is therefore a remarkable fact that the statistical incidence of topological entanglement in biomolecules such as proteins and DNA filaments, which are both long and compact, is substantially smaller than expected for general models of equilibrated polymers with equivalent length and packing conditions. It is accordingly plausible, as remarked by Levinthal in more general contexts, 7,8 that protein sequences have evolved to encode not only the thermodynamically-stable native fold, but also the sequence of steps leading to the native structure formation so to minimize the incidence of misfolded states, including knotted ones which would be very challenging to backtrack. It is possible that the sequence of naturally-occurring RNAs, some of which need to be efficiently translocated through biological pores, have evolved to harness folding kinetics and thermodynamics so as to minimize the incidence of various forms of selfentanglement, including knots, in their native structures. cache = ./cache/cord-002015-s3tdllby.txt txt = ./txt/cord-002015-s3tdllby.txt === reduce.pl bib === id = cord-002376-970934vm author = Mikel, Pavel title = Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date = 2016-12-01 pages = extension = .txt mime = text/plain words = 6581 sentences = 311 flesch = 52 summary = The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses. cache = ./cache/cord-002376-970934vm.txt txt = ./txt/cord-002376-970934vm.txt === reduce.pl bib === id = cord-001257-t21l6i3f author = Kovalev, Nikolay title = The Expanding Functions of Cellular Helicases: The Tombusvirus RNA Replication Enhancer Co-opts the Plant eIF4AIII-Like AtRH2 and the DDX5-Like AtRH5 DEAD-Box RNA Helicases to Promote Viral Asymmetric RNA Replication date = 2014-04-17 pages = extension = .txt mime = text/plain words = 10621 sentences = 624 flesch = 58 summary = Novel pro-viral function of AtRH2, AtRH5 and the yeast Dbp3p and Fal1p is to bind to the viral replication enhancer present in the tombusvirus minus-strand RNA To test if AtRH2, AtRH5 and the yeast Dbp3p and Fal1p play a comparable role with the previously analyzed yeast Ded1p (human DDX3-like) and Dbp2p (human p68-like) and the ortologous AtRH20 DEAD-box helicases [30, 49] , first we performed in vitro RNA binding experiments with affinity-purified recombinant helicase proteins. The replication process leads to the production of abundant (+)RNA progeny, while the (2)RNA templates are likely sequestered in dsRNA forms within the VRCs. The presented in vitro data based on the solubilized/purified tombusvirus replicase and the CFE assay containing the membrane-bound VRC indicate that the eIF4AIIIlike RNA helicases can mainly stimulate TBSV (+)-strand synthesis, while their effects on (2)RNA synthesis have not been observed (not shown). cache = ./cache/cord-001257-t21l6i3f.txt txt = ./txt/cord-001257-t21l6i3f.txt === reduce.pl bib === id = cord-002423-1u44tdrj author = Geoghegan, Jemma L. title = Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date = 2017-02-08 pages = extension = .txt mime = text/plain words = 6186 sentences = 267 flesch = 44 summary = While this method does not explicitly model host-switching events, it does provide a simple means to compare multiple topologies of virus-host pairs, and accounts for differences in sample size and the fact that several viruses from a specific family can infect a single host species. Across the data set as a whole we found that all virus families displayed relatively large tree topological distances with nPH85 values of !0.6, suggesting that cross-species transmission is widespread, at least at the family-level (Fig 2; S3 Table) . As with the analysis of topological distances, this revealed that cross-species transmission was the most common evolutionary event in all virus families studied here, with co-divergence consistently less frequent (with the possible exception of the Hepadnaviridae-see below), and lineage duplication and extinction playing a much more minor role. To investigate the comparative prevalence of cross-species transmission among viruses we measured the congruence between virus and host phylogenetic trees using a normalized tree topological distance-based approach (nPH85, [14] ). cache = ./cache/cord-002423-1u44tdrj.txt txt = ./txt/cord-002423-1u44tdrj.txt === reduce.pl bib === id = cord-000578-jhetyd9t author = Kovalev, Nikolay title = A Co-Opted DEAD-Box RNA Helicase Enhances Tombusvirus Plus-Strand Synthesis date = 2012-02-16 pages = extension = .txt mime = text/plain words = 8793 sentences = 509 flesch = 59 summary = In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV). In this paper, the authors show that the Ded1p DEAD-box helicase, which is an essential translation factor in yeast, is recruited by Tomato bushy stunt virus (TBSV) into its replicase complex. Interestingly, addition of purified Ded1p to the tombusvirus replicase assay containing the short RNA/DNA duplex ( Figure 7A Non-overlapping functions of Ded1p and GAPDH in promoting initiation by the tombusvirus replicase GAPDH (Tdh2p in yeast) RNA binding protein is also a host factor stimulating (+)RNA synthesis by the tombusvirus replicase [25, 50] . To test if Ded1p and GAPDH could play a complementary role during (+)RNA synthesis, we added the purified recombinant Ded1p and Tdh2p to the in vitro tombusvirus replicase assay based on the purified preparation ( Figure 8A ). cache = ./cache/cord-000578-jhetyd9t.txt txt = ./txt/cord-000578-jhetyd9t.txt === reduce.pl bib === id = cord-000556-uu1oz2ei author = Kumar, Ranjit title = RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336” date = 2012-01-20 pages = extension = .txt mime = text/plain words = 4407 sentences = 235 flesch = 46 summary = Whole genome transcriptome analysis is a complementary method to identify "novel" genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. Therefore, genome structural annotation or the identification and demarcation of boundaries of functional elements in a genome (e.g., genes, non-coding RNAs, proteins, and regulatory elements) are critical elements in infectious disease systems biology. Whole genome transcriptome studies (such as whole genome tiling arrays [13, 14, 15] and high throughput sequencing [16, 17] ) are complementary experimental approaches for bacterial genome annotation and can identify ''novel'' genes, gene boundaries, regulatory regions, intergenic regions, and operon structures. We compared the RNA-Seq based transcriptome map with the available genome annotation to identify expressed, novel, and intergenic regions in the genome. The single nucleotide resolution map helped uncover the structure and complexity of this pathogen's transcriptome and led to the identification of novel, small RNAs and protein coding genes as well as gene co-expression. cache = ./cache/cord-000556-uu1oz2ei.txt txt = ./txt/cord-000556-uu1oz2ei.txt === reduce.pl bib === id = cord-002651-9r384oxd author = Pauly, Matthew D. title = Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity date = 2017-08-16 pages = extension = .txt mime = text/plain words = 8111 sentences = 429 flesch = 50 summary = Studies of mutagen-resistant viruses have identified determinants of replicative fidelity and the importance of mutation rate to viral population dynamics. Consistent with the importance of epistatic interactions in the influenza virus polymerase, our data suggest that nucleoside analog resistance and replication fidelity are strain dependent. To this end, we identified variants within the polymerase complex of influenza virus that are able to tolerate drug-mediated increases in viral mutation rates. In most cases, mutagen-resistant variants encode polymerases that exhibit increased replication fidelity, and characterization of these mutants has elucidated the molecular mechanisms governing mutation rate. We tested each of the variant polymerases for reduced nucleoside sensitivity by comparing titers after replication of the corresponding virus populations in mock-or drug-treated cell cultures 24 h postinfection (Fig. 1A) . We used a serial passage competition assay (15) to measure the replicative fitness of each mutant virus relative to the WT PR8 and also performed growth curves to quantify RNA genome production. cache = ./cache/cord-002651-9r384oxd.txt txt = ./txt/cord-002651-9r384oxd.txt === reduce.pl bib === id = cord-001228-4eh22ek7 author = Ofori, Leslie O. title = High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity date = 2014-01-05 pages = extension = .txt mime = text/plain words = 6288 sentences = 339 flesch = 53 summary = 32 Thus, as far as we are aware, there are no reported examples of synthetic molecules able to alter HIV-1 frameshifting and interfere with viral infectivity via selective, high-affinity binding to the FSS RNA. Building on our laboratory's longstanding interest in understanding the factors that drive affinity and sequence selectivity in small molecule recognition of RNA, 33 we previously reported the use of an 11,325-member resin-bound dynamic combinatorial library 34 (designed based on the structure of DNA-binding, bisintercalating peptide antibiotics) to identify a compound (1) able to bind the HIV-1 FSS upper stem-loop with moderate affinity (K D = 4.1 ± 2.4 μM immobilized on an surface plasmon resonance (SPR) chip via one of its amine groups; K D = 350 ± 110 nM in solution as measured by fluorescence 35 ) and good selectivity. cache = ./cache/cord-001228-4eh22ek7.txt txt = ./txt/cord-001228-4eh22ek7.txt === reduce.pl bib === id = cord-000125-uvf5qzfd author = Kenworthy, Rachael title = Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation date = 2009-09-03 pages = extension = .txt mime = text/plain words = 6633 sentences = 336 flesch = 54 summary = The interaction between a PAMP and a PRR triggers activation of the interferon (IFN) pathway in mammalian cells, which significantly changes the gene-expression profile in the cells and contributes to the well-documented off-target effect of RNAi. IFN induction is especially problematic in antiviral studies employing RNAi, where the antiviral effect of IFN must be distinguished from that of RNAi. Typical IFN-inducing structure patterns include dsRNA of certain length, single-stranded RNA (ssRNA) containing 5 0 -triphosphates (5 0 -ppp), the dsRNA analogue polyinosinic-polycytidylic acid (poly I:C), and certain dsDNA molecules. Mammalian expression plasmids encoding each of these proteins, as well as the dominant negative (DN) mutants of RIG-I and MDA5, were transfected into 293FT cells with shRNAs and an IFN-b promoter reporter construct. cache = ./cache/cord-000125-uvf5qzfd.txt txt = ./txt/cord-000125-uvf5qzfd.txt === reduce.pl bib === id = cord-002320-m99amd4y author = Mathur, Kalika title = Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity date = 2016-11-30 pages = extension = .txt mime = text/plain words = 5671 sentences = 338 flesch = 56 summary = Systematic analysis of all CHIKV proteins using a Sf21 RNAi sensor cell line based assay revealed that non-structural proteins nsP2 and nsP3 exhibited RNAi suppressor activity. Using cell lysate of the transfected cell expressing nsP2 and nsP3, we evaluated their ability to bind double stranded RNA by using [γ 32P] labeled shRNA of GFP and running the bound complex in a 6% polyacrylamide gel (Fig. 3e) . Having confirmed that both nsP2 and nsP3 exhibit RNAi suppressor activities, efforts were taken to characterise the proteins better and to identify those specific domains that were and NS4B (dengue virus) were taken as positive controls and empty vector was used as negative control. Taken together, the current study has identified CHIKV proteins nsP2 and nsP3 to exhibit RNAi suppressor activity in the in-vitro system that was further demonstrated in its natural hosts, namely, an Aedes and mammalian cell line. cache = ./cache/cord-002320-m99amd4y.txt txt = ./txt/cord-002320-m99amd4y.txt === reduce.pl bib === id = cord-000063-tex6bgab author = Sui, Hong-Yan title = Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication date = 2009-05-22 pages = extension = .txt mime = text/plain words = 3501 sentences = 189 flesch = 50 summary = Using this vector that also expresses enhanced green fluorescence protein (EGFP) as surrogate marker, stable shRNA-expressing cell lines were successfully established and the inhibition efficiencies of rationally designed siRNAs targeting to conserved regions of influenza A virus genome were assessed. It was further demonstrated that no siRNA-resistant viral mutation appeared in siM2 targeting sequence even after the virus was cultured in the shRNA expressing stable cell line for 40 passages. A recent report by Zhou et al [30] also showed that several siRNAs targeting NP and M genes exhibited effective inhibition against influenza A virus replication in cultured MDCK cells and in animal models. Taken together, all the findings about effective RNAi target, lentiviral vector delivery and the establishment of stable shRNA expressing cell lines in our study provide rational information for the development of siRNAs as prophylaxis and therapy for influenza virus infection in humans. cache = ./cache/cord-000063-tex6bgab.txt txt = ./txt/cord-000063-tex6bgab.txt === reduce.pl bib === id = cord-000238-om92cx5q author = Ogbunugafor, C. Brandon title = On the possible role of robustness in the evolution of infectious diseases date = 2010-06-30 pages = extension = .txt mime = text/plain words = 6717 sentences = 347 flesch = 39 summary = We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections. [14] [15] [16] In reviewing these results, we hope to highlight the importance of empirical work in RNA viruses for testing theory pertaining to robustness, as well as for better understanding the evolutionary biology and evolvability of infectious organisms in general. 1 However, theory and artificial-life data 9 support the idea that genetic robustness should be strongly favored when populations experience elevated mutation rates, suggesting that RNA viruses would be fruitful systems to explore how genetic robustness evolves. [33] [34] [35] Regardless, preliminary experiments showed that UVC exposure for periods up to 30 min greatly increased mortality in wild type phage 6 ͑Fig. 2͒, indicating that this environmental effect should produce strong selection for UVC resistance in populations of the virus. cache = ./cache/cord-000238-om92cx5q.txt txt = ./txt/cord-000238-om92cx5q.txt === reduce.pl bib === id = cord-001542-f089bs8r author = Lai, Kang Yiu title = Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date = 2014-11-28 pages = extension = .txt mime = text/plain words = 11274 sentences = 604 flesch = 42 summary = These may include monoclonal antibody (mAbs)-based therapies (e.g. ZMapp), anti-sense phosphorodiamidate morpholino oligomers (PMO AVI-6002), lipid nanoparticle small interfering RNA (LNP-siRNA: TKM-Ebola), and an EBOV glycoprotein-based vaccine using live-attenuated recombinant vesicular stomatitis virus (rVSV-EBOGP) or a chimpanzee adenovirus (rChAd-EBOGP)-based vector. The GP2 of the EBOV is able to counter the interferon (IFN)-inducible antiviral protein tetherin which restricts the VP40-dependent budding of the progeny viral particles from infected cells [16] [17] [18] . Currently available therapeutic agents that are effective in targeting the EBOV infection in cell or animal studies may include convalescent plasma, favipiravir, chloroquine, amiodarone, dronedarone, verapamil, clomiphene, toremifene, IFN-β, Na + /K + exchangers, Na + /K + -ATPase pump inhibitors, and antioxidants. The anti-EBOV activity of clomiphene and toremifene is dependent not on its estrogen receptor antagonistic action but upon the ability of both drugs to induce a Niemann-Pick C-like phenotype to inhibit viral entry at late endosome. cache = ./cache/cord-001542-f089bs8r.txt txt = ./txt/cord-001542-f089bs8r.txt === reduce.pl bib === id = cord-000018-amvlm09p author = Pauli, Eva-K. title = Influenza A Virus Inhibits Type I IFN Signaling via NF-κB-Dependent Induction of SOCS-3 Expression date = 2008-11-07 pages = extension = .txt mime = text/plain words = 9011 sentences = 515 flesch = 53 summary = Our study was based on the observation that in cells that were infected with influenza A virus and subsequently stimulated with IFNα/β, phosphorylation of the signal transducer and activator of transcription protein 1 (STAT1) was strongly reduced. This direct viral induction of SOCS-3 mRNA and protein expression appears to be relevant for suppression of the antiviral response since in SOCS-3 deficient cells a sustained phosphorylation of STAT1 correlated with elevated expression of type I IFN-dependent genes. These results are consistent with data gained from previous experiments in Vero cells ( Figure 1E ) and indicate that neither induction of SOCS-3 mRNA nor inhibition of STAT phosphorylation is dependent on virus-induced type I IFN expression. To answer the question whether enhanced STAT phosphorylation in SOCS-3 deficient cells would also lead to enhanced expression of ISGs, total RNA was isolated at different time points p.i. from infected wild type and knock out cells and monitored for induction of SP110, IRF-1 and OAS1 ( Figure 7E, 7F and 7G ). cache = ./cache/cord-000018-amvlm09p.txt txt = ./txt/cord-000018-amvlm09p.txt === reduce.pl bib === id = cord-001109-xs7df6a7 author = Tapia, Karla title = Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity date = 2013-10-31 pages = extension = .txt mime = text/plain words = 7169 sentences = 360 flesch = 50 summary = We demonstrate that these defective viral genomes (DVGs) are generated naturally during respiratory infections in vivo even in mice lacking the type I IFN receptor, and their appearance coincides with the production of cytokines during infections with Sendai virus (SeV) or influenza virus. To further investigate the cellular mechanisms responsible for the efficient activation of the antiviral response by SeV DVGs, we evaluated the phosphorylation of transcription factors that are critical for the expression of type I IFNs in cells infected with equivalent amounts of infectious particles of a SeV strain Cantell stock containing high levels of copy-back DVGs (SeV Cantell HD) or with SeV Cantell depleted of DVGs (SeV Cantell LD). Based on the potent ability of SeV stocks containing a high content of copy-back DVGs to induce the host response to infection in vitro [23, 24, 25, 28] (Fig. 1 ) and on our prior reports of strong host responses to DVGs regardless of the presence of functional virus-encoded antagonists [23, 24] , we hypothesized that DVGs that arise in situ during viral infections provide essential stimuli to initiate an antiviral immune response. cache = ./cache/cord-001109-xs7df6a7.txt txt = ./txt/cord-001109-xs7df6a7.txt === reduce.pl bib === id = cord-000804-0hlj6r10 author = Brauburger, Kristina title = Forty-Five Years of Marburg Virus Research date = 2012-10-01 pages = extension = .txt mime = text/plain words = 14922 sentences = 730 flesch = 45 summary = While the ectodomain, which is mainly formed by GP 1 , mediates binding to entry factors and receptors [87] [88] [89] [90] [91] [92] [93] [94] [95] , the transmembrane subunit GP 2 contains the fusion peptide and is presumed to mediate fusion of the viral and the cellular membrane based on similarity to EBOV GP 2 both at the amino acid and structural level [96, 97] . The IFN-inducible antiviral protein tetherin was shown to block the release of VP40-induced virus-like MARV and EBOV particles, suggesting that tetherin might act as a restriction factor for filovirus release [102, 103] . After the nucleocapsid is released into the cytoplasm of the infected cell, transcription and replication of the viral RNA genome takes place (Figure 7 ). Virus-like particles exhibit potential as a pan-filovirus vaccine for both Ebola and Marburg viral infections cache = ./cache/cord-000804-0hlj6r10.txt txt = ./txt/cord-000804-0hlj6r10.txt === reduce.pl bib === id = cord-002746-qn34eyul author = Antzin-Anduetza, Irati title = Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication date = 2017-11-09 pages = extension = .txt mime = text/plain words = 9118 sentences = 491 flesch = 56 summary = Codon modification of nucleotides (nt) 22-261 or 22-378 in gag inhibited viral replication by decreasing genomic RNA (gRNA) abundance, gRNA stability, Gag expression, virion production and infectivity. To determine if they are necessary for inhibition of HIV-1 replication, codons introducing CpG dinucleotides were mutated back to the wild type codon, which restored efficient Gag expression and infectious virion production. Gag expression and virion production were similar for wild type HIV-1 and HIV-1 ∆22-261 (Fig. 4c) , indicating that RNA or protein sequences in this region are not necessary for these steps of the viral life cycle. When only 11 CpG dinucleotides are inserted into gag in the context of the codon modified sequence (HIV-1 CM22-165), there is a large decrease in infectivity without a substantial loss of gRNA abundance, Gag expression or virion production (Figs. [100] reported that introducing CpG dinucleotides into env inhibited HIV-1 replication by decreasing the abundance of cytoplasmic gRNA, Gag expression, Env expression and infectious virus production. cache = ./cache/cord-002746-qn34eyul.txt txt = ./txt/cord-002746-qn34eyul.txt === reduce.pl bib === id = cord-001748-7e8px4vx author = Nobach, Daniel title = Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date = 2015-08-27 pages = extension = .txt mime = text/plain words = 4873 sentences = 249 flesch = 47 summary = The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). In animals caught in 2013 (group 1: female #2, male #5, female #6), after an adaption phase of one month, samples of saliva, lacrimal fluid, skin surface, urine and excrements from the BoDV-1-infected shrews were taken weekly over a period of 4 weeks as necessary veterinary care. The five other shrews did not exhibit any evidence for BoDV-1-infection, neither infectious virus nor viral RNA was detected at any time point investigated. Current data from living shrews provide reliable evidence that natural BoDV-1-infection in these animals is indeed clinically inconspicuous over a long time period as already previously assumed [15, 18] despite persistent infection with shedding of infectious virus via various sites. Distribution of Borna Disease Virus Antigen and RNA in Tissues of naturally infected Bicolored White-Toothed Shrews, Crocidura leucodon, supporting their role as Reservoir Host Species cache = ./cache/cord-001748-7e8px4vx.txt txt = ./txt/cord-001748-7e8px4vx.txt === reduce.pl bib === id = cord-000830-jiy4cp4n author = Cobo, Fernando title = Application of Molecular Diagnostic Techniques for Viral Testing date = 2012-11-30 pages = extension = .txt mime = text/plain words = 7969 sentences = 385 flesch = 39 summary = The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. The use of amplification techniques such as polymerase chain reaction (PCR), real-time PCR or nucleic acid sequence-based amplification (NASBA) [3] for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range [4, 5] . NASBA assays could identify active infection by detecting viral messenger RNA (mRNA) but the most widely used tests in clinical virus diagnosis are quantitative real-time PCR techniques [8] . Some real-time PCR assays such as LightCycler parvovirus B19 quantitative assay (Roche Diagnostics, Indianapolis, IN) and ABI TaqMan (Applied Biosystems) have been developed for detecting B19 nucleic acids in association with infection during pregnancy or assessing the prevalence of the virus DNA in blood products [62, 63] . cache = ./cache/cord-000830-jiy4cp4n.txt txt = ./txt/cord-000830-jiy4cp4n.txt === reduce.pl bib === id = cord-002238-fyztb8d9 author = Young, D. F. title = Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family date = 2016-09-29 pages = extension = .txt mime = text/plain words = 7727 sentences = 344 flesch = 51 summary = We have previously shown that IFIT1 is primarily responsible for the antiviral action of interferon (IFN) alpha/beta against parainfluenza virus type 5 (PIV5), selectively inhibiting the translation of PIV5 mRNAs. Here we report that while PIV2, PIV5, and mumps virus (MuV) are sensitive to IFIT1, nonrubulavirus members of the paramyxoviridae such as PIV3, Sendai virus (SeV), and canine distemper virus (CDV) are resistant. Despite their limited genetic information, the majority of paramyxoviruses encode small multifunctional accessory proteins that function to aid virus multiplication and block cellular antiviral defense mechanisms; typically, these proteins can block both the production of, and the signaling response to, interferons (IFNs) (for reviews, see references 3, 4, 5, 6, and 7). These results therefore show that MuV Enders is sensitive to IFIT1 but SeV and CDV are not, the weak inhibition of SeV and CDV protein synthesis observed in A549 and A549/shIFIT1 cells pretreated with IFN presumably being due to the action of other ISGs induced by IFN. cache = ./cache/cord-002238-fyztb8d9.txt txt = ./txt/cord-002238-fyztb8d9.txt === reduce.pl bib === id = cord-002413-795wuqz5 author = Balinsky, Corey A. title = IRAV (FLJ11286), an Interferon-Stimulated Gene with Antiviral Activity against Dengue Virus, Interacts with MOV10 date = 2017-02-14 pages = extension = .txt mime = text/plain words = 5485 sentences = 278 flesch = 47 summary = title: IRAV (FLJ11286), an Interferon-Stimulated Gene with Antiviral Activity against Dengue Virus, Interacts with MOV10 IRAV is an RNA binding protein and localizes to cytoplasmic processing bodies (P bodies) in uninfected cells, where it interacts with the MOV10 RISC complex RNA helicase, suggesting a role for IRAV in the processing of viral RNA. FLJ11286, which we refer to here as IRAV (interferon-regulated antiviral gene) (also annotated as C19orf66, UPF0515, or RyDEN), encodes a protein 291 amino acids (aa) in length with a calculated molecular mass of 33.1 kDa. Analysis of published microarray data suggests that IRAV (FLJ11286) is upregulated in response to type I and type II IFNs (6, 20, (24) (25) (26) . IRAV also associates with the host RNA binding proteins UPF1 and HuR (ELAV1) and interacts with MOV10 (a RISC complex RNA helicase), suggesting a role for IRAV in processing or stability of RNA. cache = ./cache/cord-002413-795wuqz5.txt txt = ./txt/cord-002413-795wuqz5.txt === reduce.pl bib === id = cord-001655-uqw74ra0 author = Stenglein, Mark D. title = Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date = 2015-05-20 pages = extension = .txt mime = text/plain words = 8100 sentences = 479 flesch = 48 summary = The sets of viral genotypes ranged from that which would be expected for a straightforward co-infection by 2 virus strains in snake #45, to more complex combinations such as that in snake #33, which contained the sequences of 1 S and 10 distinct L segments. We applied homogenates from samples to cultures of boa constrictor-derived JK cells and monitored levels of virus RNA by qRT-PCR using genotype-discriminating primers. Thus, sequences of multiple viral genotypes Recombinant genome segments with unusual organizations. Virus populations replicate as stable ensembles in culture: (A) Liver homogenate from snake #38 was applied to cultures of JK cells and replication was monitored by measuring supernatant viral RNA levels using qRT-PCR and genotype-specific primers. Although we detected many instances of snake tissues containing multiple viral genotypes, our results do not prove that individual cells in these animals were multiply infected. cache = ./cache/cord-001655-uqw74ra0.txt txt = ./txt/cord-001655-uqw74ra0.txt === reduce.pl bib === id = cord-000822-iuglkdcp author = Sperschneider, Jana title = Predicting pseudoknotted structures across two RNA sequences date = 2012-12-01 pages = extension = .txt mime = text/plain words = 5494 sentences = 386 flesch = 61 summary = One strong point of the DotKnot method for single sequence pseudoknot prediction (Sperschneider and Datta, 2010; Sperschneider et al., 2011) is that the set of possible H-type pseudoknot candidates (and secondary structure elements) is explicitly computed and thus readily available for further investigation. (3) Use significant pairs to calculate the set of conserved structure elements and pseudoknots for the two sequences that maximizes a combined free energy and similarity score. The key point of the DotKnot-PW approach is how to score the similarity of stems, secondary structure elements and H-type pseudoknot candidates derived from sequences Seq x and Seq y . The optimal structure element alignment, which preserves the interval ordering includes structure elements p 1 , p 4 , p 7 in the first sequence and p 1 , p 4 , p 6 in the second sequence pairwise prediction with highest combined free energy and similarity score is taken, DotKnot-PW has an improved average MCC of 0.81. cache = ./cache/cord-000822-iuglkdcp.txt txt = ./txt/cord-000822-iuglkdcp.txt === reduce.pl bib === id = cord-000881-s90geszi author = Lang, Dorothy M. title = Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases date = 2012-12-25 pages = extension = .txt mime = text/plain words = 9703 sentences = 536 flesch = 60 summary = In contrast to the relatively short lengths of previously described motifs, we found that most homomorphs are long, and each provides a structural connection between the template tunnel or NTP entry tunnel and the exterior of the protein. The structurally aligned sequences that comprised homomorph of Motif F (hmF) for RdRps and HIV are summarized in Figure 3A . Using T7 DNAP as a query (lowest segment of the figure) , only a small portion of the C-terminal edge of Motif D and a few species have similar structures. In the RdRps, the combined regions of structural homology represent $75% of the sequence from the start of homomorph of Motif G (hmG) through the end of hmE in each species ($375 residues). The tertiary position of each of the homomorphs includes at least one residue (and sometimes more) in contact with the exterior surface of the protein and one or more highly conserved functional residues located within or at the wall of the template tunnel. cache = ./cache/cord-000881-s90geszi.txt txt = ./txt/cord-000881-s90geszi.txt === reduce.pl bib === id = cord-000372-wzwpyvll author = Castelló, Alfredo title = The Multifaceted Poliovirus 2A Protease: Regulation of Gene Expression by Picornavirus Proteases date = 2011-04-14 pages = extension = .txt mime = text/plain words = 16333 sentences = 781 flesch = 45 summary = These findings are in agreement with the fact that host mRNA transcription takes place in 2A pro -expressing cells when both translation and RNA nuclear export are inhibited, upon cleavage of eIF4G and Nups [17] . In this regard, PV 2A pro has been very useful for examining the requirements for eIF4G to translate different cellular or viral mRNAs. In addition to this, in this paper, we have highlighted the role of PV 2A pro not only in the processing of the poliovirus polyprotein but also in the interaction with the host-cell. In particular, PV 2A pro cleaves cell proteins involved in transcription, pre-mRNA splicing, nucleus/cytoplasm transport and translation, in order to hijack those host functions and to concentrate the cellular resources on the production of the viral progeny. cache = ./cache/cord-000372-wzwpyvll.txt txt = ./txt/cord-000372-wzwpyvll.txt === reduce.pl bib === id = cord-000937-8vk89i4h author = Law, John title = Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date = 2013-04-17 pages = extension = .txt mime = text/plain words = 6644 sentences = 332 flesch = 50 summary = RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Seven RNA libraries (aihP01, hbvP02, hcvP02, hcvP03, hcvP05, nshP01, norP01) and seven DNA libraries (aihP01D, hbvP02D, hcvP02D, hcvP03D, hcvP05D, nshP01D, norP01D) were constructed from patients with autoimmune hepatitis (AIH), hepatitis B virus (HBV) chronic infection, hepatitis C virus (HCV) chronic infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR). Plasma samples were obtained from patients with autoimmune hepatitis (AIH), chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR); each RNA library was named by diagnosis (e.g. aihP01) and a suffix 'D' was added for each DNA library (e.g. aihP01D). To a lesser extent (about one read per million), we also detected sequences resembling RNA viruses in our DNA libraries (Supplemental Tables S15-S28 ). Assembly of viral sequences was also possible for all viruses shown in Figure 2 as the most abundant virus in each library (data not shown). cache = ./cache/cord-000937-8vk89i4h.txt txt = ./txt/cord-000937-8vk89i4h.txt === reduce.pl bib === id = cord-000293-pc4x5e24 author = Yu, Chien-Hung title = Stimulation of ribosomal frameshifting by antisense LNA date = 2010-08-06 pages = extension = .txt mime = text/plain words = 3901 sentences = 194 flesch = 49 summary = The requirements for À1 ribosomal frameshifting are the presence of a slippery heptanucleotide sequence X XXY YYZ (where X can be A, U, G or C; Y can be A or U; and Z does not equal Y; the spaces indicate the original reading frame) (8) followed by a downstream structural element, such as a pseudoknot, a hairpin or an antisense oligonucleotide duplex [for reviews, see (9) ]. We and others have demonstrated that small RNA oligonucleotides are able to mimic the function of frameshifter pseudoknots or hairpins by redirecting ribosomes into new reading frames (27, 28) . These results demonstrate that LNA modifications indeed enhance the antisense-induced frameshifting efficiency probably due to higher thermodynamic stability and RNA-like structural properties. In addition to RNA oligonucleotides, we demonstrated that LNA/DNA mix-mers are also capable of stimulating efficient À1 ribosomal frameshifting in contrast to DNA oligonucleotides. Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of À1 ribosomal frameshifting cache = ./cache/cord-000293-pc4x5e24.txt txt = ./txt/cord-000293-pc4x5e24.txt === reduce.pl bib === id = cord-002990-7flusgus author = Kitano, Mitsutaka title = Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro date = 2018-04-26 pages = extension = .txt mime = text/plain words = 7080 sentences = 313 flesch = 50 summary = The application of a cell-based fluorescence resonance energy transfer (FRET) assay for protease activity demonstrated that these substitutions were involved in the enhanced resistance to rupintrivir. Furthermore, we validated the effect of these mutations using reverse genetics in murine norovirus (MNV), demonstrating that a recombinant MNV strain with a single I109V substitution in the protease also showed reduced susceptibility to rupintrivir. In the present study, we isolated replicon cells with reduced susceptibility to rupintrivir after several passages in the presence of rupintrivir and identified two amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease. To confirm the previously reported inhibitory effects of rupintrivir on human norovirus replication (10), we generated a human gastric adenocarcinoma cell line, HGT-NV, which stably maintained a Norwalk virus replicon encoding the neomycin resistance gene in place of the major capsid protein. cache = ./cache/cord-002990-7flusgus.txt txt = ./txt/cord-002990-7flusgus.txt === reduce.pl bib === id = cord-002222-rgqwm3vb author = Olarte-Castillo, Ximena A. title = Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date = 2016-09-23 pages = extension = .txt mime = text/plain words = 7544 sentences = 339 flesch = 46 summary = By screening a large number of predominantly fecal samples (n = 631) obtained from five carnivore species in the Serengeti ecosystem, East Africa, sapovirus RNA was detected in the spotted hyena (Crocuta crocuta, family Hyaenidae), African lion (Panthera leo, family Felidae), and bat-eared fox (Otocyon megalotis, family Canidae), but not in golden or silver-backed jackals (Canis aureus and C. Long-term monitoring of sapovirus in a population of individually known spotted hyenas from 2001 to 2012 revealed: i) a relatively high overall infection prevalence (34.8%); ii) the circulation of several genetically diverse variants; iii) large fluctuations in infection prevalence across years, indicative of outbreaks; iv) no significant difference in the likelihood of infection between animals in different age categories. A total of 20 partial RdRp gene sequences (16 from spotted hyenas, 3 from African lions and 1 from bat-eared foxes) were obtained and used for the phylogenetic analysis, together with publically available sequence data from 25 representatives of all sapovirus genogroups, divergent unclassified sapoviruses, and other genera in the Caliciviridae family, including Norovirus and Vesivirus. cache = ./cache/cord-002222-rgqwm3vb.txt txt = ./txt/cord-002222-rgqwm3vb.txt === reduce.pl bib === id = cord-002720-lrkscs71 author = Kurosaki, Yohei title = Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification date = 2017-10-18 pages = extension = .txt mime = text/plain words = 4950 sentences = 251 flesch = 55 summary = title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification The assay detected viral RNA at 14.5 TCID(50)/mL in virus-spiked serum or urine samples within 15 min, although it was slightly less sensitive than reference real time RT-PCR assay. We then evaluated the utility of this assay as a molecular diagnostic test using 90 plasma or serum samples and 99 urine samples collected from 120 suspected cases of arbovirus infection in the states of Paraíba and Pernambuco, Brazil in 2016. Therefore, it is difficult to detect ZIKV in blood samples from patients after the acute phase of infection, even with sensitive molecular diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) 14, 18, 19 . These results suggested that the RT-LAMP assay could be used as a rapid, sensitive diagnostic test for ZIKV, the Tp value (i.e., less than 15 min) can be used as an indicator of the number of RNA copies in each reaction. cache = ./cache/cord-002720-lrkscs71.txt txt = ./txt/cord-002720-lrkscs71.txt === reduce.pl bib === id = cord-000364-ikq38rm1 author = Rasmuson, J. title = Time to revise the paradigm of hantavirus syndromes? Hantavirus pulmonary syndrome caused by European hantavirus date = 2011-01-15 pages = extension = .txt mime = text/plain words = 2839 sentences = 178 flesch = 43 summary = Lung computer tomography (CT) on admission revealed pronounced diffuse bilateral interstitial infiltrates with pulmonary oedema, dependant atelectasis, and moderate pleural effusions (Fig. 1 ) which were later drained (>800 ml). Hantavirus infection was verified with the detection of PUUV RNA in plasma (630,000 copies/ml) on the day of admission, while IgM and IgG were negative. Consecutive plasma samples were analysed for PUUV RNA with declining viral copy numbers until negative 16 days post onset of Fig. 1 Chest CT-scans of two European patients with hantavirus pulmonary syndrome. Concerning the cases of European hantavirus infection in our present report, there was only mild or no renal impairment at the time of admission, whereas the respiratory involvement was early and severe, consistent with acute respiratory distress syndrome (ARDS), fulfilling criteria of HPS according to CDC case definition [19] . cache = ./cache/cord-000364-ikq38rm1.txt txt = ./txt/cord-000364-ikq38rm1.txt === reduce.pl bib === id = cord-002542-f7l4ty2j author = Jaworski, Elizabeth title = Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus date = 2017-05-05 pages = extension = .txt mime = text/plain words = 11789 sentences = 535 flesch = 49 summary = Using a combination of longand short-read Next-Generation Sequencing, we have characterized the formation of DI-RNAs during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms of DI-RNA emergence and evolution. By combining these data, we aimed to determine the correlation of recombination events within single RNA virus genomes, characterize the distribution of defective RNA genomes, and determine the exact make-up of DI-RNAs during serial passaging of FHV in cell culture. This observation indicates the protection of cells from infection and/or CPE when supplied with a large dose of viral particles that contain a large proportion of DI-RNAs. In this manuscript, we sought to provide a thorough and comprehensive analysis of the frequency and identity of recombination events present during the serial passaging of Flock House virus in cell culture in order to elucidate the pathways and mechanism of DI-RNA emergence and evolution. cache = ./cache/cord-002542-f7l4ty2j.txt txt = ./txt/cord-002542-f7l4ty2j.txt === reduce.pl bib === id = cord-000729-iq30z094 author = Marsh, Glenn A. title = Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date = 2012-08-02 pages = extension = .txt mime = text/plain words = 6101 sentences = 277 flesch = 49 summary = The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrinB2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. As part of our on-going field studies on HeV genetic diversity and infection dynamics in the Queensland flying fox populations, urine samples were collected on a regular basis for PCR and virus isolation. CedPV is more closely related to HeV and NiV than henipavirus-like sequences detected in African bats [26, 32] as shown in a phylogenetic tree based on the only sequences available of a 550-nt L gene fragment (Fig. S5) . cache = ./cache/cord-000729-iq30z094.txt txt = ./txt/cord-000729-iq30z094.txt === reduce.pl bib === id = cord-002102-0zbp3uqf author = Rasche, Andrea title = Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015 date = 2016-07-17 pages = extension = .txt mime = text/plain words = 1697 sentences = 106 flesch = 54 summary = title: Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015 A new hepatitis E virus (HEV-7) was recently found in dromedaries and 1 human from the United Arab Emirates. Recently, HEV sequences were reported from 3 dromedaries sampled in the United Arab Emirates (UAE) in 2013 and were classified as a new orthohepevirus A genotype, HEV-7 (2, 3) . To determine the geographic distribution of HEV-7, we conducted a geographically comprehensive study of HEV-7 prevalence in dromedaries by testing 2,438 specimens sampled in 6 countries during the past 3 decades. Serum and fecal samples were collected from dromedary camels in the UAE, Somalia, Sudan, Egypt, Kenya, and Pakistan during 1983-2015 (5-7). Detections of HEV-7 RNA in feces in this and a previous study (2) point at feces or feces-contaminated camel products, such as milk, as putative additional sources of human infection. cache = ./cache/cord-002102-0zbp3uqf.txt txt = ./txt/cord-002102-0zbp3uqf.txt === reduce.pl bib === id = cord-000979-cav9n18w author = Hoppe, Sebastian title = Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date = 2013-05-29 pages = extension = .txt mime = text/plain words = 10056 sentences = 595 flesch = 50 summary = title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. Additionally, the structure and antigenicity of the proteins and epitopes were modelled to analyze the suitability of the identified sequences for future applications like diagnostic tools or vaccine development. For a summary of the predicted characteristics, see S9: Transmembrane and antigenic potential of three potential epitope sites for cj0920c.Further, specificity control assays revealed that these signals do not drop significantly when using antibodies to Salmonella enterica indicative of nonspecific binding to occur, see S10: Specific vs. jejuni and were able to determine the important residue involved in antibody binding as well as modelling the epitope's accessibility within the full-length protein. cache = ./cache/cord-000979-cav9n18w.txt txt = ./txt/cord-000979-cav9n18w.txt === reduce.pl bib === id = cord-003254-yiqdsf9z author = Schlub, Timothy E title = A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date = 2018-08-07 pages = extension = .txt mime = text/plain words = 6313 sentences = 292 flesch = 49 summary = Herein, we present a new statistical method for detecting overlapping genes in different reading frames that relies on only a single nucleotide sequence of a gene or genome. For the synonymous mutation test (C), codons that preserve the original amino acid sequence are randomly generated and the length of ORFs on alternative reading frames subsequently measured (note that codon replacement is not restricted to the example mutations shown in the figure, all of which occur in the third nucleotide positions, and that codon replacement with the original codon is also possible). Accordingly, whole genome sequences were downloaded from 2548 reference linear RNA viruses available on GenBank; this produced a total of 6408 coding regions that were used to estimate the sensitivity and false discovery rate of each test. where C is the empirical cumulative distribution function of the theoretical distribution of lengths calculated by permuting codons in the original coding sequence: that is, C(L) is the Simple Method to Detect Candidate Overlapping Genes . cache = ./cache/cord-003254-yiqdsf9z.txt txt = ./txt/cord-003254-yiqdsf9z.txt === reduce.pl bib === id = cord-000981-6vloa2w3 author = Bálint, Zoltán title = Double-Stranded RNA Attenuates the Barrier Function of Human Pulmonary Artery Endothelial Cells date = 2013-06-03 pages = extension = .txt mime = text/plain words = 6086 sentences = 480 flesch = 56 summary = The effect of natural and synthetic double-stranded RNA (dsRNA) on hPAECs was investigated using trans-endothelial electric resistance, molecule trafficking, calcium (Ca(2+)) homeostasis, gene expression and proliferation studies. The cells were stimulated with 100 mM histamine or 15 mM 2,5-Di-t-butyl-1,4-benzohydroquinone (BHQ: selective SERCA blocker) in the presence and absence of extracellular Ca 2+ , after incubation for 24 h with 25 mg/mL Poly I:C, 25 mg/mL dsRNA, 2.5 mg/mL L-DNA, 2.5 mg/mL total RNA or control solution. Double-stranded RNA (dsRNA) or its synthetic analogue (Poly I:C) significantly decreased the electric resistance and increased the permeability of the confluent human pulmonary artery endothelial (hPAEC) monolayer as shown on Figure 1 . Altogether, these data suggest that synthetic dsRNA treatment alters the function of SERCA, which inhibits cell proliferation by inducing G1 arrest in the hPAECs and contributing to endothelial dysfunction. cache = ./cache/cord-000981-6vloa2w3.txt txt = ./txt/cord-000981-6vloa2w3.txt === reduce.pl bib === id = cord-002006-pwlybr2h author = Liu, Yuan-yuan title = Specific interference shRNA-expressing plasmids inhibit Hantaan virus infection in vitro and in vivo date = 2016-03-14 pages = extension = .txt mime = text/plain words = 3906 sentences = 197 flesch = 50 summary = AIM: To investigate the antiviral effects of vectors expressing specific short hairpin RNAs (shRNAs) against Hantaan virus (HTNV) infection in vitro and in vivo. In mice infected with lethal doses of HTNV, intraperitoneal injection of pSilencer-S or pSilencer-M (30 μg) considerably increased the survival rates and mean time to death, and significantly reduced the mean virus yields and viral RNA level, and alleviated virus-induced pathological lesions in lungs, brains and kidneys. Based on these results and the viral antigen expression results detected by IFA (data not shown), we concluded that the shRNAs that targeted the S and M segments of the HTNV gene were able to inhibit RNA transcript and virus production in the HTNV-infected cells and that shRNA-S1 and shRNA-M2 exhibited a stronger inhibitory effect against HTNV. The RNAi pSilencer-S and pSilencer-M plasmids were constructed, and their antiviral effects were further evaluated by detecting the viral protein synthesis and RNA transcript and progeny virus titers in the HTNV-infected cells. cache = ./cache/cord-002006-pwlybr2h.txt txt = ./txt/cord-002006-pwlybr2h.txt === reduce.pl bib === id = cord-002180-gsdk5x3e author = Davies, Colin title = Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date = 2016-08-24 pages = extension = .txt mime = text/plain words = 4491 sentences = 223 flesch = 52 summary = Amino acid substitutions of NS5(Y26A) and NS5(F123A) that inhibit the ability for NS5 to attach to RNA and recruit host eukaryotic translation initiation factors, respectively, retained the ability to induce an accumulation of cells in the G(0)/G(1) phase as identified for wild-type NS5. Several RNA viruses, including murine norovirus 1 (MNV-1) have been characterized to manipulate cell cycle progression at the G 1 /S restriction point, often creating favorable conditions for viral replication [14] [15] [16] [17] [18] [19] [20] [21] . The effect of NS5 on the host cell cycle was therefore determined by transfection of RAW-Blue cells with RNA transcripts, encoding individual viral genes, NS1-2 from MNV-1 was included as a negative control (Fig 1A) . Furthermore, the NS5(F123A) variant decreased cyclin A protein expression by 67% when compared to the mocktransfected population in a synonymous manner to NS5, strongly implying that the host eukaryotic initiation factor binding domain of NS5 does not play a role in its cell cycle manipulation (Fig 3D) . cache = ./cache/cord-002180-gsdk5x3e.txt txt = ./txt/cord-002180-gsdk5x3e.txt === reduce.pl bib === id = cord-000736-6f8vyziv author = Pripuzova, Natalia title = Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date = 2012-08-17 pages = extension = .txt mime = text/plain words = 6818 sentences = 328 flesch = 54 summary = FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). The analytical sensitivity of each primer set was determined in the single virus testing using FDA/CBER panels (kindly provided by Dr. Stephen Kerby, FDA/CBER) consisting of various amounts of the viruses (0-1,000 genome copies/ml) spiked into the ''normal'' human plasma. The results of sensitivity testing of the real-time PCR array primer sets specific for HIV-1, HIV-2, HBV, HCV, and WNV the with FDA/CBER analytical plasma panels. Tm and C(t) values obtained with primer sets specific for HIV-1, HCV, or HBV in testing of 17 human clinical samples in the format of PCR array targeting eight different viruses. cache = ./cache/cord-000736-6f8vyziv.txt txt = ./txt/cord-000736-6f8vyziv.txt === reduce.pl bib === id = cord-000640-t0y0b0gb author = Sumibcay, Laarni title = Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Côte d'Ivoire date = 2012-01-26 pages = extension = .txt mime = text/plain words = 2219 sentences = 109 flesch = 44 summary = Following numerous failed attempts, hantavirus RNA was detected in ethanol-fixed liver tissue from two banana pipistrelles (Neoromicia nanus), captured near Mouyassué village in Côte d'Ivoire, West Africa, in June 2011. Phylogenetic analysis of partial L-segment sequences using maximum-likelihood and Bayesian methods revealed that the newfound hantavirus, designated Mouyassué virus (MOUV), was highly divergent and basal to all other rodentand soricomorph-borne hantaviruses, except for Nova virus in the European common mole (Talpa europaea). After innumerable failed attempts, hantavirus RNA was detected by RT-PCR in ethanol-fixed liver tissues from two of 12 banana pipistrelles (Neoromicia nanus Peters 1852), captured during June 2011 near Mouyassué village (5°22'07"N, 3°05'37"W) in Aboisso District, 130 km from Abidjan, in the extreme southeastern region of Côte d'Ivoire in West Africa ( Figure 1 ). The newfound hantavirus, designated Mouyassué virus (MOUV), exhibited low nucleotide and amino acid sequence similarity of less than 69% to all representative soricomorph-and rodent-associated hantaviruses, except for the 76.3% sequence similarity with Nova virus (NVAV), previously reported in the European common mole (Talpa europaea) [12] . cache = ./cache/cord-000640-t0y0b0gb.txt txt = ./txt/cord-000640-t0y0b0gb.txt === reduce.pl bib === id = cord-000547-adfigzc1 author = Beniac, Daniel R. title = The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date = 2012-01-11 pages = extension = .txt mime = text/plain words = 7782 sentences = 392 flesch = 51 summary = METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. From the same image data set, we combined extracted volumes from tomograms with 2-D single particle processing to determine the structure of the GP spikes ( Figure 5 ) to a resolution of 14 Å as measured by the Fourier Shell Correlation (FSC) 0.5 criterion. Analysis of 2090 distinct intact virions with a nucleocapsid from cryo-electron micrographs shows that the most common class length (53%) of virus particles is 982679 nm ( Figure 1A , Table S1 ). cache = ./cache/cord-000547-adfigzc1.txt txt = ./txt/cord-000547-adfigzc1.txt === reduce.pl bib === id = cord-002312-jyk7f8hz author = Branton, W. G. title = Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis date = 2016-11-28 pages = extension = .txt mime = text/plain words = 4611 sentences = 231 flesch = 41 summary = Massively parallel (deep) sequencing (RNAseq) of total RNA permitted analysis of all RNA sequences in MS (n = 6) and nonMS (n = 6) white matter samples, revealing that bacterial RNA (ribosomal and non-ribosomal) sequences were detected in all nonMS and MS brain specimens, including MS patients with relapsing-remitting disease (receiving disease modifying therapy) (RR-MS, n = 3) and progressive (untreated) MS (P-MS; n = 3) ( Fig. 2A) . The current study shows the presence of bacterial RNA and DNA sequences and proteins in human brain which are disrupted in conjunction with inflammatory demyelination in patients with MS. The present studies revealed the ratio of bacterium-encoded 16s rDNA to rRNA in matched brain samples to be ~1:2 in both white matter (and cortex, data not shown) with bacterial numbers of 1200-1400 genomes/cm 3 suggesting both bacterial burden and replication were low compared to active pathogenic infections in other tissues. cache = ./cache/cord-002312-jyk7f8hz.txt txt = ./txt/cord-002312-jyk7f8hz.txt === reduce.pl bib === id = cord-001152-v6uc0ijw author = Girardi, Erika title = Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells date = 2013-11-19 pages = extension = .txt mime = text/plain words = 7021 sentences = 383 flesch = 52 summary = Here, we provide evidence for the presence of discrete small RNAs of viral origin that are not associated with the RNA-induced silencing complex (RISC), that are highly expressed and detected by Northern blot analysis, and that accumulate as 21to 28-nucleotide (nt) species during infection. We report that the cellular antiviral endoribonuclease RNase L cleaves the viral genome, producing in turn the small RNAs. Surprisingly, we uncovered the presence of a modification on the 3′-end nucleotide of SINV-derived viral small RNAs (SvsRNAs) that might be at the origin of their stability. The identification of small RNAs from RNA viruses could be seen either as a result of a productive mechanism for the pathogen (as for virus-encoded miRNAs) or as the consequence of a host response to control the infection by degrading viral RNAs. SINV expresses four enzymes that play key functions during the viral replicative cycle. cache = ./cache/cord-001152-v6uc0ijw.txt txt = ./txt/cord-001152-v6uc0ijw.txt === reduce.pl bib === id = cord-002608-zn7tm1ww author = Sokoloski, Kevin J. title = Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants date = 2017-06-29 pages = extension = .txt mime = text/plain words = 11224 sentences = 549 flesch = 41 summary = A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. The data presented in this report indicates that the SINV capsid protein binds to specific viral RNA sequences in the cytoplasm of infected cells, but its interaction with genomic RNA in mature extracellular viral particles is largely non-specific in terms of nucleotide sequence. This report details our efforts to identify and characterize the sites of interaction between the viral capsid protein and the genomic RNA using the model alphavirus Sindbis virus (SINV). C) The infectivity of the individual SINV C:R interaction site mutants and parental wild type virus as reported as the ratio of total particles per infectious unit as determined using BHK-21 cells. cache = ./cache/cord-002608-zn7tm1ww.txt txt = ./txt/cord-002608-zn7tm1ww.txt === reduce.pl bib === id = cord-001963-4wjvykx7 author = Liu, Chia-Lin title = Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development date = 2016-02-26 pages = extension = .txt mime = text/plain words = 5457 sentences = 304 flesch = 56 summary = title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development By interrupting the stacking interaction between Y148 and an RNA base, we identified an influenza virus NP inhibitor, (E, E)-1,7-bis(4-hydroxy-3-methoxyphenyl) -1,6-heptadiene-3,5-dione; this inhibitor reduced the NP's RNA-binding affinity and hindered viral replication. As shown in Fig. 7A , upon H7 treatment at 15μM, the M1 viral RNA synthesis in the influenza virus-infected cells was reduced by 75% at T2. NP is the most abundant RNA-binding viral protein in influenza virus-infected cells and is responsible for recognizing RNA and forming a filamentous nucleocapsid 24 . Using fluorescence titration and an SPR assay of the NPs, we identified one potential natural compound, curcumin (H7), that targets Y148 of influenza virus NP and potently interferes with its RNA-binding activity. cache = ./cache/cord-001963-4wjvykx7.txt txt = ./txt/cord-001963-4wjvykx7.txt === reduce.pl bib === id = cord-001829-rwnbxmt4 author = Lu, Yi-Fan title = IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance date = 2015-11-04 pages = extension = .txt mime = text/plain words = 7156 sentences = 384 flesch = 48 summary = Genome-wide association studies performed on diverse patient populations have identified polymorphisms near the interferon-λ 3 (IFNL3; formerly IL28B) gene that predict the efficacy of interferon-based therapy for chronic infection. The differential effects on mRNA versus protein levels strongly suggest that the IFNL3 3′ UTR regulates gene expression by repressing the efficiency of mRNA translation rather than mRNA abundance in HeLa cells. We used polysome profiling to examine whether the variant IFNL3 reporter mRNAs were differentially associated with translating ribosomes in stable HeLa cell lines. Although rs4803217 is not independently associated with patient phenotypes in the cohort we analyzed, this SNP occurs in the 3′ UTR of IFNL3 and showed clear functional effects on reporter gene expression, suggesting a role for this variant in control of HCV infection. cache = ./cache/cord-001829-rwnbxmt4.txt txt = ./txt/cord-001829-rwnbxmt4.txt === reduce.pl bib === id = cord-002398-0a3okta0 author = Myllykoski, Matti title = Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase date = 2017-01-31 pages = extension = .txt mime = text/plain words = 6151 sentences = 363 flesch = 56 summary = Here, we studied the structure of the 2H family member LigT from Escherichia coli both in the apo form and complexed with different active-site ligands, including ATP, 2′-AMP, 3′-AMP, phosphate, and NADP(+). coli LigT bound to tRNA in solution, and provide a model for RNA binding by LigT, involving flexible loops lining the active site cavity. The crystal structure of LigT with 2 0 -AMP was superimposed on the corresponding complex of CNPase, in order to distinguish common and divergent ligand binding determinants in 2H enzymes. Structural data [29] from these enzymes incidate that the 2 0 ,5 0 -adenosine bisphophate substrate binds along the opposite side of the active site, compared to LigT and CNPase (Fig 7A) . As the different structures predicted an RNA-binding surface on LigT, we further modeled a 3-residue RNA molecule with a terminal 2 0 -phosphate into the active site. cache = ./cache/cord-002398-0a3okta0.txt txt = ./txt/cord-002398-0a3okta0.txt === reduce.pl bib === id = cord-002179-v8lpw4r7 author = Viktorovskaya, Olga V. title = Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements date = 2016-08-24 pages = extension = .txt mime = text/plain words = 8021 sentences = 418 flesch = 49 summary = title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements Previously, we have described a high-throughput mass spectrometry method termed TUX-MS (thiouracil cross-linking mass spectrometry) to identify host factors that interact with viral RNA during a live infection in cell culture [15] . Development of a quantitative thiouridine cross-linking mass spectrometry (qTUX-MS) method for identification of proteins associated with the DENV RNA TUX-MS can be used to identify host factors by incorporating 4-thiouridine (4sU), a zero-distance cross-linker, into the viral RNA (vRNA) to enable cross-linking of proteins bound to vRNA during a live infection in cell culture [15] . Since some of hnRNPs are known to modulate cellular gene expression in response to dengue infection [60, 61] , we can not rule out that some of the observed effects on virus titers derive from their roles in regulating host mRNAs. Among the numerous qTUX-MS identified factors of interest, our study is the first to demonstrate the involvement of HMCES (or C3orf37) in viral infection. cache = ./cache/cord-002179-v8lpw4r7.txt txt = ./txt/cord-002179-v8lpw4r7.txt === reduce.pl bib === id = cord-002763-n952re94 author = Niu, Xiaosai title = Transcriptome analysis of avian reovirus-mediated changes in gene expression of normal chicken fibroblast DF-1 cells date = 2017-11-25 pages = extension = .txt mime = text/plain words = 4307 sentences = 245 flesch = 50 summary = title: Transcriptome analysis of avian reovirus-mediated changes in gene expression of normal chicken fibroblast DF-1 cells In this study, RNA-Seq technology was applied to investigate the transcriptome-wide changes of DF-1 cells upon ARV infection at the middle stage. CONCLUSIONS: Overall, the differential expression profile presented in this study can be used to expand our understanding of the comprehensive interactions between ARV and the host cells, and may be helpful for us to reveal the pathogenic mechanism on the molecular level. In this study, we tried to build a complete expression profile of ARV-mediated changes at the transcriptional level using RNA-Seq to unveil the complex interactions between ARV and host cells. The results show a similar pattern of ARV-mediated changes as was seen in the DEG analysis of RNA-Seq data (Fig. 4 ). cache = ./cache/cord-002763-n952re94.txt txt = ./txt/cord-002763-n952re94.txt === reduce.pl bib === id = cord-002937-7xauocti author = Huang, Chung-Guei title = A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date = 2018-02-20 pages = extension = .txt mime = text/plain words = 6238 sentences = 293 flesch = 46 summary = We aimed to investigate whether primary cultures of human respiratory tract epithelial cells are helpful to understand H7N9 virus pathogenesis and tissue tropism, and to evaluate how patient-related characteristics can affect the host's response to infection. In this scenario, primary cultures of human respiratory tract epithelial cells would be invaluable to understand H7N9 virus tissue tropism and pathogenesis, as well as to evaluate how patient-related characteristics can modulate the host's response to infection. With regard to virus tropism, viral RNA quantities were significantly higher in epithelial cells obtained from the upper anatomical locations than from the lower anatomical locations, without adjustment (P = 0.030); however, the difference lost significance after adjustment for age, sex, medical comorbidities, and obesity (P = 0.490; Figure 2B ). cache = ./cache/cord-002937-7xauocti.txt txt = ./txt/cord-002937-7xauocti.txt === reduce.pl bib === id = cord-002994-1zjrunzc author = Faye, Martin title = Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus date = 2018-04-13 pages = extension = .txt mime = text/plain words = 11495 sentences = 517 flesch = 45 summary = Based on these alignments, we investigated the genetic properties of these different isolates circulating in West Africa, such as genome length and location of main conserved amino acid motifs previously described in mosquito-borne flaviviruses (MBFVs) with sometimes mutations which include no physicochemical properties changes [3] . The RNAz method [21] implemented in the Vienna RNA Websuite (http://rna.tbi.univie.ac.at/) [22] was used to detect thermodynamically stable and evolutionarily conserved structural RNA domains on complete non-coding regions of the 11 West African BAGV isolates characterized in this study and the isolates from Spain and CAR, because complete non-coding sequences are not currently available for the isolate from India. Here, we described location of main conserved amino acid motifs on BAGV proteins using in silico analysis of complete genome sequences of the 11 West African BAGV isolates characterized in this study and sequences from India, CAR and Spain. cache = ./cache/cord-002994-1zjrunzc.txt txt = ./txt/cord-002994-1zjrunzc.txt === reduce.pl bib === id = cord-001541-5d64esp4 author = Walker, Peter J. title = Evolution of Genome Size and Complexity in the Rhabdoviridae date = 2015-02-13 pages = extension = .txt mime = text/plain words = 9157 sentences = 398 flesch = 45 summary = We demonstrate that remarkable changes in genome size and complexity have occurred in rhabdoviruses in a clade-specific manner, primarily by extension and insertion of additional transcriptional units in the structural protein gene junctions, followed by occasional losses. All rhabdovirus genomes contained the five canonical structural protein genes (N, P, M, G and L); however, there was remarkable diversity in the number and location of other long ORFs. Across the data set, we identified 179 additional ORFs 180 nt in length of which 142 shared no detectable protein sequence similarity with any other protein in our data set or with those in public databases (S2 Table) . Interestingly, although substantial variation in the length of gene junctions was observed in several genera (including ephemeroviruses and lyssaviruses), most variation in genome size occurred as the result of the presence of new, non-canonical ORFs in the regions between the structural protein genes (Table 1) . cache = ./cache/cord-001541-5d64esp4.txt txt = ./txt/cord-001541-5d64esp4.txt === reduce.pl bib === id = cord-002482-2t09zqqi author = Miras, Manuel title = Non-canonical Translation in Plant RNA Viruses date = 2017-04-06 pages = extension = .txt mime = text/plain words = 13890 sentences = 732 flesch = 51 summary = Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. In this review, we describe current knowledge on the mechanisms used by positive-sense single-stranded (+ss) RNA plant viruses to initiate translation, focusing on cis-acting sequences present in viral mRNAs. We also describe other protein translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. cache = ./cache/cord-002482-2t09zqqi.txt txt = ./txt/cord-002482-2t09zqqi.txt === reduce.pl bib === id = cord-003006-lk2ny1wd author = Cantoni, Diego title = Ebolaviruses: New roles for old proteins date = 2018-05-03 pages = extension = .txt mime = text/plain words = 6045 sentences = 274 flesch = 44 summary = These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Lastly, VP35 is a suppressor of RNA silencing, functionally equivalent to the human immunodeficiency virus (HIV-1) Trans-activator of transcription (Tat) protein and important for viral evasion of the innate immune response [34] . The authors propose that this mutation is likely a result of EBOV adaptation to the human host, as several viral variants have been seen to increase human cell infectivity while decreasing virus entry in nonhuman primates [83] [84] [85] . In addition, many ebolavirus proteins are seen to interact with immune cells, causing cell activation and/or cell death and facilitating both viral replication and spread (e.g., by recruiting monocytes to infected cells or by increasing vascular leakage) as well as enabling immune evasion (e.g., antibody neutralisation by sGP and by cleaved GP), roles that were previously solely attributed to VP24 and VP35. cache = ./cache/cord-003006-lk2ny1wd.txt txt = ./txt/cord-003006-lk2ny1wd.txt === reduce.pl bib === id = cord-000866-dr2uow4m author = Picard-Jean, Frédéric title = The Immunosuppressive Agent Mizoribine Monophosphate Is an Inhibitor of the Human RNA Capping Enzyme date = 2013-01-17 pages = extension = .txt mime = text/plain words = 7046 sentences = 368 flesch = 50 summary = In the present study, we investigated the ability of MZP to directly inhibit the human RNA capping enzyme (HCE), a protein harboring both RNA 5′-triphosphatase and RNA guanylyltransferase activities. An RNA guanylyltransferase (GTase) then catalyzes a two-step reaction in which it initially utilizes GTP as a substrate to form a covalent enzyme-GMP (EpG) intermediate, with the concomitant release of pyrophosphate (PPi). Since ribavirin triphosphate and MZP share functional similarities, we investigated the attractive possibility that MZP could also inhibit the GTase activity of the human RNA capping enzyme (HCE). The enzyme-GMP complex formation assays were carried out for 3 min at 37uC in a buffer containing 1 mM [a-32 P]GTP, 4 mM HCE, 50 mM Tris-HCl, pH 7.5, 5 mM MgCl 2 , 500 mM DTT, 0.5 ng/ml pyrophosphatase (Roche), and various concentration of MZP (as indicated). cache = ./cache/cord-000866-dr2uow4m.txt txt = ./txt/cord-000866-dr2uow4m.txt === reduce.pl bib === id = cord-001453-l1r416w7 author = Hou, Linlin title = Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome date = 2014-11-10 pages = extension = .txt mime = text/plain words = 8358 sentences = 420 flesch = 54 summary = title: Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome Consistently, a fusion protein containing full-length Csl4 and NTD of DnaG led to enhanced degradation of A-rich RNA by the exosome. The RNase PH-domain containing subunits Rrp41 and Rrp42 are arranged in a catalytically active hexamer, on the top of which a trimeric cap composed of the RNA-binding proteins Rrp4 and Csl4 is bound ( Figure 1B ; 4, 5, [22] [23] [24] . The bacterial primase DnaG is composed of an NTD containing a Zn-finger motif involved in DNA binding, the central, catalytic TOPRIM domain and a CTD neces-sary for the interaction with the replicative helicase DnaB ( Figure 1A , refs. coli cell-free extract was easily detectable by pull-down assays with Strep-Tactin Sepharose beads (for an example see Figure 7A be-low), we conclude that the CTD of DnaG is important for the binding to the archaeal exosome. cache = ./cache/cord-001453-l1r416w7.txt txt = ./txt/cord-001453-l1r416w7.txt === reduce.pl bib === id = cord-003158-mhlqnj52 author = Wang, Qi title = Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date = 2018-07-13 pages = extension = .txt mime = text/plain words = 5186 sentences = 291 flesch = 56 summary = Previous studies have demonstrated that the HCV JFH1 NS5A C-terminal is a flexible region which is capable of accommodating foreign gene inserts (such as EGFP, 720bp and Rennilla luciferase [Rluc] , 930bp) and still permit HCV replication and viral production (18, 19, (24) (25) (26) (27) (28) (29) . In this study, we used the JFH1-AM120 as a vector to explore if infectious reporter virus would be produced following insertion of LacZ gene that was three time larger than Rluc, into the NS5A C-terminus. This result provided evidence that fusion protein of NS5A and β-galactosidase can be co-expressed in Huh7.5 cells after transfection of JFH1-AM120-LacZ RNA. Our results demonstrate that the LacZ reporter gene can be inserted into the NS5A C-terminus of HCV JFH1-AM120 and will express the predicted NS5A-LacZ fusion protein, which can be detected by western blotting three days after RNA transfection of cells. cache = ./cache/cord-003158-mhlqnj52.txt txt = ./txt/cord-003158-mhlqnj52.txt === reduce.pl bib === id = cord-001964-iy6qzq58 author = Muñoz-González, Sara title = Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar date = 2016-02-26 pages = extension = .txt mime = text/plain words = 6933 sentences = 319 flesch = 48 summary = The wild boars persistently infected with CSFV were protected from superinfection by the virulent CSFV Margarita strain, as evidenced by the absence of clinical signs and the absence of Margarita RNA detection in serum, swabs and tissue samples. Additionally, in PBMCs, a well-known target for CSFV viral replication, only the primary infecting virus RNA (Cat01 strain) could be detected, even after the isolation in ST cells, demonstrating SIE at the tissue level in vivo. Interestingly, the RNA of the vaccinal C-strain was undetectable by specific RT-PCR [8] in any of the samples analysed after vaccination, including blood, nasal and rectal swabs, or organs throughout the experiment, suggesting a phenomenon of homologous interference, also known as superinfection exclusion (SIE), between the high viral load generated by the primary persistent infection and the CSFV vaccine strain. cache = ./cache/cord-001964-iy6qzq58.txt txt = ./txt/cord-001964-iy6qzq58.txt === reduce.pl bib === id = cord-002439-wesyiymn author = Le, My-Tra title = Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch date = 2017-02-13 pages = extension = .txt mime = text/plain words = 12389 sentences = 589 flesch = 60 summary = For this current report, optical tweezers (OT), a type of single molecule force spectroscopy, and steered molecular dynamic simulations (SMD) were used to examine the folding/unfolding pathways of the TSS. One possibility for why the TSS-only fragment was not stable was the omission of the upstream 5A, as it was subsequently shown that adjacent doublet mutations in 5A (positions 8 and 9 in Figure 1A ) or single mutations disrupting É 3 caused identical enhancements in flexibility of residues throughout the 5A/H4a/É 3 region as assayed Hairpins H4a, H4b and H5 and tertiary interactions É 2 and É 3 comprise the TSS. Initial explicit solvent SMD simulations performed on fragment TSS108 (C 5 through A 112 ) at pulling speeds of 1.0 Å /ps and 0.5 Å /ps terminated with H5 and H4b helices remaining partly basepaired, indicating that the RNA chain was ahead of its approximate equilibrium state. cache = ./cache/cord-002439-wesyiymn.txt txt = ./txt/cord-002439-wesyiymn.txt === reduce.pl bib === id = cord-003187-qdbcdn2j author = Bassi, Maria Rosaria title = Extinction of Zika Virus and Usutu Virus by Lethal Mutagenesis Reveals Different Patterns of Sensitivity to Three Mutagenic Drugs date = 2018-08-27 pages = extension = .txt mime = text/plain words = 6701 sentences = 337 flesch = 41 summary = Although the two viruses are inhibited by the same three drugs, ZIKV is relatively more susceptive to serial passage in the presence of purine analogues (favipiravir and ribavirin), while USUV replication is suppressed more efficiently by 5-fluorouracil. We observe that ribavirin, favipiravir, and 5-fluorouracil are all inhibitors of both ZIKV and USUV, and that consecutive passage of virus in the presence of these drugs can lead to the complete extinction of infectivity. To investigate whether ZIKV replication could be affected by increased mutagenesis, we tested four different compounds known to be mutagenic for diverse viruses, 5-fluorouracil, ribavirin, favipiravir, and decitabine (25, 32, 35, (37) (38) (39) . To investigate whether the antiviral activities observed during treatment with favipiravir, ribavirin, and 5-fluorouracil are connected to their predicted mutagenic activity, we analyzed the mutation frequencies of both ZIKV and USUV rescued after 5 passages in the presence of these compounds. cache = ./cache/cord-003187-qdbcdn2j.txt txt = ./txt/cord-003187-qdbcdn2j.txt === reduce.pl bib === id = cord-002676-zwkl1ywk author = Yu, Dong-Shan title = The lifecycle of the Ebola virus in host cells date = 2017-06-15 pages = extension = .txt mime = text/plain words = 5322 sentences = 287 flesch = 45 summary = However, the mechanisms of EBOV lifecycle in host cells, including viral entry, membrane fusion, RNP formation, GP-tetherin interaction, and VP40-inner leaflet association remain poorly understood. Then, the Tyro3 protein kinase (TAM) family, including Axl, Dtk, and Mer, which widely expressed in many cell types, span the plasma membrane and contain intracellular tyrosine kinase domains, are facilitate EBOV GP-dependent attachment [39, 40] . In addition, folate receptor-α (FR-α) was reported to be a co-receptor in binding cells that expressed MARV or EBOV GP, mediated syncytia formation triggered by GP, and facilitated cellular entry of the virus [28] . After the virus has been internalized into the endosome, fusion induced by cleaved GP is fundamentally independent of pH, which indicated an unidentified host cell factor critical for filovirus entry is sensitive to an acidic pH [56] . Host Cell Plasma Membrane Phosphatidylserine Regulates the Assembly and Budding of Ebola Virus cache = ./cache/cord-002676-zwkl1ywk.txt txt = ./txt/cord-002676-zwkl1ywk.txt === reduce.pl bib === id = cord-003070-6oca1mrm author = Shen, Wen-Jun title = RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date = 2018-02-28 pages = extension = .txt mime = text/plain words = 5476 sentences = 339 flesch = 56 summary = On the non-redundant benchmark test sets extracted from the PRIDB, the RPiRLS method outperformed RPI-Pred and IPMiner in terms of accuracy, specificity and sensitivity. The computational results showed that the RPiRLS classifier outperformed the RPiRLS-7G classifier in terms of various performance measurements, indicating that the diversity of amino acids at a sequence is important for the prediction of RPIs. The performance of predicting RPIs was evaluated by using 10-fold stratified cross-validation on the RPI2662 data set. For the RPI369 data set as shown in Table 4 , the performance of the RPiRLS method was 0.85, 0.92, 0.84 and 0.86 for predictive accuracy, AUC, specificity and sensitivity, respectively. The work presented here provided a computational method, called RPiRLS, to classify RNA-protein pairs as interacting or non-interacting by integrating a sequence-based derived kernel with regularized least squares. cache = ./cache/cord-003070-6oca1mrm.txt txt = ./txt/cord-003070-6oca1mrm.txt === reduce.pl bib === id = cord-000794-l565gha4 author = Yan, Huan title = Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus date = 2012-11-13 pages = extension = .txt mime = text/plain words = 13364 sentences = 698 flesch = 54 summary = Here, by using near zero distance photo-cross-linking and tandem affinity purification, we revealed that the receptor-binding region of pre-S1 specifically interacts with sodium taurocholate cotransporting polypeptide (NTCP), a multiple transmembrane transporter predominantly expressed in the liver. Photoreactive ligand peptides for identification of interacting protein(s) of pre-S1 domain of L envelope protein To identify the pre-S1 interacting molecule(s), we employed a photo-cross-linking approach using a synthetic peptide derived from the native pre-S1 peptide with particular residues replaced by eLife digest Liver diseases related to the human hepatitis B virus (HBV) kill about 1 million people every year, and more than 350 million people around the world are infected with the virus. In this study, by employing a unique approach of tandem affinity purification combined with MS analysis against a Tupaia hepatocyte proteome database established by deep sequencing, we revealed that the liver bile acid transporter, NTCP, specifically interacts with a key region in the pre-S1 domain of the HBV envelope L protein. cache = ./cache/cord-000794-l565gha4.txt txt = ./txt/cord-000794-l565gha4.txt === reduce.pl bib === id = cord-003044-9uqa39j9 author = Cervera, Héctor title = Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date = 2018-03-19 pages = extension = .txt mime = text/plain words = 10863 sentences = 533 flesch = 46 summary = As viral fitness is reduced, interactions are less optimal and, consequently, the gene expression profile of the plant will be increasingly different from that resulting from the infection with the WT virus. Figure 2A shows the clustering (unweighted average distance method; UPGMA) of average expression data for those genes that significantly changed expression (62-fold) among plants infected with the seven viral genotypes (1-way ANOVAs with false discovery rate (FDR) correction; overall P < 0.05) relative to the mock-inoculated plants. tabacum into a novel, poorly susceptible one, Arabidopsis thaliana, have shown that adaptation of TEV to the novel host (i.e., concomitant to large increases in fitness) was associated with a profound change in the way the ancestral and evolved viruses interacted with the plant's transcriptome, with genes involved in the response to biotic stresses, including signal transduction and innate immunity pathways, being significantly underexpressed in plants infected with the evolved virus than in plants infected with the ancestral one (Agudelo-Romero et al. cache = ./cache/cord-003044-9uqa39j9.txt txt = ./txt/cord-003044-9uqa39j9.txt === reduce.pl bib === id = cord-002687-ql6zo8ka author = Li, Dan title = A potent human neutralizing antibody Fc-dependently reduces established HBV infections date = 2017-09-26 pages = extension = .txt mime = text/plain words = 14698 sentences = 772 flesch = 55 summary = Neutralizing antibodies (nAbs), in addition to their capacity to specifically block viral entry via Fab (fragment of antigen binding) recognition of virus, have been found to exert a variety of immunological 'effector' functions, including clearance of circulatory viruses as well as by mediating cytotoxic killing or phagocytosis of infected cells (DiLillo et al., 2014; Corti et al., 2011; Bournazos et al., 2014; Bruel et al., 2016; Lu et al., 2016; Hessell et al., 2007) , or even possibly triggering sustained host immune responses in vivo Pelegrin et al., 2015) . In the present study, we took advantage of a large non-immune phage display human antibody library and our human NTCP-enabled HBV cell culture system (Yan et al., 2012; Sun et al., 2016) to identify a panel of nAbs that specifically target the preS1 domain. cache = ./cache/cord-002687-ql6zo8ka.txt txt = ./txt/cord-002687-ql6zo8ka.txt === reduce.pl bib === id = cord-002673-5a1rfi6k author = Knibb, Wayne title = Regional genetic diversity for NNV grouper viruses across the Indo-Asian region – implications for selecting virus resistance in farmed groupers date = 2017-09-06 pages = extension = .txt mime = text/plain words = 6692 sentences = 298 flesch = 48 summary = This study uses statistical approaches and assessment of "characteristic attributes" (i.e. nucleotide positions that discriminate among strains) to assess whether published and new NNV RNA2 cds sequences show genetic differentiation over geography, host species and years. Within the red spotted grouper nervous necrosis virus (RGNNV) strain, to which all Asian grouper NNV belong, however, no one so far has reported evidence of genetic subgrouping by region, species or year in a formal statistical manner, especially when we restrict hosts just to Asian grouper. The goal of this report was to collate the most comprehensive data set to date on NNV RNA2 sequences for warm water Asian marine finfish, whether published and/or lodged in Genbank over the last 20 years, including some sequence data produced by our group for Vietnamese and Taiwanese grouper, to statistically test the data for evidence of NNV strain variation that associates with geography, host species and year and also to determine whether there are "characteristic attributes" that indicate regional (or host, year) specific differences among the strains. cache = ./cache/cord-002673-5a1rfi6k.txt txt = ./txt/cord-002673-5a1rfi6k.txt === reduce.pl bib === id = cord-002764-px0cz6qn author = Lin, Yuan title = Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs date = 2017-11-17 pages = extension = .txt mime = text/plain words = 8369 sentences = 429 flesch = 51 summary = These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline–rich-motif (polyPRM) ligand. These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline-rich-motif (polyPRM) ligand. Tyrosine mutations also block recruitment of IDRs into hydrogels and/or phase-separated liquids formed by the RNA-binding protein hnRNPA2 (47) and FUS (29) , as well as into RNA granules in cells (29) . We found that, when tethered to a polySH3 domain protein that phase-separates when mixed with a cognate poly-proline-rich motif (polyPRM) ligand, wildtype FUS decreases the threshold concentration for LLPS by 8-fold. cache = ./cache/cord-002764-px0cz6qn.txt txt = ./txt/cord-002764-px0cz6qn.txt === reduce.pl bib === id = cord-003104-9cx1gdze author = Fitzsimmons, William J. title = A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus date = 2018-06-28 pages = extension = .txt mime = text/plain words = 8643 sentences = 457 flesch = 55 summary = Here, we present data for an alternative model whereby RNA viruses evolve high mutation rates as a byproduct of selection for increased replicative speed. However, the observed attenuation of antimutator RNA viruses in vivo has led many to argue for the adaptive benefit of high mutation rates, as genetic diversity provides a rich substrate for a virus's evolution in the face of varying intrahost environments [7, 10, [34] [35] [36] [37] [38] . This is a moderate fitness defect, falling in the 64th percentile in a dataset of 8,970 fitness values obtained for point mutants of poliovirus under similar conditions [16] (e.g., human epithelial cells [HeLa] multiplicity of infection [MOI] 0.1, 8-hour infection cycle, and 6 passages; Fig 1B) . The adaptability of WT and high-fidelity viruses have generally been compared using assays that measure the acquisition of drug resistance, the reversion of an attenuating point mutation, or escape from microRNA in a limited number of replication cycles [5] [6] [7] 34, 36] . cache = ./cache/cord-003104-9cx1gdze.txt txt = ./txt/cord-003104-9cx1gdze.txt === reduce.pl bib === id = cord-003130-p2h8p5bm author = Lindqvist, Richard title = Tick-Borne Flaviviruses and the Type I Interferon Response date = 2018-06-21 pages = extension = .txt mime = text/plain words = 8350 sentences = 481 flesch = 48 summary = There are more than 70 viruses in the genus flavivirus, and they are transmitted by arthropods such as mosquitoes (dengue virus (DENV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV) and ticks (tick-borne encephalitis virus (TBEV), Langat virus (LGTV), Kyasanur forest disease virus (KFDV), Omsk hemorrhagic fever virus (OHFV), Powassan virus (POWV), and Louping-ill virus (LIV)) [1] [2] [3] [4] [5] . Two other ISGs which have been shown to be antivirally active against TBEV are virus inhibitory protein endoplasmic reticulum associated interferon inducible (viperin) and tripartite motif-79α (TRIM79α). The role of interferon in tick-borne encephalitis virus-infected l cells. A functional toll-like receptor 3 gene (tlr3) may be a risk factor for tick-borne encephalitis virus (tbev) infection Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection cache = ./cache/cord-003130-p2h8p5bm.txt txt = ./txt/cord-003130-p2h8p5bm.txt === reduce.pl bib === id = cord-003045-r707jl16 author = Bhuvaneshwar, Krithika title = viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date = 2018-06-05 pages = extension = .txt mime = text/plain words = 6546 sentences = 359 flesch = 54 summary = The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. Available online at: https:// www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts/ licensedproductsblas/blooddonorscreening/infectiousdisease/ucm080466.htm Abbreviations: HBV, Hepatitis B virus; HCV, Hepatitis C Virus; HERV K113, Human Endogenous Retrovirus K113; TCGA, The Cancer Genome Atlas; HCC, Hepatocellular carcinoma; NAFLD, nonalcoholic fatty liver disease; Hep B, Hepatitis B; Hep C, Hepatitis C; HepB + HepC, coinfected with both Hepatitis B and C virus; HBsAg, Hepatitis B surface antigen; HBeAg, Hepatitis B type e antigen; NGS, next-generation sequencing; RNA-seq, whole transcriptome sequencing; BAM, Binary version of Sequence alignment/map format; CDS, coding sequence; Cox PH, Cox Proportional Hazard; HBx, viral gene X; STS, Sequence-tagged sites; NCBI, National Center for Biotechnology Information; GFF, general-feature-format. cache = ./cache/cord-003045-r707jl16.txt txt = ./txt/cord-003045-r707jl16.txt === reduce.pl bib === id = cord-003122-a3f4l6iu author = Dou, Dan title = Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date = 2018-07-20 pages = extension = .txt mime = text/plain words = 10272 sentences = 565 flesch = 43 summary = The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. Influenza A viruses (IAVs) and type B viruses (IBVs) contain 8, negative-sense, single-stranded viral RNA (vRNA) gene segments ( Figure 1A ) (3, 4) , which encode transcripts for 10 essential viral proteins, as well as several strain-dependent accessory proteins ( Figure 1B) . In contrast to the early steps in IAV entry, vRNP trafficking to the nucleus following the fusion event is highly dependent on the host cell machinery and transport pathways [reviewed in Ref. cache = ./cache/cord-003122-a3f4l6iu.txt txt = ./txt/cord-003122-a3f4l6iu.txt === reduce.pl bib === id = cord-003050-n25wnmq5 author = Nibert, Max L. title = A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date = 2018-03-07 pages = extension = .txt mime = text/plain words = 3324 sentences = 159 flesch = 53 summary = The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on − 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. Based on similar genome sizes, coding organizations, and P2-and P3-region sequence similarities, both MBV and RsBV1 appear to be most closely related to plant viruses in the unassigned genus Sobemovirus [12, 16] . As a result, the consensus sequence for the apparent new barnavirus reported here (GenBank MG686618) is 4206 nt long, appears to be coding complete for ORFs 1-4 ( Fig. 1) , and was newly assembled from a total of 821 individual reads (reads per position: mean, 19; range, 2-35). cache = ./cache/cord-003050-n25wnmq5.txt txt = ./txt/cord-003050-n25wnmq5.txt === reduce.pl bib === id = cord-003284-hjx2d5rq author = Márquez-Jurado, Silvia title = An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo date = 2018-10-07 pages = extension = .txt mime = text/plain words = 9917 sentences = 409 flesch = 51 summary = Furthermore, using this infectious clone we have generated a mutant ZIKV containing a single amino acid substitution (A175V) in the NS2A protein that presented reduced viral RNA synthesis in cell cultures, was highly attenuated in vivo and induced fully protection against a lethal challenge with ZIKV wild-type. To analyze the genetic stability of the recombinant ZIKV harboring the point mutation A175V in the coding region of the NS2A protein (rZIKV-RGN-mNS2A), total RNA was purified from Vero cells infected with viruses from passage 1 (P1) to passage 5 (P5) using the RNeasy minikit (Qiagen), according to the manufacturer's specifications. To investigate whether the reduced RNA synthesis of rZIKV-RGN-mNS2A in Vero cells could result in viral attenuation in vivo, the ability of the mutant virus to induce pathogenesis was analyzed in A129 mice and compared with that of the parental rZIKV-RGN ( Figure 6 ). cache = ./cache/cord-003284-hjx2d5rq.txt txt = ./txt/cord-003284-hjx2d5rq.txt === reduce.pl bib === id = cord-003305-ya0siivm author = Liu, Weichi title = A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase date = 2018-11-16 pages = extension = .txt mime = text/plain words = 8861 sentences = 427 flesch = 54 summary = The intra-molecular NTD interactions with the RdRP palm that controls the active site closure, together with the observation of the NTD deletion mutant N-91 exhibited higher level of misincorporation in the de novo RNA synthesis, suggesting a unique mode of fidelity modulation. In order to quantitatively assess whether the fidelity levels are modulated by the intra-molecular NTD-RdRP interface interactions, we established the 32 P-radioactivity based NTP misincorporation assays using the T30/P2 construct utilized in the aforementioned de novo-mode synthesis assessment ( Figure 1B and C) . The effect of E472A mutation was highly consistent with AA mutation ( Figure 4B and Supplementary Figure S3A Since polymerase misincorporation level can be affected by the type of misincorporation and the sequence context of the misincorporation site, we established the second type of regular NTP misincorporation assays using the same T30/P2 construct for a more adequate assessment of the RdRP fidelity modulation brought by the NTD. cache = ./cache/cord-003305-ya0siivm.txt txt = ./txt/cord-003305-ya0siivm.txt === reduce.pl bib === id = cord-001835-0s7ok4uw author = nan title = Abstracts of the 29th Annual Symposium of The Protein Society date = 2015-10-01 pages = extension = .txt mime = text/plain words = 138514 sentences = 6150 flesch = 40 summary = Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues. cache = ./cache/cord-001835-0s7ok4uw.txt txt = ./txt/cord-001835-0s7ok4uw.txt === reduce.pl bib === id = cord-003505-qr6ukfti author = Tabraue-Chávez, Mavys title = A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date = 2019-03-06 pages = extension = .txt mime = text/plain words = 5655 sentences = 331 flesch = 50 summary = In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. Once the abasic PNA probes hybridize with target sequences, the SMART-C-Biotin dynamic incorporation takes place, enabling the unequivocal identification of the parasite present in the amplicon sample, because of the unique colorimetric pattern that each Trypanosomatid amplicon generates. DNA amplicon products were denatured and then together with the dynamic chemistry reaction reagents added directly into the internal column of the Spin-Tube that supports the nylon membrane for the color-development assay (Fig. 4) . 20 ng of human gDNA were used as PCR template for its amplification with the set of primers described in our study and neither colorimetric signals nor bands were detected using the Spin-Tube and capillary electrophoresis analysis respectively (Fig. 5 , column 2: 2A and 2B), hence probing the specificity when human gDNA is present. cache = ./cache/cord-003505-qr6ukfti.txt txt = ./txt/cord-003505-qr6ukfti.txt === reduce.pl bib === id = cord-003711-l3brhmzq author = Munnur, Deeksha title = Reversible ADP-ribosylation of RNA date = 2019-06-20 pages = extension = .txt mime = text/plain words = 6854 sentences = 410 flesch = 58 summary = ADP-ribosylation is a reversible chemical modification catalysed by ADP-ribosyltransferases such as PARPs that utilize nicotinamide adenine dinucleotide (NAD(+)) as a cofactor to transfer monomer or polymers of ADP-ribose nucleotide onto macromolecular targets such as proteins and DNA. We further reveal that ADP-ribosylation of RNA mediated by PARP10 and TRPT1 can be efficiently reversed by several cellular ADP-ribosylhydrolases (PARG, TARG1, MACROD1, MACROD2 and ARH3), as well as by MACROD-like hydrolases from VEEV and SARS viruses. Importantly, PARP3 could only ADP-ribosylate DNA ends and did not have any activity on RNA oligos, while PARP10 specifically modified phosphorylated ssRNA oligo in the conditions tested ( Figure 1A and B). Since PARP10 can ADP-ribosylate both 5 and 3 phosphorylated ends of RNA, we tested both of these modified oligos as substrates for well characterized human ADP-ribosylhydrolases: PARG, TARG1, MACROD1, MACROD2 and ARH1-3. cache = ./cache/cord-003711-l3brhmzq.txt txt = ./txt/cord-003711-l3brhmzq.txt === reduce.pl bib === id = cord-003482-f1uvohf0 author = Malmlov, Ashley title = Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date = 2019-02-04 pages = extension = .txt mime = text/plain words = 7503 sentences = 400 flesch = 53 summary = Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. cache = ./cache/cord-003482-f1uvohf0.txt txt = ./txt/cord-003482-f1uvohf0.txt === reduce.pl bib === id = cord-004827-bnf3mvaf author = Desselberger, U. title = Report on an ICTV-sponsored symposium on Virus Evolution date = 2005-01-13 pages = extension = .txt mime = text/plain words = 2766 sentences = 164 flesch = 48 summary = Phylogenetic relationships have been found useful for virus identification, work on origin, speed and mechanisms of evolution, taxonomy, and the elucidation of transmission pathways (e.g. the transmission of HIV from a source to a victim [16] ). In vitro, a single round of replication of HIV-1 in T lymphocytes generated on average 9 recombination events per virus [14] . Approximately 50% of sequence changes are consistent with evolution by point mutations; other changes are due to multiple recombination events. After an introduction in which basic genetic terms were defined (mutation and mutation rate, hypermutation, recombination, reassortment, segmentation etc), the quasispecies concept was presented according to which any sample of an RNA virus represents a 'swarm' of closely related mutants. 'To maintain RNA structure, evolution selects against better alternatives elsewhere in the genome'. The aim of the talk was to show the significance of RNA structural considerations for the evolution of viruses. Plant RNA virus evolution cache = ./cache/cord-004827-bnf3mvaf.txt txt = ./txt/cord-004827-bnf3mvaf.txt === reduce.pl bib === id = cord-003792-v48xeqdz author = Izquierdo-Suzán, Mónica title = Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date = 2019-08-17 pages = extension = .txt mime = text/plain words = 4017 sentences = 182 flesch = 47 summary = We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Several studies carried out under laboratory conditions have demonstrated that Zika virus can infect many different Aedes mosquito species (3) ; still, the key species for the transmission of Zika virus to humans are Ae. aegypti and Ae. albopictus (4) (5) (6) . In this study, we sought to demonstrate natural vertical transmission in Ae. aegypti mosquitoes by detecting viral RNA and isolating infectious Zika virus from larvae hatched from field-collected eggs. In this work, we were also able to demonstrate the natural vertical transmission of Zika virus in Ae. aegypti mosquitoes by the successful isolation of infectious Zika virus (31N) from larvae raised from field-collected eggs. cache = ./cache/cord-003792-v48xeqdz.txt txt = ./txt/cord-003792-v48xeqdz.txt === reduce.pl bib === id = cord-004280-c470nlie author = Coleman, Kristen K. title = Airborne Influenza A Virus Exposure in an Elementary School date = 2020-02-05 pages = extension = .txt mime = text/plain words = 4118 sentences = 212 flesch = 46 summary = In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Significantly different (p = 0.049) airborne IAV densities were detected between all three indoor locations (i.e., gymnasium, classroom, and corridor) and all positive samples were collected during the last two weeks of 66 , and a 20-30% relative humidity level; Descriptive of an average elementary school student in the USA weighing ~23-32 kg with an assumed tidal volume (V T ) of 7 mL per kg of body mass. Given the high airborne IAV densities detected in the school corridor, along with elevated student contact rates, it is plausible to conclude that the school corridor is a "hotspot" for influenza virus transmission. cache = ./cache/cord-004280-c470nlie.txt txt = ./txt/cord-004280-c470nlie.txt === reduce.pl bib === id = cord-004848-2cfphi88 author = Carter, M. J. title = Transcription of feline calicivirus RNA date = 1990 pages = extension = .txt mime = text/plain words = 3361 sentences = 190 flesch = 60 summary = In this way these workers have identified three intracellular RNAs (4.8, 4.2, and 2.4 kb) as well as the genome (8.2 kb) and shown that these form a nested set of 3' co-terminal molecules similar to that observed in coronavirus infected cells. We have used this to probe FCV-infected cells for the synthesis of virus specific RNA and confirm and extend the observations of Neill and Mengeling. Subcloning of the virus 3' end into a single stranded vector has allowed us to examine the occurrence of positive and negative sense RNA separately. Finally this inference was confirmed by subcloning the terminal EcoRI/PstI fragment into M13 and determining its sequence (Fig. 3a) , This showed a poly A stretch preceded by a short run ofpoly C which is exactly that structure expected for cDNA clones derived by this method from an mRNA 3' end. However, the negative strand-specific probe also showed hybridization to subgenomic messages 2-4, but this was not observed until later in infection than the detection of the positive forms of these molecules. cache = ./cache/cord-004848-2cfphi88.txt txt = ./txt/cord-004848-2cfphi88.txt === reduce.pl bib === id = cord-003382-v3w1wi5c author = Rahmatpanah, Farah title = Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors date = 2018-10-02 pages = extension = .txt mime = text/plain words = 5543 sentences = 342 flesch = 56 summary = We examined the effect of human primary bronchial epithelial cells (PBECs) on PDC functions by performing RNA-sequencing of PDCs after co-culture with air liquid interface differentiated PBECs. Functional analysis revealed that PDCs co-cultured with PBECs displayed upregulation of type I IFN production and response genes. In keeping with the RNA-seq data, we observe increased secretion of type I IFN and other cytokines in response to influenza in PDCs co-cultured with PBECs. The PDCs also primed Th1 responses in T cells. PDCs exposed to PBECs secreted significantly higher levels of type I IFNs (p = 0.0001) on stimulation with influenza as compared to PDCs cultured alone (Fig. 3a) , which is in keeping with the RNA-seq data. In keeping with the activation genes in RNA-seq, we also observed increased secretion of type I IFN from influenza stimulated PDCs co-cultured with PBECs. The expression of TLR9 and ZBP1 was upregulated. cache = ./cache/cord-003382-v3w1wi5c.txt txt = ./txt/cord-003382-v3w1wi5c.txt === reduce.pl bib === id = cord-003707-fbe47bgi author = Russo, Alice G title = Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date = 2019-06-18 pages = extension = .txt mime = text/plain words = 9010 sentences = 611 flesch = 55 summary = I. scapularis NIRVS are enriched in bunyaand orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. NIRVS arise from the reverse transcription of viral RNA into cDNA and its integration into the genome of a host germ cell, followed by vertical transmission to offspring (Katzourakis and Gifford 2010) . Yet recent evidence has highlighted the abundance of NIRVS in some arthropod genomes-e.g., Ae. aegypti and Ae. albopictus contain >100 NIRVS from over eight RNA virus families encompassing þssRNA, ÀssRNA, and dsRNA viral groups (Palatini et al. Using the well-studied genomes of Aedes mosquitoes to validate our analysis, we employed a bioinformatic pipeline to characterise NIRVS in seven non-Aedes arbovirus vectors that have representative genomic sequences (Table 1 and Fig. 1 ). scapularis lacked NIRVS from positive-sense RNA viruses, which comprise about one tenth of NIRVS in Aedes mosquitoes ( Fig. 3; Supplementary Table S2 ). cache = ./cache/cord-003707-fbe47bgi.txt txt = ./txt/cord-003707-fbe47bgi.txt === reduce.pl bib === id = cord-003596-6dg7i06i author = Xiong, Qingqing title = Biomedical applications of mRNA nanomedicine date = 2018-07-27 pages = extension = .txt mime = text/plain words = 12783 sentences = 666 flesch = 36 summary = The rise of mRNA nanomedicines is rapidly advancing their applications in a wide range of biomedical fields, such as vaccination, protein-replacement therapy, gene editing, and cell reprogramming and engineering. The four major biomedical applications of mRNA nanomedicine include: 1) nanovaccines derived from antigen-encoded mRNA for the activation of the immune system; 2) proteinreplacement therapy for the treatment of genetic disorder diseases and cancer due to the mutation or loss of protein expression; 3) gene-editing achieved by the co-delivery of Cas9-encoded mRNA and gRNA; and 4) cell programming and engineering through the introduction of mRNA encoding for transcript factors or other functional molecules. In other studies, SAM vaccines encoding influenza antigens were successfully delivered to DCs by chitosan-nanoparticles and PEI-based polyplexes, which were also reported to successfully induce humoral and cellular immune responses in mice [145, 146] . Phosphorothioate cap analogs increase stability and translational efficiency of RNA vaccines in immature dendritic cells and induce superior immune responses in vivo cache = ./cache/cord-003596-6dg7i06i.txt txt = ./txt/cord-003596-6dg7i06i.txt === reduce.pl bib === id = cord-005281-wy0zk9p8 author = Blinov, V. M. title = Viral component of the human genome date = 2017-05-09 pages = extension = .txt mime = text/plain words = 6583 sentences = 306 flesch = 44 summary = In the human genome, this capacity is determined by the portion of chromosomal DNA, which does not contain species-specific protein-encoding sequences and, thus, can basically make a place for novel information that will be modified to reach a new balance. In fact, the scope of the described phenomena is not limited to retroviruses as such, since the ubiquity of retroviral elements in animal genomes, their activity in germline cells [31] , along with the fact that viral replication depends significantly on RNA expression, allow retroviruses to contribute in different ways to the insertion of nonretroviral genes into animal germline cells. Finally, the ability to incorporate parts of the viral genome into the chromosomal DNA of host germline cells can vary strongly among different taxonomic groups of viruses, i.e., orders, families, genera, and even species If insertions of viral sequences remain functionally active in the host cell genome, they can give rise to either proteins that function in a new environment or untranslated RNAs of different sizes. cache = ./cache/cord-005281-wy0zk9p8.txt txt = ./txt/cord-005281-wy0zk9p8.txt === reduce.pl bib === id = cord-001521-l36f1gp7 author = nan title = Oral and Poster Manuscripts date = 2011-04-08 pages = extension = .txt mime = text/plain words = 183363 sentences = 11362 flesch = 53 summary = The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. cache = ./cache/cord-001521-l36f1gp7.txt txt = ./txt/cord-001521-l36f1gp7.txt === reduce.pl bib === id = cord-005010-xg2bv9gy author = Dayer, Mohammad Reza title = Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date = 2015-01-30 pages = extension = .txt mime = text/plain words = 4251 sentences = 213 flesch = 46 summary = title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus In the present work, by analyzing genomic sequences of RNA viruses either with negative or positive sense, performing different docking experiments and carrying out molecular dynamic (MD) simulations, we undertook to study the mechanism conferring different affinities to CCHFV nucleoprotein for negative and positive sense RNAs'. Figure 1 , also, shows that irrespective of their senses, long RNAs have comparatively higher affinities to nucleoprotein than short RNAs. Based on the results of aforementioned docking experiments, we then selected CCHFV nucleoproteins-RNA complexes of maximum binding energies for positive and negative sense RNAs (both short and long) to carry out MD simulations. cache = ./cache/cord-005010-xg2bv9gy.txt txt = ./txt/cord-005010-xg2bv9gy.txt === reduce.pl bib === id = cord-006331-s2qf98lj author = Spiridonova, V. A. title = Molecular recognition elements: DNA/RNA-aptamers to proteins date = 2010-05-23 pages = extension = .txt mime = text/plain words = 7144 sentences = 412 flesch = 57 summary = After 16 rounds of selection from the 2' amino modified RNA library the isolated aptamers formed a complex with FVIIa characterized by the K d value of 11.3 ± 1.3 nM. performed RNA selection to FIXa; after eight rounds of selection they found an aptamer, which bound to FIXa with the K d value of 0.65 ± 0.2 nM and exhibited 5000 fold higher affinity to FIXa compared with FVIIa, FXa, FXIa and activated protein C [20] . These aptamers formed a complex with ΔNS3 with the K d value of 10 nM, caused 90% inhibition of protease activity of the ΔNS3 peptide and full sized NS3 bound to a maltose binding protein (MBP NS3). Four teen rounds of selection yielded the RNA aptamer, exhibiting high affinity binding to p50 and inhibition of NF kB binding to DNA by preventing protein dimerization [91] . cache = ./cache/cord-006331-s2qf98lj.txt txt = ./txt/cord-006331-s2qf98lj.txt === reduce.pl bib === id = cord-004656-n4h295e5 author = Olson, Ann Louise title = Developmental Regulation of Angiotensinogen Gene Expression in Sheep date = 1990 pages = extension = .txt mime = text/plain words = 2412 sentences = 151 flesch = 57 summary = In an effort to determine if this phenomenon is specific to the rat or applicable to other species, we compared the ontogenic changes in hepatic and renal angiotensinogen mRNA expression in fetal (60, 90, 118, and 138 d of gestation, term being 145 d), newborn (7 d postnatal), and adult sheep. Angiotensinogen mRNA sequences were detected in all fetal liver samples and appeared to increase 3-fold from 60 to 138 d gestation and then to decrease after birth. In an effort to determine if this phenomenon is specific to the rat or applicable to other species, we compared the ontogenic Received January 18, 1990 ; accepted April 16, 1990 changes in hepatic and renal angiotensinogen gene expression during the last trimester of gestation in fetal sheep. Northern blot analysis of liver and kidney RNA from fetal sheep (1 18 and 138 d gestational age) 1 and newborn lamb are shown in Figure 3 . cache = ./cache/cord-004656-n4h295e5.txt txt = ./txt/cord-004656-n4h295e5.txt === reduce.pl bib === id = cord-006049-sw1hki4r author = Keefe, Anthony D. title = Aptamers as therapeutics date = 2010 pages = extension = .txt mime = text/plain words = 9789 sentences = 510 flesch = 42 summary = Nucleic acid aptamers can be selected from pools of random-sequence oligonucleotides to bind a wide range of biomedically relevant proteins with affinities and specificities that are comparable to antibodies. Although this is true for biological nucleic acids [1] [2] [3] [4] , it was only recently that a series of technological advances allowed the development of in vitro evolutionary methods for the discovery of additional, non-biological oligonucleotides that can bind to protein targets. Since the invention of the SELEX process around 1990 (REfS 5, 6) , researchers have identified high-affinity aptamers that target a broad cross-section of protein families including cytokines, proteases, kinases, cell-surface receptors and cell-adhesion molecules (TABLE 1) . In particular, the site-specific placement of functional groups for conjugation means that the modification of aptamers after the solid-phase step (for example with high molecular mass PEG 46 ) leads to products with discrete stoichiometries and defined chemical structures. Selection of a RNA aptamer that binds to human activated protein C and inhibits its protease function cache = ./cache/cord-006049-sw1hki4r.txt txt = ./txt/cord-006049-sw1hki4r.txt === reduce.pl bib === id = cord-006452-mmdk2xom author = Chen, Jing title = Nucleic Acid-Based Therapeutics for Pulmonary Diseases date = 2018-10-18 pages = extension = .txt mime = text/plain words = 6605 sentences = 361 flesch = 38 summary = Nucleic acid-based therapeutics present huge potential in the treatment of pulmonary diseases ranging from lung cancer to asthma and chronic pulmonary diseases, which are often fatal and widely prevalent. In this review, we provide a comprehensive overview of the nucleic acid application for pulmonary diseases, covering action mechanism of the nucleic acid drugs, the novel delivery systems, and the current formulation for the administration to lungs. To overcome these biological barriers, strategies like chemical modification, conjugation, vector encapsulation, and selection of administration route have been utilized to improve the delivery of nucleic acids to lungs. One direction for developing new drugs to treat asthma is to target central pathways to the pathogenesis of the disease, and nucleic acid-mediated therapies silencing the specific effector or the upstream regulator can be a potential approach. Nucleic acid drugs hold great promises as new classes of therapeutic agents for pulmonary diseases, and some candidates have entered into clinical trials (Table III) . cache = ./cache/cord-006452-mmdk2xom.txt txt = ./txt/cord-006452-mmdk2xom.txt === reduce.pl bib === id = cord-003898-y6zpvw84 author = Tan, Kai Sen title = RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date = 2019-08-27 pages = extension = .txt mime = text/plain words = 7671 sentences = 386 flesch = 44 summary = title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications The aim of this study was to utilize RNA sequencing (RNAseq) technology to not only reveal the hNEC responses (from multiple individuals) against influenza infection, but also to identify those genes with high magnitude changes to serve as potential reference markers of the innate responses of influenza infection. After deriving the transcriptomes by RNAseq, we then further investigated whether the changes in expression of genes resulted in alterations in secretory cytokines and chemokines early in the infection of hNECs. Initially, we detected significant reductions in multiple cytokines at 8 hpi, with the exception of IL-15 which was increased ( Figure S2 ). In conclusion, RNAseq technology allowed us to accurately quantify the magnitude of gene expression changes, as well as the relevant enriched pathways during H3N2 influenza virus infection of hNECs, which can serve as a baseline for future clinical studies. cache = ./cache/cord-003898-y6zpvw84.txt txt = ./txt/cord-003898-y6zpvw84.txt === reduce.pl bib === id = cord-004851-h9ppa064 author = Plagemann, P. G. W. title = Hepatitis C virus date = 1991 pages = extension = .txt mime = text/plain words = 6835 sentences = 320 flesch = 48 summary = The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pestiand flaviviruses, the following genome organization has been predicted. A recent study of stored blood samples from prospective studies of 15 U.S.A. patients with transfusion-associated chronic hepatitis documented by liver biopsies indicated that the time course of changes in plasma ALT activity and of the formation of anti-HepCV antibodies can vary considerably between patients [4] . The putative nucleocapsid protein sequence derived from PCR products of RNA extracted from healthy Japanese carrier plasma exhibited a 97.4% amino acid identity with the sequence determined for the original chimpanzee HepCV isolate (HepCV-1) but only a 90.5 % identity at the nucleotide level [45] [46] [47] . cache = ./cache/cord-004851-h9ppa064.txt txt = ./txt/cord-004851-h9ppa064.txt === reduce.pl bib === id = cord-007819-51h2jrsy author = Schommer, Susan K. title = Use of a PRRSV Infectious Clone to Evaluate in Vitro Quasispecies Evolution date = 2006 pages = extension = .txt mime = text/plain words = 1393 sentences = 82 flesch = 52 summary = Use of the infectious clone also allows us to begin with a single DNA sequence, providing a well-defined starting point for studying PRRSV evolution. 8 The ORF3 protein has the greatest percentage of amino acid changes between the modified live vaccine (Ingelvac) and its parent strain, VR-2332, the isolate from which the infectious clone used in this study was derived. These sequences were then compared to a low passage VR-2332 cell culture propagated stock to determine if the use of an infectious clone was able to decrease the quasispecies variation as compared to a viral stock. The master sequence for each sample derived from the infectious clone was the same as the original plasmid for all genetic regions investigated. Generation of an infectious clone of VR-2332, a highly virulent North American-type isolate of porcine reproductive and respiratory syndrome virus cache = ./cache/cord-007819-51h2jrsy.txt txt = ./txt/cord-007819-51h2jrsy.txt === reduce.pl bib === id = cord-003676-kr4o8hoc author = Tan, Chee Wah title = Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans date = 2019-05-28 pages = extension = .txt mime = text/plain words = 3944 sentences = 217 flesch = 55 summary = title: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans In this study, we screened 517 cynomolgus macaques caught in Singapore for evidence of exposure to PRV3M (also known as Melaka virus), which was first isolated from human patients in Melaka, Malaysia. We provide evidence that PRV exposure in the macaque population in Singapore occurs at a relatively high prevalence and this study suggests that cynomolgus macaques may be an intermediate or reservoir host for PRVs. Pteropine orthoreoviruses (PRVs) are a group of emerging bat-borne viruses, belonging to the genus Orthoreovirus within the family Reoviridae. Given the cross-species transmission of PRVs and frequent human-monkey interaction in Singapore and surrounding regions, we initiated this study to determine the seroprevalence of PRV3M in wild cynomolgus macaques and to examine the susceptibility of cynomolgus macaques to experimental infection with PRV3M and their potential role in acting as hosts facilitating cross-species transmission. cache = ./cache/cord-003676-kr4o8hoc.txt txt = ./txt/cord-003676-kr4o8hoc.txt === reduce.pl bib === id = cord-003435-ke0az7nf author = Schlake, Thomas title = mRNA as novel technology for passive immunotherapy date = 2018-10-17 pages = extension = .txt mime = text/plain words = 15190 sentences = 850 flesch = 40 summary = Recombinant technologies further expanded the available therapies based on mAbs. In vitro antibody selection technologies like phage or ribosome display were developed to enable the generation of highly specific human mAbs out of libraries that may even be naïve for the specific antigens [31] [32] [33] [34] [35] [36] 1 Schematic illustration comparing active immunization and passive antibody immunotherapies. While T cell engineering for adoptive transfer inevitably requires the use of nucleic acids encoding a target-specific receptor, antibody immunotherapy can deploy recombinant proteins. However, the effects of mRNA modifications on translation, immunostimulation and resulting protein expression appear to be variable, for instance dependent on the type of target cells. In comparison to a single transfer of cells with retroviral CAR expression, an mRNA-encoded receptor required three consecutive lymphocyte infusions to obtain a comparable antitumor effect [262] . cache = ./cache/cord-003435-ke0az7nf.txt txt = ./txt/cord-003435-ke0az7nf.txt === reduce.pl bib === id = cord-007714-n3omlvfl author = Brown, J. W. S. title = The Role of the Plant Nucleolus in Pre-mRNA Processing date = 2008 pages = extension = .txt mime = text/plain words = 7260 sentences = 364 flesch = 46 summary = In recent years, molecular and proteomic approaches have begun to dissect the pathways of ribosomal subunit assembly and transport from the nucleolus and examine the composition of protein complexes and RNPs involved in these processes (Grandi et al. In plants, the best-characterised nuclear bodies are the nucleolus and CBs. The plant nucleolus differs to some extent in organisation and structure from the animal nucleolus, although its major function in rRNA and ribosomal subunit production remains the same Shaw and Brown 2004) . Finally, the Arabidopsis nucleolus contains exon junction complex proteins, involved in linking transcription and splicing to translation, export and mRNA surveillance (Pendle et al. As with other large RNP complexes such as the spliceosome, correct assembly occurs in a regulated and co-ordinated step-wise pathway involving non-ribosome factors and ribosomal proteins required for correct rRNA folding, protein association and ultimately export of the ribosomal subunits through the nuclear pore complex to the cytoplasm (Venema and Tollervey 1999; Fatica and Tollervey 2002; Grannemann and Baserga 2004) . cache = ./cache/cord-007714-n3omlvfl.txt txt = ./txt/cord-007714-n3omlvfl.txt === reduce.pl bib === id = cord-004507-ezuyjcxs author = Tomazatos, Alexandru title = Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix) date = 2020-02-21 pages = extension = .txt mime = text/plain words = 6326 sentences = 348 flesch = 49 summary = The study provided complete genome sequences for nine Letea virus strains and new information about orbivirus diversity, host range, ecology and evolution. The phylogenetic clustering of Orbivirus members results in clades indicating their putative or potential arthropod vectors: Culicoidesor sand fly-borne (C/SBOV), mosquito-borne (MBOV) and tick-borne orbiviruses (TBOV) [9] . Evolutionary relationship of LEAV with representative members of the Orbivirus genus were analyzed by inferring phylogenetic trees with amino acid and nucleotide ORF sequences of conserved genes encoding the polymerase (VP1), the subcore shell protein T2 (VP2/VP3) and the major core surface protein T13 (VP7) [5, 6] . Inclusion and demarcation of species within the Orbivirus genus considers several criteria, such as sequence identity of segments encoding the polymerase (VP1) and major subcore shell protein T2, gene reassortment between close strains, high levels of serological cross-reactivity against conserved antigens like the T13 protein, conservation of UTR terminal nucleotides, range of hosts and vectors or the clinical signs associated with orbivirus infection [1] . cache = ./cache/cord-004507-ezuyjcxs.txt txt = ./txt/cord-004507-ezuyjcxs.txt === reduce.pl bib === id = cord-005654-n9u2em10 author = Campbell, David A. title = Apparent discontinuous transcription of Trypanosoma brucei variant surface antigen genes date = 1984 pages = extension = .txt mime = text/plain words = 4241 sentences = 218 flesch = 58 summary = 41 The repeated mini-exon sequence that encodes the first 35 base pairs of all variant surface antigen mRNAs of Trypanosoma brucei directs the synthesis of a discrete I37-nucleotide transcript. 41 The repeated mini-exon sequence that encodes the first 35 base pairs of all variant surface antigen mRNAs of Trypanosoma brucei directs the synthesis of a discrete I37-nucleotide transcript. This result could be interpreted as protection by a short RNA of 137 nucleotides derived from the mini-exon repeats and/or by a longer transcript with a discontinuity at this position in the RNA/DNA duplex. The second method to detect and size transcripts from the mini-exon repeat used Northern blot analysis 31 • For this procedure, total trypanosome RNA was resolved by polyacrylamide gel electrophoresis (PAGE) in denaturing conditions, transferred to GeneScreen membrane 32 and hybridized with a [5/ -32 P]_labelled, synthetic oligonucleotide complementary to positions + 117 to +133. cache = ./cache/cord-005654-n9u2em10.txt txt = ./txt/cord-005654-n9u2em10.txt === reduce.pl bib === id = cord-000083-3p81yr4n author = nan title = Poster Exhibition date = 2009-01-31 pages = extension = .txt mime = text/plain words = 112815 sentences = 7542 flesch = 56 summary = R. China Background: The objective of this study was to evaluate the early virologic response for prediction of achievement of HBeAg seroconversion and hepatitis B virus (HBV) DNA negativity after two years of lamivudine treatment in chronic hepatitis B (CHB) patients. Methods: A total of 620 patients who tested positive for hepatitis B surface antigen and were referred to Chiba University Hospital between February 1985 and March 2008 were included in the study, and their following characteristics were analyzed: age, gender, the status of HBeAg, ALT, HBV-DNA level, and PLT. Methods: A total of 60 patients with chronic hepatitis B, 32 (53.3%) were HBeAg positive (group A) while 28(46.7%) were HBeAg negative (group B) were included in this study after meeting the following criteria: age 18 to 60 years, HBsAg positive for more than 6 months, serum HBV-DNA was >5 log(10) copies/mL and ALT more than two times the upper normal limit. cache = ./cache/cord-000083-3p81yr4n.txt txt = ./txt/cord-000083-3p81yr4n.txt === reduce.pl bib === id = cord-007236-8hiymqyb author = Sun, Ji-Min title = Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway date = 2011-11-09 pages = extension = .txt mime = text/plain words = 4983 sentences = 276 flesch = 47 summary = title: Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway We demonstrated that a group of Monascus orange pigment (MOP) derivatives effectively inhibited NS5B RdRp activity and interfered with the mevalonate synthesis pathway, thereby suppressing HCV replication in cells harbouring an HCV genotype 1b subgenomic replicon and in cells infected with genotype 2a HCV. As shown in Figure 2 (a), among the selected group of MOP AADs that inhibited NS5B RdRp activity in vitro, Lys, Phe, Val, Leu and Ile derivatives also inhibited HCV replication in Huh7 cells, which harbour a HCV subgenomic replicon RNA. Together, these results suggest that in addition to a direct inhibition of NS5B RdRp activity, these MOP AAD compounds also inhibit HCV replication by interfering with the cholesterol biosynthetic pathway downstream of the HMG-CoA reductase step. cache = ./cache/cord-007236-8hiymqyb.txt txt = ./txt/cord-007236-8hiymqyb.txt === reduce.pl bib === id = cord-007009-4wbvdg1r author = Takahashi, Toru title = The First Identification and Retrospective Study of Severe Fever With Thrombocytopenia Syndrome in Japan date = 2014-03-15 pages = extension = .txt mime = text/plain words = 4686 sentences = 236 flesch = 47 summary = Severe fever with thrombocytopenia syndrome (SFTS), an infectious disease with a high case-fatality rate, is caused by SFTS virus (SFTSV), a novel bunyavirus reported to be endemic to central and northeastern parts of China [1, 2] . Vero cells were inoculated with RT-PCR-positive patient sera for virus isolation, cultured for 4-7 days, and examined for SFTSV antigen detection by indirect immunofluorescence assay (IFA) with a polyclonal antibody raised against SFTSV recombinant NP (rNP; rabbit anti-SFTSV rNP serum), which was produced as follows. Physicians were asked to volunteer information if they had treated patients who satisfied the following case definition: (1) fever of >38°C; (2) gastrointestinal tract symptoms, such as nausea, vomiting, abdominal pain, diarrhea, and melena; (3) thrombocytopenia, with <100 × 10 9 platelets/L; (4) leukopenia, with <4 × 10 9 white blood cells/L; (5) elevated levels of aspartate aminotransferase, alanine aminotransferase, and lactate dehydrogenase; (6) absence of other causes; and (7) death or admission to an intensive care unit because of the severity symptoms. Detection of severe fever with thrombocytopenia syndrome virus (SFTSV) RNA in the right cervical lymph node by the in situ hybridization ATtailing method. cache = ./cache/cord-007009-4wbvdg1r.txt txt = ./txt/cord-007009-4wbvdg1r.txt === reduce.pl bib === id = cord-004274-cot05vx7 author = Jackson, Nicholas A. C. title = The promise of mRNA vaccines: a biotech and industrial perspective date = 2020-02-04 pages = extension = .txt mime = text/plain words = 4253 sentences = 251 flesch = 38 summary = "STATE-OF-THE-ART" mRNA CONSTRUCTS AND DELIVERY TECHNOLOGIES The core principle behind mRNA as a technology for vaccination is to deliver the transcript of interest, encoding one or more immunogen(s), into the host cell cytoplasm where expression generates translated protein(s) to be within the membrane, secreted or intracellularly located. Perspective #2: Translational sciences will inform preclinical and clinical studies to promote rapid downselection of constructs and formulations A key aspect of vaccine development efforts is the goal of making early informed decisions, based on objective data that favor or disfavor a particular candidate. 64 The current focus from a clinical perspective is to optimize the benefit (immunogenicity and efficacy) while reducing the risk (safety) profile of a candidate mRNA vaccine by optimizing the quality attributes that dictate expression and/or augmenting delivery. Thus, early-phase clinical trials need to be designed in a way to appropriately capture the inflammatory component intrinsic to all mRNA vaccines, given that several intracellular innate immune response sensors are activated by RNA. cache = ./cache/cord-004274-cot05vx7.txt txt = ./txt/cord-004274-cot05vx7.txt === reduce.pl bib === id = cord-007041-rloey02j author = Harel, Noam title = Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations date = 2019-12-16 pages = extension = .txt mime = text/plain words = 7126 sentences = 333 flesch = 50 summary = We sequenced virus populations in parallel using both MinION and Illumina, allowing us to corroborate the inferences of AssociVar. This then allowed us to directly infer relationships between mutations and to deduce the entire genome sequences of viral strains in the population. We then determined the population frequency of each mutation at passage 1 and passage 15 through whole genome deep sequencing as described below, using Illumina and MinION. After applying AssociVar to the data, we were able to identify five out of the six mutations appearing at a frequency above 10% in the Illumina results in p15A, and all eight positions within the p15B sample (Figure 4 , Supplementary Table S2 ). We applied AssociVar to sequencing data from an evolved population of phages where Illumina sequencing was available, allowing us to corroborate whether mutations we found based on analysis of the MinION data alone were indeed real. cache = ./cache/cord-007041-rloey02j.txt txt = ./txt/cord-007041-rloey02j.txt === reduce.pl bib === id = cord-006129-5rog0s98 author = Hemida, Maged Gomaa title = Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date = 2012-08-16 pages = extension = .txt mime = text/plain words = 7443 sentences = 508 flesch = 50 summary = [12] Answering back, certain host miRNAs alter the cell gene expression to defend the cells against the viral infection by interfering with viral proteins or other cellular factors as a type of immune response against these particular viruses. [40] These virus-encoded miRNAs play important roles in the establishment of latent infection, as well as the pathogenesis of virally induced diseases. According to the most recent studies, herpesviruses utilize their encoded miRNAs in a wide range of biologic functions, such as inhibition of apoptosis, immune evasion, control of cellular proliferation, and regulation of viral replication. [58] Downregulation of UL114 protein, using miR-UL112-1, results in inhibition of viral DNA replication and subsequently triggers the latent phase of infection, making the virus able to evade the host immune system. cache = ./cache/cord-006129-5rog0s98.txt txt = ./txt/cord-006129-5rog0s98.txt === reduce.pl bib === id = cord-003597-zj3w9ptj author = Altman, Matthew C. title = Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children date = 2019-04-08 pages = extension = .txt mime = text/plain words = 13552 sentences = 661 flesch = 44 summary = We combined nasal virus PCR, nasal and peripheral blood cell differentials, and nasal and blood RNA-seq for serial sample collections at baseline and longitudinally during episodes when participants reported cold symptoms to determine the key molecular pathways associated with subsequent asthma exacerbations. The primary aim of the study was to identify patterns of gene expression induced during events that progressed to asthma exacerbations (exacerbation, Ex + ), defined by clinical symptoms that resulted in systemic corticosteroid use within 10 d of cold Fig. 1 | Study design and primary and secondary endpoints. From nasal and blood samples, we combined measured cell percentages with RNA-seq data and used cell deconvolution and WGCNA to construct and validate a repertoire of 94 distinct gene expression modules representing a diverse array of biological functions (Supplementary Fig. 1 and Supplementary Table 1 ). cache = ./cache/cord-003597-zj3w9ptj.txt txt = ./txt/cord-003597-zj3w9ptj.txt === reduce.pl bib === id = cord-004719-3stcx0dd author = Mushegian, A. R. title = Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date = 1993 pages = extension = .txt mime = text/plain words = 6347 sentences = 280 flesch = 44 summary = In several groups of positive-strand RNA viruses, the movement function is provided by the proteins encoded by the so-called triple gene block including two putative small membrane-associated proteins and a putative RNA helicase. It is concluded that classification of movement proteins based on comparison of their amino acid sequences does not correlate with the type of genome nucleic acid or with grouping of viruses based on phylogenetic analysis of replicative proteins or with the virus host range. Limited sequence similarities were observed between i) movement proteins of dianthoviruses and the MIP family of cellular integral membrane proteins, and ii) between movement proteins of bromoviruses and cucumoviruses and M1 protein of influenza viruses which is involved in nuclear export of viral ribonucleoproteins. With representative sequences of plant virus genomes from many groups available, efforts were made to identify regions of similarity between known movement proteins and to predict movement functions for uncharacterized ORFs. Early observations made by this approach have been reviewed previously (e.g. cache = ./cache/cord-004719-3stcx0dd.txt txt = ./txt/cord-004719-3stcx0dd.txt === reduce.pl bib === id = cord-004509-jkzqmkz6 author = Thirion, Laurence title = Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology date = 2020-01-30 pages = extension = .txt mime = text/plain words = 4393 sentences = 194 flesch = 47 summary = In conclusion, Lyoph-P&P holds several advantages over extemporaneously preparer liquid formulation that merit to be considered when a novel real-time molecular assay is implemented in a laboratory in charge of routine diagnostic activity. Selected assays target two emerging viruses that are listed on the blueprint of the WHO as to be considered for preparedness and response actions [5] : chikungunya virus (CHIKV), a single-stranded positive-sense RNA alphavirus, and Rift Valley fever phlebovirus (RVFV), a tri-segmented, single-stranded negative-sense RNA phlebovirus. Detection of CHIKV RNA using Lyoph-P&P provides results in clinical samples that are at least equal and often better than those obtained with the extemporaneously prepared liquid formulation used as reference. Indeed, at laboratory level, it is likely that one or two different formats (number of tests per vial) will be either prepared or ordered; as a consequence, the time during which rehydrated material can be stored without affecting the expected performances of the assay is a key factor. cache = ./cache/cord-004509-jkzqmkz6.txt txt = ./txt/cord-004509-jkzqmkz6.txt === reduce.pl bib === id = cord-007463-8g0zklzy author = Pocock, D.H. title = Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis date = 2002-11-13 pages = extension = .txt mime = text/plain words = 1932 sentences = 91 flesch = 49 summary = The 3′ terminal labelling method for the analysis of genome profiles used in this study required only 1 ng of viral RNA, an increase of 1000-fold in sensitivity over ethidium bromide staining for detecting all rotavirus genome segments. To investigate the latter, mixtures containing known amounts of ds-RNA from two rotavirus isolates with disparate genome profiles (UK strain and a C7 type) were used to simulate the type of samples that might be recovered from calves concurrently infected with these two viruses. After 3' terminal labelling the RNA segments were analysed by electrophoresis (Fig. 3) profiles, and meant that in a faecal sample containing two rotaviruses if one virus was present at a concentration 10-fold less than the other, i.e. 1 log10 dilution, it would not be detected. Rotaviruses isolated from 43 sub-clinically infected calves were characterised by genome profile analysis. cache = ./cache/cord-007463-8g0zklzy.txt txt = ./txt/cord-007463-8g0zklzy.txt === reduce.pl bib === id = cord-009662-ntjngiem author = Moulton, Jon D. title = Using Morpholinos to Control Gene Expression date = 2007-01-15 pages = extension = .txt mime = text/plain words = 11606 sentences = 583 flesch = 48 summary = When delivering Morpholinos to cell cultures using Endo-Porter, starting with a 10 µM Morpholino concentration for both fluorescent delivery assays and functional experiments increases the chances that the fluorescence will be visible in the cytosol and that the first functional experiment will produce measurable results. However, assaying only for a phenotypic effect becomes problematic if the expected change in phenotype does not occur; if antisense activity is not separately assessed at the level of protein concentration or mRNA mass, the experimenter will not be able to discern whether (1) the oligo failed to reach and interact with its target mRNA to produce the knockdown or splice-block, or (2) the knockdown or spliceblock was successful but did not cause the expected phenotypic change. The negative control shows that the effects observed during the antisense experiment are due to the sequence of the targeting oligo and not to the backbone chemistry of the Morpholino or the cytosolic delivery method used. cache = ./cache/cord-009662-ntjngiem.txt txt = ./txt/cord-009662-ntjngiem.txt === reduce.pl bib === id = cord-009376-a35a92gh author = Lovatt, Archie title = Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date = 2002-01-07 pages = extension = .txt mime = text/plain words = 9214 sentences = 523 flesch = 48 summary = Applications of Q-PCR within biotechnology are discussed with particular emphasis on the following areas of biosafety and genetic stability testing: (a) determination of the biodistribution of gene therapy vectors in animals; (b) quantification of the residual DNA in final product therapeutics; (c) detection of viral and bacterial nucleic acid in contaminated cell banks and final products; (d) quantification of the level of virus removal in process validation viral clearance studies; (e) specific detection of retroviral RT activity in vaccines with high sensitivity; and (f) transgene copy number determination for monitoring genetic stability during production. We are developing Q-PCR assays for these repeat regions for rodent and primate residual DNA to obtain sensitivity in the fg range, however, one advantage of using a gene such as ␤-actin is gene stability, as this target should not undergo copy number changes within a stable cell line. cache = ./cache/cord-009376-a35a92gh.txt txt = ./txt/cord-009376-a35a92gh.txt === reduce.pl bib === id = cord-007382-5kb16qb7 author = Hartmann, G. title = Nucleic Acid Immunity date = 2016-12-15 pages = extension = .txt mime = text/plain words = 16155 sentences = 915 flesch = 47 summary = With the additions of RNAi and the CRISPR/Cas system, specific nucleases including the restriction-modification (R-M) systems, and antiviral effector proteins partially discovered only recently in the context of rare hereditary inflammatory diseases, the new concept of nucleic acid immunity evolves. While innate nucleic acid immune-sensing receptors elicit antiviral signaling pathways, a number of nucleic acid-detecting effector proteins (viral restriction factors, e.g., PKR, ADAR1, IFIT1) directly detect and restrict nucleic acid function and replication. Another member of the RIG-I-like helicase family of receptors is MDA5 which was found to be responsible for the long sought after type I IFN-inducing activity of cytosolic long double-stranded RNA including poly(I:C) . Extrinsic effects inside the same cell include degradation of the nucleic acid (e.g., RNase L activated by 2 0 -5 0 -OA generated by OAS1 upon binding of long double-stranded RNA). cache = ./cache/cord-007382-5kb16qb7.txt txt = ./txt/cord-007382-5kb16qb7.txt === reduce.pl bib === id = cord-007474-ckqghr3b author = Johnson, Michael E. title = Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes date = 2002-11-13 pages = extension = .txt mime = text/plain words = 6487 sentences = 362 flesch = 51 summary = Recombinant complementary DNA (cDNA) representing gene 9 (the gene encoding the neutralization antigens in VP7 glycoprotein) from OSU (porcine rotavirus serotype 1) and Gottfried (porcine rotavirus serotype 2) strains were used to determine the optimal hybridization conditions which allow specific detection of group A porcine rotaviruses. In the present study, a dot blot hybridization assay is described for the detection and serotypic differentiation of porcine rotavirus utilizing hybridization probes prepared from recombinant cDNA representing gene 9 from OSU and Gottfried strains (porcine rotavirus serotypes 1 and 2, respectively). Five subfragments of gene 9 from OSU and Gottfried (Table 1 ) were 32p-labeled and hybridized to heterologous rotavirus RNA under both high and low stringency conditions. They reported that rotavirus serotypes 2 and 3 could be differentiated with the gene 9 cDNA probe by using conditions of low stringency (56 ° C), and comparison with the results obtained with hybridization at 56°C, 13% formamide. cache = ./cache/cord-007474-ckqghr3b.txt txt = ./txt/cord-007474-ckqghr3b.txt === reduce.pl bib === id = cord-008556-oetrdm8g author = Kozak, Marilyn title = Regulation of Protein Synthesis in Virus-Infected Animal Cells date = 2008-03-01 pages = extension = .txt mime = text/plain words = 23945 sentences = 1270 flesch = 51 summary = One consequence of the scanning mechanism is that deleting the "ribosome binding site" (i.e., the normal initiator codon and flanking sequences) will not abolish translation; ribosomes will simply use the next AUG codon downstream, which, in some cases, has been shown to direct the synthesis of a biologically active, truncated protein (Downey et al., 1984; Halpern and Smiley, 1984; Katinka and Yaniv, 1982) . The best evidence for this is the ability of both EMC and SFV 26 S mRNA to be translated in EMC virus-infected cells, in which host translation is drastically inhibited by a mechanism that has not been difined, but that clearly does not involve cap binding protein (Mosenkis et al., 1985) . In wild-type adenovirus-infected cells, in which host protein synthesis is drastically reduced, both adenovirus and influenza virus mRNAs are translated efficiently. cache = ./cache/cord-008556-oetrdm8g.txt txt = ./txt/cord-008556-oetrdm8g.txt === reduce.pl bib === id = cord-005865-7lohh5ty author = Pipper, Juergen title = Catching bird flu in a droplet date = 2007-09-23 pages = extension = .txt mime = text/plain words = 4167 sentences = 207 flesch = 52 summary = Here we present a microfluidic platform that can detect the highly pathogenic avian influenza virus H5N1 in a throat swab sample by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. Here we present a microfluidic platform that can detect the highly pathogenic avian influenza virus H5N1 in a throat swab sample by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. Starting from a throat swab sample, we show how HPAI H5N1 can be detected by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. (h) After SPE, the immobilized viral RNA is magnetically pulled out of the raw sample solution, washed four times to remove residual contaminants, and desorbed into an RT-PCR solution positioned on top of a miniaturized real-time thermocycler (see also Supplementary Fig. 1 ). cache = ./cache/cord-005865-7lohh5ty.txt txt = ./txt/cord-005865-7lohh5ty.txt === reduce.pl bib === id = cord-007621-rapinodd author = Vidovic, Maria title = Induction and regulation of class II major histocompatibility complex mRNA expression in astrocytes by interferon-γ and tumor necrosis factor-α date = 2002-11-13 pages = extension = .txt mime = text/plain words = 6680 sentences = 365 flesch = 57 summary = Previous data from this laboratory had shown that the cytokine tumor necrosis factor-α (TNF-α) enhances IFN-γ-mediated class II antigen expression on astrocytes. To determine the steady-state level of mRNA for class II, Northern blot analysis was performed using a eDNA probe for murine class Ii genes (E-a), with total RNA isolated from cultured astrocytes. The duration of protein synthesis required to allow expression of the class II MHC gene in astrocytes was examined in cells that were pretreated with IFN-y or IFN-7/TNF-a for different lengths of time prior to the addition of CHX. In this study we have shown that primary neonatal rat astrocytes, upon stimulation with IFN-~,, express mRNA transcripts for class II MHC genes, and that TNF-a enhances the expression of IFN-~,-induced class II mRNA. The expression of class II mRNA was completely inhibited when CHX was included with IFN-~, and IFN-'t/TNF-~ treatment, indicating that newly synthesized protein is required for astrocyte class II MHC gene expression. cache = ./cache/cord-007621-rapinodd.txt txt = ./txt/cord-007621-rapinodd.txt === reduce.pl bib === id = cord-007066-zn10rnrm author = Park, Noh Jin title = Characterization of RNA in Saliva date = 2006-06-01 pages = extension = .txt mime = text/plain words = 4637 sentences = 285 flesch = 62 summary = RNA can enter the oral cavity through various routes, including saliva secretions from the 3 major salivary glands (the parotid, submandibular, and sublingual glands) and minor glands, gingival crevice fluid (GCF), and desquamated oral epithelial cells. It is therefore possible that the RPS9 PCR products in panels B and C of Fig. 1 are produced from both RPS9 and RPS9P2 mRNAs. Previous expression-based microarray analysis showed that 185 different transcripts were consistently detected in the supernatants of 10 healthy human saliva samples (6 ) . Although individual variations exist, we detected ␤-actin mRNA in all 3 major salivary glands, GCF, and desquamated oral epithelial cells ( Fig. 2A) , suggesting that RNA enters the oral cavity from different sites. In addition to the saliva samples, we also measured RNA-macromolecule associations in serum and found that ϳ8% and Ͻ1% of ␤-actin mRNA could be detected in serum filtered through 0.45 and 0.22 m pores, respectively (see Fig. 1c in the online Data Supplement). cache = ./cache/cord-007066-zn10rnrm.txt txt = ./txt/cord-007066-zn10rnrm.txt === reduce.pl bib === id = cord-005378-u2bbgn8k author = Yun, Sang-Im title = Overview: Replication of porcine reproductive and respiratory syndrome virus date = 2013-12-19 pages = extension = .txt mime = text/plain words = 6583 sentences = 349 flesch = 49 summary = Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that causes significant losses in the pig industry, is one of the most important animal pathogens of global significance. Similarly, mutagenesis studies have shown that EAV NSP1 (which contains a tandem of the PCPα and PCPβ domains, with PCPα having lost its enzymatic activity) is involved in regulating the accumulation of minusstrand templates to control the relative abundance of viral mRNAs, thereby coordinating genome replication, subgenomic mRNA synthesis, and virus production (Tijms et al., 2001 (Tijms et al., , 2007 Nedialkova et al., 2010) . Structure and cleavage specificity of the chymotrypsin-like serine protease (3CLSP/nsp4) of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Identification of the CD163 protein domains involved in infection of the porcine reproductive and respiratory syndrome virus cache = ./cache/cord-005378-u2bbgn8k.txt txt = ./txt/cord-005378-u2bbgn8k.txt === reduce.pl bib === id = cord-005392-0pgcfk6b author = Sidoti, Francesca title = Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes date = 2011-07-05 pages = extension = .txt mime = text/plain words = 3621 sentences = 167 flesch = 41 summary = title: Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes In this study, we developed the first quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes. Aim of this study was to develop the first quantitative real-time nucleic acid sequence-based amplification assay internally controlled using molecular beacon for selective and sensitive detection of HRV serotypes. To estimate the dynamic range of the real-time NASBA assay (range of concentrations over which the method performs in a linear manner with an acceptable level of trueness and precision), we used HRV standard dilutions from 10 8 copies/ll to 1 copy/ll. Evaluation of a real-time nucleic acid sequence-based amplification assay using molecular beacons for detection of human immunodeficiency virus type 1 cache = ./cache/cord-005392-0pgcfk6b.txt txt = ./txt/cord-005392-0pgcfk6b.txt === reduce.pl bib === id = cord-006951-tj22dh5o author = Li, Siyu title = The effect of RNA stiffness on the self-assembly of virus particles date = 2018-01-31 pages = extension = .txt mime = text/plain words = 4913 sentences = 218 flesch = 59 summary = While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging. In this paper, we vary the degree of branching as well as the effective Kuhn length and linear charge density of a model RNA, and study their impact on the optimal length of encapsulated genome by capsid proteins. cache = ./cache/cord-006951-tj22dh5o.txt txt = ./txt/cord-006951-tj22dh5o.txt === reduce.pl bib === id = cord-006960-9pho3hk6 author = Prakash, R. title = Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date = 2013-12-27 pages = extension = .txt mime = text/plain words = 6279 sentences = 286 flesch = 51 summary = In this work, we have utilized electro-actuation based DMF technology, integrated with suitably tailored resistive micro-heaters and temperature sensors, to achieve chip based real-time, quantitative PCR (qRT-PCR). Performance of the integrated DMF device was analyzed in real-time chip based qRT-PCR detection of in-vitro synthesized influenza A and C virus RNAs during 30-35 PCR cycles. Among the contact temperature control methods, the micro-fabricated resistive heaters/RTDs have smaller power requirement, faster thermal response and higher heating ramp rates and are therefore preferred for the proposed qRT-PCR micro-device. Mixing of the influenza C RNA sample and the off-chip prepared PCR reagents, followed by the RT reaction and thermal cycling over Micro-electrode 1, is shown in Figure 7 . This article demonstrates the design and micro-fabrication of integrated droplet microfluidic device, with nano-textured superhydrophobic top surface, that is capable of electro-handling of PCR samples/reagents, facilitating chip based mixing/sample preparation and chip based qRT-PCR amplification and detection of influenza viruses. cache = ./cache/cord-006960-9pho3hk6.txt txt = ./txt/cord-006960-9pho3hk6.txt === reduce.pl bib === id = cord-005377-36io7zsm author = Sidoti, Francesca title = Alternative Molecular Tests for Virological Diagnosis date = 2012-04-09 pages = extension = .txt mime = text/plain words = 5994 sentences = 292 flesch = 35 summary = The main isothermal methods reviewed here include loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), and helicase-dependent amplification (HDA). Development and evaluation of a novel loop mediated isothermal amplification (LAMP) method for rapid detection of SARS Corona virus Rapid detection of norovirus from fecal specimens by real-time reverse transcription-loop-mediated isothermal amplification assay Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification. Rapid and real-time detection of chikungunya virus by reverse transcription loop mediated isothermal amplification assay Development and evaluation of reverse transcription Loop mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus Development of a quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes Development and evaluation of a real-time nucleic acid sequence based amplification assay for rapid detection of influenza A cache = ./cache/cord-005377-36io7zsm.txt txt = ./txt/cord-005377-36io7zsm.txt === reduce.pl bib === id = cord-005147-mvoq9vln author = nan title = Autorenregister date = 2017-02-23 pages = extension = .txt mime = text/plain words = 86573 sentences = 4356 flesch = 45 summary = Using whole-exome sequencing and trio-based de novo analysis, we identified a novel heterozygous de novo frameshift variant in the leukemia inhibitory factor receptor (LIFR) gene causing instability of the mRNA in a patient presenting with bilateral CAKUT and requiring kidney transplantation at one year of age. Loss of cdkl5 associated with deficient mammalian target of rapamycin (mTOR) signaling in mice and human cells We and other groups have shown that mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene cause a severe neurodevelopmental disorder with clinical features including intellectual disability, early-onset intractable seizures and autism, that are closely related to those present in Rett syndrome (RTT) patients. Functional characterization of novel GNB1 mutations as a rare cause of global developmental delay Over the past years, prioritization strategies that combined the molecular predictors of sequence variants from exomes and genomes of patients with rare Mendelian disorders with computer-readable phenotype information became a highly effective method for detecting disease-causing mutations. cache = ./cache/cord-005147-mvoq9vln.txt txt = ./txt/cord-005147-mvoq9vln.txt === reduce.pl bib === id = cord-007689-0vpp3xdl author = Schlee, M. title = Beyond Double-Stranded RNA-Type I IFN Induction by 3pRNA and Other Viral Nucleic Acids date = 2007 pages = extension = .txt mime = text/plain words = 7735 sentences = 488 flesch = 53 summary = Since the discovery of type I IFNs in 1957, long double-stranded RNA formed during replication of many viruses was thought to be responsible for type I IFN induction, and for decades double-stranded RNA-activated protein kinase (PKR) was thought to be the receptor. It now became evident that not PKR but two members of the Toll-like receptor (TLR) family, TLR7 and TLR9, and two cytosolic helicases, RIG-I and MDA-5, are responsible for the majority of type I IFNs induced upon recognition of viral nucleic acids. Based on the recent progress in the field, we now know that TLR7, TLR9, and RIG-I do not require long double-stranded RNA for type I IFN induction. These two cytosolic receptors are then responsible for the second and prolonged wave of type I IFN production and for the induction of apoptosis of virally infected cells. Small interfering RNAs mediate sequence-independent gene suppression and induce immune activation by signaling through toll-like receptor 3 cache = ./cache/cord-007689-0vpp3xdl.txt txt = ./txt/cord-007689-0vpp3xdl.txt === reduce.pl bib === id = cord-008541-0u2fatbg author = Bujarski, Jozef J. title = Molecular Studies of Genetic RNA–RNA Recombination in Brome Mosaic Virus date = 2008-02-28 pages = extension = .txt mime = text/plain words = 6347 sentences = 356 flesch = 49 summary = The idea was to develop an infectious RNA3 molecule stable in infection with a possibility of inserting sequences of interest and studying their recombinational activity. This indicated that progeny recombinants easily accumulated, because they easily outcompeted their parental RNAs. Figure 3 shows that all legitimate crossover events occurred within the long (197-to 220-nt) 3' region of M4 or DM4 (homologous among three BMV RNA components) and the corresponding part of either wt RNAl or wt RNA2. The recombination activity between pairs of these mutants was determined by coinoculation rearrangements was tested by inserting long palindromic sequences into RNA3 molecules (Section IV,D). The sequence of the inserted region and the presence of a marker mutation a t the 3' end indicated that B x 4 might have been formed through rearrangements between two mutant B RNA3 molecules. cache = ./cache/cord-008541-0u2fatbg.txt txt = ./txt/cord-008541-0u2fatbg.txt === reduce.pl bib === id = cord-006826-vnmg0zid author = Rayaprolu, Vamseedhar title = Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles date = 2017-12-06 pages = extension = .txt mime = text/plain words = 6543 sentences = 338 flesch = 56 summary = In this work, we wanted to determine how the length of the cargo impacts the stability and structure of the assembled CLPs. We hypothesized that cargo neutralizes the basic region of the alphavirus capsid protein and if the cargo is long enough, it will also act to scaffold the CP monomers together. Modest differences in particle size on DLS and EM suggest that changes in light scattering intensity indicate that similar amounts of CLPs were formed using 48hp, 48lin, and 90mer oligos than with the shorter 27mer ( figure 1(B) ). From our ionic strength stability results (figure 1(B)), we postulated that longer cargo that functioned to both neutralize charge and scaffold CP would favor the formation of complete, closed, spherical cores. This model provides an explanation for the structural defects observed in the cryo-EM classification, but does not account for the possible role of longer cargo in scaffolding or bridging between CP monomers to promote CLP assembly. cache = ./cache/cord-006826-vnmg0zid.txt txt = ./txt/cord-006826-vnmg0zid.txt === reduce.pl bib === id = cord-005060-n901y2d4 author = ZHANG, Feiyun title = Complete Nucleotide Sequence of Ryegrass Mottle Virus : A New Species of the Genus Sobemovirus date = 2001 pages = extension = .txt mime = text/plain words = 2602 sentences = 173 flesch = 62 summary = The largest ORF 2 encodes a polyprotein of 947 amino acids (103.6 kDa), which codes for a serine protease and an RNA-dependent RNA polymerase. The genome sequence of sobernoviruses has been determined in Southern bean mosaic virus (SBMV)'2,24), CfMV8315), Rice yellow mottle virus (RYMV)") and Lucerne transient streak virus (LTSV, accession number U31286). However, the con-served sequence, WAG + E/D rich sequence is detected in the region, and putative E/S cleavage sites are present on both sides of the region : proteolytic cleavage would result in a protein of 9 kDa. Possibly, the VPg of RGMoV is located between the protease and the RNA-dependent RNA polymerase domains in the same order as in the SBMV ORF 222) (Fig. 3) . In the RGMoV RNA sequence, no ORF corresponds to the second largest product of 68 kDa. The putative replicase of CfMV is translated as part of a single polyprotein by -1 ribosomal frameshifting between two overlapping ORFs having a coding capacity for 60.9 kDa and 56.3 kDa proteins7J8). cache = ./cache/cord-005060-n901y2d4.txt txt = ./txt/cord-005060-n901y2d4.txt === reduce.pl bib === id = cord-010161-bcuec2fz author = Matson, David O. title = IV, 6. Calicivirus RNA recombination date = 2004-09-14 pages = extension = .txt mime = text/plain words = 3335 sentences = 168 flesch = 45 summary = With the description of statistically significant phylogenetic clades within CV genera, data were available to recognize strains that might be natural recombinants within CVs. Two examples are the well-characterized Argentine strain 320 (Arg320) and Snow Mountain virus (SMV), one of the prototype CVs, recognized to be recombinants when the RNA polymerase and capsid regions of these strains were characterized (Hardy et al., 1997; Jiang et al., 1999) (Fig. 2) . While SMV was likely also to be a recombinant virus, the capsid and RNA polymerase region amplicons of SMV were generated separately and that fact did not exclude the possibility of different sources of strains. Infection of single cells simultaneously by two CVs implies absence of immune or molecular and of 40 nt near the 5' end of that strain's capsid gene (ID="B" sequence for this Fig.) . The sequence data indicated that recombination in strain Arg320 occurred at the ORF1/capsid gene junction where high sequence identity exists between the putative parent clades. cache = ./cache/cord-010161-bcuec2fz.txt txt = ./txt/cord-010161-bcuec2fz.txt === reduce.pl bib === id = cord-007181-qpahuqld author = YOGO, Yoshiaki title = Polyadenylate in the Virion RNA of Mouse Hepatitis Virus date = 1977-10-17 pages = extension = .txt mime = text/plain words = 2058 sentences = 122 flesch = 59 summary = Sedimentation Analysis-PH]Virion RNA dissolved in 0.1 ml NET was layered on a 15-30% sucrose gradient in NET containing 0.3% SDS, then sedimented at 48,000 rpm for 90 min at room temperature in an SW 50.1 rotor. Isolation of Poly(A)-fHJAdenosine-or P'P]labeled MH virion RNA containing 50 (ig of carrier tRNA was digested with a combination of ribonuclease A (2//g) and Tl (50 units The hydrolysate was neutralized with HC1O, at 0°C and the precipitate was removed by centrifugation. We therefore extracted RNA from [*H]uridine-labeled MH virions with phenol/chloroform as well as 1 % SDS, and RNA's obtained by both methods were compared by sucrose gradient centrifugation. To isolate poly(A), ['HJadenosine-labeled total virion RNA was digested with a combination of ribonuclease A and Tl. The digest was adjusted to 0.3 M NaCl-0.001 M EDTA-0.02 M Tris-HCl (pH 7.5)-7 M urea and applied to a DEAE-Sephadex column equilibrated with the same buffer. cache = ./cache/cord-007181-qpahuqld.txt txt = ./txt/cord-007181-qpahuqld.txt === reduce.pl bib === id = cord-006935-wzz5t3sv author = Gorbalenya, Alexander E. title = Viral cysteine proteinases date = 1996 pages = extension = .txt mime = text/plain words = 8112 sentences = 460 flesch = 59 summary = Only one conserved cysteine residue, thought to be the catalytic nucleophile, was identified in 3C p~° sequences of different origin [41, 47] and its indispensability for the PV 3C pr° proteolytic activity was proven by site-directed mutagenesis [48] . All RNA viral cysteine proteinases are synthesized as a domain in a polyprotein [17] and three major trends were discovered with respect to the position occupied by these enzymes. However, in an N-terminally extended precursor of 3C pr°, the Nterminal region of the proteinase could adopt a different structure that would fit the substrate binding pocket and might be processed in cis [5] . The $5-$2 subsites of the substrate-binding pocket, which interact with the less conserved P5-P2 positions of the cleavage sites, were recognized in the enzyme-substrate model of the HRV-14 3C pr° as well [5] . cache = ./cache/cord-006935-wzz5t3sv.txt txt = ./txt/cord-006935-wzz5t3sv.txt === reduce.pl bib === id = cord-009943-fzynh14x author = Ai‐Nakib, W. title = Detection of Human Rhinoviruses and Their Molecular Relationship Using cDNA Probes date = 2005-12-11 pages = extension = .txt mime = text/plain words = 2879 sentences = 158 flesch = 58 summary = Further, evidence is provided in this study that indicates that it would be feasible to use cDNA probes to detect human rhinoviruses in nasal washings. In a preliminary study we found that this probe does indeed cross-hybridize with a number of human rhinoviruses indicating the feasibility of cDNA:RNA hybridization for rhinovirus detection [Al-Nakib et al, 19861 . We have now extended these studies to include a larger series of human rhinoviruses (totalling some 56 viruses) and looked in more detail at the molecular relationship between these viruses, the limits of detection, and the feasibility of applying these procedures for the direct detection of viral RNA in nasal washings. However, in addition to detecting virus at lower titres, the strength of the hybridization signals obtained with 20 x SSC-37 % formaldehyde were particularly strong at all virus dilutions in nasal washings compared with phenol/chloroform extraction, indicating that more viral RNA has been immobilised onto the nitrocellulose filters. cache = ./cache/cord-009943-fzynh14x.txt txt = ./txt/cord-009943-fzynh14x.txt === reduce.pl bib === id = cord-011794-ejoufvvj author = Binder, Florian title = Isolation and characterization of new Puumala orthohantavirus strains from Germany date = 2020-04-23 pages = extension = .txt mime = text/plain words = 5972 sentences = 309 flesch = 51 summary = Additionally, glycoprotein precursor (GPC)-derived virus-like particles of a German PUUV sequence allowed the generation of monoclonal antibodies that allowed the reliable detection of the isolated PUUV strain in the immunofluorescence assay. Finally, the reactivity of the isolates was determined with novel monoclonal antibodies raised against PUUV GPC VLPs. Bank voles were trapped in spring 2019 in the PUUV endemic region around Osnabrück following a standard snap trapping protocol [25, 26] . Dissection on site and inoculation of VeroE6 and bank vole MGN-2-R cells with homogenized lung samples resulted after three blind passages in four potential isolates that were detected by a novel PUUV RT-qPCR (Table S1 , Fig. 1) . Reactivity of novel PUUV GPC-specific monoclonal antibodies with hantavirus-infected VeroE6 cells in immunofluorescence assay (IFA). In conclusion, the PUUV isolate described here replicates in a bank vole cell line and its N and GPC proteins can be detected by specific monoclonal antibodies. cache = ./cache/cord-011794-ejoufvvj.txt txt = ./txt/cord-011794-ejoufvvj.txt === reduce.pl bib === id = cord-010120-mqvm9zn4 author = Dinman, Jonathan D. title = Ribosomal frameshifting in yeast viruses date = 2004-01-29 pages = extension = .txt mime = text/plain words = 6721 sentences = 406 flesch = 64 summary = Ribosomal frameshifting is different from frameshift suppression in that these events are directed by specific mRNA sequences and structures, rather than being a consequence of mutations in host gene products, e.g. tRNAs containing four base anticodon loops. In eukaryotes, frameshifting in the +1, or 3' direction has been observed in the Ty retrotransposable elements in yeast (for review, see reference 25), and in the ornithine decarboxylase antizyme gene in mammalian ~e l l s .~~,~~ In Tyl and Ty3, +1 they splice their RNA.4 I: s6 All of these classes ribosomal frameshifting between the T Y A and T Y B genes in Tyl and the GAG3 and POL3 genes in Ty3 also results in the production of Gag-Pol fusion proteins. A longer ribosomal pause over the slippery site would follow, yielding increased efficiencies of -1 ribosomal frame~hifting.~.'~ A weak point of this model is that, in some mRNA pseudoknots, stem 1 is only five or six base pairs in slippery site, eliminating frameshifting. cache = ./cache/cord-010120-mqvm9zn4.txt txt = ./txt/cord-010120-mqvm9zn4.txt === reduce.pl bib === id = cord-008575-bbpmlo3c author = Lawton, Jeffrey A title = Mechanism of genome transcription in segmented dsRNA viruses date = 2004-01-07 pages = extension = .txt mime = text/plain words = 15879 sentences = 753 flesch = 43 summary = Although no reconstitution system is yet available for any of the reoviruses, studies conducted using baculovirusexpressed recombinant rotavirus-like particles containing the viral RNA polymerase coexpressed with the inner capsid protein have begun to clarify the mechanism by which the dsRNA genome is synthesized from the mRNA templates in rotavirus Patton et al., 1996; Zeng et al., 1996) . One of the more interesting observations about the life cycle of dsRNA viruses is that genome transcription occurs only within structurally intact TCPs. In rotavirus, the transcriptionally competent form of the virus has a double-layered capsid consisting of the structural proteins VP2 and VP6 surrounding the dsRNA genome segments and the enzymatic machinery in the core. Although observation of the actively transcribing rotavirus particle by electron cryomicroscopy has not provided a clear definition of the pathway of mRNA translocation through the inner capsid layer, atomic resolution structural studies of the bluetongue virus TCP have suggested a possible route (Grimes et al., 1998) . cache = ./cache/cord-008575-bbpmlo3c.txt txt = ./txt/cord-008575-bbpmlo3c.txt === reduce.pl bib === id = cord-010273-0c56x9f5 author = Simmonds, Peter title = Virology of hepatitis C virus date = 2001-10-10 pages = extension = .txt mime = text/plain words = 7897 sentences = 337 flesch = 41 summary = 1,2 The identification of HCV led to the development of diagnostic assays for infection, based either on detection of antibody to recombinant polypeptides expressed from cloned HCV sequences or direct detection of virus ribonucleic acid (RNA) sequences by polymerase chain reaction (PCR) using primers complimentary to the HCV genome. 6 '13 Remarkably, a series of plant viruses that are structurally distinct from each of the mammalian virus groups, and with different genome organizations, have RNA-dependent RNA polymerase amino acid sequences that are perhaps more similar to those of HCV than are the flaviviruses. In contrast to the highly restricted sequence diversity of the 5'NCR and adjacent core region, the two putative envelope genes are highly divergent between different variants of HCV (Table III) 111-114 and show a three-to-four-times higher rate of sequence change with time in persistently infected patients, ll5 Because these proteins are likely to lie on the outside of the virus, they would be the principal targets of the humoral immune response to HCV elicited on infection. cache = ./cache/cord-010273-0c56x9f5.txt txt = ./txt/cord-010273-0c56x9f5.txt === reduce.pl bib === id = cord-008407-jbp8bxjz author = Derdeyn, Cynthia A. title = Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date = 1995-01-10 pages = extension = .txt mime = text/plain words = 6710 sentences = 298 flesch = 56 summary = During serial undiluted passage of rubella virus (RUB) in Vero cells, two species of defective-interfering (DI) RNAs of approximately 7000 and 800 nucleotides (nts) in length were generated (Frey, T. Finally, to determine whether the majority of DI RNAs present in P12 RNA contained a deletion in the SP-ORF, an oligonucleotide probe which is complementary to a sequence located within the E1 protein coding region (nts 8472 to 8488, eligonucleotide 83, Fig. 3E ) that was deleted in all three cDNA clones was hybridized to P12 RNA. Analysis of the 5' terminus of DI RNA generated during serial passage As shown in Figure 3A , oligonucleotide probes complementary to the exact 5' terminal sequences of the RUB genome hybridized to the large DI RNAs. To confirm that these DI RNAs contained the authentic 5' end of the genome, primer extension was performed on intraceilular RNA from standard RUB-infected cells and P12 RNA. cache = ./cache/cord-008407-jbp8bxjz.txt txt = ./txt/cord-008407-jbp8bxjz.txt === reduce.pl bib === id = cord-011803-9122f1zc author = Zhao, Yang title = The RNA quality control pathway nonsense-mediated mRNA decay targets cellular and viral RNAs to restrict KSHV date = 2020-07-03 pages = extension = .txt mime = text/plain words = 8355 sentences = 493 flesch = 50 summary = Collectively, our study describes an intricate relationship between cellular targets of an RNA quality control pathway and KSHV lytic gene expression, and demonstrates that NMD can function as a cell intrinsic restriction mechanism acting upon DNA viruses. EJCs are deposited at the exon-exon junction, thus we determined whether the EJC component eukaryotic translation initiation factor 4A3 (eIF4A3) is associated with spliced KSHV RNAs. To test EJC association with KSHV transcripts we performed eIF4A3 formaldehyde crosslinking RNA immunoprecipitation (fRIP) coupled to reverse transcription quantitative PCR (RT-qPCR) on lytic iSLK.219 and TREx-BCBL-RTA cells (Fig. 1g, h) . Leveraging p-UPF1 fRIP-seq we identified NMD targets transcriptome-wide in both latent and lytic PEL cells and targets include both host and viral RNAs. Remarkably, the mRNA encoding RTA, the master transcription factor governing KSHV reactivation, is targeted by NMD via its 3′UTR and silencing of UPF1 is sufficient to potentiate RTA-mediated transactivation. cache = ./cache/cord-011803-9122f1zc.txt txt = ./txt/cord-011803-9122f1zc.txt === reduce.pl bib === id = cord-012784-c74jr4ga author = Zhang, Le-le title = Identification of nagilactone E as a protein synthesis inhibitor with anticancer activity date = 2020-02-11 pages = extension = .txt mime = text/plain words = 4879 sentences = 265 flesch = 48 summary = We previously reported that nagilactone E (NLE), a dinorditerpenoid isolated from Podocarpus nagi, possessed anticancer effects against lung cancer cells in vitro. To better understand the potential biological processes associated with the effects of NLE in lung cancer A549 cells, GO analysis was performed using the online DAVID 6.8 bioinformatics resource. To clarify the mechanisms underlying the anticancer effect of NLE in A549 lung cancer cells, we further analyzed the DEGs using the CMap dataset. As shown in Fig. 4a , the mRNA levels of NRF2, p21, STAT3, and ATF4 were upregulated after NLE treatment, which was consistent with the results obtained by RNA-seq analysis. Thereafter, the inhibitory effect of NLE on de novo protein synthesis in A549 cells was further confirmed using the Click-iT assay. CMap dataset analysis supported NLE as a protein synthesis inhibitor, which was further confirmed by the Click-iT assay. cache = ./cache/cord-012784-c74jr4ga.txt txt = ./txt/cord-012784-c74jr4ga.txt === reduce.pl bib === id = cord-004584-bcw90f5b author = nan title = Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date = 2011-08-06 pages = extension = .txt mime = text/plain words = 106850 sentences = 5038 flesch = 41 summary = Our goals are two-fold: (1) to monitor conformational changes in each domain upon its binding to specific ligands and then to correlate the observed changes with structural differences between the CRDs and (2) to investigate the interaction between the CRDs and lipid model membranes. Cholesterol-assisted lipid and protein interactions such as the integration into lipid nanodomains are considered to play a functional part in a whole range of membrane-associated processes, but their direct and non-invasive observation in living cells is impeded by the resolution limit of [200nm of a conventional far-field optical microscope. Therefore, to investigate the dynamic and complex membrane lateral organization in living cells, we have developed an original approach based on molecule diffusion measurements performed by fluorescence correlation spectroscopy at different spatial scales (spot variable FCS, svFCS) (1). cache = ./cache/cord-004584-bcw90f5b.txt txt = ./txt/cord-004584-bcw90f5b.txt === reduce.pl bib === id = cord-006068-w3if1hns author = Marshak-Rothstein, Ann title = Toll-like receptors in systemic autoimmune disease date = 2006 pages = extension = .txt mime = text/plain words = 10093 sentences = 442 flesch = 41 summary = This Review summarizes recent in vitro and in vivo studies that point to an important connection between DNA-and RNA-containing immune complexes, the production of type I interferons (IFNs; that is, IFNα and IFNβ), the activation of TLRs and subsequent events in the development and/or the progression of systemic autoimmune diseases. . b | IFNα upregulates expression of Toll-like receptor 7 (TLR7) by B cells, promotes cell death and increased release of certain RNA autoantigens, and primes pDCs to respond more effectively to immune complexes. A limited number of studies have now provided data consistent with the idea that TLR7 and TLR9 have key roles in the production of pathogenic autoantibodies and/or in the development of clinical features of autoimmunity in experimental animals ( Mice that are homozygous for the lpr mutation do not express a functional form of the death receptor CD95 (also known as FAS), and they develop a lymphoproliferative disease that is similar to Canale-Smith syndrome in humans. cache = ./cache/cord-006068-w3if1hns.txt txt = ./txt/cord-006068-w3if1hns.txt === reduce.pl bib === id = cord-008613-tysyq6o4 author = Thomas, Sheila M. title = Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5 date = 1988-09-09 pages = extension = .txt mime = text/plain words = 8410 sentences = 433 flesch = 60 summary = Simian virus 5 (SV5), a prototype paramyxovirus, has a single-stranded, negative sense genomic RNA (vRNA) approximately 15,000 nucleotides in chain length that is transcribed in infected cells by the virion-associated RNA transcriptase to yield virus-specific mRNAs. The SV5 "P" gene has been shown to encode both the P protein (Mr = 44,000), and protein V (Mr = 24,000) by the arrest of translation in vitro of both P and V using a cDNA clone derived from SV5-specific mRNAs (Paterson et al., 1984) . Antigenic Region Mapping of the P and V Monoclonal Antibodies on the P and V Gene Using T7 RNA Polymerase Runoff Transcripts, In Vitro Translation, and Immunoprecipitation The full-length P203-1 DNA insert cloned using Xbal linkers (XX) and a Hindlll to Xbal fragment (HX) containing the 3' two-thirds of the P203-1 DNA were placed under the control of the T7 promoter in the plasmid pGEM-2. cache = ./cache/cord-008613-tysyq6o4.txt txt = ./txt/cord-008613-tysyq6o4.txt === reduce.pl bib === id = cord-004879-pgyzluwp author = nan title = Programmed cell death date = 1994 pages = extension = .txt mime = text/plain words = 81677 sentences = 4465 flesch = 51 summary = Furthermore kinetic experiments after complementation of HIV=RT p66 with KIV-RT pSl indicated that HIV-RT pSl can restore rate and extent of strand displacement activity by HIV-RT p66 compared to the HIV-RT heterodimer D66/D51, suggesting a function of the 51 kDa polypeptide, The mouse mammary tumor virus proviral DNA contains an open reading frame in the 3' long terminal repeat which can code for a 36 kDa polypeptide with a putative transmembrane sequence and five N-linked glycosylation sites. To this end we used constructs encoding the c-fos (and c-jun) genes fused to the hormone-binding domain of the human estrogen receptor, designated c-FosER (and c-JunER), We could show that short-term activation (30 mins.) of c-FosER by estradiole (E2) led to the disruption of epithelial cell polarity within 24 hours, as characterized by the expression of apical and basolateral marker proteins. cache = ./cache/cord-004879-pgyzluwp.txt txt = ./txt/cord-004879-pgyzluwp.txt === reduce.pl bib === id = cord-010374-z9ygudv6 author = Siddell, S.G. title = Coronaviridae1 date = 2008-07-24 pages = extension = .txt mime = text/plain words = 1541 sentences = 111 flesch = 51 summary = The main characteristics of the member viruses are: (i) Morphological: Enveloped pleomorphic particles typically 100 nm in diameter (range 60-220 nm), bearing about 20 nm long club-shaped surface projections, (ii) Structural: A single-stranded infectious molecule of genomic RNA of about (5-7) × 10(6) molecular weight. (iv) Antigenic: 3 major antigens, each corresponding to one class of virion protein, (v) Biological: Predominantly restricted to infection of natural vertebrate hosts by horizontal transmission via the fecal/oral route. Recently, there have been reports of virus-specific RNA poly merases in coronavirus-infected cells, but the components of the enzyme have not been iden tified. UV inactivation studies in dicate that coronavirus mRNAs are not pro duced by the processing of a larger RNA, although extensive sequence homologies have been detected at the 5' ends of ail murine hepatitis virus-specific subgenomic RNAs. For murine hepatitis virus, the mRNA function of each of the subgenomic viral RNAs has been demonstrated in vitro, and the mRNAs encod ing each of the virion proteins, or its precur sors, have been identified ( fig. cache = ./cache/cord-010374-z9ygudv6.txt txt = ./txt/cord-010374-z9ygudv6.txt === reduce.pl bib === id = cord-010045-eqzs01au author = Britton, P. title = Sequence of the nucleoprotein gene from a virulent British field isolate of transmissible gastroenteritis virus and its expression in Saccharomyces cerevisiae date = 2006-10-27 pages = extension = .txt mime = text/plain words = 6185 sentences = 353 flesch = 57 summary = Yeast cells containing recombinant plasmids, with the nucleoprotein gene in the correct orientation, produced a polypeptide of M, 47000, identical to the viral product, that reacted with a specific monoclonal antibody. Three recombinant plasmids, shown to contain cDNA inserts of 1.5 kbp and designated pTS13-2, pTS15-1 and pTSi 5-2, were labelled with p^S]-dATP by nick translation and hybridized to glyoxylated TGEV mRNA species separated on 1 % agarose gels as described in Experimentat procedures. The plasmid also contained the smaller 3' ORF which initiates, in a different reading frame, 6 bp 3' from the end of the nucleoprotein gene and terminates 166 bp 5' to the Drall Sma\ combined site between the TGEV cDNA insert and the pUC9 DNA. A recombinant plasmid, pYNGI, was found to contain the TGEV nucleoprotein gene in the correct orientation for expression under the control of the yeast GAL1 promoter. cache = ./cache/cord-010045-eqzs01au.txt txt = ./txt/cord-010045-eqzs01au.txt === reduce.pl bib === id = cord-008588-4eu9v5d3 author = Chastain, Michael title = Structural Elements in RNA date = 2008-02-29 pages = extension = .txt mime = text/plain words = 13667 sentences = 617 flesch = 54 summary = The structures of the tRNA anticodon loop and the UUCG loop suggest that the specific loop sequences adopt conformations that are more stable because they contain more hydrogen bonding and stacking interactions-particularly interactions with the sugar-phosphate backbone. Determining the conformation of these loops in RNA is important for understanding how these nucleotides interact with other elements of secondary structure to form tertiary interactions and for understanding how proteins bind to bulge loops. In general, this could occur between any of the secondary structure regions containing unpaired nucleotides (single-stranded regions, hairpin loops, bulge loops, internal loops, and junction loops). There are several examples of RNA molecules containing tertiary contacts between nucleotides that are in loop regions of secondary structure. The high frequency with which known RNA structures contain tertiary pairing between nucleotides that are unpaired in the secondary structure stresses the importance of learning more about such interactions. cache = ./cache/cord-008588-4eu9v5d3.txt txt = ./txt/cord-008588-4eu9v5d3.txt === reduce.pl bib === id = cord-012032-zolowuhj author = Yu, Peifa title = 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705 date = 2020-08-08 pages = extension = .txt mime = text/plain words = 3499 sentences = 197 flesch = 45 summary = To further examine the antiviral effects, another murine macrophage cell line, J774A.1, was used, and a similar inhibitory effect of 2'-FdC on MNV-1 replication was observed, with decreased viral RNA and NS1/2 protein expression ( Supplementary Fig. 1 ). As shown in Fig. 3D and E, the viral NS1/2 protein expression and viral titers were further decreased when the antivirals were used in combination, supporting the synergistic antiviral effects of 2'-FdC with MPA, ribavirin, or T705 against MNV replication. The combined effect of 2'-FdC and ribavirin on viral replication was analyzed using a qRT-PCR assay (n = 2-4) and mathematical modeling using MacSynergy. RAW264.7 cells were infected with MNV-1 at an MOI of 1 for 1 h and then left untreated or treated with 2'-FdC and MPA, ribavirin, or T705 at the indicated concentrations for 20 h, alone or in combination. cache = ./cache/cord-012032-zolowuhj.txt txt = ./txt/cord-012032-zolowuhj.txt === reduce.pl bib === id = cord-008426-ktn8c0zx author = Othman, Yasmin title = Nucleotide sequence of the bean strain of southern bean mosaic virus() date = 1995-01-10 pages = extension = .txt mime = text/plain words = 5393 sentences = 276 flesch = 57 summary = From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses. Southern bean mosaic virus (SBMV) is the type member of the sobemovirus group of small icosahedral positive-strand RNA viruses (for reviews see Sehgal, 1981 ; Tremaine and Hamilton, 1983; Hull, 1988) . The recently published nucleotide sequence (4450 nt) of rice yellow mottle virus (RYMV), another sobemovirus (Ngon A Yassi et aL, 1994) , shows that it has a similar genome organization to SBMV-C (Fig. 1) . Amino acid sequence of southern bean mosaic virus coat protein and its relation to the three dimensional structure of the virus cache = ./cache/cord-008426-ktn8c0zx.txt txt = ./txt/cord-008426-ktn8c0zx.txt === reduce.pl bib === id = cord-007208-wnkjdg6y author = Li, Sheng-Hsiang title = Demonstration of a Glycoprotein Derived From the Ceacam10 Gene in Mouse Seminal Vesicle Secretions(1) date = 2005-09-01 pages = extension = .txt mime = text/plain words = 5610 sentences = 289 flesch = 56 summary = Here we report the purification and identification of an androgen-stimulated 36-kDa glycoprotein, a minor protein component of mouse SVS that is able to enhance sperm motility in vitro. The following materials were obtained from commercial sources: DEAE-Sephacel (Amersham Pharmacia Biotech, Uppsala, Sweden); Protein PAK SP 5PW column (Waters, Milford, MA); Vydac 218TP54 C 18 column (Separations Group, Hesperia, CA); AminoLink coupling gel, bicinchoninic protein assay kit (Pierce, Rockford, IL); testosterone propionate, nitroblue tetrazolium, 5-bromo-4-chloro-3-indolyl phosphate (BCIP), PMSF, periodic acid Schiff reagent, and silanated glass slides (Sigma Chemical Co., St Louis, MO); cDNA integrity kit, alkaline phosphataseconjugated streptavidin, and biotin-conjugated goat anti-rabbit immunoglobulin G (IgG; Kirkegaard & Perry Laboratories, Gaithersburg, MD); rhodamine-conjugated goat anti-rabbit IgG (Zymed Laboratories, San Francisco, CA); Nuclear Fast Red (Vector Laboratories, Burlingame, CA); enhanced chemiluminescent substrate and [␣32 A) Fractionation of soluble mouse SVS proteins by ion exchange chromatography on a DEAE-Sephacel column. A novel heat-labile phospholipid-binding protein, SVS VII, in mouse seminal vesicle as a sperm motility enhancer cache = ./cache/cord-007208-wnkjdg6y.txt txt = ./txt/cord-007208-wnkjdg6y.txt === reduce.pl bib === id = cord-007920-mh3tesdc author = Dhar, Arun K. title = Genomic Organization, Biology, and Diagnosis of Taura Syndrome Virus and Yellowhead Virus of Penaeid Shrimp date = 2004-11-11 pages = extension = .txt mime = text/plain words = 19308 sentences = 1000 flesch = 52 summary = The three most detrimental shrimp viruses are white spot syndrome virus (WSSV), yellowhead virus (YHV), and Taura syndrome virus (TSV), all of which have caused serious epizootics in various regions of Asia and are considered notifiable by the Office International de Epizooties (OIE, 2002) . The RNA helicase consensus sequence, Gx 4 GK, is present at ORF1 amino acid positions 752 to 758, and the TSV helicase domain shows significant similarity with the cognate domain of insect picorna-like viruses (Drosophila C virus, DCV; Rhophalosiphum padi virus, RhPV; Plautia stali intestinal virus, PSIV; black queen cell virus, BQCV; Triatoma virus of the fungus Triatoma infestans, TrV; and Himetobi P virus, HiPV). In addition to helicase, protease, and RdRp motifs, the TSV genome contains a short aa sequence at the N-terminal end of ORF1 (positions 166 to 230) that shows significant similarity with the inhibition of apoptosis (IAP) proteins found in mammals, yeast, insects, and some DNA viruses (Mari et al., 2002) . cache = ./cache/cord-007920-mh3tesdc.txt txt = ./txt/cord-007920-mh3tesdc.txt === reduce.pl bib === id = cord-010762-c01wgg4v author = Wu, Jiqin title = A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase date = 2020-05-01 pages = extension = .txt mime = text/plain words = 9021 sentences = 382 flesch = 50 summary = Previously reported NS5 structures represented by those from the Japanese encephalitis virus (JEV) and Dengue virus serotype 3 (DENV3) exhibit two apparently different global conformations, defining two sets of intra-molecular MTase-RdRP interactions. Data from in vitro polymerase assays further demonstrate that perturbing the JEV-mode but not the DENV3-mode intra-molecular interactions inhibits catalysis only at initiation, while the cell-based virological analysis suggests that both modes of interactions are important for virus proliferation. NS5 constructs bearing mutations specifically probing two modes of MTase-RdRP intra-molecular interfaces were tested in in vitro polymerase assays, and only the JEV-mode interface related mutants inhibited polymerase initiation primarily through a three-fold reduction in the Michaelis constant of the initiating NTP (K M, NTP ), while polymerase EC properties were not much affected by mutations probing both modes of interactions. cache = ./cache/cord-010762-c01wgg4v.txt txt = ./txt/cord-010762-c01wgg4v.txt === reduce.pl bib === id = cord-014397-7b88ycv8 author = Gavora, JS title = Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date = 1996-12-15 pages = extension = .txt mime = text/plain words = 11583 sentences = 528 flesch = 41 summary = Thus introduction of new mechanisms of disease resistance in livestock by gene transfer may be viewed as a logical continuation of the creative influence of humans on the evolution of farm animals and birds that could benefit mankind by improvements in food safety and production efficiency. As background for the discussion of the subject, the article deals briefly with coevolution of hosts and parasites and principal elements of virus-host interactions, and reviews past improvement of disease resistance in plants and livestock by conventional breeding and genetic engineering, as well as the potential 'biological cost' of genetic manipulation. Basic understanding of the parallel evolution of viruses and their hosts provides a useful starting point for the consideration of strategies for genetic engineering of new mechanisms of resistance. Genetic engineering strategies that prevent entry of viruses into host cells would be effective against all three types of viral infection. cache = ./cache/cord-014397-7b88ycv8.txt txt = ./txt/cord-014397-7b88ycv8.txt === reduce.pl bib === id = cord-010977-fwz7chzf author = Myserlis, Pavlos title = Translational Genomics in Neurocritical Care: a Review date = 2020-02-20 pages = extension = .txt mime = text/plain words = 11990 sentences = 519 flesch = 31 summary = In this review, we describe some of the approaches being taken to apply translational genomics to the study of diseases commonly encountered in the neurocritical care setting, including hemorrhagic and ischemic stroke, traumatic brain injury, subarachnoid hemorrhage, and status epilepticus, utilizing both forward and reverse genomic translational techniques. Termed "reverse translation," this approach starts with humans as the model system, utilizing genomic associations to derive new information about biological mechanisms that can be in turn studied further in vitro and in animal models for target refinement (Fig. 1) . These results highlight the value of reverse genomic translation in first identifying human-relevant genetic risk factors for disease, and using model systems to understand the pathways impacted by their introduction to select rationally-informed modalities for potential treatment. These observations provide vital information about cellular mechanisms impacted by human disease-associated genetic risk factors without requiring the expense and time investment of creating, validating, and studying animal models. cache = ./cache/cord-010977-fwz7chzf.txt txt = ./txt/cord-010977-fwz7chzf.txt === reduce.pl bib === id = cord-012484-c9ajmbw2 author = Wahlund, Martina title = The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia date = 2020-07-26 pages = extension = .txt mime = text/plain words = 5085 sentences = 241 flesch = 45 summary = The blood transcriptome of the children (n = 63) was investigated at time of FN diagnosed as viral, bacterial, co-infection or unknown etiology, respectively, and compared to control samples derived from 12 of the patients following the FN episode. In the present study of children during cancer treatment, the blood transcriptome was not suitable for determining the etiology of FN because of too few circulating immune cells for reliable gene expression analysis. To determine whether it is possible to detect pathogen-specific immune responses on the basis of gene expression in immunosuppressed children, we compared the blood transcriptomes of samples with viral infection, bacterial infection, co-infection, or unknown etiology with those of the control samples. To determine whether it is possible to detect pathogen-specific immune responses on the basis of gene expression in immunosuppressed children, we compared the blood transcriptomes of samples with viral infection, bacterial infection, co-infection, or unknown etiology with those of the control samples. cache = ./cache/cord-012484-c9ajmbw2.txt txt = ./txt/cord-012484-c9ajmbw2.txt === reduce.pl bib === id = cord-010680-lc1onm53 author = Patel, Ami title = In Vivo Delivery of Nucleic Acid-Encoded Monoclonal Antibodies date = 2020-03-10 pages = extension = .txt mime = text/plain words = 13044 sentences = 659 flesch = 41 summary = Some of these hurdles may be overcome through transient in vivo gene delivery platforms, such as non-viral synthetic plasmid DNA and messenger RNA vectors that are engineered to encode optimized mAb genes. In this review, we focus on nucleic acid delivery of antibody employing synthetic plasmid DNA vector platforms, and RNA delivery, these being important approaches that are advancing simple, rapid, in vivo expression and having an impact in animal models of infectious diseases and cancer, among others. The original studies surrounding in vivo antibody gene delivery focused primarily on gene delivery using recombinant viral vectors such as AAV and adenovirus (Ad), which were advanced clinically, building on work in the traditional gene therapy-based field. Additional studies to help evaluate fully human pDNA-mAbs in mouse models would be highly informative for both non-viral and viral delivery and provide an important path forward for preclinical evaluation of in vivo-delivered antibodies [109] . cache = ./cache/cord-010680-lc1onm53.txt txt = ./txt/cord-010680-lc1onm53.txt === reduce.pl bib === id = cord-010188-884d196k author = Schlesinger, Sondra title = Alphaviruses — vectors for the expression of heterologous genes date = 2004-08-26 pages = extension = .txt mime = text/plain words = 3049 sentences = 140 flesch = 47 summary = Sindbis virus and Semliki Forest vires are best known as valuable models for molecular and cell biology, and it is these two viruses that are presently being developed as vectors for the expression of heterologous genes. The basic strategy for using alphaviruses as vectors for the expression of heterologous genes has been to construct cDNAs of the alphavirus genome, in which the heterologous gene is placed downstream from the promoter used to transcribe a subgenomic RNA 13 (Fig. 2a) . A second potential problem is recombination between the packaging helper virus RNA and vector RNAs. The two Sindbis RNAs can undergo recombination to produce a single molecule of RNA containing the genes that encode both the nonstructural and structural proteins m. The initial studies with Sindbis and Semliki Forest virus suggest that both viruses are promising as vectors for heterologous gene expression. cache = ./cache/cord-010188-884d196k.txt txt = ./txt/cord-010188-884d196k.txt === reduce.pl bib === id = cord-013243-1hj5clsw author = Brewer, Gary title = Editorial for “Methods to characterize virus small RNAs and RNA structures” date = 2020-10-16 pages = extension = .txt mime = text/plain words = 576 sentences = 41 flesch = 48 summary = title: Editorial for "Methods to characterize virus small RNAs and RNA structures" One of the advantages of this enzymatic approach is that it minimizes problems that can arise upon annealing two complementary RNA strands, e.g., secondary structure within a ssRNA due to selfannealing; and low yields of long dsRNAs. These RNAs can be subsequently modified (e.g., Here, the small molecule dimethyl sulfate (DMS) preferentially methylates unpaired or dynamic adenosine and cytosine residues within a viral RNA genome. Methods for detection and study of virus derived small RNAs produced from the intramolecular base-pairing region of the picornavirus genome A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells Functional analyses of mammalian virus 5'UTR-derived, small RNAs that regulate virus translation From current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants cache = ./cache/cord-013243-1hj5clsw.txt txt = ./txt/cord-013243-1hj5clsw.txt === reduce.pl bib === id = cord-012420-llh22iq2 author = Stott, Robert J. title = Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins date = 2020-07-21 pages = extension = .txt mime = text/plain words = 12015 sentences = 579 flesch = 41 summary = Interestingly, non-pathogenic OW Mopeia virus (MOPV), a close genetic relative to LASV, induces a strong initial IFN and cytokine response in infected moDCs and macrophages leading to a sustained T cell activation and immune response [67, 68] . Similar to NP, interaction of arenavirus Z proteins with RIG-I prevents further binding to MAVS and therefore inhibits the production of IFN-β and reduces antiviral host immune responses. Although the inhibition of RIG-I signalling by highly pathogenic arenaviruses in vitro suggests that there should be limited IFN1 response, it is notable that in vivo infection with some of these viruses (LCMV, JUNV) induces high levels of IFN1, ISGs and cytokines suggesting that this strategy is not completely effective or is widely varied in cell type and differs from host to host [134, 135, 186] . cache = ./cache/cord-012420-llh22iq2.txt txt = ./txt/cord-012420-llh22iq2.txt === reduce.pl bib === id = cord-012909-o6t2srim author = Chaudhari, Jayeshbhai title = Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain date = 2020-07-28 pages = extension = .txt mime = text/plain words = 9281 sentences = 490 flesch = 43 summary = Both virulent and live-attenuated porcine reproductive and respiratory syndrome virus (PRRSV) strains can establish persistent infection in lymphoid tissues of pigs. In this study, expression of several important chemokine ligands (CCL19, CCL21, CCL24, CCL22, CX3CL1, and CCL14) and chemokine receptors (CCR6 and CCR10) which play an essential role in migration and localization of lymphocytes and antigen-presenting cells (APCs) to the lymphoid tissues was down regulated in ILN of CON90-infected pigs (Figure 6a ). In this study, expression of several important chemokine ligands (CCL19, CCL21, CCL24, CCL22, CX3CL1, and CCL14) and chemokine receptors (CCR6 and CCR10) which play an essential role in migration and localization of lymphocytes and antigen-presenting cells (APCs) to the lymphoid tissues was down regulated in ILN of CON90-infected pigs (Figure 6a ). GO terms and KEGG analysis revealed that genes involved in the innate immune (complement and TLR) pathways, apoptosis, cytokine-chemokine signaling, T-cell exhaustion, and humoral responses are highly differentially expressed in PRRSV-infected animals compared to control. cache = ./cache/cord-012909-o6t2srim.txt txt = ./txt/cord-012909-o6t2srim.txt === reduce.pl bib === id = cord-013176-6ckuya1w author = Ninfali, Paolino title = Antiviral Properties of Flavonoids and Delivery Strategies date = 2020-08-21 pages = extension = .txt mime = text/plain words = 8102 sentences = 372 flesch = 35 summary = Quercetin, extracted from Embelia ribes (Mirsinaceae), exhibited antiviral effects against HCV, exerted through activity inhibition of the viral protease Non-Structural protein 3 (NS3), leading to a decrease in HCV replication [36] . The natural extract of Tetrastigma hemsleyanum (Vitaceae) contains many flavonoids, including vitexin, vitexin-2-O-rhamnoside, isorhamnetin, rutin, kaempferol, astragalin, quercitrin, quercetin and iso-quercetin, which were shown to be able to exert anti-influenza virus activity, with different efficiency, through the reduction of the number of plaques induced by the influenza virus in infected Madin-Darby Canine Kidney (MDCK) cells [21] . In future perspective, this approach could be considered in order to possibly improve the antiviral activity of some flavonoids, like baicalin, that was able, like fludarabine [65] , to act against HIV-1 chronic infection of human monocytes and macrophages, inhibiting the fusion of HIV virus envelope proteins with these cells [73] . cache = ./cache/cord-013176-6ckuya1w.txt txt = ./txt/cord-013176-6ckuya1w.txt === reduce.pl bib === id = cord-013280-kczj24se author = Yang, Bo title = Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus date = 2020-09-04 pages = extension = .txt mime = text/plain words = 11293 sentences = 608 flesch = 46 summary = Viral capsid protein VP1 and leading protein L pro can inhibit the production of interferon (IFN) and innate immune response by interacting with soluble resistance-related calcium-binding protein (sorcin) or host transcription factor ADNP [12, 13] . Viral capsid protein VP1 and leading protein L pro can inhibit the production of interferon (IFN) and innate immune response by interacting with soluble resistance-related calcium-binding protein (sorcin) or host transcription factor ADNP [12, 13] . FMDV VP1 interacts with host ribosomal protein SA (RPSA) to continually activate the MAPK signal pathway and promote virus replication by inhibiting the RPSA-mediated function [59] (Figure 2 , Table 1 ). It interacts with the VISA protein to inhibit the formation of VISA-regulated complex, thereby inhibiting the dimerization and phosphorylation of IRF3, inhibiting the expression of antiviral genes induced by IFN-β, and promoting FMDV replication [60] (Figure 2 , Table 1 ). cache = ./cache/cord-013280-kczj24se.txt txt = ./txt/cord-013280-kczj24se.txt === reduce.pl bib === id = cord-013412-gj443yei author = Lebedeva, Natalya Sh. title = The Application of Porphyrins and Their Analogues for Inactivation of Viruses date = 2020-09-23 pages = extension = .txt mime = text/plain words = 13428 sentences = 626 flesch = 46 summary = The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. cache = ./cache/cord-013412-gj443yei.txt txt = ./txt/cord-013412-gj443yei.txt === reduce.pl bib === id = cord-013177-whd0znan author = Han, Zhenzhi title = The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales date = 2020-09-07 pages = extension = .txt mime = text/plain words = 5049 sentences = 265 flesch = 44 summary = Novel posa-like viral genomes were first identified in swine fecal samples using metagenomics and were designated as unclassified viruses in the order Picornavirales. These posa-like viruses have undergone a complex evolutionary process, and have a wide geographic distribution, complex host spectrum, deep phylogenetic divergence, and diverse genomic organizations. Novel posa-like virus genomes were first identified in swine fecal samples using metagenomics and were assigned as unclassified viruses to the order Picornavirales [12] . Further reports of novel posaviruses with low amino acid sequence identity revealed novel genomic organization features and phylogenetic characteristics of posa-like viruses [15, 16] . Due to the low genomic sequence similarity between the husavirus and unclassified posa-like viruses in Picornavirales, it was difficult to perform a phylogenetic analysis at the full-length genome level. Posa-like viruses identified in previous reports and in the present study formed a single group and clustered with the genomes of family Marnaviridae (Figure 4) . cache = ./cache/cord-013177-whd0znan.txt txt = ./txt/cord-013177-whd0znan.txt === reduce.pl bib === id = cord-013171-wgn529rc author = Zhong, Yi title = STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway date = 2020-09-16 pages = extension = .txt mime = text/plain words = 6746 sentences = 410 flesch = 50 summary = title: STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway They extended this analysis to multiple cell types of diverse origin, including human embryonic STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway carcinoma stem cells (NT2), mouse neural progenitor cells (N2A), human retinal epithelial cells (ARPE19), and primary mouse embryonic fibroblasts (MEFs). RASEs detected by qPCR were consistent with those by RNA-seq, which demonstrated that STAU1 may play a significant regulatory role in the AS of 'nerve growth factor receptor signaling pathway'. In addition, the AS of multiple genes was also regulated by STAU1, and the main enriched pathways not only include 'retrograde transport' and 'muscle cell differentiation', but also the 'nerve growth factor receptor signaling pathway'. cache = ./cache/cord-013171-wgn529rc.txt txt = ./txt/cord-013171-wgn529rc.txt === reduce.pl bib === id = cord-014685-ihh30q6f author = nan title = Posters P788 - P999 date = 2005-09-21 pages = extension = .txt mime = text/plain words = 38354 sentences = 1784 flesch = 45 summary = This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes. cache = ./cache/cord-014685-ihh30q6f.txt txt = ./txt/cord-014685-ihh30q6f.txt === reduce.pl bib === id = cord-013854-wadpugbj author = Fratter, Carl title = EMQN best practice guidelines for genetic testing in dystrophinopathies date = 2020-05-18 pages = extension = .txt mime = text/plain words = 12725 sentences = 536 flesch = 38 summary = Since whole-exon deletions or duplications are the predominant type of pathogenic variant in the DMD gene (~78%; Table 1 ), an initial screen which detects the majority of these copy number variations (CNVs) should be the first diagnostic test offered (refer to Genetic testing strategy section and Fig. 1 ). In patients with an ascertained clinical diagnosis of dystrophinopathy but no CNVs or small variants identified, RNA-based methods offer a valuable tool with a high likelihood of being able to detect variants that escape detection using level 1 and 2 DNA approaches, such as complex rearrangements or deep intronic variants leading to pseudo-exon insertion or cryptic splice site recognition in the mature transcripts. If a pathogenic DMD variant is not identified by analysis for whole-exon deletions and duplications or after DMD gene sequencing, then in some cases alternative diagnoses should be considered, depending on the available clinical evidence and test results. cache = ./cache/cord-013854-wadpugbj.txt txt = ./txt/cord-013854-wadpugbj.txt === reduce.pl bib === id = cord-015642-p46abodr author = Backofen, Rolf title = Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures date = 2013 pages = extension = .txt mime = text/plain words = 4201 sentences = 278 flesch = 66 summary = On a more technical level, the problem to compute the partition function over RNA secondary structures with given end-to-end distance d, usually measured as the number of external bases (plus possibly the number of structural domains) arises for instance when predicting nucleic acid secondary structure in the presence of single-stranded binding proteins [9] or in models of RNA subjected to pulling forces (e.g. in atom force microscopy or export through a small pore) [10, 23, 11] . can be split as follows, This gives the recursion [10] , the investigate of loop entropy dependence [7] , the analysis of FRET signals in the presence of single-stranded binding proteins [9] , as well as in mathematical studies of RNA panhandle-like structures [2, 13] . As the graph-distance for a pair of nucleotides in a given secondary structure can be computed in O(n log n) time, even large samples can be evaluated efficiently 2 . The equilibrium partition function and base pair binding probabilities for RNA secondary structure cache = ./cache/cord-015642-p46abodr.txt txt = ./txt/cord-015642-p46abodr.txt === reduce.pl bib === id = cord-012552-porty653 author = Tan, Kun title = The role of the NMD factor UPF3B in olfactory sensory neurons date = 2020-08-10 pages = extension = .txt mime = text/plain words = 11512 sentences = 600 flesch = 52 summary = Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. We identified UPF3B-regulated genes in mOSNs by performing RNA-seq analysis on FACSpurified mOSNs (YFP+ cells) from R26-eYFP; Omp-Cre mice (Figure 1-figure supplement 1B) . Among the antimicrobial genes expressed and upregulated in Upf3b-null OSN precursors and OSNs was Camp (also known as 'Cramp'), which encodes a member of the cathelicidin family of antimicrobial peptides that has an important role in the defense against microbial infections, and functions in cell chemotaxis, immune mediator induction, and inflammatory response regulation (Zhang and Gallo, 2016) . cache = ./cache/cord-012552-porty653.txt txt = ./txt/cord-012552-porty653.txt === reduce.pl bib === id = cord-015376-z739ifu5 author = Savarino, Andrea title = Potential therapies for coronaviruses date = 2006-08-31 pages = extension = .txt mime = text/plain words = 6361 sentences = 313 flesch = 48 summary = These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. The potential usefulness of 3CLpro as a drug target is supported by: i) its fundamental role in coronavirus replication; ii) its well defined 3D structure; and iii) preliminary clinical observation indicating that drugs cross-targeting this enzyme, that is, the HIV-1 protease inhibitors (HIV-1 PIs; 2 -6) produced some clinical benefits in patients treated with IFNs and ribavirin. cache = ./cache/cord-015376-z739ifu5.txt txt = ./txt/cord-015376-z739ifu5.txt === reduce.pl bib === id = cord-015527-ph576eji author = Mostajo, Nelly F title = A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date = 2019-09-30 pages = extension = .txt mime = text/plain words = 8386 sentences = 441 flesch = 56 summary = Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species. cache = ./cache/cord-015527-ph576eji.txt txt = ./txt/cord-015527-ph576eji.txt === reduce.pl bib === id = cord-004534-jqm1hxps author = nan title = Abstract date = 2009-06-09 pages = extension = .txt mime = text/plain words = 139023 sentences = 6450 flesch = 42 summary = HIV-1 to efficiently complete a replication cycle has to integrate its genome into the host cellular DNA.After HIV-1 enters target cells,neosynthesized viral DNA forms along with other proteins the pre-integration complex (PIC).PICs are then transported into the nucleus where integration,catalyzed by the viral integrase,takes place.HIV-1 viral particles engineered to incorporate integrase fused to EGFP have proven effective to study PICs within nuclei of infected cells.In this study we report the live imaging analysis of nuclear PIC dynamics obtained by time-lapse microscopy.Intranuclear trajectories of IN-EGFP-labeled PIC were collected in three dimensions and examined by both mean squared displacement (MSD) and cage diameter (CD) analysis.In CD the maximum distances measured between two positions occupied by a PIC in a time window of 2 minutes were calculated while in our MSD analysis 5-minute long trajectory segments were considered.Remarkably,MSD revealed the presence of an underlying active transport mechanism.To test the possible role of actin filaments,PIC nuclear trafficking was analyzed in cells treated with latrunculin B (actin polymerization inhibitor).Preliminary results suggest that the disruption of actin function impairs the active nuclear movement of PICs. Second harmonic generation microscopy reveals sarcomere contractile dynamics of cardiomyocytes N. cache = ./cache/cord-004534-jqm1hxps.txt txt = ./txt/cord-004534-jqm1hxps.txt === reduce.pl bib === id = cord-015673-rz74sh32 author = Lamers, Anne E. title = RNA Interference Mechanisms and Therapeutic Applications date = 2006 pages = extension = .txt mime = text/plain words = 2953 sentences = 177 flesch = 54 summary = RNA interference (RNAi) is a technology developed after the recent discovery of well-conserved cellular processes that induce posttranscriptional gene silencing triggered by small fragments of double-stranded RNA. An ancient process for defense against viral infections and transposons, and in higher developed organisms an endogenous process that regulates gene expression, triggered by double-stranded RNA (dsRNA) was recently revealed (for reviews see Carrington and Ambros, 2003; Hammond et al., 2001; Sharp, 2001) . Furthermore, longer fragments seem to be more effective than short RNA particles, because they are more efficiently processed into more different siRNAs. The convenient method of introducing small dsRNA fragments into the cell by hairpin-expressing plasmids (Fig. 2) can overcome these disadvantages (Kawasaki and Taira, 2003; Yu et al., 2002) . Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells cache = ./cache/cord-015673-rz74sh32.txt txt = ./txt/cord-015673-rz74sh32.txt === reduce.pl bib === id = cord-014908-jys1y0k9 author = Yadav, Rakesh title = Trends and Perspectives of Biosensors for Food and Environmental Virology date = 2010-05-19 pages = extension = .txt mime = text/plain words = 5113 sentences = 259 flesch = 32 summary = Unluckily, the PCR-based tools do not persistently amplify nucleic acids if viruses are found in infected food or environmental samples at critically low level. Another successful innovative biosensor with combined microfluidics and biosensing capabilities, furnish real time and automated affinity bioanalysis (e.g. for antigen-antibody assays) through surface plasmon resonance (SPR)-based original optical transduction mechanism. Since molecular recognition trait is central in the biosensing systems, all the structural components can be targeted to device a biosensor for detection of the specific virion particles present in food and environment samples. Molecular nanotechnology-based new nanostructures/nanomaterials such as aptamers are capable for developing highly specific biosensor for target elements detection. DNA-based biosensors have great applications in food and environmental analysis including determination of the pathogenic bacteria , and virus DNA sequence such as that of SARS virus (Abad-Valle et al. Quartz crystal microbalance (QCM)-based piezoelectric sensors can detect the hybridized viral DNA and also the capsid protein-ligand interactions. cache = ./cache/cord-014908-jys1y0k9.txt txt = ./txt/cord-014908-jys1y0k9.txt === reduce.pl bib === id = cord-013784-zhgjmt2j author = Tang, Min title = Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions date = 2020-06-04 pages = extension = .txt mime = text/plain words = 13704 sentences = 794 flesch = 45 summary = To move beyond serum-free sphere culture-based models, we utilized a DLP-based rapid 3D bioprinting system to generate 3D tri-culture or tetra-culture glioblastoma tissue models, with a background "normal brain" made up of NPCs and astrocytes and a tumor mass generated by GSCs, with or without macrophage, using brain-specific extracellular matrix (ECM) materials (Fig. 1a ). 35 While patient-derived glioblastoma cells grown under serum-free conditions enrich for stem-like tumor cells (GSCs) that form spheres and more closely replicate transcriptional profiles and invasive potential than standard culture conditions, we previously demonstrated that spheres display differential transcriptional profiles and cellular dependencies in an RNA interference screen compared to in vivo xenografts. [49] [50] [51] g Therapeutic efficacy prediction of drugs in all cancer cells in the CTRP dataset based on differentially expressed genes between the 3D tetra-culture model and GSCs grown in sphere culture as defined by RNA-seq. cache = ./cache/cord-013784-zhgjmt2j.txt txt = ./txt/cord-013784-zhgjmt2j.txt === reduce.pl bib === id = cord-016144-280kwlev author = Maan, Sushila title = Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date = 2018-04-26 pages = extension = .txt mime = text/plain words = 6526 sentences = 364 flesch = 45 summary = Further, modifications in PCR-based molecular detection techniques have generated a vast array of fast, reliable and specific assays which have widespread applications in veterinary diagnostics. The sensitivity of any genome detection-based method can be enhanced to a very high degree by manipulating any of the three pillars of the assay, i.e. by amplification of target, signal and probe. Common real-time PCRs include (1) SYBR green method where the fluorescent dye SYBR green binds to random dsDNA and can also give nonspecific amplification and (2) dual dyelabelled probe method which involves the use of sequence-specific DNA probes that are labelled with a fluorescent reporter, permitting specific detection after hybridization of the probe with its complementary sequence. To overcome these limitations and to increase efficiency comparable to symmetric PCRs, linear after the exponential (LATE)-PCR was developed based on primer pairs purposely designed for use at unequal concentrations to yield specific single-stranded DNA products in a robust way (Pierce et al. cache = ./cache/cord-016144-280kwlev.txt txt = ./txt/cord-016144-280kwlev.txt === reduce.pl bib === id = cord-016108-jlono0x7 author = Marthaler, Douglas title = Next-Generation Sequencing for Porcine Coronaviruses date = 2015-09-10 pages = extension = .txt mime = text/plain words = 1439 sentences = 97 flesch = 57 summary = In this chapter, we describe a method to deep genome sequence porcine coronavirus on the Illumina MiSeq, avoiding the number of contaminating reads associated with the host and other microorganisms. (e) Remap the reads to the contig to verify accurate generation of the viral genome and suffi cient coverage. (a) Open the SeqManNGen program, select reference-based assembly, and load the Susscrofa genome and the correlating paired fastq fi les to the sample. However, the concentration by RT-PCR may not indicate successful generation of the complete viral genome since total RNA was used in the library preparation. If libraries have limited host contamination and have an acceptable concentration of viral RNA (Ct value <25), a 1 million read output per sample should be suffi cient for assembly. Since the MiSeq generates reads from total RNA, host reads need to be removed to facilitate de novo assembly, which can be done by fi rst mapping the reads to the swine genome and saving the unmapped reads. cache = ./cache/cord-016108-jlono0x7.txt txt = ./txt/cord-016108-jlono0x7.txt === reduce.pl bib === id = cord-016209-6p9btua0 author = Merl, S. title = Targeting Viral Heart Disease by RNA Interference date = 2008 pages = extension = .txt mime = text/plain words = 7170 sentences = 429 flesch = 41 summary = The use of highly specific siRNAs targeting distinct regions of the viral genome ( Fig. 1) as well as host genes that are relevant for virus entry and maturation represents a novel therapeutic strategy to cure or attenuate in particular coxsackievirus-mediated diseases. Several laboratories obtained significant inhibition of the HIV-1 replication applying both synthetic and vector-derived siRNAs/shRNAs directed against the viral genome and HIV-encoded RNAs, such as the TAR element, tat, rev, gag, env, vif, nef and reverse transcriptase (Boden et al. In our previous work, the application of the most effective siRNA directed against the RNA dependent RNA polymerase 3D resulted in an approximately fourfold prolonged survival of coxsackievirus-infected cells and an inhibition of viral replication by more than 10 5 -fold compared to control siRNAs (Merl and Wessely 2007) . Even though previous studies reported efficient suppression of hepatitis C virus replication by siRNAs targeting single-stranded regions inbetween two stem-loop motifs of the viral 5′ UTR (Yokota et al. cache = ./cache/cord-016209-6p9btua0.txt txt = ./txt/cord-016209-6p9btua0.txt === reduce.pl bib === id = cord-016095-jop2rx61 author = Vignais, Pierre V. title = Challenges for Experimentation on Living Beings at the Dawn of the 21(st) Century date = 2010-06-08 pages = extension = .txt mime = text/plain words = 42843 sentences = 1503 flesch = 43 summary = Instead of setting out to discover unknown mechanisms by analyzing effects that are dependent on specific causes, with some uncertainty as to the possible success of the enterprise being undertaken, which is the foundation stone of the Bernardian paradigm of the experimental method, many current research projects give themselves achievable and programmable objectives that depend upon the means available to them: sequencing of genomes with a view to comparing them, recognition of sequence similarities in proteins coded for by genes belonging to different species, with the aim of putting together phylogenetic trees, synthesis of interesting proteins in transgenic animals and plants, analysis of the three-dimensional structure of proteins, in order to find sites that are likely to fix medicinal substances, and synthesis of molecular species able to recognize pathogenic targets. cache = ./cache/cord-016095-jop2rx61.txt txt = ./txt/cord-016095-jop2rx61.txt === reduce.pl bib === id = cord-014462-11ggaqf1 author = nan title = Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date = 2011-04-21 pages = extension = .txt mime = text/plain words = 35453 sentences = 1711 flesch = 49 summary = Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. cache = ./cache/cord-014462-11ggaqf1.txt txt = ./txt/cord-014462-11ggaqf1.txt === reduce.pl bib === id = cord-016808-gy8d8285 author = Agol, Vadim I. title = The Origin and Evolution of Viruses date = 2008 pages = extension = .txt mime = text/plain words = 3255 sentences = 172 flesch = 44 summary = Modern hypotheses of viral origin are based on two major developments of the molecular biology: discovery of ribozymes (RNA-based enzymes) and formulation of the "RNA World" theory (RNA had been "invented" before proteins and DNA), on the one hand, and achievements of genomics (determination of the nucleotide sequences of a great number of cellular and viral genomes), on the other. Three distinct DNA viruses, which had infected RNA genome-containing cells, gave rise to the three distinct domains of life, bacteria, archea, and eukarya (Forterre, 2006) . To infect a human, an avian flu virus should change its receptor specificity, which depends on the interaction of viral hemagglutinin (HA) with a cellular membrane glycoprotein receptor. Such a change in the host range may be achieved by either mutations in the avian HA or acquisition by an avian virus of the HA gene from human influenza virus as a result of genetic exchange (reassortment) between these viruses during mixed infections. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain cache = ./cache/cord-016808-gy8d8285.txt txt = ./txt/cord-016808-gy8d8285.txt === reduce.pl bib === id = cord-016343-wc3i54fc author = Frese, Michael title = Interferon-Induced Effector Proteins and Hepatitis C Virus Replication date = 2008 pages = extension = .txt mime = text/plain words = 10097 sentences = 503 flesch = 45 summary = RdRp, RNA-dependent RNA polymerase; IRES, internal ribosome entry site; 5BSL3.2, stem loop 3.2 within the coding sequence of NS5B normally result in the production of type I IFNs and the subsequent expression of IFN-induced effector proteins, which in turn would establish an antiviral state in the IFN-producing cell itself and in neighboring cells. Since MxA has the ability to efficiently inhibit a variety of different RNA viruses, MxA was the first IFN-induced effector protein to be analyzed for its antiviral activity in the HCV replicon system (Frese et al., 2001) . Rather indirect evidence that the OAS/RNase L pathway may indeed target HCV replication/translation was recently provided by Taguchi and co-workers, who reported that the N-terminal portion of NS5A (amino acids 1 to 148), which lacks the so-called PKR-binding domain, binds to OAS proteins and there by counteract the antiviral activity of IFN-α (Taguchi et al., 2004) . cache = ./cache/cord-016343-wc3i54fc.txt txt = ./txt/cord-016343-wc3i54fc.txt === reduce.pl bib === id = cord-016261-jms7hrmp author = Liu, Chunmei title = Profiling and Searching for RNA Pseudoknot Structures in Genomes date = 2005 pages = extension = .txt mime = text/plain words = 4330 sentences = 221 flesch = 53 summary = Profiling models based solely on sequence content such as Hidden Markov Model (HMM) [12] may miss structural homologies when directly used to search genomes for noncoding RNAs containing complex secondary structures. ERPIN searches genomes by sequentially looking for single stem loop motifs contained in the noncoding RNA gene, and reports a hit when significant alignment scores are observed for all the motifs at their corresponding locations. In this paper, we propose a new method to search for RNA pseudoknot structures using a model of multiple CMs. Unlike the model of Brown and Wilson, we use independent CM components to profile the interleaving stems in a pseudoknot. Finally, in order to test the ability of our program to cope with noncoding RNA genes with complex pseudoknot structures, we carried out an experiment where the complete DNA genomes of two bacteria were searched to find the locations of the tmRNA genes. cache = ./cache/cord-016261-jms7hrmp.txt txt = ./txt/cord-016261-jms7hrmp.txt === reduce.pl bib === id = cord-015237-8cxfa8wf author = nan title = Structure Watch date = 2005 pages = extension = .txt mime = text/plain words = 274 sentences = 23 flesch = 66 summary = The solution structures of the four RNA-binding domains (RBDs) of polypyrimidine-tract-binding protein-1 (PTB1) in complex with RNA have now been solved by Oberstrass et al., leading to new models for the function of PTB1 as a repressor of alternative splicing. used NMR to look at the structure of RBD1-4 in complex with a 5′-CUCUCU-3′ oligonucleotide, which is a common feature of intronic regulatory sequences. Each RBD binds independently to one RNA molecule and recognizes a different consensus sequence within the oligonucleotide. The nucleotides interact with the flat β-sheet surface of each RBD but, unlike other RBD-RNA structures, the third β-strand is only weakly involved in RNA binding. A single PTB1 molecule can therefore bring two distant pyrimidine tracts into close proximity and induce RNA looping -a feature that has led to the proposal of various models for the function of this protein in alternative splicing. Structure of PTB bound to RNA: specific binding and implications for splicing regulation cache = ./cache/cord-015237-8cxfa8wf.txt txt = ./txt/cord-015237-8cxfa8wf.txt === reduce.pl bib === id = cord-015606-h9bbvpzd author = Highfield, P.E. title = Translation of infectious bronchitis virus RNA date = 2006-03-27 pages = extension = .txt mime = text/plain words = 1125 sentences = 72 flesch = 63 summary = When RNA extracted from IBV-infected and uninfected chick embryo kidney cells was added to the reticulocyte system there was a stimulation of methionine incorporation (Table 1 ) and a whole spectrum of polypeptides could be found in the product (Fig. la) . It has a molecular weight of 55 000, co-migrates with one of the bands formed by translation of the virion RNA and is also present in the IBV capsid. When the products formed in the wheat germ synthesis by IBV infected cellular RNA were compared with those formed by uninfected cellular RNA, two new bands could be identified, with molecular weights Lomniczi [4] have demonstrated that the RNA is infectious and that the virion does not contain any transcriptase activity (Lomniczi, unpublished results) . In the reticulocyte system one of the products formed by the virion RNA appears to have the same molecular weight as one of the virion proteins. cache = ./cache/cord-015606-h9bbvpzd.txt txt = ./txt/cord-015606-h9bbvpzd.txt === reduce.pl bib === id = cord-016179-4i1n9j4x author = Chen, Yi-Ning title = Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues date = 2015-09-10 pages = extension = .txt mime = text/plain words = 2078 sentences = 133 flesch = 62 summary = title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues A specific one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay using TCoV-specific primers and dual-labeled fluorescent probe for detection and quantitation of TCoV in feces and intestine tissues is described in this chapter. In this chapter, the protocol for one-step real-time RT-PCR to detect, differentiate, and quantitative TCoV RNA in the feces and intestinal tissue is presented. In step 3, the extracted RNA was subjected to one-step real-time RT-PCR for detection and quantitation of TCoV in feces or intestine tissues. Specific real time reverse transcription polymerase chain reaction for detection and quantitation of turkey coronavirus RNA in tissues and feces from turkeys infected with turkey coronavirus The protocol "Real-time reverse transcription-polymerase chain reaction for detection and quantitation of turkey coronavirus RNA in feces and intestine tissues" outlined in this chapter had been successfully carried out in the authors' studies on molecular diagnostics, molecular virology, immunology, and/or vaccinology of turkey coronaviral enteritis. cache = ./cache/cord-016179-4i1n9j4x.txt txt = ./txt/cord-016179-4i1n9j4x.txt === reduce.pl bib === id = cord-016309-6mw8okmt author = Bule, Mohammed title = Antivirals: Past, Present and Future date = 2019-06-06 pages = extension = .txt mime = text/plain words = 8200 sentences = 405 flesch = 36 summary = Those included usage restricted to a single virus and specific animal species, problems with high spectrum activity and low cytotoxicity, high costs of development of new chemical compounds and absence of rapid diagnostic techniques allowing prompt use of a specific antiviral agent in the course of an acute infection (Rollinson 1992a, b) . Nevertheless, several licensed human antiviral agents are being used with cascade principle for treatment of animal diseases (e.g. acyclovir, idoxuridine and trifluridine against feline herpesvirus-1 ocular infection in cats) (Thiry et al. The discovery of PAA (Fig. 22.4) as an antiviral drug gave rise to intense research on its biological activities, which demonstrated PAA and its derivatives' ability to inhibit the replication of a number of viruses such as immunodeficiency, hepatitis and herpes viruses. To conclude with, equine herpesvirus type 1 (EHV-1) infection causes outbreak of respiratory and various neurological diseases in horses, against which acyclovir and valacyclovir are the most common drugs, but also IFN targeting IFNGR complex as a key mediator of virus-specific cellular immunity (Poelaert et al. cache = ./cache/cord-016309-6mw8okmt.txt txt = ./txt/cord-016309-6mw8okmt.txt === reduce.pl bib === id = cord-015871-1tuf4zxi author = Ergonul, Onder title = Treatment of Crimean-Congo Hemorrhagic Fever date = 2007 pages = extension = .txt mime = text/plain words = 8234 sentences = 474 flesch = 44 summary = In contrast, a dose of ribavirin at least nine times greater was required to induce a comparable inhibitory effect on the yields of Rift Valley fever virus, for which the drug has been shown to inhibit replication in monkeys and rodents [104] . However hemorrhagic fever virus infections can be approached by the following different therapeutic strategies [6] : (i) administration of high-titered neutralizing antibodies and/or (ii) treatment with antiviral drugs. In recent times, several groups have studied the antiviral activities of interferons against hemorrhagic fever viruses. Human MxA protein inhibits the replication of Crimean-Congo hemorrhagic fever virus Type I interferon inhibits Crimean-Congo hemorrhagic fever virus in human target cells Genotoxic effect of ribavirin in patients with Crimean-Congo hemorrhagic fever Ribavirin efficacy in an in vivo model of Crimean-Congo hemorrhagic fever virus (CCHF) infection Inhibition of Crimean-Congo hemorrhagic fever viral infectivity yields in vitro by ribavirin cache = ./cache/cord-015871-1tuf4zxi.txt txt = ./txt/cord-015871-1tuf4zxi.txt === reduce.pl bib === id = cord-017181-ywz6w2po author = Maus, Carsten title = Component-Based Modelling of RNA Structure Folding date = 2008 pages = extension = .txt mime = text/plain words = 5364 sentences = 284 flesch = 51 summary = As this regulating process depends largely on structure formation, modelling of RNA folding would be a big step in the right direction for reflecting attenuation dynamics. Additionally, modelling interactions between mRNA and RNAP as well as mRNA and the ribosome are needed because both influence the kinetic folding process and RNA termination structures break up gene transcription. If observed structures are present during folding simulation, the macro level model can signalise this information and thus trigger dynamics to other components by adding new ports to itself (representing docking sites) or send messages over existing ports. Simulating the RNA folding with Kinfold [12] results in a five times higher amount of the 2-helix conformation than the single hairpin, but their total sum is about 60% of all molecules and thus less misfolded structures can be observed. The pattern observation function of the RNA folding model, which is realised at macro level, allows us to look for an intrinsic transcription termination structure [2] during simulation. cache = ./cache/cord-017181-ywz6w2po.txt txt = ./txt/cord-017181-ywz6w2po.txt === reduce.pl bib === id = cord-017968-17d37a2z author = Lewinski, Martin title = Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana date = 2018-08-30 pages = extension = .txt mime = text/plain words = 6560 sentences = 389 flesch = 50 summary = Here, we discuss recent progress to obtain a systems-level understanding of in vivo RNA–protein interactions in the reference plant Arabidopsis thaliana using protein-centric and RNA-centric methods as well as combined protein binding site and structure probing. Among the RBPs present in the Arabidopsis genome are 197 proteins with an RNA recognition motif (RRM), the most abundant type of RNA-binding domain, and 28 K homology (KH) domain proteins first identified in mammalian heterogeneous nuclear protein hnRNP K (Silverman et al. Functional characterization of a glycine-rich RNA-binding protein 2 in Arabidopsis thaliana under abiotic stress conditions Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with target transcripts in Arabidopsis thaliana cache = ./cache/cord-017968-17d37a2z.txt txt = ./txt/cord-017968-17d37a2z.txt === reduce.pl bib === id = cord-016293-pyb00pt5 author = Newell-McGloughlin, Martina title = The flowering of the age of Biotechnology 1990–2000 date = 2006 pages = extension = .txt mime = text/plain words = 22402 sentences = 943 flesch = 47 summary = In the course of the project, especially in the early years, the plan stated that "much new technology will be developed that will facilitate biomedical and a broad range of biological research, bring down the cost of many experiments (mapping and sequencing), and finding applications in numerous other fields." The plan built upon the 1988 reports of the Office of Technology Assessment and the National Research Council on mapping and sequencing the human genome. These DNA chips have broad commercial applications and are now used in many areas of basic and clinical research including the detection of drug resistance mutations in infectious organisms, direct DNA sequence comparison of large segments of the human genome, the monitoring of multiple human genes for disease associated mutations, the quantitative and parallel measurement of mRNA expression for thousands of human genes, and the physical and genetic mapping of genomes. cache = ./cache/cord-016293-pyb00pt5.txt txt = ./txt/cord-016293-pyb00pt5.txt === reduce.pl bib === id = cord-016499-5iqpl23p author = Mackay, Ian M. title = Rhinoviruses date = 2014-02-27 pages = extension = .txt mime = text/plain words = 23394 sentences = 1156 flesch = 45 summary = A convenience population of 15 healthy children (1-9 years old) without asthma were followed during at least three seasons, and picornaviruses were detected in 5 % of 740 specimens (21 % of infections) not associated with symptoms, The impact of HRV typing and of sampling based only on symptoms. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines cache = ./cache/cord-016499-5iqpl23p.txt txt = ./txt/cord-016499-5iqpl23p.txt === reduce.pl bib === id = cord-015933-x5cq4k4x author = Verbrugh, H.A. title = 1 Micro-organismen, de mens en het ontstaan van infectieziekten: algemene principes date = 2011 pages = extension = .txt mime = text/plain words = 19354 sentences = 1625 flesch = 54 summary = Virussen vormen een geheel aparte groep biologische agentia die ziekte bij de mens kunnen veroorzaken; hun meest karakteristieke eigenschap is dat zij voor hun vermeerdering afhankelijk zijn van levende gastheercellen. Dit duidt er dus tevens op dat een micro-organisme over een complex geheel van genetische eigenschappen moet beschikken, wil het pathogene betekenis voor de mens krijgen; dergelijke eigenschappen worden ook wel virulentiefactoren genoemd. Een aantal virussen staat bekend als tumorvirus omdat zij een permanente maligne transformatie in hun gastheercel kunnen teweegbrengen; het virus beïnvloedt dan de transcriptie van specifieke cellulaire oncogenen of andere gastheergenen, genen die betrokken zijn bij de regulatie van celdeling of spontane celdood (apoptose). Hoewel sommige micro-organismen (stafylokokken) zich direct aan dergelijke kunststoffen kunnen hechten, is het in de praktijk zo dat het oppervlak ervan snel door neerslag met bovengenoemde matrixeiwitten als fibronectine wordt bedekt, een proces dat ook wel conditionering van het biomateriaal wordt genoemd. cache = ./cache/cord-015933-x5cq4k4x.txt txt = ./txt/cord-015933-x5cq4k4x.txt === reduce.pl bib === id = cord-015850-ef6svn8f author = Saitou, Naruya title = Eukaryote Genomes date = 2013-08-22 pages = extension = .txt mime = text/plain words = 7424 sentences = 484 flesch = 53 summary = General overviews of eukaryote genomes are first discussed, including organelle genomes, introns, and junk DNAs. We then discuss the evolutionary features of eukaryote genomes, such as genome duplication, C-value paradox, and the relationship between genome size and mutation rates. Most of the protein coding genes of melon mitochondrial DNAs are highly similar to those of its congeneric species, which are watermelon and squash whose mitochondrial genome sizes are 119 kb and 125 kb, respectively. There are various genomic features that are specifi c to eukaryotes other than existence of introns and junk DNAs, such as genome duplication, RNA editing, C-value paradox, and the relationship between genome size and mutation rates. The Perigord black truffl e ( Tuber melanosporum ), shown as A i n Fig. 8.9 , has the largest genome size (~125 Mb) among the 88 fungi species whose genome sequences were so far determined, yet the number of genes is only ~7,500 [ 81 ] . cache = ./cache/cord-015850-ef6svn8f.txt txt = ./txt/cord-015850-ef6svn8f.txt === reduce.pl bib === id = cord-017297-q3qtgrfc author = Rajagopal, Vaishnavi title = Viral Helicases date = 2008-11-01 pages = extension = .txt mime = text/plain words = 11546 sentences = 654 flesch = 52 summary = In a recent study on HSV-1 UL9 helicase, mutational analysis of the residues in the Ia motif implicated in DNA binding resulted in moderate to severe defects in single-stranded nucleic-acids binding and ssNA stimulated ATPase activity, while retaining the intrinsic ATPase activity similar to that of wildtype enzyme (Marintcheva and Weller 2003) . Thus, in order to understand the mechanism of helicase catalyzed unwinding reactions, it is important to understand all the individual steps to it, namely: nucleic-acid binding, NTP binding and hydrolysis, single-stranded translocation, and then finally the strand-separation function. Two early genes of bacteriophage T5 encode proteins containing an NTP-binding sequence motif and probably involved in DNA replication, recombination and repair Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases A functional interaction of ICP8, the herpes simplex virus single-stranded DNA-binding protein, and the helicase-primase complex that is dependent on the presence of the UL8 subunit cache = ./cache/cord-017297-q3qtgrfc.txt txt = ./txt/cord-017297-q3qtgrfc.txt === reduce.pl bib === id = cord-018804-wj35q88f author = Lázaro, Ester title = Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date = 2007 pages = extension = .txt mime = text/plain words = 8510 sentences = 398 flesch = 44 summary = High error prone replication, together with the short replication times and large population sizes typical of RNA viruses, instead of being a handicap for survival provides an extraordinary evolutionary advantage by permitting the generation of a wide reservoir of mutants with different phenotypic properties [7] . However, the fact that DNA organisms, which usually live in constant environments, have evolved corrector activities, whereas RNA viruses have not, suggests that replication with high error rates is a selected character that strongly favours viral adaptation to fast changing conditions. Quasi-species replicating during a long time in a near-constant environment in the absence of large population size fluctuations can present a low rate of fixation of mutations in the consensus sequence, despite the continuous occurrence of mutants that is characteristic of the underlying dynamics of the population. The infection of a new host constitutes a sudden change in the environment in which viral replication takes place, usually with the consequence of a drastic decrease in the average fitness of the virus population, which prevents further transmission. cache = ./cache/cord-018804-wj35q88f.txt txt = ./txt/cord-018804-wj35q88f.txt === reduce.pl bib === id = cord-018944-du42ho11 author = Shin, Jeong Hwan title = Nucleic Acid Extraction and Enrichment date = 2018-11-10 pages = extension = .txt mime = text/plain words = 6857 sentences = 355 flesch = 41 summary = [6, 7] as follows: (1) extraction should be simple and rapid and should show high sensitivity and specificity; (2) it is preferred that there be no requirements for specialized equipment or special knowledge and skills; (3) the final nucleic acid should be pure and easy to modify for various amplification techniques; (4) the reagents and their product should be harmless; and (5) the process of preparation should resist contamination with other specimens. Although the phenolchloroform method is relatively easy compared with the CsCl/EtBr gradient and is very useful for the extraction of nucleic acids, it also is problematic for the clinical microbiology laboratory because phenol has important limitations due to its being toxic, caustic, and flammable [5, 15, 16] . In recent years, it has become possible to extract viral nucleic acid from clinical specimens having cellular components, and there have been trials of these commercially available kits to detect various clinically important viruses [30] [31] [32] . cache = ./cache/cord-018944-du42ho11.txt txt = ./txt/cord-018944-du42ho11.txt === reduce.pl bib === id = cord-016313-n4ewq0pt author = Baranyi, Lajos title = Advances in Lentiviral Vector-based Cell Therapy with Mesenchymal Stem Cells date = 2012-09-27 pages = extension = .txt mime = text/plain words = 20575 sentences = 824 flesch = 39 summary = The field of possible application of mesenchymal stem cells in medicine and research expanded tremendously with the advent of improved Lentiviral-vectors capable of inserting stable copies of genes of interest and expressing proteins or biologically active RNA species ad libitum, performing delicate gene editing or active gene silencing or serving as advanced drug delivery systems utilized in ex vivo cell therapy. Implantation of Lentiviral vector-transduced human bone marrow mesenchymal cells using collagen scaffolds into immunode fi cient mice resulted in ef fi cient engraftment of gene-engineered cells and provided sites for transgene-expression in vivo. Moreover, it did not alter the differentiation potential of either HSCs or MSCs. In addition, the therapeutic potential of CD133+ and MSC progenitor cells transduced ex vivo with Lentiviral vector encoding the mature form of vascular endothelial growth factor D (VEGF-D ) or the enhanced green fl uorescent protein (eGFP) marker gene achieved permanent gene expression. cache = ./cache/cord-016313-n4ewq0pt.txt txt = ./txt/cord-016313-n4ewq0pt.txt === reduce.pl bib === id = cord-018164-h5k1zsyg author = Taylor, Milton W. title = What Is a Virus? date = 2014-07-22 pages = extension = .txt mime = text/plain words = 4769 sentences = 260 flesch = 60 summary = Studies of viral replication indicate that most viruses self-assemble as a result of interactions between the viral proteins to form a viral capsid that interacts with the nucleic acid to form the whole. The viral proteins are produced in one part of the cell, the replicated nucleic acid in another, and somehow they find each other, interact, and form virus particles that are expelled from the cell. Indirect contact spread includes cases where mucus from a runny nose may get onto the hands, or virus may be left on a surface such as a doorknob, telephone, or countertops, and is picked up by a second individual, who then touches his eyes or nose, resulting in infection. Vector transmission is a very common means of transmission; the best studied cases include yellow fever, dengue virus, and West Nile fever-viruses all transmitted by mosquitoes. As many as 400 million people are infected annually by dengue virus, which is caused by any one of four related viruses transmitted by mosquitoes. cache = ./cache/cord-018164-h5k1zsyg.txt txt = ./txt/cord-018164-h5k1zsyg.txt === reduce.pl bib === id = cord-017167-8cdbcrh7 author = Ahola, Tero title = Functions of Chikungunya Virus Nonstructural Proteins date = 2016-12-03 pages = extension = .txt mime = text/plain words = 10491 sentences = 530 flesch = 49 summary = The nonstructural proteins (nsPs) of chikungunya virus (CHIKV) are expressed as one or two polyprotein precursors, which are translated directly from the viral genomic RNA. Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis. However, recent studies of SFV P1234 processing reveal that a second mechanism, the presentation of cleavage sequences via long-range interactions between different domains of the polyprotein, Processing of CHIKV ns polyprotein P1234 and RNA synthesis. The main interaction appears to be mediated by a membrane-binding peptide located in the central part of the protein (approximately residues 244-263 in CHIKV nsP1; Fig. 2 ), which forms an amphipathic alpha helix, as characterized for the corresponding peptide from SFV (Ahola et al. However, the effects of mutations introduced into the NTPase/helicase active site were different for these viruses: in SINV such a mutation strongly reduced the nsP2-dependent degradation of Rpb1 whereas CHIKV nsP2 mostly retained its ability to block host gene expression. cache = ./cache/cord-017167-8cdbcrh7.txt txt = ./txt/cord-017167-8cdbcrh7.txt === reduce.pl bib === id = cord-021115-2fkghukw author = Guo, Yun title = Molecular dynamics simulation of RNA pseudoknot unfolding pathway date = 2013-03-12 pages = extension = .txt mime = text/plain words = 3271 sentences = 178 flesch = 63 summary = It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (MMTV) RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynamics simulation method in this paper. To study the factors that affect the stability and the unfolding pathways of the pseudoknots, the MMTV RNA was studied by all-atom molecule dynamics simulation methods under different ion concentrations and temperatures. The structural features of MMTV RNA pseudoknot in different ion concentration, the unfolding process of RNA pseudoknot, and two hairpin helices that constituted the RNA pseudoknot were studied with all atom molecular dynamics simulation method in this paper. cache = ./cache/cord-021115-2fkghukw.txt txt = ./txt/cord-021115-2fkghukw.txt === reduce.pl bib === id = cord-020969-lh2ergpm author = STRAUSS, JAMES H. title = Gene Therapy date = 2012-07-27 pages = extension = .txt mime = text/plain words = 11793 sentences = 597 flesch = 52 summary = Together with methods for cloning and manipulating viral genomes, this information has made possible the use of viruses as vectors to express foreign genes. The use of minus-strand RNA viruses as vectors was delayed because the virion RNA itself is not infectious, but recent developments has made it possible to rescue virus from cloned DNA by using coexpression of the appropriate viral proteins in a transfected cell. It is also possible to transfect cells with the E1 or E3 expression cassette together with DNA clones encoding the rest of the adenovirus genome, in which case homologous recombination results in the production of virus. Because the poliovirus replicon lacks a full complement of the structural genes (it is a suicide vector), packaging to produce particles requires infection of a cell that expresses the polioviral structural proteins by some mechanism. cache = ./cache/cord-020969-lh2ergpm.txt txt = ./txt/cord-020969-lh2ergpm.txt === reduce.pl bib === id = cord-016419-v1f6dx3e author = Gupta, Varsha title = Production of Recombinant Pharmaceutical Proteins date = 2016-10-23 pages = extension = .txt mime = text/plain words = 9648 sentences = 602 flesch = 50 summary = Usage of recombinant DNA technology for large-scale production of proteins requires ample amount of time, labor, and resources, but it also offers many opportunities for economic growth. The recombinant proteins approved by FDA are obtained either from Escherichia coli or other prokaryotes; from Saccharomyces cerevisiae or other fungal species; from insect cells , mammalian cells , or human cells ; or from transgenic plants or animals. Their advantages are low cost, high mass production, scale-up, lack of human pathogens , and addition of eukaryotic PTMs. The fi rst recombinant protein obtained in 1986 from tobacco plants was human growth hormone . The vector can be modifi ed to express genes for insulin (tomato) or Hep-B surface antigen (HBsAg) for recombinant therapeutics providing a human glycosylation pattern have increased attention, and the efforts are being made for the development of novel glycoengineered cell lines for production of fully glycosylated protein therapeutic. cache = ./cache/cord-016419-v1f6dx3e.txt txt = ./txt/cord-016419-v1f6dx3e.txt === reduce.pl bib === id = cord-018437-yjvwa1ot author = Mitchell, Michael title = Taxonomy date = 2013-08-26 pages = extension = .txt mime = text/plain words = 9283 sentences = 561 flesch = 48 summary = Classifi cation is based on the genomic nucleic acid used by the virus (DNA or RNA), strandedness (single or double stranded), and method of replication. The nucleocapsids of some viruses are surrounded by envelopes composed of lipid bilayers and host-or viral-encoded proteins. The sequence of negative-sense ssRNA is complementary to the coding sequence for translation, so mRNA must be synthesized by RNA polymerase, typically carried within the virion, before translation into viral proteins. Among the families of viruses able to infect humans and other vertebrate hosts, there are many species that target and cause disease in the lung. The nucleocapsid is surrounded by an envelope derived from host-cell membrane and viral envelope proteins, including hepatitis B surface antigen. The genome of human parainfl uenza viruses is ~15 kb in length with an organization and six reading frames (N, P, M, F, HN, L) typical of the Paramyxoviridae (Karron and Collins 2007 ) . cache = ./cache/cord-018437-yjvwa1ot.txt txt = ./txt/cord-018437-yjvwa1ot.txt === reduce.pl bib === id = cord-019076-4qu9j953 author = Ulferts, Rachel title = Expression and Functions of SARS Coronavirus Replicative Proteins date = 2009-07-22 pages = extension = .txt mime = text/plain words = 10036 sentences = 516 flesch = 52 summary = In this chapter, we review our current understanding of the expression and functions of key replicative enzymes, such as RNA polymerases, helicase, ribonucleases, ribose-2′-O-methyltransferase and other replicase gene-encoded proteins involved in genome expression, virus–host interactions and other processes. The RTC includes the key replicative proteins of the virus, such as RNA-dependent RNA polymerase (RdRp) and helicase activities, as well as enzymes that are thought to be involved in the processing and modification of viral and/or cellular RNAs, such as primase, endoribonuclease, exoribonuclease and ribose-2 0 -O-methyltransferase activities (for recent reviews, see Masters 2006; Ziebuhr 2005 Ziebuhr , 2008 . SARS-CoV pp1a and pp1ab are co-and post-translationally processed by two proteases, a papain-like protease (PL pro ) and the main protease (M pro , nsp5), resulting in 16 mature products called nonstructural proteins (nsps) 1-16 The 5 0 -terminal ORF(s) expressed from specific RNAs is/are shown as boxes. cache = ./cache/cord-019076-4qu9j953.txt txt = ./txt/cord-019076-4qu9j953.txt === reduce.pl bib === id = cord-022084-hap7flng author = ARRUDA, EURICO title = Respiratory Tract Viral Infections date = 2009-05-15 pages = extension = .txt mime = text/plain words = 19181 sentences = 1041 flesch = 43 summary = The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. cache = ./cache/cord-022084-hap7flng.txt txt = ./txt/cord-022084-hap7flng.txt === reduce.pl bib === id = cord-016755-ye37z5h9 author = Li, Jiandong title = The Discovery Process of SFTS in China date = 2019-10-12 pages = extension = .txt mime = text/plain words = 2310 sentences = 116 flesch = 52 summary = Sequence from a novel species of phlebovirus was identified by sequence independent single primer amplification (SISPA) from the serum of a patient with SFTS. The virus was isolated in Vero cell culture and its complete genome sequence was determined, only distantly related to other known phleboviruses. Phylogenetic trees based on complete viral genomic sequence of L, M and S segments from strains (HB29, HN6, AN12, LN2, JS3 and SD4) from 6 provinces in China in comparison with other known phleboviruses showed that SFTS virus was related to prototypic viruses of Phlebovirus. The novel phlebovirus was isolated in cultured Vero cells inoculated with acute-phase serum of patient HB29 from Shuizhou area, Hubei province. Specificity, sensitivity and cross reactivity of the methods were verified with serum samples collected from patients with SFTS confirmed by RT-PCR and sera collected from healthy donors from the areas without reported SFTS cases. cache = ./cache/cord-016755-ye37z5h9.txt txt = ./txt/cord-016755-ye37z5h9.txt === reduce.pl bib === id = cord-017732-1pwa6zsk author = Miller, W. Allen title = Ribosomal Frameshifting in Decoding Plant Viral RNAs date = 2009-07-21 pages = extension = .txt mime = text/plain words = 10588 sentences = 477 flesch = 56 summary = As in animal viruses, the −1 ribosomal frameshift site in the viral mRNA consists of a canonical shifty heptanucleotide followed by a highly structured frameshift stimulatory element, and the gene translated as a result of frameshifting usually encodes the RNA-dependent RNA polymerase. We suggest that these experiments may not have revealed all of the sequence requirements for frameshifting on the full-length viral RNA because the frameshifting constructs tested contained a very short (10 codon) first (zero frame) ORF from the start codon through the shifty site which is followed immediately by a stop codon. The 25-kDa protein that could be generated by a frameshift followed by cleavage at the HC-Pro/P3 cleavage site is indicated (Chung et al., 2008) anticipate results of future research and structural analysis to determine how these diverse plant viral RNAs induce ribosomes to change reading frames by what may be novel mechanisms. cache = ./cache/cord-017732-1pwa6zsk.txt txt = ./txt/cord-017732-1pwa6zsk.txt === reduce.pl bib === id = cord-016652-x8t3lf1x author = Matthews, David title = Viruses and the Nucleolus date = 2011-05-23 pages = extension = .txt mime = text/plain words = 6630 sentences = 348 flesch = 33 summary = This process is crucial for virus biology because if the viral proteins that are required for cytoplasmic functions such as RNA synthesis and encapsidation are sequestered in the nucleolus or nucleus, then progeny virus production will be affected as has been revealed by inhibitor and genetic studies (Lee et al. Viruses may interact with the nucleolus to usurp host cell functions and recruit nucleolar proteins to facilitate virus replication. Initial studies utilising the prototype g-2 herpesvirus, herpes virus saimiri (HVS), demonstrated that the HVS nucleolar trafficking ORF57 protein induces nucleolar redistribution of the host cell human TREX proteins, which are involved in mRNA nuclear export (Boyne and Whitehouse 2006) . The localisation of porcine reproductive and respiratory syndrome virus nucleocapsid protein to the nucleolus of infected cells and identification of a potential nucleolar localization signal sequence Sequence requirements for nucleolar localization of human T cell leukemia virus type I pX protein, which regulates viral RNA processing cache = ./cache/cord-016652-x8t3lf1x.txt txt = ./txt/cord-016652-x8t3lf1x.txt === reduce.pl bib === id = cord-021481-tvs1pnib author = Singh, Gatikrushna title = Cellular RNA Helicases Support Early and Late Events in Retroviral Replication date = 2018-08-17 pages = extension = .txt mime = text/plain words = 6039 sentences = 359 flesch = 43 summary = Introns FIGURE 7.1 Critical events in HIV-1 replication are supported by RNA helicases Early steps in HIV-1 replication involve reverse transcription in the cytosol of capsid-associated viral RNA (n = 2) to double-stranded cDNA that transits the nuclear pore and integrates into the host chromosome (blue lines) to form a provirus (red line surrounded by black dotted line) with the involvement of at least two RHs (DHX9, DDX19A). The study of CTE/TAP activity significantly expanded knowledge of nucleocytoplasmic transport of cell mRNAs and regulation by many virus RNAs. Ten years ago and in context RSV, a genetically simple avian retrovirus, DDX19B/yeast DBP5 was determined to facilitate nuclear export of genome-length unspliced RNA (LeBlanc et al., 2007) . Influenza A virus polymerase recruits the RNA helicase DDX19 to promote the nuclear export of viral mRNAs RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs cache = ./cache/cord-021481-tvs1pnib.txt txt = ./txt/cord-021481-tvs1pnib.txt === reduce.pl bib === id = cord-022348-w7z97wir author = Sola, Monica title = Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date = 2007-09-02 pages = extension = .txt mime = text/plain words = 10892 sentences = 671 flesch = 56 summary = An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. Under the rubric replication, a virus could vary to increase its fitness, exploit different target cells or evade adaptive immune responses. For a given virus, different protein sequence sets were compared to a given reference such as RT in the case of HIV/SIV. Although these data were derived from completely sequenced primate immunodeficiency viral genomes, analyses on larger data sets, such as p17 Gag/p24 Gag or gp120/gp41, yielded relative values that differed from those given in Table 6 .1 by at most 14%. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships (Table 6 .1). In the clear cases where genetic variation is exploited by RNA viruses, it is used to overcome barriers to transmission set up by the host population, e.g. herd immunity. cache = ./cache/cord-022348-w7z97wir.txt txt = ./txt/cord-022348-w7z97wir.txt === reduce.pl bib === id = cord-018724-ss8x2g3b author = Stobbe, Anthony title = Plant Virus Diversity and Evolution date = 2016-06-22 pages = extension = .txt mime = text/plain words = 7456 sentences = 360 flesch = 47 summary = The variation we see within a single plant host has profound effects on the how the virus responds to selective pressures associated with new hosts, and factors such as the bottleneck events associated with cell-to-cell movement or vectoring. However, several forms of virus variation, such as the high mutation rates of RNA and some DNA viruses, recombination, and reassortment lead to resistance breaking (Duffy and Holmes 2008; McDonald and Linde 2002; Harrison 2002) . For example, genetic diversity (heterosis) induced tolerance to Turnip mosaic virus in wild cress (Lepidium sp.) hybrids, while plants that were selfed were more susceptable to disease, suggesting that small populations with low genetic diversity could lead to increased disease symptoms, and infection rates (Houliston et al. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus cache = ./cache/cord-018724-ss8x2g3b.txt txt = ./txt/cord-018724-ss8x2g3b.txt === reduce.pl bib === id = cord-016538-4og05fuo author = Dolja, V. V. title = Biotechnology Applications of Grapevine Viruses date = 2017-03-30 pages = extension = .txt mime = text/plain words = 6266 sentences = 292 flesch = 44 summary = Although in theory any of the grapevine-infecting viruses can be engineered into transient gene expression or VIGS vector, in practice, only one of them, the filamentous Grapevine leafroll-associated virus-2 (GLRaV-2) from the genus Closterovirus (family Closteroviridae), was demonstrated to fulfill these roles (Dolja and Koonin 2013; Kurth et al. Among these viruses, only GLRaV-2, a closterovirus, has been so far engineered into a vector capable of systemic infection of grapevine that either produces recombinant protein or elicits VIGS response (Kurth et al. The more recently developed CTV-based gene expression vectors were shown to be not only capable of systemic infection in the natural citrus hosts but also exhibited remark-able genetic stability in regard to retention of the inserted recombinant gene, as well as VIGS capability (Dawson et al. Another candidate to be developed as a vector for protein expression and VIGS is GRSPaV, which is the only grapevine-infecting member of the genus Foveavirus that was recently characterized (Meng et al. cache = ./cache/cord-016538-4og05fuo.txt txt = ./txt/cord-016538-4og05fuo.txt === reduce.pl bib === id = cord-018798-yzxy9ogf author = Jain, Pradeep Kumar title = RNAi for Resistance Against Biotic Stresses in Crop Plants date = 2018-07-10 pages = extension = .txt mime = text/plain words = 12555 sentences = 711 flesch = 47 summary = This chapter also reviews the rich history of RNAi research, gene regulation by small RNAs across different organisms, and application potential of RNAi for generating transgenic plants resistant to major pests(.) But, there are some limitations too which restrict wider applications of this technology to its full potential. Different delivery methods of dsRNA that have been used for successful RNAi in insects and nematodes include microinjection, feeding on either artificial diet (Table 4 .2), and/or host-mediated delivery through transgenic plants (Fig. 4.1) . RNAi mechanism partly occurs in the host itself and partly in nematodes feeding on the transgenic host plant expressing dsRNA for the target gene. despite the absence of Sid-1 and Sid-2 genes exhibit systemic RNAi when subjected to silencing technology indicating a presence of similar receptor-mediated endocytic process for dsRNA uptake as reported in insects ). cache = ./cache/cord-018798-yzxy9ogf.txt txt = ./txt/cord-018798-yzxy9ogf.txt === reduce.pl bib === id = cord-023865-6rafp3x3 author = Surjit, Milan title = The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date = 2009-07-22 pages = extension = .txt mime = text/plain words = 9210 sentences = 448 flesch = 45 summary = Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. Interestingly, biochemically mediated inhibition of GSK3 activity in SARS-CoV infected cells also leads to around 80% reduction in viral titer and subsequent induction of a virus-induced cytopathic effect. Further, S-phase specific gene products like cyclin E and CDK2 were found to be downregulated in SARS-CoV infected cell lysate, which suggested that the observed phenomenon may be relevant in vivo. Based on this observation, Palese's laboratory has studied the IFN inhibitory property of different SARS-CoV proteins, which revealed that ORF3, ORF6 as well as the N-protein have the ability to independently inhibit IFN production through different mechanisms. Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells cache = ./cache/cord-023865-6rafp3x3.txt txt = ./txt/cord-023865-6rafp3x3.txt === reduce.pl bib === id = cord-019051-gtruu1op author = Weber, Olaf title = The role of viruses in the etiology and pathogenesis of common cold date = 2009-11-10 pages = extension = .txt mime = text/plain words = 12321 sentences = 734 flesch = 44 summary = Viruses with an established role in common cold are rhinoviruses, adenoviruses, parainfluenza viruses, coronaviruses and the respiratory syncytial virus, and these are reviewed in greater detail here. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex and it is safe to say, not fully understood for each and every virus that is linked to respiratory tract infection. RSV infection is assumed to be frequently misdiagnosed, particularly in adults [56] , because the symptoms are similar to those caused by other respiratory viruses like influenza. Human parainfluenza viruses (HPIV) are important causes of respiratory diseases in infants and children. HMPV is thought to be the second or third cause of severe acute respiratory tract infection in children, just ranking behind RSV and influenza virus [146, 148] . Retinoic acid-inducible gene I mediates early Antiviral Response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells cache = ./cache/cord-019051-gtruu1op.txt txt = ./txt/cord-019051-gtruu1op.txt === reduce.pl bib === id = cord-023724-5at0rhqk author = Cann, Alan J. title = Infection date = 2015-07-24 pages = extension = .txt mime = text/plain words = 14979 sentences = 755 flesch = 48 summary = The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins. cache = ./cache/cord-023724-5at0rhqk.txt txt = ./txt/cord-023724-5at0rhqk.txt === reduce.pl bib === id = cord-022262-ck2lhojz author = Gromeier, Matthias title = Genetics, Pathogenesis and Evolution of Picornaviruses date = 2007-09-02 pages = extension = .txt mime = text/plain words = 28035 sentences = 1423 flesch = 46 summary = The following viruses have been recognized as picornaviruses on the basis of their genome sequences and physico-chemical properties as well as the result of comparative sequence analyses (see the section on Evolution): equine rhinovirus types I and 2, Aichi virus, porcine enterovirus, avian encephalomyelitis virus, infectious flacherie virus of silkworm Clusters of enteroviruses refer to groups of enteroviruses arranged predominantly according to genotypic kinship (Hyypia et al., 1997) . Briefly, when expression vectors ( Figure 12 .6E) consisting of a gag gene (encoding p17-p24; 1161 nt) of human immunodeficiency virus that was fused to the N-terminus of the poliovirus polyprotein (Andino et al., 1994; Mueller and Wimmer, 1998) were analysed after transfection into HeLa cells, the genomes were not only found to be severely impaired in viral replication but they were also genetically unstable (Mueller and Wimmer, 1997) . cache = ./cache/cord-022262-ck2lhojz.txt txt = ./txt/cord-022262-ck2lhojz.txt === reduce.pl bib === id = cord-023208-w99gc5nx author = nan title = Poster Presentation Abstracts date = 2006-09-01 pages = extension = .txt mime = text/plain words = 70854 sentences = 3492 flesch = 43 summary = In order to develop a synthetic protocol by an automated instrumentation, increasing yield, purity of the crude, and reaction time, a microwave-assisted solid phase peptide synthesis was validated comparing the use of the new generation of Triazine-Based Coupling Reagents (TBCRs) with a series of commonly used ones. Ubiquitinium is a well known mechanism in protein degredation of Eukaryotic cells ,in which many obsolte and corrupted three dimentional structure protein ,become marked by covalent attachment of ubuquitin through a multi-step enzymatic pathway.Ubiquitin is a small ,8.5 kDa peptide of 76 amino acid residues that targets such substrtes for proteolysis in proteasome .Recnt studies showed that an extra cellular ubiquitination process also taking place in the epididymes of humans and other animals marks protein on the surface of the defective sperm .it appears that structurally and functionally defective sperm become surface ubiquitinated by epididymal epithelial cells. This head-to-tailcyclized 14-amino-acid peptide contains one disulfide bridge and a lysine residue (Lys5) present in the P1 position, which is responsible for inhibitor specificity.As was reported by us and other groups, SFTI-1 analogues with one cycle only retain trypsin inhibitory activity. cache = ./cache/cord-023208-w99gc5nx.txt txt = ./txt/cord-023208-w99gc5nx.txt === reduce.pl bib === id = cord-016796-g4kqqpy1 author = Bramhachari, Pallaval Veera title = Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date = 2019-11-05 pages = extension = .txt mime = text/plain words = 5646 sentences = 305 flesch = 34 summary = As a part of modern research on immunotechniques, a diagnostic approach for chronic hepatitis C infection (CHC), detects specific antibody to HCV (anti-HCV) (indirect tests) and assays that can detect, quantify, or characterize components of HCV viral particles, viz. Nonetheless, recent studies on respiratory syncytial virus (RSV) developed Luciferase Immunoprecipitation Systems (LIPS) assay to detect IgG Antibodies against Human RSV G-Glycoprotein. Sensitive and specific detection of Crimean-Congo hemorrhagic fever virus (CCHFV) was developed employing specific IgM and IgG antibodies in human sera using recombinant CCHFV nucleoprotein as antigen in μ-capture and IgG immune complex (IC) ELISA tests (Emmerich et al. A rapid diagnostic platform for colorimetric differential detection of DENV and CHIKV viral infections was recently developed with a possibility to alter clinical diagnosis of acute febrile illnesses in resource-limited settings. This novel antibody demonstrates noteworthy specificity to identify H7N9 virus compared to homemade target-captured ELISA, qRT-PCR, and rapid influenza diagnostic test (RIDT) with high sensitivity (Chang et al. cache = ./cache/cord-016796-g4kqqpy1.txt txt = ./txt/cord-016796-g4kqqpy1.txt === reduce.pl bib === id = cord-018017-c8myq6bi author = Iversen, Patrick L. title = The Threat from Viruses date = 2018-09-30 pages = extension = .txt mime = text/plain words = 11563 sentences = 615 flesch = 51 summary = Numerous emerging infections caused by viral agents have imposed high impact on human survival (Table 3 .3). The apparent success of these viruses is that as they move from reservoir hosts to humans and as humans become immune to the initial infection, the population of diverse genomes offers multiple chances to adapt by finding a "fit" genome version which can propagate until the next transition requiring adaption. Human T-cell Lymphotropic Virus (HTLV-1) HTLV-1 is a single-stranded RNA retrovirus, defined by their use of reverse transcriptase, a polymerase, that makes a DNA copy of the RNA 7 kb viral genome. If we combine cardiovascular events and neoplasia caused by infection, then infectious disease is the most significant threat to human life and qualifies as the area of greatest impact. Adeno-associated Virus (AAV) is a single stranded DNA virus that infects humans but are not known to cause disease. is a 5229 base double-stranded DNA virus infecting less than 5 percent of the human population. cache = ./cache/cord-018017-c8myq6bi.txt txt = ./txt/cord-018017-c8myq6bi.txt === reduce.pl bib === id = cord-023017-k6edtg58 author = nan title = AASLD Abstracts (pp. 282A–382A) date = 2006-02-10 pages = extension = .txt mime = text/plain words = 65796 sentences = 3553 flesch = 51 summary = 14/55 (25%) patients in AC who did not discontinue by week 24 received ribavirin dose reduction in comparison to 31/108 ( The clinical outcome in response to combination therapy for treatment of chronic hepatitis C virus (HCV) infection appears to be different for Caucasian versus African American patients. Over the period of combination therapy, most patients in which serum virus titers were reduced to non detectable levels had significant increases in T cell responses to HCV proteins. CHRONIC Background: Recent large prospective trials demonstrated that the combination therapy of interferon (1FN)-alphalribavirin significantly increased the ratio of a sustained virological response in patients with chronic hepatitis C in comparison with IFN monotherapy, especially in patients with high HCV-RNA titer and genotype lb. Results: Patients with chronic HCV infection showed higher MxA gene expression levels than healthy controls, indicating that hepatitis C virus induces IFN production. cache = ./cache/cord-023017-k6edtg58.txt txt = ./txt/cord-023017-k6edtg58.txt === reduce.pl bib === id = cord-020235-stcrozdw author = nan title = Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date = 2012-03-15 pages = extension = .txt mime = text/plain words = 13494 sentences = 843 flesch = 58 summary = Hepatitis A virus (HAV) was isolated directly from human stool in diploid human fibroplasrs, Viral antigen was expressed only after 210 days of incubation of the infected cultures. Univ., 0-8700 Wiirzburg Effect of Measles (SSPE) Antiserum on Viral Surface Proteins and Hormone Receptor Activity in C6/SSPE Persistently Infected Cells BARRETT, P. Inst, of Genetics, Univ., 0-5000 Co logne Virus-Cell DNA Recombinants in Human Cells Lytically Infected by Ad2 NEUMANN, R., WEYER, U., and DOERFLER, W. In vitro, however, the gag-specific peptide sequences are cleaved off upon addition of the purified viral piS protease; in the case of the replication-defective, transforming avian sarcoma virus PRC II the cleaved nongag part has a ryrosine-phosphorylaring kinase activity similar to that described for the RSV src-gene product pp60 src . f. Virologie, Univ., D·6300 Giefen, 3 A protein of a molecular weight of about 38.000 d has been found to be phosphorylated 1 h after the onset of cell transformation by Rous sarcoma virus (RSV). cache = ./cache/cord-020235-stcrozdw.txt txt = ./txt/cord-020235-stcrozdw.txt === reduce.pl bib === id = cord-025181-eg108wcd author = Zheng, Zhihang title = Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date = 2020-05-25 pages = extension = .txt mime = text/plain words = 5919 sentences = 340 flesch = 59 summary = In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. Further, we compared the infectivity of these two viral variants in a self-limited infection model, in which type I IFN receptor of wild-type Balb/c mice had been transiently blocked before infection, and found only the virus strain exhibiting larger plaque size caused infectious viral particles in sera. We have recently developed a ZIKV infection model in Balb/c mice with transient blockage of type I IFN Fig. 2 Phylogenetic analysis of DENV-2 1D4-5-SP and DENV-2 8H2-7-LP with representative serotype-2 dengue viruses of different genotypes isolated from different geographical regions. cache = ./cache/cord-025181-eg108wcd.txt txt = ./txt/cord-025181-eg108wcd.txt === reduce.pl bib === id = cord-021568-tdfn6up8 author = STRAUSS, JAMES H. title = Subviral Agents date = 2012-07-27 pages = extension = .txt mime = text/plain words = 10937 sentences = 588 flesch = 59 summary = The conserved domains highlighted in the figure are thought to be important for the replication of the viroid (i.e., to form promoters recognized by RNA polymerase II) and for its cleavage to produce unit-length molecules. GSS, most FFI, and some cases of CJD occur as dominant inherited diseases, associated with mutations in the gene for the prion protein. The pattern of symptoms associated with a particular TSE may vary, however, depending in part on how the disease was contracted; on the source of the infecting agent; and on the nature of mutations in the prion protein. Studies in mice and other animals, as well as the finding that mutations in the prion protein are associated with inherited TSEs in humans, have made clear that the prion protein, abbreviated PrP, is intimately involved in the transmission of TSE and in the disease process. cache = ./cache/cord-021568-tdfn6up8.txt txt = ./txt/cord-021568-tdfn6up8.txt === reduce.pl bib === id = cord-022336-zqnczjpp author = Robertson, Hugh D. title = Virus Origins: Conjoined RNA Genomes as Precursors to DNA Genomes date = 2007-09-02 pages = extension = .txt mime = text/plain words = 6163 sentences = 229 flesch = 47 summary = The chapter also outlines the significance of work on viroid-like pathogens, circular RNA replication, and their potential relation to early RNA; and relates the early emergence of RNA mosaics to developments leading to today's DNA-based systems of viral gene expression. Recent work to be reviewed below shows that there is one class of primitive life forms-the viroid-like pathogens -whose properties today could help us to understand how primitive RNA-based self-replication may have been compatible with expansion to produce more complex RNAs. In summary, the causative agent for human hepatitis delta contains two specialized domains, one concerned with replication and the other encoding a single protein (Branch et al., 1989; Purcell and Gerin, 1996; Taylor, 1996) . It is evident that if RNA conjunction leading to delta-like RNA mosaics with both replicating and functionally translatable protein-coding domains has taken place, we need to consider the consequences both for the evolution of primitive RNA systems, yielding today's DNA-based cellular information system, and for presentday RNA-level events. cache = ./cache/cord-022336-zqnczjpp.txt txt = ./txt/cord-022336-zqnczjpp.txt === reduce.pl bib === id = cord-023120-jcgf2401 author = nan title = Animal virus genetics date = 2004-06-18 pages = extension = .txt mime = text/plain words = 17801 sentences = 1474 flesch = 67 summary = We suggest that, (1) c regions contain promotors for viral RNA synthesis, (2) cx contains a more efficient promotor than c" and (3) non-acute disease foliows the formation of critical viral-cell recombinants in which ( 2 ) The r e s u l t i n g CDNA i s f r a c t i o n a t e d and a l l fragments having a length g r e a t e r than 300 nucleotides are i s o l a t e d and c u t with a r e s t r i c t i o n endonuclease capable of d i g e s t i n g single-stranded DNA. Studies of the synthesis and processing of viral proteins in simian sarcoma associated virus (SSAV)infected and SSV(SSAV)transformed marmoset and human cell lines has demonstrated polyprotein precursors precipitable by anti-SSAV p30 and anti-SSAV gp70. cache = ./cache/cord-023120-jcgf2401.txt txt = ./txt/cord-023120-jcgf2401.txt === reduce.pl bib === id = cord-030028-s6sxi8uj author = Rubio, Luis title = Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date = 2020-07-17 pages = extension = .txt mime = text/plain words = 14687 sentences = 698 flesch = 40 summary = This technique has been used to differentiate isolates of some plant viruses, such as prunus necrotic ringspot virus (PNRSV), TYLCV and CTV (Gillings et al., 1993; Hammond et al., 1998; Font et al., 2007) ; iii) Single-strand conformation polymorphism (SSCP) analysis is based on electrophoresis of denatured dsDNA in non-denaturing gels so migration of single-stranded DNA depends on its conformation determined by its nucleotide sequence and the electrophoretic conditions. This technique followed by sequencing of the different haplotypes detected has been used to evaluate the genetic variation of some plant viruses, such as cucumber mosaic virus (CMV), citrus psorosis virus (CPsV) and CTV (Rubio et al., 1996; Rubio et al., 1999; Vives et al., 2002; Lin et al., 2003; Martıń et al., 2006) . Procedures to detect and identify various viruses or virus strains in a single assay simultaneously reduce time and cost of the analysis (see Pallaś et al., 2018 for a comprehensive review), and are especially suitable for evaluating mixed infections in individual plants. cache = ./cache/cord-030028-s6sxi8uj.txt txt = ./txt/cord-030028-s6sxi8uj.txt === reduce.pl bib === id = cord-023770-ymxapsv6 author = nan title = Closteroviridae date = 2011-11-23 pages = extension = .txt mime = text/plain words = 3662 sentences = 197 flesch = 53 summary = In general, capsid proteins and their homologs (CPm) show a significant degree of sequence conservation and the duplicate copies probably retain the general spatial folding and some crucial properties of the CPs. Notable exception are a group of ampeloviruses with the smallest genomes in the family [e.g. grapevine leafrollassociated virus 4 (GLRaV-4), GLRaV-5, GLRaV-6, GLRaV-9, pineapple mealybug wilt-associated virus 1(PMWaV-1) and PMWaV-3] which do not appear to possess CPm. The genome expression strategy is based on: (i) proteolytic processing of the polyprotein encoded by ORF1a; (ii) 1 Pos. ssRNA ribosomal frameshift for the expression of the RdRp domain encoded by ORF1b, a mechanism not found in other ()RNA plant viruses; (iii) expression of the downstream ORFs via the formation of a nested set of 3 co-terminal sub-genomic RNAs (sgRNAs). cache = ./cache/cord-023770-ymxapsv6.txt txt = ./txt/cord-023770-ymxapsv6.txt === reduce.pl bib === id = cord-023726-2fduzqyb author = STRAUSS, JAMES H. title = The Structure of Viruses date = 2012-07-27 pages = extension = .txt mime = text/plain words = 10614 sentences = 633 flesch = 57 summary = Also shown for each family is the presence or absence of an envelope in the virion, the triangulation number (defined later) if the virus is icosahedral, the morphology of the nucleocapsid or core, and figure numbers where the structures of members of a family are illustrated. Structural studies of viruses have shown that the capsid proteins that form the virions of many plant and animal icosahedral viruses have a common fold. The largest particle is the nucleocapsid of herpes simplex virus, which is 1250 Å in diameter and has T=16 symmetry (the virion is enveloped but only the nucleocapsid is regular FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. cache = ./cache/cord-023726-2fduzqyb.txt txt = ./txt/cord-023726-2fduzqyb.txt === reduce.pl bib === id = cord-027975-77544sed author = Tars, Kaspars title = ssRNA Phages: Life Cycle, Structure and Applications date = 2020-06-30 pages = extension = .txt mime = text/plain words = 11655 sentences = 582 flesch = 55 summary = Several of the studied ssRNA characteristics, such as coat protein–RNA interactions and the ability to readily form virus-like particles in recombinant expression systems, have fueled many practical applications such as RNA labeling and tracking systems and vaccine development. Bacteriophages belonging to the family Leviviridae are among the simplest known viruses, exhibiting positive-sense single-stranded RNA (ssRNA) genomes of just 3.5-4.5 kilobases, typically encoding only 4 proteins. Due to their simplicity, ssRNA phages have been used as models to study various processes in molecular biology and virology, including translation repression, RNA-protein interactions and virus evolution. For quite some time, the only available structural information about protein-RNA interactions in ssRNA phage particles came from the studies of CP dimers in complex with a 19 nucleotide-long stem-loop fragment known as TR (translation repression) from the genome region located around the replicase start codon in bacteriophage MS2 ). cache = ./cache/cord-027975-77544sed.txt txt = ./txt/cord-027975-77544sed.txt === reduce.pl bib === id = cord-027865-p1epjn51 author = Sterchi, Diane L. title = Molecular pathology date = 2020-06-22 pages = extension = .txt mime = text/plain words = 13228 sentences = 841 flesch = 54 summary = ISH is a method of localizing and detecting specific mRNA sequences in preserved tissue sections or cell preparations by hybridizing the complementary strand of a nucleotide probe to the sequence of interest. (See Data Sheet Kappa and Lambda Probe ISH Kit, Novacastra.) (Fig. 21.3.) Chromogenic in situ hybridization (CISH) is a method 'that enables the detection of gene expression in the nucleus using a conventional histochemical reaction' (White 2005) ; it is used for the detection of abnormal genes and to identify a gene therapy treatment direction. However, FISH still has an advantage over chromogenic methods for labeling specific nucleic acid sequences in cells and tissues. This may be done by using the normal detection procedure for the ISH method on dots of labeled nucleic acid sequence and a labeled control applied at matching descending concentrations on a positively charged nylon membrane. cache = ./cache/cord-027865-p1epjn51.txt txt = ./txt/cord-027865-p1epjn51.txt === reduce.pl bib === id = cord-033692-txfuuu7d author = Lim, Byeonghwi title = Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection date = 2020-10-13 pages = extension = .txt mime = text/plain words = 7927 sentences = 371 flesch = 44 summary = In this study, we investigated the molecular mechanisms of PRRSV infection by integrating the differences in the expression of various genes in tissues responsible for respiration (lungs) and immunity (bronchial lymph nodes [BLNs] , and tonsils) using RNA-Seq data at serial time points. To validate the results of specific groups, GSEA based on the KEGG database were performed using log 2 -normalised TMM counts at each time point for each tissue to identify the maximum gene expression changes for each group, and the GSEA results were consistent with the KEGG enrichment analyses of DEGs. GSEA using the 3-dpi data for all tissues revealed many significant pathways related to viral infection, among which influenza A showed the highest NES ( Figure 5A ). Significant KEGG terms related to viral infections and immune signalling were identified through KEGG enrichment analyses performed for each up-and down-regulated genes (343 and 287 genes, respectively), based on the time point for each tissue with a maximum FC value in the GCN, which was constructed using serial DEGs ( Figure 4A ). cache = ./cache/cord-033692-txfuuu7d.txt txt = ./txt/cord-033692-txfuuu7d.txt === reduce.pl bib === id = cord-035067-ic843wr9 author = de Almeida, Joana Ferro Machado title = COVID-19 and the gastrointestinal tract: what do we already know? date = 2020-11-05 pages = extension = .txt mime = text/plain words = 5453 sentences = 336 flesch = 56 summary = Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools. Information on country of origin, mean age, different comorbidities, typical symptoms (fever, cough, and dyspnea, among others), gastrointestinal symptoms (diarrhea, nausea, vomiting, and abdominal pain), and the presence of viral RNA in feces, when cited, were included in this study for analysis. (19) According to the descriptive, cross-sectional, multicenter study (three hospitals in Hubei, China) by Pan et al., with 204 patients, in which 107 were male, mean age of 52.91±15.98 years, 103 (50.5%) reported some gastrointestinal symptom, such as lack of appetite (81; 78.6%), diarrhea (35; 34.0%), vomiting (4; 3.9%), and abdominal pain (2; 1.9%). (26) Cipriano et al., conducted a systematic review with six studies of patients from China, which points to the possibility of SARS-CoV-2 infection in the gastrointestinal tract and fecal-oral transmission. cache = ./cache/cord-035067-ic843wr9.txt txt = ./txt/cord-035067-ic843wr9.txt === reduce.pl bib === id = cord-018564-3igg5s57 author = Schomburg, Dietmar title = RNA helicase 3.6.4.13 date = 2013 pages = extension = .txt mime = text/plain words = 12324 sentences = 1241 flesch = 67 summary = Driven by the energy of ATP hydrolysis, this movement allows the protein to displace complementary strands of DNA or RNA [13] ; <38> the DEAD-box protein DED1 has the ability to balance RNA unwinding with a profound strand annealing activity in a highly dynamic fashion [11] ; <10,20> RNA helicase activity [2, 4] ; <12> multifunctional enzyme possessing serine protease, NTPase, and RNA unwinding activities [42] ; <12> NTPase activity analyzed, ambiguous helicase activity, enzyme capable for unwinding RNA and DNA [38] ; <39> RNA-stimulated ATPase activities determined, interaction between the replicative component nonstructural protein 3 (NS3) with the nonstructural protein 4A (NS4A) [44] ; <12> the Arg-rich amino acid motif HCV1487-1500, a fragment of domain 2 NS3 of Hepatitis C virus, as well as the complete domain 2, and domain 2 lacking the flexible loop localized between Val1458 and Thr1476, mediate competitive inhibition of diverse protein kinase C functions, inhibition of rat brain PKC, overview [39] ; <17> the West Nile virus RNA helicase uses the energy derived from the hydrolysis of nucleotides to separate complementary strands of RNA [62] ; <13> translation of HIV-1 gag mRNA is reliant on the ATP-dependent helicase activity of RNA helicase A [61] ) (Reversibility: ?) [2, 4, 5, 6, 11, 12, 13, 21, 22, 28, 30, 31, 32, 37, 38, 39, 41, 42, 43, 44, 45, 46, 61, 62 ] P ADP + phosphate S RNA + H 2 O <2,5,10,42> (<5> helicase/unwinding activity [43] ; <42> helicase/unwinding activity, either ATP or dATP is required for the unwinding activity [32] ; <2> RNA unwinding activity, the enzyme contains two RecA-like domains, opening and closing of the interdomain cleft during RNA unwinding [45] ) (Reversibility: ?) [32, 41, 43, 45 ] P ? cache = ./cache/cord-018564-3igg5s57.txt txt = ./txt/cord-018564-3igg5s57.txt === reduce.pl bib === id = cord-017764-h1w9gbxk author = Meanwell, Nicholas A. title = The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date = 2018-06-08 pages = extension = .txt mime = text/plain words = 9250 sentences = 389 flesch = 39 summary = A groundbreaking clinical trial that combined daclatasvir (1) with the protease inhibitor asunaprevir (52) established that a chronic HCV infection could be cured with small molecule therapy in the absence of immune stimulation, setting the stage for approval of this regimen for the treatment of GT-1b-infected subjects by the Japanese health authorities on July 4, 2014. The discovery of the hepatitis C virus (HCV) nonstructural 5A (NS5A) replication complex inhibitor daclatasvir (1) began with the development of a genotype 1b (GT-1b) replicon that was implemented as a phenotypic screen using a design that conferred a stringent triaging of hit molecules [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] . A screen of compounds selected from the library of HCV NS5A inhibitors assessed in the presence of 1 using the Tyr93Asn GT-1aresistant replicon, followed by SAR optimization, identified Syn-395 (52) as a molecule capable of restoring the sensitivity of resistant virus to the inhibitory effects of 1. Discovery of daclatasvir, a pan-genotypic hepatitis C virus NS5A replication complex inhibitor with potent clinical effect cache = ./cache/cord-017764-h1w9gbxk.txt txt = ./txt/cord-017764-h1w9gbxk.txt === reduce.pl bib === id = cord-023705-3q9yr6np author = FENNER, FRANK title = Viral Replication date = 2014-06-27 pages = extension = .txt mime = text/plain words = 8331 sentences = 424 flesch = 51 summary = Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. Many important biochemical phenomena, such as splicing and other types of posttranscriptional processing of RNA, posttranslational cleavage and glycosylation of proteins, replica tion of RNA, reverse transcription, integration, and transposition of viral genes and cellular oncogenes, were first elucidated by virologists and have general application in cell biology. The proteins translated from the early transcripts of DNA viruses include enzymes and other proteins required for the replication of viral nucleic acid, as well as proteins that suppress host cell RNA and protein synthesis. cache = ./cache/cord-023705-3q9yr6np.txt txt = ./txt/cord-023705-3q9yr6np.txt === reduce.pl bib === id = cord-024282-t5wl0bih author = Mao, Shunfu title = BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance date = 2020-02-01 pages = extension = .txt mime = text/plain words = 3451 sentences = 226 flesch = 58 summary = title: BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance For example, RNA-Seq assembly tools typically require hyper-parameter tuning to achieve good performance for particular datasets. Results: Here we propose BOAssembler, a framework that enables end-to-end automatic tuning of RNA-Seq assemblers, based on Bayesian Optimization principles. The reference-based assembler together with its performance evaluation can be represented as an abstract function f (D, θ), where D includes both the read alignments used for assembly and the reference transcriptome (a set of ground truth RNA transcripts) used for evaluation, and θ refers to the parameters of f . After read alignments are assembled with given parameter θ, the assembly output (a set of RNA transcripts) will be compared with the reference transcriptome, and the quality of assembly is measured by scalar metrics such as precision p and sensitivity s. cache = ./cache/cord-024282-t5wl0bih.txt txt = ./txt/cord-024282-t5wl0bih.txt === reduce.pl bib === id = cord-023766-qx0qdjmt author = Nirwan, Sonam title = Rhinovirus RNA Polymerase: Structure, Function, and Inhibitors date = 2018-11-02 pages = extension = .txt mime = text/plain words = 10466 sentences = 477 flesch = 51 summary = Differences observed in the secondary structure of these polymerases reflect not only the substrate diversity but also divergent mechanisms for initiation of RNA synthesis (primer dependent for HRV and RHDV but primer independent for HCV and bacteriophage ϕ6). Conserved aspartic acid residues in the polymerase palm domains coordinate the two magnesium ions needed for the catalytic polymerization reaction of the enzyme, with one metal activating the primer 3 0 OH for the attack of the nucleotide α-phosphate, and the other metal serving to stabilize the triphosphate moiety ( Fig. 11 .1). The EC of PV polymerase provided a required view about how the template and the RNA strand interact as they thread through the active site and showed that viral RdRPs use a unique palm-based structural change to close their active site for catalysis (Gong and Peersen, 2010) . cache = ./cache/cord-023766-qx0qdjmt.txt txt = ./txt/cord-023766-qx0qdjmt.txt === reduce.pl bib === id = cord-007890-bie1veti author = nan title = ECC-4 Abstracts date = 2002-04-16 pages = extension = .txt mime = text/plain words = 85992 sentences = 5665 flesch = 50 summary = Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children's Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections. cache = ./cache/cord-007890-bie1veti.txt txt = ./txt/cord-007890-bie1veti.txt === reduce.pl bib === id = cord-022290-p0l1kv6n author = Bergmann, Ernst M. title = Proteolytic Enzymes of the Viruses of the Family Picornaviridae date = 2007-05-09 pages = extension = .txt mime = text/plain words = 9450 sentences = 480 flesch = 56 summary = The primary function of the picornaviral proteinases is the cotranslational, specific cleavage of the viral polyprotein into the structural and nonstructural proteins. This is true even for some families of + RNA viruses which have developed additional strategies to generate individual gene products from a single RNA genome, e.g., subgenomic RNAs or multiple ORFs. Proteolytic cleavage as a covalent modification of the precursors of viral structural proteins is even more common and occurs even in DNA viruses. The sequence of the residues which form the last turn of this helix is highly conserved throughout the picornaviral 3C genes (K/RR/KNL/I), It is interesting that the structural and functional details of the proteolytic active site of the 3C proteinases are not the most conserved part of the 3C structure (Gorbalenya et al., 1988) . While the details of the specific enzyme substrate interactions gleaned from the crystal structures of 3C proteinases provide valuable information for the design of effective inhibitors, there is little experimental evidence for the mechanism of the chymotrypsin-like cysteine proteinases. cache = ./cache/cord-022290-p0l1kv6n.txt txt = ./txt/cord-022290-p0l1kv6n.txt === reduce.pl bib === id = cord-023608-w2g7v7g1 author = nan title = ISAR News date = 2017-10-20 pages = extension = .txt mime = text/plain words = 6059 sentences = 284 flesch = 48 summary = ICAR retains its flavor and personality, providing an interdisciplinary forum at which investigators involved in basic, translational, and clinical research worldwide meet to review recent developments in all areas of antiviral research, drug and vaccine development. Additionally, satellite activities such as the Women in Science Roundtable, the Career Development Panel and the New Member and First Time Attendee luncheon (The Happy Hour) provided an opportunity to discuss other issues of relevance. With so many different competing conferences and meetings to attend and a long economic crisis of which scientific research did not escape, ISAR has gone through great financial efforts to continue supporting the participation of students, postdocs and young investigators. The TCFF Awards support the professional development of women with potential to make significant contributions to the field of Antiviral Research by providing funds to attend a conference, visit another laboratory, take a course, or acquire specialized training. cache = ./cache/cord-023608-w2g7v7g1.txt txt = ./txt/cord-023608-w2g7v7g1.txt === reduce.pl bib === id = cord-034648-vfqth54o author = nan title = WITHDRAWN date = 2020-10-12 pages = extension = .txt mime = text/plain words = 2000 sentences = 145 flesch = 55 summary = To determine if gene expression changes were associated with changes in cellular response, transwell assays were performed to assess HTR-8 cell migration and invasion after exposure to 2.5% O 2 or 21% O 2 for 6hrs and 24hrs. Outcome parameters monitored were estradiol levels, follicle morphology and survival throughout the in vitro culture interval (IVC), germinal vesicle breakdown (GVBD), oocyte maturation to metaphase II stage, fertilization and development to blastocyst. Cell number in blastocysts was determined by Hoechst staining RESULTS: Pre-antral follicles measured 121.9 AE 40.9 mM with oocyte diameters of 61.1AE 4.1 mM at time of seeding. RESULTS: Based on scRNAseq data in non-human primate ovarian tissue, ACE2 and TMPRSS2 co-localize in a sub-population of oocytes in antral follicles (62% of cells, Pearson correlation¼0.37), but to a lesser extent in less mature oocytes and not at all in ovarian somatic cells. cache = ./cache/cord-034648-vfqth54o.txt txt = ./txt/cord-034648-vfqth54o.txt === reduce.pl bib === id = cord-048204-6lvn10f4 author = Shi, Stephanie T. title = Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus date = 2000-09-01 pages = extension = .txt mime = text/plain words = 7656 sentences = 378 flesch = 56 summary = In order to demonstrate the involvement of hnRNP A1 in MHV RNA replication and transcription, we established several DBT cell lines stably expressing either the wildtype (wt) hnRNP A1 or a C-terminus-truncated mutant lacking the M9 sequence and part of the glycine-rich domain. We showed that the mutant hnRNP A1, which was localized predominantly in the cytoplasm, exhibited dominant-negative effects on viral genomic RNA replication and subgenomic mRNA transcription. Cells infected with P0 viruses did not yield detectable amounts of DIssE, but contained the naturally occurring A59 DI RNA, whose replication was inhibited more strongly than the synthesis of MHV genomic and subgenomic RNAs in DBT-A1DC cells ( Figures 5B, lanes 8±10 and 6B, lanes 1± 3). In the present study, we established that MHV RNA transcription and replication were enhanced by overexpression of the wt hnRNP A1 protein, but inhibited by expression of a dominant-negative hnRNP A1 mutant in DBT cell lines. cache = ./cache/cord-048204-6lvn10f4.txt txt = ./txt/cord-048204-6lvn10f4.txt === reduce.pl bib === id = cord-048471-7jszm1nd author = Salim, Omar title = Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus date = 2008-05-14 pages = extension = .txt mime = text/plain words = 5646 sentences = 246 flesch = 49 summary = Although slightly larger than predicted the N-term protein was detected in a processed form in vivo, thus not only demonstrating initial translation of the ORF1 polyprotein but also activity of the viral protease. Previous studies of norovirus polyprotein processing have yielded three major products following in vitro transcription and translation, representing the uncleaved 3ABCD, N-term and 2C proteins. In addition, this important observation also confirms for the first time that the JV 3C protease was active in cells transfected with capped RNA as the size of the V5/N-term indicated successful cleavage of the protein from the ORF1 polyprotein. Unlike similarly studied human noroviruses JV initially did not appear to express the N-terminal protein, presenting the possibility that the encoding RNA sequence had a regulatory function itself, most likely involved in translation initiation in an IRES-like manner. cache = ./cache/cord-048471-7jszm1nd.txt txt = ./txt/cord-048471-7jszm1nd.txt === reduce.pl bib === id = cord-022196-1tionxun author = FENNER, FRANK title = The Nature and Classification of Animal Viruses date = 2013-11-17 pages = extension = .txt mime = text/plain words = 9588 sentences = 406 flesch = 46 summary = With most isometric particles and in all complex virions, the capsid encloses another protein structure containing the viral genome, called the core. All animal viruses with tubular nucleocapsids are enveloped, and in these the lipid layer from which glycoprotein peplomers project is probably applied to a protein shell (the membrane protein; see Fig. 1 -1), which may be relatively rigid, as in Rhabdovirus, or readily distorted (as in the myxoviruses) so that in negatively stained electron micrographs the virions appear to be pleomorphic. The RNA viruses that have the largest (single-stranded) genomes, those of the Leukovirus genus, also have a highly complex structure with an envelope enclosing an icosahedral capsid that, in turn, surrounds a tubular nucleocapsid. The conventional physicochemical criteria [(a) nucleic acid: type, strandedness, fragmentation, and molecular weight; (b) virion: shape, size, and symmetry] are suitable for classification at this level of family/genus, perhaps assisted by the serological cross-reactivity of "group" antigens where these have been recognized. cache = ./cache/cord-022196-1tionxun.txt txt = ./txt/cord-022196-1tionxun.txt === reduce.pl bib === id = cord-020010-q58x6xb0 author = nan title = 19th ICAR Abstracts: date = 2006-03-13 pages = extension = .txt mime = text/plain words = 46663 sentences = 2181 flesch = 44 summary = In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression. cache = ./cache/cord-020010-q58x6xb0.txt txt = ./txt/cord-020010-q58x6xb0.txt === reduce.pl bib === id = cord-048327-xgwbl8em author = Henderson, Clark M. title = Antisense-induced ribosomal frameshifting date = 2006-08-18 pages = extension = .txt mime = text/plain words = 4337 sentences = 232 flesch = 49 summary = The ability of cis-acting RNA structures or trans-acting 2 0 -O-Methyl antisense oligonucleotides to induce ribosomal frameshifting was determined by in vitro transcription and translation of a dual luciferase reporter vector, p2Luc. p2Luc contains the Renilla and firefly luciferase genes on either side of a multiple cloning site, and can be transcribed using the T7 promoter located upstream of the Renilla luciferase gene (45) . As the AZ1A antisense oligonucleotide was designed to anneal directly adjacent to the UGA codon of the shift site, it was of interest to determine whether the wild-type antizyme pseudoknot could induce À1 frameshifting when located in the equivalent position. The ability of spermidine to stimulate antisense oligonucleotide induced ribosome frameshifting to the +1 reading frame at the UCC UGA shift site in the absence of the natural 3 0 stimulator demonstrates that this cis-acting element is not required for polyamine responsiveness. cache = ./cache/cord-048327-xgwbl8em.txt txt = ./txt/cord-048327-xgwbl8em.txt === reduce.pl bib === id = cord-022128-r8el8nqm author = Domingo, Esteban title = Molecular basis of genetic variation of viruses: error-prone replication date = 2019-11-08 pages = extension = .txt mime = text/plain words = 17663 sentences = 798 flesch = 39 summary = In the case of viral genomes, mutations can result from different mechanisms: (i) template miscopying (direct incorporation of an incorrect nucleotide); (ii) primer-template misalignments that include miscoding followed by realignment, and misalignment of the template relative to the growing chain (polymerase "slippage" or "stuttering"); (iii) activity of cellular enzymes (i.e., deaminases), or (iv) chemical damage to the viral nucleic acids (deamination, depurination, depyrimidination, reactions with oxygen radicals, direct and indirect effects of ionizing radiation, photochemical reactions, etc.) (Naegeli, 1997; Bloomfield et al., 2000; Friedberg et al., 2006) . In addition to the general environmental and sequence context consequences for templatecopying fidelity that may affect any genome type, mutation rates for DNA viruses will also be influenced by: (i) whether the DNA polymerase that catalyzes viral DNA synthesis includes or lacks a functional proofreading-repair activity. cache = ./cache/cord-022128-r8el8nqm.txt txt = ./txt/cord-022128-r8el8nqm.txt === reduce.pl bib === id = cord-022889-lv6fy6e6 author = Dávalos, Alberto title = Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date = 2019-08-07 pages = extension = .txt mime = text/plain words = 96011 sentences = 5041 flesch = 51 summary = This report suggests that some plant ncRNAs (e.g miRNAs and siRNAs) show higher stability as compared to other ncRNAs due to peculiar chemical characteristics (2'‐O‐methylation at 3' end).However, ingested or administered ncRNA must overcome many extracellular and cellular barriers to reach the intended target tissue or functional location in sufficient amount to exert any biological effect. Finally, the publications reporting the outcome of two EFSA procurements aiming respectively at investigating and summarising the state of knowledge on the mode-of-action of dsRNA and miRNA pathways, the potential for non-target gene regulation by dsRNA-derived siRNAs or miRNAs, the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing 6 ; and reviewing relevant scientific information on RNA interference that could serve as baseline information for the environmental risk assessment of RNAi-based GM plants ) 7 were also used. cache = ./cache/cord-022889-lv6fy6e6.txt txt = ./txt/cord-022889-lv6fy6e6.txt === reduce.pl bib === id = cord-048198-zjufx4fo author = Pasternak, Alexander O. title = Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis date = 2001-12-17 pages = extension = .txt mime = text/plain words = 7614 sentences = 366 flesch = 58 summary = Here we present results of a comprehensive co-variation mutagenesis study of equine arteritis virus TRSs, demonstrating that discontinuous RNA synthesis depends not only on base pairing between sense leader TRS and antisense body TRS, but also on the primary sequence of the body TRS. Synthesis of sg mRNAs initially was proposed to be primed by free leader transcripts, which would base-pair to the complementary TRS regions in the full-length minus strand, and would be extended subsequently to make sg plus strands ( Figure 1B ; Baric et al., 1983 Baric et al., , 1985 . 7220±7228, 2001 Using site-directed mutagenesis of TRSs of the arterivirus equine arteritis virus (EAV), we have shown previously that base pairing between the sense leader TRS and antisense body TRSs is crucial for sg mRNA synthesis (van Marle et al., 1999a) . cache = ./cache/cord-048198-zjufx4fo.txt txt = ./txt/cord-048198-zjufx4fo.txt === reduce.pl bib === id = cord-102547-nxut8ov1 author = Grädel, C. title = Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing date = 2020-06-09 pages = extension = .txt mime = text/plain words = 6505 sentences = 349 flesch = 53 summary = DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. Taxonomic classification of viral reads (Oxford Nanopore) and contigs (Illumina MiSeq) using MEGAN based on BLASTN matches against NCBI's nucleotide (nt) database at the species and genotype levels. In order to confirm the genotype identification and to obtain a highly accurate whole genome sequence of the enterovirus genome, we subsequently subjected the sample E590 also to cDNA sequencing using Illumina MiSeq. In this case, the cDNA was produced using genotype-specific primers given that low number of reads was obtained by DRS and MiSeq . Illumina sequencing of the cDNA from sample E026 produced using oligo-dT primers and random hexamers showed similar distributions on the domain level: The majority of contigs belonged to bacterial species (98.6% and 98.9%, respectively for oligo-dT and random hexamer approaches), with a minority of reads mapping to eukaryotes (0.49%, 0.50%) and viruses (0.87%, 0.56%). cache = ./cache/cord-102547-nxut8ov1.txt txt = ./txt/cord-102547-nxut8ov1.txt === reduce.pl bib === id = cord-035110-5lkzhjfh author = Zhu, Le title = Isolation and characterization of exosomes for cancer research date = 2020-11-10 pages = extension = .txt mime = text/plain words = 14672 sentences = 743 flesch = 34 summary = Another study reported that triple-negative breast cancer (TNBC) cells can activate stromal cells by releasing exosomes containing unshielded RNAs that mimic viral components to co-opt anti-viral immune responses, thereby promoting tumor growth [115] . Furthermore, CAF-derived exosomes contain intact metabolites, including amino acids, lipids, and TCA-cycle intermediates, which are internalized by prostate cancer cells to promote tumor growth [122] . EGFR carried in exosomes secreted from gastric cancer cells can be delivered to the liver and integrated into the plasma membrane of liver stromal cells, thus favoring the development of a liver-like microenvironment and promoting liver-specific metastasis [147] . In addition, abundant studies have demonstrated that tumor-derived exosomes can modulate the cell biology of MDSCs, including increasing their expansion, promoting their activation, and enhancing their immunosuppressive function [162] . Tumor-associated macrophages-derived exosomes promote the migration of gastric cancer cells by transfer of functional Apolipoprotein E cache = ./cache/cord-035110-5lkzhjfh.txt txt = ./txt/cord-035110-5lkzhjfh.txt === reduce.pl bib === id = cord-048222-1pq6dkl5 author = Imbeaud, Sandrine title = Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces date = 2005-03-30 pages = extension = .txt mime = text/plain words = 7001 sentences = 313 flesch = 47 summary = With that prospect in mind, and with the aim of anticipating future standards by pre-normative research, we identified and tested two software packages recently developed to gauge the integrity of RNA samples with a user-independent strategy: one open source, the degradometer software for calculation of the degradation factor and 'true' 28S:18S ratio based on peak heights (24) and the freely available RIN algorithm of the Agilent 2100 expert software, based on computation of a 'RNA Integrity Number' (RIN) (25) . A RIN number is computed for each RNA profile (see Supplementary Table 4 online) resulting in the classification of RNA samples in 10 numerically predefined categories of integrity. The values of the mean fold changes, calculated according to the 2 ÀDDCt quantification method (see Materials and Methods), were found lower than 1.0, corresponding to the expression level (1·) in the sample exhibiting the highest RNA quality (Table 2 and Figure 5 ). cache = ./cache/cord-048222-1pq6dkl5.txt txt = ./txt/cord-048222-1pq6dkl5.txt === reduce.pl bib === id = cord-102892-nt1zoktv author = Sweeney, Blake A. title = R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types date = 2020-09-11 pages = extension = .txt mime = text/plain words = 3366 sentences = 188 flesch = 54 summary = Consensus tRNA primary 213 sequence with 2D structure for each isotype of each taxonomic domain was generated based 214 on the tRNA alignments used for building the isotype-specific covariance models in tRNAscan-215 SE 2.0 16 . 270 R2DT templates model the conserved core of most structured RNAs We classified each nucleotide in the resulting diagrams according to whether it matched a 282 template and found that 90.6% of nucleotides were displayed using the nucleotide locations 283 encoded in the templates, while 6.0% of nucleotides represented insertions compared to the 284 templates, and 3.4% of nucleotides matched the templates but required automatic repositioning 285 by the Traveler software (Table 2) . In addition, R2DT will benefit from the ongoing development Isotype-specific consensus tRNA sequences and 2D structures were generated using R-scape 52 389 from the alignments that were used to train and build the corresponding covariance models in 390 tRNAscan-SE 16 . cache = ./cache/cord-102892-nt1zoktv.txt txt = ./txt/cord-102892-nt1zoktv.txt === reduce.pl bib === id = cord-102967-dx0tg077 author = Mahajan, Lakshmi S. title = Mapping RNA dependent RNA polymerase activity and immune gene expression using PRO-seq date = 2020-06-16 pages = extension = .txt mime = text/plain words = 2853 sentences = 163 flesch = 57 summary = Coupled to PRO-seq in human blood samples, we propose to use PRO-seq as a single package method to detect (+)ssRNA virus RdRp activity and its interaction with host immune response through transcriptome-wide profiling of leukocyte gene expressions at once. This is different from Drosophila RNA Polymerase II, which appears to have comparable substrate specificity for all 4 biotin-NTPs. The ORF-proximal accumulation coincides with quadruplet rich regions of the template-strand of the DAV genome ( Figure 1D ). From this data, we did not detect significant PRO-seq sequences from (+)ssRNA viral genomes, indicating that none of the individuals had direct viral infections in the blood immune cells. Our PRO-seq data show expression levels of immune-response related genes from human peripheral blood leukocytes. PRO-seq density on DAV genome and base-quadruplet counts.The read count is indicated along the left side of each graph. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) cache = ./cache/cord-102967-dx0tg077.txt txt = ./txt/cord-102967-dx0tg077.txt === reduce.pl bib === id = cord-102931-vxkbctiz author = Mao, Kai title = Induction of RNA interference by C. elegans mitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme date = 2020-06-06 pages = extension = .txt mime = text/plain words = 8680 sentences = 503 flesch = 49 summary = Here, we report that mitochondrial dysfunction in Caenorhabditis elegans activates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. elegans compared to most animals, and surprisingly, loss of function mutations in some of those genes cause an increase in the response to siRNAs: mutations in the RdRp RRF-3, the specialized Argonaute ERGO-1, the RNA helicase ERI-6/7, or the exoribonuclease ERI-1 enhance silencing by siRNAs (Fischer et al., 2008; Kennedy et al., 2004) . We find that reduction of function mutations in a wide range of mitochondrial components robustly enhanced RNA interference-mediated silencing of endogenous genes as well as a variety of reporters of RNAi. These antiviral responses to mitochondrial dysfunction are homologous to the RIG-I-based mitochondrial response in mammals because they depend on the RIG-I homologue, the DRH-1 RNA helicase. Our analysis of the eol-1 and drh-1 pathway from mitochondrial dysfunction to enhanced RNA interference and antiviral activity is a key output from mitochondria for anti-aging. cache = ./cache/cord-102931-vxkbctiz.txt txt = ./txt/cord-102931-vxkbctiz.txt === reduce.pl bib === id = cord-030654-8yxa1r1c author = Zhang, Changhui title = Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4281 sentences = 289 flesch = 62 summary = This structure was revealed to be a horseshoe-like tetramer, which may play an essential role in nsp9 oligomerization and in the regulation of viral nucleic acid binding during the replication of the virus. The initial structure solved by molecular replacement showed that six SARS-CoV-2 nsp9 protomers form an OB-fold cluster in an asymmetric unit ( Supplementary Fig. 1a ). To obtain more information about the protein interfaces and the likely biological assemblies of the OB-fold cluster, we calculated the structure of SARS-CoV-2 nsp9 using PDBe-PISA [27] . These three contact surfaces in interface I b/c contribute a hydrophobic base with eight hydrogen bonds and one salt bridge, making the SARS-CoV-2 nsp9 tetramer extremely stable in the crystal structure. In this present study, we observed the nucleic acid-binding ability of SARS-CoV-2 nsp9, using the electrophoretic mobility The molecules in these two interfaces are shown as cartoons and colored and labeled as in Fig. 2a . cache = ./cache/cord-030654-8yxa1r1c.txt txt = ./txt/cord-030654-8yxa1r1c.txt === reduce.pl bib === id = cord-048485-b8xb1f12 author = Hulst, Marcel title = Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date = 2008-06-04 pages = extension = .txt mime = text/plain words = 6269 sentences = 313 flesch = 45 summary = RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. However, the fluorescence intensity was not higher than the background threshold for any of these probes, indicating that mRNA concentrations of these cytokines (including IFN-c) in infected and uninfected mucosal scrapings were too low to detect by microarray analysis, probably due to the relatively low percentage of cytokine-producing (immune) cells present in intestinal mucosa [6] . Using microarray analysis, we detected a set of genes that are differently expressed in rotavirus-infected jejunal mucosa compared to uninfected mucosa. Perhaps, enhanced expression of a PLA2-inh in our study may be a countermeasure of specific intestinal epithelial cells to normalize and/or inhibit PLA2 enzyme activity in response to extra-and intracellular changes in [Ca 2+ ] evoked by rotavirus replication, either to protect specific cells from extra-and intracellular membrane-damage or to negatively regulate A-acid production. cache = ./cache/cord-048485-b8xb1f12.txt txt = ./txt/cord-048485-b8xb1f12.txt === reduce.pl bib === id = cord-102898-eyyd7ent author = Rizvi, Vaseef A. title = Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date = 2020-07-17 pages = extension = .txt mime = text/plain words = 3048 sentences = 159 flesch = 44 summary = Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. downstream polyprotein, 2) Significant modulation in levels of a distinct subset of ribosome-bound tRNAs 48 that cannot be explained by virtue of codon usage and 3) Translation from an upstream ORF (uORF) using 49 a non-canonical initiation codon in the 5 UTR region of JEV. However, these sites do not represent commonly associated Studies on RNA viruses have suggested adaptations in codon usage of viral genes to the host translation [30] . Interestingly, JEV infection appears to stimulate 251 expression from UUG start site by almost 67% suggesting viral or virus-induced host trans-regulatory factors 252 promoting uORF translation (Fig.4D) . We also identify a subset of ribosome associated 286 tRNAs whose levels are modulated globally upon JEV infection (Fig.3) . cache = ./cache/cord-102898-eyyd7ent.txt txt = ./txt/cord-102898-eyyd7ent.txt === reduce.pl bib === id = cord-048322-5eqdrd52 author = Aigner, Achim title = Delivery Systems for the Direct Application of siRNAs to Induce RNA Interference (RNAi) In Vivo date = 2006-05-18 pages = extension = .txt mime = text/plain words = 7333 sentences = 363 flesch = 41 summary = The antitumorigenic effects of PEI/siRNA-mediated in vivo gene-targeting of tumor-relevant proteins like in mouse tumor xenograft models are described. The efficient protection against enzymatic or nonenzymatic degradation is particularly important for RNA molecules including siRNAs. In fact, while the therapeutic potential of siRNAs for the treatment of various diseases is in principle very promising, limitations of transfer vectors may turn out to be rate-limiting in the development of RNAi-based therapeutic strategies. Their ultimate success, however, will Figure 4 : Systemic treatment of mice with PEI-complexed HER-2-specific siRNAs leads to reduced growth of subcutaneous SKOV-3 tumor xenografts due to decreased HER-2 expression. RNAi-mediated gene-targeting through systemic application of polyethylenimine (PEI)-complexed siRNA in vivo Atelocollagenmediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo cache = ./cache/cord-048322-5eqdrd52.txt txt = ./txt/cord-048322-5eqdrd52.txt === reduce.pl bib === id = cord-102336-ex3zlq38 author = De Wijngaert, Brent title = Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase date = 2020-04-14 pages = extension = .txt mime = text/plain words = 2266 sentences = 127 flesch = 60 summary = Cryo-EM structures of transcription pre-initiation complex (PIC) and initiation complex (IC) of yeast mitochondrial RNA polymerase show fully resolved transcription bubbles and explain promoter melting, template alignment, DNA scrunching, transition into elongation, and abortive synthesis. Hence, the structural basis for promoter melting, DNA scrunching, and transcription initiation remains largely unknown for the mtRNAPs. RPO41 (∆N100) and MTF1 were assembled on a pre-melted promoter (-21 to +12, 15S yeast mtDNA promoter; Fig. 1A ) to generate the yeast mitochondrial transcription preinitiation complex (y-mtPIC) (Fig. S1 ). The 3.7 Å density map of IC locates many previously uncharacterized structural elements, including the C-tail of MTF1 and the scrunched DNA ( Fig. 2B-C) , and reveals the mechanism of template alignment and RNA synthesis during initiation. During the transition, the upstream DNA from position -1 onward is locked in the MTF1 NT-groove while the template strand undergoes a large conformational switching to align with the 2-mer RNA and the incoming UTPaS at the active site ( Fig. 2C; Movie S2). cache = ./cache/cord-102336-ex3zlq38.txt txt = ./txt/cord-102336-ex3zlq38.txt === reduce.pl bib === id = cord-102934-7e2mqooe author = Dogra, N. title = exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer date = 2020-09-30 pages = extension = .txt mime = text/plain words = 5830 sentences = 385 flesch = 51 summary = Here, we established 60 total small RNA-sequencing profiles from 17 aggressive prostate cancer (PCa) patients tumor and adjacent normal tissue, and EVs isolated from urine, serum, and cancer cell culture media. We interrogated the key satellite alteration in tumor-derived EVs and found that resection of tumor prostate tissue leads to differential expression of reactive oxygen species (ROS), P53 pathways, inflammatory/cytokines, oncogenes, and tumor suppressor genes in the EV nanosatellites. We have conducted the total small RNA sequencing (n = 60) of aggressive prostate cancer patients (n = 17) tumor and adjacent normal tissue and EVs from urine, serum, and 22RV1 PCa cell line. We interrogated the key satellite alteration in tumor-derived EVs and found that resection of tumor prostate cancer tissue leads to differential expression of novel RNA biomarkers, ROS, P53 pathways, inflammatory/cytokines, major oncogenes, and tumor suppressors in the EV nanosatellites. cache = ./cache/cord-102934-7e2mqooe.txt txt = ./txt/cord-102934-7e2mqooe.txt === reduce.pl bib === id = cord-048478-ftlb5b95 author = Mroczek, Seweryn title = Apoptotic signals induce specific degradation of ribosomal RNA in yeast date = 2008-04-01 pages = extension = .txt mime = text/plain words = 9796 sentences = 418 flesch = 45 summary = One striking characteristic, which accompanies apoptosis in both vertebrates and yeast, is a fragmentation of cellular DNA and mammalian apoptosis is often associated with degradation of different RNAs. We show that in yeast exposed to stimuli known to induce apoptosis, such as hydrogen peroxide, acetic acid, hyperosmotic stress and ageing, two large subunit ribosomal RNAs, 25S and 5.8S, became extensively degraded with accumulation of specific intermediates that differ slightly depending on cell death conditions. For example, in metazoans the programmed cell death (PCD) called apoptosis, in addition to irreversible DNA damage, which is considered an apoptotic hallmark (3) , also involves specific cleavage of several RNA species, including 28S rRNA, U1 snRNA or Ro RNP-associated Y RNAs (4) . Together, this strongly suggests that rRNA degradation observed in apoptotic and oxidative stress conditions is not simply a result of cell death but is produced in the process that requires enzymatic activity and functional cellular machinery. cache = ./cache/cord-048478-ftlb5b95.txt txt = ./txt/cord-048478-ftlb5b95.txt === reduce.pl bib === id = cord-029779-9b6zs1sb author = Casey, Sophie title = Temporally Altered miRNA Expression in a Piglet Model of Hypoxic Ischemic Brain Injury date = 2020-07-27 pages = extension = .txt mime = text/plain words = 11367 sentences = 662 flesch = 52 summary = miR-181a inhibition increased neurite length in vitro in two different types of cell culture-the SH-SY5Y cell line and primary cultures of E14 rat midbrain-and increased expression of BMPR2 in differentiating SH-SY5Ys. Therefore, this miRNA may be a potential therapeutic target with neuroprotective effects. Analyses of previously performed microarray data showed altered expression levels in 70 miRNAs in umbilical cord whole blood in infants with moderate and severe HIE compared with controls and this data have been previously reported by our group [5] . The predicted downstream targets of the six miRNAs were predicted to exert neuroprotective effects, and functional examination of one of the associated pathways-the BMP signalling pathway (a member of the TGFβ superfamily [31] )-in differentiating SH-SY5Y cells revealed inhibition of miR-181a increases expression of the type II receptor BMPR2. cache = ./cache/cord-029779-9b6zs1sb.txt txt = ./txt/cord-029779-9b6zs1sb.txt === reduce.pl bib === id = cord-103511-31njndob author = Broggi, Achille title = Type III interferons disrupt the lung epithelial barrier upon viral recognition date = 2020-05-05 pages = extension = .txt mime = text/plain words = 3886 sentences = 283 flesch = 61 summary = Accordingly, sorted lung resident dendritic cells express 192 high levels of IFN-λ transcript after 5 days of poly (I:C) treatment, in contrast to epithelial cells, 193 alveolar macrophages and monocytes (Fig. 4A) , which, instead, express inflammatory cytokines (Fig. S8A, B) . Moreover, diphtheria toxin (DT)-mediated depletion of 195 CD11c + cells in CD11c-DT receptor (DTR) mice was sufficient to completely abolish IFN-λ 9 transcript and protein upregulation upon 6 days of poly (I:C) treatment (Fig. 4B, C) , while production remained unaltered (Fig. S8C with the response measured in vivo, TLR7 stimulation did not induce IFN production while it 207 induced upregulation of pro-inflammatory cytokines, and intracellular delivery of poly (I:C) induced 208 high levels of IFN-I but not IFN-λ (Fig.4D, Fig. S9A , B). Dendritic cells sorted from Ticam1 -/mice treated with poly (I:C) for six 222 days did not express appreciable levels of IFN-λ transcripts while still produced type I interferons 223 ( Fig. 4E, F) . cache = ./cache/cord-103511-31njndob.txt txt = ./txt/cord-103511-31njndob.txt === reduce.pl bib === id = cord-103015-3dxwbmd2 author = Shengjuler, Djoshkun title = The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain date = 2017-08-04 pages = extension = .txt mime = text/plain words = 7069 sentences = 411 flesch = 63 summary = Molecular-docking simulations revealed a putative site of PIP binding to poliovirus (PV) 3C protein that was validated using NMR spectroscopy. 93 Validation of PIP-binding sites by NMR 94 In order to test the validity of our docking observations, we titrated 15 N-labeled 3C protein 95 with soluble dibutyl-PI4P to observe potential NMR chemical shift perturbations (CSPs), which 96 would indicate chemical environment changes in the presence of PI4P (Figure 2) . Out of the three 97 basic residues of the major cluster that were predicted to interact with the PI4P, R13 showed the 98 largest CSP (Figure 2A ). Titration of PI4P into a solution containing 3C caused CSPs that were consistent 249 with the major PI4P-binding site observed computationally (Figure 2A) . cache = ./cache/cord-103015-3dxwbmd2.txt txt = ./txt/cord-103015-3dxwbmd2.txt === reduce.pl bib === id = cord-102766-n6mpdhyu author = Alam, Md. Nafis Ul title = Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses date = 2020-06-25 pages = extension = .txt mime = text/plain words = 3193 sentences = 192 flesch = 56 summary = title: Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses Machine Learning methods are becoming more reliable for characterizing sequence data, but virus genomes are more variable than all forms of life and viruses with RNA-based genomes have gone overlooked in previous machine learning attempts. We designed a novel short k-mer based scoring criteria whereby a large number of highly robust numerical feature sets can be derived from sequence data. Here, we present a novel short k-mer based sequence 28 scoring method that generates robust sequence information for training machine learning 29 classifiers. Here, we present a novel short k-mer based sequence 28 scoring method that generates robust sequence information for training machine learning 29 classifiers. VirFinder: a novel k-mer based tool for identifying viral sequences from 558 assembled metagenomic data. cache = ./cache/cord-102766-n6mpdhyu.txt txt = ./txt/cord-102766-n6mpdhyu.txt === reduce.pl bib === id = cord-104162-fe51v2pt author = Zhang, Chiyu title = Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3745 sentences = 208 flesch = 49 summary = Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. Assays of the base order-dependent component of the folding energy have shown that a highly conserved region, in otherwise rapidly mutating HIV-1 genomes, associates with an RNA structure corresponding, not to a protein-encoding function, but to an RNA packaging signal. This high GC% value can obscure the contribution of the base order-dependent component of the folding energy, which provides a sensitive indicator of local intraspecies pressures for the conservation of function within a population (i.e. a mutated organism is eliminated by natural selection so no longer can be assayed for function in the population). cache = ./cache/cord-104162-fe51v2pt.txt txt = ./txt/cord-104162-fe51v2pt.txt === reduce.pl bib === id = cord-025948-6dsx7pey author = Maitra, Arindam title = Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date = 2020-06-04 pages = extension = .txt mime = text/plain words = 7218 sentences = 382 flesch = 56 summary = Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. We have initiated a study on sequencing of SARS-CoV-2 genome from swab samples obtained from infected individuals from different regions of West Bengal in Eastern India and report here the first nine sequences and the results of analysis of the sequence data with respect to other sequences reported from the country until date. The A2a clade is characterized by the signature nonsynonymous mutations leading to amino acid changes of P323L in the RdRp which is involved in replication of the viral genome and the change of D614G in the Spike glycoprotein which is essential for the entry of the virus in the host cell by binding to the ACE2 receptor. We have also detected emergence of mutations in the important regions of the viral genome including Spike, RdRP and nucleocapsid coding genes. cache = ./cache/cord-025948-6dsx7pey.txt txt = ./txt/cord-025948-6dsx7pey.txt === reduce.pl bib === id = cord-103914-ppgx7mci author = Maughan, Elizabeth F. title = Cell-intrinsic differences between human airway epithelial cells from children and adults date = 2020-04-20 pages = extension = .txt mime = text/plain words = 8186 sentences = 419 flesch = 47 summary = Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We found no significant differences in the proportion of cells in these three cellular compartments in paediatric and adult biopsies either by immunohistochemistry ( Figure 1A /1B), or by assessing basal, mucosecretory or ciliated cellassociated gene expression (Table S2 ) in bulk RNA sequencing in which we had laser-capture microdissected the whole epithelium ( Figure 1C ; Figure S1 ). Analysing this laser-capture microdissected whole epithelium RNA sequencing dataset using DESeq2 (Love et al., 2014) with a false discovery rate (FDR) of 1% and log2 fold change threshold of 1.2, we identified 37 genes with significant differential expression between paediatric and adult donors of which 17 were upregulated in adults and 20 were expressed at higher levels in children ( Figure 2A ; Table S3 ). cache = ./cache/cord-103914-ppgx7mci.txt txt = ./txt/cord-103914-ppgx7mci.txt === reduce.pl bib === id = cord-252268-o63ep08b author = Carolan, Louise A. title = TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date = 2014-09-01 pages = extension = .txt mime = text/plain words = 6643 sentences = 358 flesch = 52 summary = As this equation relies on consistency between samples in the RNA quantity assayed, and the optimum reaction efficiency, as well as minimal fluctuation in the expression of housekeeping genes (endogenous controls) (Peters et al., 2007; Mane et al., 2008; Bruder et al., 2010) , these parameters were optimized using RNA extracted from cultured ferret lymph node cells stimulated with mitogens or with influenza virus. To test the ability of ferret leukocytes to produce mRNA cytokines and chemokines, lymph node cells from naïve ferrets were cultured with various mitogens known to activate T and B lymphocyte and macrophage/monocyte responses (Fig. 5) and with live or heat inactivated influenza virus (Fig. 6 ) and the cytokine and chemokine expression profiles were determined (summarized in (ConA) or Phytohaemagglutinin (PHA), which act by cross linking T cell receptors via sugars on the surface of human T lymphocytes (Chilson and Kelly-Chilson, 1989) , induced similar cytokine profiles, increasing expression of IL2, IL4, IL6, IL10, IL17, Granzyme A, TNF␣ and IFN␥, most with high fold changes, consistent with effective stimulation of T lymphocytes (Fig. 5) . cache = ./cache/cord-252268-o63ep08b.txt txt = ./txt/cord-252268-o63ep08b.txt === reduce.pl bib === id = cord-102412-cnlvyey4 author = Tekman, Mehmet title = A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework date = 2020-08-28 pages = extension = .txt mime = text/plain words = 6419 sentences = 300 flesch = 53 summary = Results Here we outline several Galaxy workflows and learning resources for scRNA-seq, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The analysis of scRNA-seq within Galaxy was a two-pronged e ort concentrated on bringing high quality single-cell tools into Galaxy, and providing the necessary work ows and training to accompany them. The training pictographically guides users through the concepts of extracting cell barcodes from the protocol, explains the signi cance of UMIs in the process of read deduplication with illustrative examples, and instructs the user in the process of performing further quality controls on their data during the post-mapping process via RNA STAR and other tools that are native to Galaxy. A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses cache = ./cache/cord-102412-cnlvyey4.txt txt = ./txt/cord-102412-cnlvyey4.txt === reduce.pl bib === id = cord-026641-eemp6b5j author = Kabiljo, Julijan title = From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date = 2020-06-11 pages = extension = .txt mime = text/plain words = 6689 sentences = 373 flesch = 37 summary = In the absence of NS1 apoptosis appears to be induced through the viral-RNA-mediated induction of retinoic acidinducible gene I (RIG-I) and interferon (IFN) signaling including protein kinase R (PKR) and eukaryotic initiation factor 2 alpha (eIF2α) activation and subsequent block of translation [39] [40] [41] . Another study screened a variety of wild-type influenza A viruses for their infectivity in pancreatic carcinoma cell lines and showed oncolytic effectiveness in a mouse model of human pancreatic cancer 67 . expressed a recombinant humanized cytotoxic T-lymphocyte-associated protein 4 (CTLA4) immune checkpoint inhibiting antibody from two different RNA fragments of the influenza A virus genome in order to enhance its anti-cancer effectiveness in a murine B16 melanoma model 96 . Further effects of oncolytic influenza A viruses on the cancer-immune microenvironment shown in murine models include activation of NK-cells and macrophage polarization towards immuno-stimulatory M1 phenotypes 66, 114 . cache = ./cache/cord-026641-eemp6b5j.txt txt = ./txt/cord-026641-eemp6b5j.txt === reduce.pl bib === id = cord-146406-85usg3uh author = Morelli, Marco J. title = Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing date = 2011-01-27 pages = extension = .txt mime = text/plain words = 4376 sentences = 221 flesch = 55 summary = Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the Inoculum used to initiate experimental infection. Some of the higher frequency polymorphisms identified encoded changes within codons associated with heparan sulphate binding and were present in both feet lesions revealing intermediate stages in the evolution of a tissue-culture adapted virus replicating within a mammalian host. The sequence diversity of viral populations within individual hosts is the starting 24 material for selection and subsequent evolution of RNA viruses such as foot--and--mouth 25 disease virus (FMDV). The sequence diversity of viral populations within individual hosts is the starting 24 material for selection and subsequent evolution of RNA viruses such as foot--and--mouth 25 disease virus (FMDV). Validation and analysis of sequence diversity in the samples 148 The frequency of site--specific polymorphisms was estimated from the frequency of 149 mismatches of the aligned reads to the reference genome. cache = ./cache/cord-146406-85usg3uh.txt txt = ./txt/cord-146406-85usg3uh.txt === reduce.pl bib === id = cord-243806-26n22jbx author = Vandelli, Andrea title = Structural analysis of SARS-CoV-2 and prediction of the human interactome date = 2020-03-30 pages = extension = .txt mime = text/plain words = 5252 sentences = 317 flesch = 52 summary = Here, we performed sequence and structural alignments among 62 SARS-CoV-2 strains and identified the conservation of specific elements in the spike S region, which provides clues on the evolution of domains involved in the binding to ACE2 and sialic acid. As highly structured regions of RNA molecules have strong propensity to form stable contacts with proteins 14 and promote assembly of specific complexes 15, 16 , SARS-CoV-2 domains enriched in double-stranded content are expected to establish interactions within host cells that are important to replicate the virus 17 . Analysis of functional annotations carried out with GeneMania 46 revealed that proteins interacting with the 5' of SARS-CoV-2 RNA are associated with regulatory pathways involving NOTCH2, MYC and MAX that have been previously connected to viral infection processes ( Fig. 4E) 47, 48 . cache = ./cache/cord-243806-26n22jbx.txt txt = ./txt/cord-243806-26n22jbx.txt === reduce.pl bib === id = cord-103807-x4hrwhkz author = Prokop, J. W. title = Viral Induced Genetics Revealed by Multi-Dimensional Precision Medicine Transcriptional Workflow date = 2020-04-06 pages = extension = .txt mime = text/plain words = 6843 sentences = 375 flesch = 50 summary = Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Using multi-time point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology vs. The power of RNA generated data likely is in its potential to effect therapeutic changes in individual patients with diverse clinical presentations, such as Multiple Organ Dysfunction Syndrome (MODS). Additional insights from the top mapped bacteria include normal flora elevation of Polynucleobacter necessarius and Bordetella parapertussis in patient 24 suggested to have issues in antigen processing and presentation (case study presented below for RNASEH2B), multiple Streptococcus strains (including pyogenes) identified in patients 11 and 5 that were culture positive, Pandoraea faecigallinarum in patient 10, and Cryobacterium arcticum in patient 10 day 0. cache = ./cache/cord-103807-x4hrwhkz.txt txt = ./txt/cord-103807-x4hrwhkz.txt === reduce.pl bib === id = cord-102866-40s64455 author = Bhadra, Sanchita title = One enzyme reverse transcription qPCR using Taq DNA polymerase date = 2020-05-30 pages = extension = .txt mime = text/plain words = 2863 sentences = 161 flesch = 58 summary = To verify this activity and to determine whether Taq polymerasemediated reverse transcription might be leveraged for single enzyme RNA detection, we carried out the CDC-approved SARS-CoV-2-specific N1 TaqMan RT-qPCR assay using only Taq DNA polymerase and its accompanying commercial reaction buffer, ThermoPol, (New England Biolabs) seeded with different copies of N gene armored RNA (Asuragen), a commercial template preparation that is devoid of DNA. Even though the only polymerase present in these reactions was Taq DNA polymerase (NEB), and no dedicated reverse transcriptase was added, amplification curves were generated in response to 3 x 10 5 , 3 x 10 4 , and 3 x 10 3 copies of the SARS-CoV-2 N gene armored RNA templates (Figure 1 ). Similar to our results with armored N gene RNA, the NEB Taq DNA polymerase was able to perform TaqMan RT-qPCR analysis of SARS-CoV-2 viral genomic RNA with all three CDC assays (Figure 2 ). cache = ./cache/cord-102866-40s64455.txt txt = ./txt/cord-102866-40s64455.txt === reduce.pl bib === id = cord-254192-86ksgl5t author = Li, Liang title = IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia date = 2019-10-17 pages = extension = .txt mime = text/plain words = 7233 sentences = 324 flesch = 50 summary = Here, to resolve the mechanism responsible for the disparity between IFN-λ3 and type I IFN in anti-mucosal virus infection, we compared the transcription profiles induced by the two IFNs in porcine intestinal epithelial (IPEC-J2) cells by RNA-Seq. Our results showed that the pretreatment of IPEC-J2 cells with IFN-λ3 resulted in the differential expression of 983 genes. Here, to resolve the mechanism responsible for the disparity between IFN-λ3 and type I IFN in anti-mucosal virus infection, we compared the transcription profiles induced by the two IFNs in porcine intestinal epithelial (IPEC-J2) cells by RNA-Seq. Our results showed that the pretreatment of IPEC-J2 cells with IFN-λ3 resulted in the differential expression of 983 genes. In this study, we comprehensively compared the transcriptional profiling of IFN-λ3-and IFN-α-induced genes in a porcine intestinal epithelial cell line (IPEC-J2) and verified the RNA-Seq results by reverse transcriptase quantitative PCR (RT-qPCR) in vitro, and further confirmed the transcriptional profile difference in crypt-derived porcine enteroids. cache = ./cache/cord-254192-86ksgl5t.txt txt = ./txt/cord-254192-86ksgl5t.txt === reduce.pl bib === id = cord-103853-ar09nzmw author = Wayment-Steele, Hannah K. title = RNA secondary structure packages ranked and improved by high-throughput experiments date = 2020-05-31 pages = extension = .txt mime = text/plain words = 4328 sentences = 201 flesch = 42 summary = 20 In this work, we evaluate the performance of commonly-used packages capable of making thermodynamic predictions in two tasks that have been crowdsourced on Eterna and are emerging as central to RNA characterization and design: 1) predicting chemical reactivity data through calculating probabilities that nucleotides are unpaired, and 2) predicting relative stabilities of multiple structural states that underlie the functions of riboswitch molecules, a task that involves predicting affinities of both small molecules and proteins of interest. We evaluated commonly used secondary structure modeling packages in their ability to make thermodynamic predictions on a compilation of large datasets of diverse synthetic molecules from Eterna, which we termed EternaBench ( Figure 1A ). We trained models with a variety of combinations of data types to explore interactions in multitask training (Table 1) and evaluated performance on held-out test sets for single-structure prediction accuracy, chemical mapping prediction accuracy, and riboswitch fold change prediction. cache = ./cache/cord-103853-ar09nzmw.txt txt = ./txt/cord-103853-ar09nzmw.txt === reduce.pl bib === id = cord-253115-ekgdsv4f author = Mehta, Meenu title = Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases date = 2019-08-01 pages = extension = .txt mime = text/plain words = 7317 sentences = 457 flesch = 39 summary = Commonly used drug delivery systems for respiratory diseases are polymer-based, lipid-based and peptide-based, and among these three, the lipid-based carriers are the most commonly used vectors for delivering RNAi. They include solid lipid nanoparticles, cationic liposomes, lipidoids, solid nanostructured lipid carriers and pH-responsive lipids [26] . The effective delivery of the drug and siRNA induced cell death of lung tumor cells by targeted gene silencing [56] . Glud et al., investigated pulmonary gene silencing effect of small interfering locked nucleic acid (siLNAs), targeting enhanced-greenfluorescent-protein (EGFP) in lung bronchoepithelium upon intravenous delivery of naked siLNAs and intranasal delivery of naked siLNA or chitosan based siLNA mucoadhesive nanoparticles. This study demonstrated that SAMiRNA nanoparticle is a stable siRNA silencing platform with less toxicity for effective in vivo targeting of genes involved in the pathogenesis of respiratory diseases [96] . Overcoming cisplatin resistance in non-small cell lung cancer with Mad2 silencing siRNA delivered systemically using EGFR-targeted chitosan nanoparticles cache = ./cache/cord-253115-ekgdsv4f.txt txt = ./txt/cord-253115-ekgdsv4f.txt === reduce.pl bib === id = cord-253282-zwl0safn author = Plant, Ewan P. title = Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date = 2013-01-18 pages = extension = .txt mime = text/plain words = 5007 sentences = 266 flesch = 55 summary = In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. Here, analyses using synonymous protein coding mutations demonstrate that the region of the genome that harbors the frameshift signal affects the regulation of genomic and subgenomic RNA production without altering protein sequence. Here we describe deletion and mutagenesis experiments with a dual luciferase reporter to show that the effect the sequence between stems 1 and 2 has on frameshifting efficiency is due to structural changes those mutations cause in the pseudoknot. Similar to previously described viruses containing mutations in the slippery site of the frameshift signal [7] , here we show that mutations to the SARS-CoV frameshift stimulating mRNA pseudoknot can also affect the production of viral genomic RNA. cache = ./cache/cord-253282-zwl0safn.txt txt = ./txt/cord-253282-zwl0safn.txt === reduce.pl bib === id = cord-254250-l0v602x9 author = Hooper, Chantelle title = A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date = 2020-10-02 pages = extension = .txt mime = text/plain words = 6440 sentences = 309 flesch = 48 summary = title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. rnaSPAdes assembly of combined libraries produced 38,826 contigs; 23 contigs, of average length 4560 bp, had similarity in protein sequence to YHV or gill-associated virus (GAV), but when the trimmed reads were aligned against the YHV genome (accession number GCA_003972805.1), no alignment was seen. rosenbergii were negative: MrNV and XSV, the causative agents of white tail disease [9, 10] ; MrTV, a virus associated with mass larval mortalities in China [15] , Spiroplasma eriocheiris [8] , and WSSV-shown to be able to infect M. cache = ./cache/cord-254250-l0v602x9.txt txt = ./txt/cord-254250-l0v602x9.txt === reduce.pl bib === id = cord-253024-b393ea2u author = Fu, Kaisong title = Evidence for variable rates of recombination in the MHV genome date = 1992-07-31 pages = extension = .txt mime = text/plain words = 8420 sentences = 488 flesch = 56 summary = Six RNA+ mutants that reside within a single complementation group mapping within the S glycoprotein gene of MHV-A59 were isolated which did not cause syncytium at the restrictive temperature. Since these mutants do not produce syncytium at the restrictive temperature ( Fig. 1) and sequence analysis of RNA recombinant viruses suggested that the defect in LA7 mapped within the first 1 .l kb of the S glycoprotein gene (Banner et al., 1990; Keck eta/., 1987 Keck eta/., , 1988a Makino eta/., 1986b Makino eta/., , 1987 , these data provided an anchor for mapping the location of the remaining group F RNA+ mutants. Since the distance between the group Fl and F2 mutants would have required sizable deletions (>lOO bp) to result in ts+ virus (Fig. 4) these data suggested that large deletions were rare events in these crosses, and did not contribute to an increase in the recombination frequency within the S glycoprotein gene. cache = ./cache/cord-253024-b393ea2u.txt txt = ./txt/cord-253024-b393ea2u.txt === reduce.pl bib === id = cord-103638-n5kpvsvg author = Nguyen, Long T. title = Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date = 2020-04-14 pages = extension = .txt mime = text/plain words = 5357 sentences = 388 flesch = 60 summary = By extending the 3'or 5'-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes. However, the ENHANCE showed 5.4-fold and 3.4-fold and higher trans-cleavage activity compared to the wild-type crRNA for targeting the methylated dsDNA and ssDNA, respectively (Fig. 3e, Supplementary Fig. 20a) . While no clinical samples were tested, the results indicated the 3'DNA7-modified crRNA consistently demonstrated higher sensitivity for detecting CoV-2 dsDNA within 30 minutes as compared to the wild-type crCoV-2 ( Supplementary Figs. cache = ./cache/cord-103638-n5kpvsvg.txt txt = ./txt/cord-103638-n5kpvsvg.txt === reduce.pl bib === id = cord-103377-j1mmx7k7 author = Karasik, Agnes title = Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences date = 2020-09-11 pages = extension = .txt mime = text/plain words = 11779 sentences = 646 flesch = 58 summary = Since it was reported that RNase L activation increased translation of 3'UTR regions downstream of stop codons by interfering with factors that promote translation termination (eRF3) or ribosome recycling (ABCE1) (Le Roy et al., 2005) , we assessed the level of ribosome footprints in 3'UTRs. This level was assayed by computing the ratio of footprints in every 3'UTR relative to its respective main ORF within the coding sequence (density ratio, 3'UTR:ORF) for each transcript . The similarity in the effects suggests that translation of non-canonical regions occurs when RNase L is activated via naturally produced 2-5A from broad activation of the antiviral response by double-stranded RNAs. It should be noted that poly I:C treatment did result in slightly elevated 3'UTR ribosome footprints on some genes in a RNase L KO cell line (Supplemental Figure 4A ). cache = ./cache/cord-103377-j1mmx7k7.txt txt = ./txt/cord-103377-j1mmx7k7.txt === reduce.pl bib === id = cord-103735-nil1vv6h author = Alfano, Niccolo title = Non-invasive surveys of mammalian viruses using environmental DNA date = 2020-03-29 pages = extension = .txt mime = text/plain words = 5829 sentences = 373 flesch = 53 summary = Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. We provide evidence that environmental and invertebrate-derived DNA samples including waterhole water, sediment and wild haematophagous terrestrial leeches can be used to survey known and unknown viruses. cache = ./cache/cord-103735-nil1vv6h.txt txt = ./txt/cord-103735-nil1vv6h.txt === reduce.pl bib === id = cord-103899-6tqm99g1 author = Mirzaei, Rasoul title = The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date = 2020-11-13 pages = extension = .txt mime = text/plain words = 9756 sentences = 554 flesch = 47 summary = Hence, analyzing the role of these types of nucleotides in antiviral immune responses and the characterization of miRNA target genes might contribute to understanding the mechanisms of the interplay between the host and viruses, and in the future, potentially result in discovering therapeutic strategies for the prevention and treatment of acute COVID-19 infection. This review will summarize the recent discoveries associated with miRNAs in various respiratory infections caused by viruses, especially coronavirus, and address all feasible therapeutic options to mitigate the burden of VRIs. The humoral immunity is immunologically categorized as an acquired immune response in which T helper cells collaborate with B cells to differentiate these types of cells to plasma cells [17] [18] [19] . The immune responses against VRIs, such as IV, hRV, human coronavirus (HcoV), hMPV, and RSV, are correlated with the aberrant expression of several miRNAs in epithelial cells and participate in the pathogenesis of chronic and acute forms of respiratory disorders (Table 1 ) [16] . cache = ./cache/cord-103899-6tqm99g1.txt txt = ./txt/cord-103899-6tqm99g1.txt === reduce.pl bib === id = cord-253616-7jyui5ca author = Lai, Zheng-Zong title = Harringtonine Inhibits Zika Virus Infection through Multiple Mechanisms date = 2020-09-07 pages = extension = .txt mime = text/plain words = 4969 sentences = 286 flesch = 48 summary = To investigate the anti-ZIKV activity of harringtonine, we assessed the inhibition of virus infection in Vero cells with MOI = 0.01 under different concentrations of harringtonine for 48 h. Intracellular viral RNA levels, protein expression levels and virus progeny in supernatants were respectively determined by RT-qPCR, western blotting and fluorescent focus assay (FFA). The dose-dependent anti-ZIKV activities of harringtonine were observed to decrease viral RNA/protein production and progeny yield ( Figure 1B-D) , indicating that virus propagation was suppressed. Harringtonine (625 nM) was administered at different stages of ZIKV infection with MOI = 0.1, and then the levels of ZIKV RNA in cells, as well as virus titers in supernatants, were determined after 24 h treatment. Harringtonine (625 nM) was administered at different stages of ZIKV infection with MOI = 0.1, and then the levels of ZIKV RNA in cells, as well as virus titers in supernatants, were determined after 24 h treatment. cache = ./cache/cord-253616-7jyui5ca.txt txt = ./txt/cord-253616-7jyui5ca.txt === reduce.pl bib === id = cord-253862-jl1zhg13 author = Khalaf, Khalil title = SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date = 2020-10-06 pages = extension = .txt mime = text/plain words = 14595 sentences = 760 flesch = 45 summary = Although this novel virus is less severe than the first SARS-CoV outbreak, human-to-human transmission remains very high and the number of cases continues to rise exponentially in major urban areas, highlighting the urgent need to develop new containment, diagnostic, and treatment protocols. In the case of SARS-CoV-2, viral evasion of the innate immune system leads to an increase in cytokine production and late CD4+/CD8+ response, which then leads to pathogenic inflammation in patients with high viral loads. (ChiCTR2000029308), involving severe SARS-CoV-2 cases, compared lopinavir/ritonavir treatment with standard care alone, and they showed that the antivirals yielded no clinical benefits. In an open-label control study conducted by Cai et al., the antiviral activity of favipiravir + IFN-α was compared to that of lopinavir/ritonavir + IFN-α in patients with confirmed SARS-CoV-2 infection. cache = ./cache/cord-253862-jl1zhg13.txt txt = ./txt/cord-253862-jl1zhg13.txt === reduce.pl bib === id = cord-253539-0kcujnfa author = Agranovsky, A. A. title = Principles of Molecular Organization, Expression, and Evolution of Closteroviruses: Over The Barriers date = 1996-12-31 pages = extension = .txt mime = text/plain words = 10620 sentences = 481 flesch = 55 summary = It has been suggested that the genes for CP homologues arose by gene duplication that probably occurred in a common closterovirus ancestor; it is noteworthy that, despite significant divergence, the CP homologues of BYV and CTV have retained the profile of conserved amino acid residues that are believed to ensure the characteristic fold of the filamentous plant virus CPs (Boyko et al., 1992 , Dolja et al., 1991 . L I W RNA-2 contains genes for the small hydrophobic protein, the HSP7O homologue, the 59-kDa protein distantly related to the B W 64-kDa and CTV 61-kDa products, the 9-kDa protein, the 28-kDa CP, the 52-kDa protein whose C-terminal domain is homologous to the CP, and the 26-kDa protein The monopartite genome of another whitefly-transmissible closterovirus, cucumber chlorotic spot virus (CCSW, has a size of approximately 15.5 kb (Woudt et al., 1993a,b) . cache = ./cache/cord-253539-0kcujnfa.txt txt = ./txt/cord-253539-0kcujnfa.txt === reduce.pl bib === id = cord-122092-gdyt02er author = Fatehi, Farzad title = Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date = 2020-10-18 pages = extension = .txt mime = text/plain words = 10080 sentences = 511 flesch = 55 summary = Comparison of different scenarios is based on tissue damage and viral load, highlighting the impact(s) of antibodies and adaptive cell-mediated immune response on infection dynamics. Surprisingly, our model also suggests that early treatment by either therapy alone can actually increase the duration of infection compared with a later therapy start, likely because suppressing virus production results in a reduced immune response. The model also includes non-structural proteins that are important for the viral life cycle, such as the replicase-transcriptase complex (RTC), and keeps track of the numbers of gRNAs (and subgenomic sgRNAs) at different stages of the replication process. We have included additional reactions into the model that describe remdesivir binding to the RTC complexes on the gRNAs and sgRNAs to capture this (see SI for details), and track the effect of a given, fixed number of remdesivir molecules per cell on the release of viral particles from an infected host cell. cache = ./cache/cord-122092-gdyt02er.txt txt = ./txt/cord-122092-gdyt02er.txt === reduce.pl bib === id = cord-102968-mhawyect author = Desirò, Daniel title = SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs date = 2018-09-23 pages = extension = .txt mime = text/plain words = 4044 sentences = 233 flesch = 58 summary = Results Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate destructive and compensatory mutants of two interacting single-stranded RNAs. This will facilitate a fast and accurate assessment of key regions, possibly involved in functional long-range RNA-RNA interactions and finally help virologists to design appropriate experiments. In this study, we present a tool called SilentMutations (SIM) that effectively simulates synonymous (silent) compensatory mutations in two single-stranded viral RNAs and is therefore appropriate for the in vitro assessment of predicted LRIs. Here, we present a command-line tool, called SilentMutations (SIM), that can simulate synonymous structure-destroying and structurepreserving mutation pairs within coding regions for long-range RNA-RNA interaction experiments. Figure 1 : Overall workflow of the SilentMutations tool, exemplary shown for two sequences from a negative single-stranded RNA virus genome (ssRNA-) (a) The first step will extract the defined range in each sequence and possibly increase the range to preserve codons in the given reading frame. cache = ./cache/cord-102968-mhawyect.txt txt = ./txt/cord-102968-mhawyect.txt === reduce.pl bib === id = cord-103823-3rchp9yy author = Taufer, Michela title = RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology date = 2008-11-30 pages = extension = .txt mime = text/plain words = 10168 sentences = 462 flesch = 50 summary = Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. Of course, the scientist who uses such an approach of sampling and rebuilding from segments to predict longer secondary structures has to benefit from the computing capabilities of such a framework without being required to cut and paste results from one code output to another, redirecting or reformatting output files (e.g., from FASTA to EMBL format) before forwarding them to the next step in the analysis, or dealing with distributed computer systems. RNAVLab addresses the challenges above by combining sampling of nucleotide sequences, predictions based on different codes and supported by grid computing technology, and analysis of large sets of secondary structures with different scientific scopes. cache = ./cache/cord-103823-3rchp9yy.txt txt = ./txt/cord-103823-3rchp9yy.txt === reduce.pl bib === id = cord-023354-f2ciho6o author = nan title = TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130046 sentences = 7333 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023354-f2ciho6o.txt txt = ./txt/cord-023354-f2ciho6o.txt === reduce.pl bib === id = cord-103163-0rreoh4o author = Smith, Sydni Caet title = Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date = 2020-10-22 pages = extension = .txt mime = text/plain words = 8965 sentences = 456 flesch = 46 summary = We determined the titers and RNA segment profiles of reovirus (rsT1L and rsT3D I ) and rotavirus (rsSA11) laboratory strains that had been rescued by reverse genetics then serially passaged ten times, each in triplicate lineages, in cultured cells. The two reoviruses accumulated non-canonical RNAs that retain 5′ and 3′ termini and feature one or more large internal deletions, while the rotavirus rarely accumulated such DVGs. Analyses of next-generation RNA-sequencing data sets from purified rsT1L reovirus RNA revealed many junctions, with hot spots for recombination in specific viral gene segments. Taken together, lin1 RNA profiles suggest non-canonical RNA species that differ in length but have identical termini to the parental segments accumulate variably during reovirus and rotavirus serial passage in cultured cells. cache = ./cache/cord-103163-0rreoh4o.txt txt = ./txt/cord-103163-0rreoh4o.txt === reduce.pl bib === id = cord-103925-i73ymrov author = Hill, Chris H. title = Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus date = 2020-08-11 pages = extension = .txt mime = text/plain words = 11552 sentences = 550 flesch = 53 summary = Finally, we use metabolic labelling and ribosome profiling to study 2A-mediated frameshifting and translation of the TMEV genome at sub-codon resolution in infected cells. A meta-analysis of the inferred P site positions of ribosomes relative to host mRNA start and stop codons reveals that RPFs map to coding sequences with a triplet periodicity reflective of the length of a codon ( Figure S3D ). Moving on to look specifically at the frameshift site, a single-nucleotide resolution plot of reads mapping to this region reveals a peak on the SS mutant genome corresponding to a ribosome paused with the GUU codon of the slippery sequence in the P site ( Figure 5G , Figure S4C ). These read lengths were selected for analysis as potential "disome-protected fragments", and their density plotted on the viral genome at the inferred P site position of the upstream, colliding ribosome ( Figure 6C and D). cache = ./cache/cord-103925-i73ymrov.txt txt = ./txt/cord-103925-i73ymrov.txt === reduce.pl bib === id = cord-103430-x6zzuu7v author = Contu, Lara title = Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date = 2020-10-12 pages = extension = .txt mime = text/plain words = 8272 sentences = 461 flesch = 56 summary = Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus' hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. Gene ontology (GO) enrichment analyses of protein complexes that could 10 form between the identified host interactors revealed highly significant GO terms related to 11 translation and Nonsense-mediated mRNA Decay (NMD). In addition to ribosomal proteins, many other RNA binding proteins were also 37 identified as having a potential role in SFV replication (Figure 3a (nsP1, nsP2, nsP3-Z, nsP4, capsid and Env) as well as for the merged list (All baits) was also applied. cache = ./cache/cord-103430-x6zzuu7v.txt txt = ./txt/cord-103430-x6zzuu7v.txt === reduce.pl bib === id = cord-103787-qhftb6d7 author = Garcia, Elizabeth P. title = Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date = 2005-10-31 pages = extension = .txt mime = text/plain words = 7354 sentences = 355 flesch = 47 summary = Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. We have developed STAR (scalable transcription analysis routine), a gene expression analysis platform that represents an innovative integration of real-time multiplex PCR and capillary electrophoresis (CE), allowing the simultaneous quantitative measurement of multiple targets in a single sample with high sensitivity. In a typical STAR experiment (diagrammatically shown in Figure 1A ), a PCR reaction is set up in a single tube containing the analyte, common PCR reagents (eg, DNA polymerase, dNTPs), and, for each target to be amplified, gene-specific primers where at least one of each pair is labeled with a fluorophore. cache = ./cache/cord-103787-qhftb6d7.txt txt = ./txt/cord-103787-qhftb6d7.txt === reduce.pl bib === id = cord-252485-cxi3cr15 author = Yoshida, Asuka title = IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date = 2015-08-04 pages = extension = .txt mime = text/plain words = 7074 sentences = 306 flesch = 50 summary = We and other groups have recently reported that recombinant viruses of Sendai virus (SeV), a prototype of the family Paramyxoviridae, in which the C proteins are knocked-out or mutated, generate dsRNA in infected cells at levels similar to the production of IFN-β (Takeuchi et al., 2008; Irie et al., 2010) . These unusual RNAs exhibited distinct properties in infected cells in terms of encapsidation with the viral N protein and subcellular distribution with SG marker proteins and RLRs. Our results suggest that RNA-typedependent mechanisms recognize and accumulate virus-derived, IFN-β-inducible, unusual RNAs into specific compartment to trigger the production of IFN-β, and that SeV may evade detection by the host innate immune system by preventing the production of these RNA species. Since the naked cbDI genomes have been reported readily to form an ideal structure as the RIG-I ligands of 5 -triphosphated, blunt-ended dsRNA (Kolakofsky, 1976) , these results indicated that the major IFN-β-inducing viral RNA species produced in the cells infected with CNT was encapsidated cbDI genomes, whereas those for SeV-4C(-) and NDV were not. cache = ./cache/cord-252485-cxi3cr15.txt txt = ./txt/cord-252485-cxi3cr15.txt === reduce.pl bib === id = cord-184744-oyc2djxk author = Parvez, Md Sorwer Alam title = Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3653 sentences = 224 flesch = 49 summary = The present study evaluated the possibility of plant originated approved 117 therapeutics against the main protease protein (MPP), RNA-dependent RNA polymerase (RdRp) and spike protein (S) of SARS-CoV-2 including drug surface analysis by using molecular docking through drug repurposing approaches. The molecular interaction study revealed that Rifampin (-16.3 kcal/mol) were topmost inhibitor of MPP where Azobechalcone were found most potent plant therapeutics for blocking the RdRp (-15.9 kcal /mol) and S (-14.4 kcal/mol) protein of SARS-CoV-2. The main protease proteins, RNA-dependent RNA polymerase and spike protein of SARS-CoV-2 were employed to molecular docking study with the repurposed drug candidates from plant origin for find out the better drug option towards the COVID-19 pandemic. In the present study, five plantr based therapeutics such as Azobechalcone, Rifampin, Isolophirachalcone, Tetrandrine and Fangchinoline were suggested for potential inhibitors for the Main Protease protein, RNA dependent RNA polymerase and Spike protein of SARS-CoV-2 by using molecular docking based virtual screening study. cache = ./cache/cord-184744-oyc2djxk.txt txt = ./txt/cord-184744-oyc2djxk.txt === reduce.pl bib === id = cord-254210-3mi2aop5 author = Haddad, Rodrigo title = Silencing of HTLV-1 gag and env genes by small interfering RNAs in HEK 293 cells date = 2011-01-26 pages = extension = .txt mime = text/plain words = 4490 sentences = 281 flesch = 57 summary = title: Silencing of HTLV-1 gag and env genes by small interfering RNAs in HEK 293 cells Three small interference RNAs (siRNAs) corresponding to gag and three corresponding to env were designed to analyze the effect of silencing by RNAi technology. In the present study, siRNAs were used for inhibition of the expression of the HTLV-1 structural genes gag and env. Forty-eight hours after transfection, the expression of EGFP-target (gag or env) fusion proteins was observed directly under an inverted fluorescence microscope. HEK 293 cells were observed 48 h posttransfection under a fluorescence microscope to determine the silencing effect of siRNAs on Gag and Env protein expression in cultured cells (Fig. 2B and C) . Based on the fluorescence data, flow cytometry and real time quantitative PCR, two siRNAs targeted to the HTLV-1 gag gene reduced efficiently gene expression by different amounts compared to the negative siRNA, scrambled siRNAs and controls without siRNA. cache = ./cache/cord-254210-3mi2aop5.txt txt = ./txt/cord-254210-3mi2aop5.txt === reduce.pl bib === id = cord-104186-fyw1xfgi author = Cui, Y title = Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. date = 1996-10-15 pages = extension = .txt mime = text/plain words = 7815 sentences = 361 flesch = 58 summary = Cells harboring the above hybrid UPFJ gene had the same three phenotypes as the mof4-1 strain, including: (i) elevated abundance of CYH2 precursor and frameshift reporter LacZ mRNA (Figures 2B and IC); (ii) inability to propagate the M1 killer virus (Table IV, Table IV , #5). A upflA strain (YGC106) containing the lacZ frameshift reporter construct in the zero or -1 frame relative to the translation start site (p315-JD86-ter or p315-JD85-ter) was transformed with a single copy plasmid harboring either the wild-type UPFJ gene, the mof4-1 allele or the vector alone. Thus, the higher expression level of the lacZ gene product in the -1 reading frame in mof4-1 cells as compared Hybrid genes between the wild-type UPFI and the mof4-1 alleles schematically represented in (A) were constructed, transformed into a upflA strain (Y52-) and CYH2 precursor abundance was determined by RNA blotting analysis as described in Figure 1 . cache = ./cache/cord-104186-fyw1xfgi.txt txt = ./txt/cord-104186-fyw1xfgi.txt === reduce.pl bib === id = cord-252871-qfrpuy3t author = Nasir, Arshan title = Investigating the Concept and Origin of Viruses date = 2020-11-03 pages = extension = .txt mime = text/plain words = 5153 sentences = 298 flesch = 46 summary = We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. In turn, the origin of archaeoviruses from Archaea, bacterioviruses from Bacteria, and eukaryoviruses from Eukarya also seems less likely as these viruses share several conserved protein folds involved in virion synthesis and other functions, indicating that they may have evolved prior to the diversification of LUCA into modern cells. cache = ./cache/cord-252871-qfrpuy3t.txt txt = ./txt/cord-252871-qfrpuy3t.txt === reduce.pl bib === id = cord-253466-7gpije5d author = Netherton, Christopher title = A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date = 2007-08-31 pages = extension = .txt mime = text/plain words = 26372 sentences = 1363 flesch = 45 summary = Significantly, Poliovirus infection causes enrichment of GEFs in membranes containing replicase proteins, and this would provide a mechanism for increasing levels of Arf1-GTP at sites of virus replication. There is evidence that Tobacco mosaic virus also uses the ER as a site of replication because the replicase enzyme and viral RNA are located on the ER of infected cells, and infection causes major changes in ER morphology (Reichel and Beachy, 1998) , including ER aggregation and formation of lamella structures. Even though these viruses infect a diverse range of hosts from different phyla, including vertebrates [poxviruses, African swine fever virus (ASFV)], arthropods (entomopox, ASFV, chloriridoviruses), amphibians and fish (Ranavirus, Megalocytivirus, and Lymphocystivirus genera of the Iridoviridae family), marine algae (phycodnaviruses), and protozoa (mimivirus), they all generate cytoplasmic factories as major sites of virus assembly and replication (illustrated in Fig. 4 ). Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein cache = ./cache/cord-253466-7gpije5d.txt txt = ./txt/cord-253466-7gpije5d.txt === reduce.pl bib === id = cord-103739-mmkrwj8t author = Snijder, Eric J. title = A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date = 2020-03-24 pages = extension = .txt mime = text/plain words = 3808 sentences = 223 flesch = 48 summary = Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). 106 double-membrane spherules (DMSs) 107 We first set out to analyse the ultrastructure of MERS-CoV-infected Huh7 cells under sample 108 preparation conditions favourable for autoradiography (see Materials and Methods) (Fig 1, S1 109 Video). Association of polioviral proteins of the P2 89 genomic region with the viral replication complex and virus-induced membrane synthesis as 90 visualized by electron microscopic immunocytochemistry and autoradiography cache = ./cache/cord-103739-mmkrwj8t.txt txt = ./txt/cord-103739-mmkrwj8t.txt === reduce.pl bib === id = cord-252466-usrpodjx author = Yun, Nadezhda E. title = Pathogenesis of Lassa Fever date = 2012-10-09 pages = extension = .txt mime = text/plain words = 5668 sentences = 290 flesch = 40 summary = Apparently, failure to develop the cellular immune response that would control dissemination of LASV, which is indicated by high serum virus titers, combined with disseminated replication in tissues and absence of neutralizing antibodies, leads to the development of fatal Lassa fever [64] . Downregulation of immune responses caused by LASV infection demonstrated in vitro is also in agreement with the results of clinical observations showing that fatal outcome of Lassa fever correlates with low levels or absence of interleukin (IL) 8 and IFN inducible protein 10 (IP-10) in circulation [70] . These data indicate that T cells are essential for rapid resolution of LASV infection; however, if the host fails to control virus replication due to inadequate activation of the immune system, T lymphocytes may play a key role in Lassa fever pathogenesis. cache = ./cache/cord-252466-usrpodjx.txt txt = ./txt/cord-252466-usrpodjx.txt === reduce.pl bib === id = cord-254747-vox5xsgd author = Deng, Xufang title = An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date = 2018-04-01 pages = extension = .txt mime = text/plain words = 5730 sentences = 323 flesch = 53 summary = Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways. cache = ./cache/cord-254747-vox5xsgd.txt txt = ./txt/cord-254747-vox5xsgd.txt === reduce.pl bib === id = cord-253480-qchrw337 author = Pu, Jieying title = Antiviral activity of Carbenoxolone disodium against dengue virus infection date = 2016-12-23 pages = extension = .txt mime = text/plain words = 5289 sentences = 287 flesch = 52 summary = Here, we found that the production of infectious DENV particles was significantly decreased by CBX treatment in DENV‐permissive cells, while the viral RNA and viral protein synthesis were not affected. Moreover, results from time-of-addition study showed that the inhibitory effect of CBX on DENV was exhibited by targeting the virus itself, not the host cells. In this study, we investigated whether CBX treatment inhibits dengue infection by measuring the production of progeny virions and viral RNA as well as viral protein expression. To determine whether CBX inhibits the production of infectious progeny DENV in other dengue-permissive cells, TCID 50 assay was performed to measure the virus titer in CBX-treated THP-1 and HUVEC cells, both of which are widely used in DENV studies [Halstead, 1988; Wu et al., 2000] . CBX treatment did not inhibit DENV-1 or DENV-2 RNA synthesis and protein expression in one replication cycle, but markedly reduced progeny virus The total RNA was isolated from the infected cells and analyzed by quantitative RT-PCR. cache = ./cache/cord-253480-qchrw337.txt txt = ./txt/cord-253480-qchrw337.txt === reduce.pl bib === id = cord-252433-0e9lonq4 author = Cullen, Bryan R. title = Viral RNAs: Lessons from the Enemy date = 2009-02-20 pages = extension = .txt mime = text/plain words = 3564 sentences = 172 flesch = 52 summary = As a result, HIV-1 mutants lacking a functional rev gene are able to express the proteins encoded by fully spliced viral mRNAs, that is, Tat, Nef, and the defective Rev protein itself, but cannot express any of the proteins encoded by incompletely spliced viral mRNAs, including Gag, Pol, and Env. The transcripts encoding these viral structural proteins, however, can be detected in the nucleus of cells infected by Rev-deficient viruses, where they are either degraded or eventually fully spliced and then exported (Cullen, 2003) . MPMV has a simpler genomic organization than HIV-1 and only encodes the three structural proteins Picornaviruses and some flaviviruses Recruits cellular translation factors and ribosomal subunits to viral translation initiation codons in the absence of an mRNA cap Gag, Pol, and Env. Nevertheless, MPMV expresses both a genome-length Gag/ Pol mRNA and a spliced Env mRNA. cache = ./cache/cord-252433-0e9lonq4.txt txt = ./txt/cord-252433-0e9lonq4.txt === reduce.pl bib === id = cord-253307-4bpdfgau author = Sanz, Miguel A. title = Inhibition of host protein synthesis by Sindbis virus: correlation with viral RNA replication and release of nuclear proteins to the cytoplasm date = 2014-11-19 pages = extension = .txt mime = text/plain words = 10157 sentences = 537 flesch = 49 summary = Analysis of a SINV variant with a point mutation in nsP2, exhibiting defects in the shut‐off of host protein synthesis, indicates that both viral RNA replication and the release of nuclear proteins to the cytoplasm are greatly inhibited. Furthermore, nucleoside analogues that inhibit cellular and viral RNA synthesis impede the blockade of host mRNA translation, in addition to the release of nuclear proteins. Therefore, in SINV nsP2 (P726G)-replicating BHK cells, a correlation exists between the inhibition of viral RNA replication and the release of nuclear proteins, in addition to the failure to completely block cellular mRNA translation. Thus, in agreement with previous results, these findings indicate that the shutoff of host translation after SINV infection is restricted when viral RNA synthesis is blocked and nuclear proteins are not released to the cytoplasm. Indeed, in cells co-transfected with rep C+luc(ΔnsPs) and EMCV(IRES)-nsP1-4 mRNA, there is low-level RNA replication, no release of nuclear proteins and the synthesis of cellular proteins is not blocked. cache = ./cache/cord-253307-4bpdfgau.txt txt = ./txt/cord-253307-4bpdfgau.txt === reduce.pl bib === id = cord-254592-wa5il5go author = Brierley, Liam title = Tissue tropism and transmission ecology predict virulence of human RNA viruses date = 2019-11-26 pages = extension = .txt mime = text/plain words = 5887 sentences = 269 flesch = 37 summary = To quantify the effects of the most informative risk factors, averaged partial dependence was extracted from the random forests, describing the marginal predicted probabilities of severe virulence associated with each virus trait (Fig 4, S2 Table) . Predicted probability of classifying virulence as 'severe' for each of the most informative risk factors in random forest models applied to all known human RNA viruses and zoonotic viruses only (primary tissue tropism, any known neural tropism, any known renal tropism, level of human-to-human transmissibility, primary transmission route, and any known vector-borne transmission). In both classification tree and random forest models, viruses were more likely to be predicted to cause severe disease if they caused systemic infections, had neural or renal tropism, transmitted via direct contact or respiratory routes, or had limited capability to transmit between humans (0 < R 0 � 1). cache = ./cache/cord-254592-wa5il5go.txt txt = ./txt/cord-254592-wa5il5go.txt === reduce.pl bib === id = cord-254100-u6x5zd4i author = Taliansky, M.E. title = Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date = 2010-10-15 pages = extension = .txt mime = text/plain words = 13988 sentences = 662 flesch = 40 summary = An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. As their name suggests, MPs are involved in virus spread in infected plants, and the potential role of fibrillarin in this process will be discussed in Section IV.B. The multifunctional PVA (potato virus A)-encoded viral genomelinked protein (VPg) is also able to interact with fibrillarin (Rajamäki and Bonfiglioli et al. cache = ./cache/cord-254100-u6x5zd4i.txt txt = ./txt/cord-254100-u6x5zd4i.txt === reduce.pl bib === id = cord-254916-y1rw9q11 author = Ogando, Natacha S. title = SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date = 2020-06-22 pages = extension = .txt mime = text/plain words = 8571 sentences = 423 flesch = 50 summary = The overall level of amino acid sequence identity of viral proteins ranges from about 65 % in the least conserved parts of the S protein to about 95 % in the most conserved replicative enzyme domains, prompting the coronavirus study group of the International Committee on the Taxonomy of Viruses to classify the new agent within the species Severe acute respiratory syndrome-related coronavirus, which also includes the 2003 SARS-CoV [1] . In this report, we describe a comparative study of the basic replication features of SARS-CoV and SARS-CoV-2 in Vero E6 cells, including growth kinetics, virus titres, plaque phenotype and an analysis of intracellular viral RNA and protein synthesis. One of them is the rapid evolution -during virus passaging in Vero cells -of a specific region of the SARS-CoV-2 S protein that contains the so-called furin-like cleavage site. cache = ./cache/cord-254916-y1rw9q11.txt txt = ./txt/cord-254916-y1rw9q11.txt === reduce.pl bib === id = cord-253501-hkxlq3os author = Anang, Saumya title = Recent Advances Towards the Development of a Potent Antiviral Against the Hepatitis E Virus date = 2018-06-28 pages = extension = .txt mime = text/plain words = 4416 sentences = 290 flesch = 38 summary = [29] [30] [31] [32] Ribavirin inhibits host inosine monophosphate dehydrogenase, thereby depleting cellular GTP pools and blocking viral replication during HEV infection. Sofosbuvir, a prodrug of a uridine nucleoside analogue that acts as a direct-acting antiviral against hepatitis C virus (HCV) RNA-dependent RNA polymerase in its active form, was reported by Dao Thi et al. 63, 64 Zinc salts were shown to block the replication of both genotype 1 and genotype 3 HEV by inhibiting the activity of viral RNA-dependent RNA polymerase in cultured human hepatoma cells. Zinc directly inhibits HEV RNA-dependent RNA polymerase activity in vitro and displays moderate cooperativity with ribavirin in inhibiting viral replication in mammalian cell culture models of HEV infection. Ribavirin therapy inhibits viral replication on patients with chronic hepatitis e virus infection Zinc salts block hepatitis E virus replication by inhibiting the activity of viral RNA-dependent RNA polymerase cache = ./cache/cord-253501-hkxlq3os.txt txt = ./txt/cord-253501-hkxlq3os.txt === reduce.pl bib === id = cord-254070-v9gabn1a author = Bordería, Antonio V. title = Fidelity Variants and RNA Quasispecies date = 2015-10-25 pages = extension = .txt mime = text/plain words = 7003 sentences = 386 flesch = 48 summary = For retroviruses, some base analog-resistant HIV strains were reported with reverse transcriptase mutations (e.g., M184V) that altered the fidelity of this RNA-dependent DNA polymerase. Several observations supported this last mechanism: G64S exhibited the same replication as wild-type virus in single-cycle infections; G64S generated fewer escape mutants to antiviral compounds; and G64S was also resistant to base analogs of different structure (Pfeiffer and Kirkegaard 2003; Vignuzzi et al. Finally, a high-fidelity polymerase variant was found for foot-and-mouth disease virus (FMDV, also in the Picornaviridae family), selected by serial passage in the RNA mutagen, 5-fluorouracil (5-FU). As with picornavirus high-fidelity variants, this variant was resistant to multiple RNA mutagens and generated populations with more restricted genetic diversity than wild-type virus. A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity cache = ./cache/cord-254070-v9gabn1a.txt txt = ./txt/cord-254070-v9gabn1a.txt === reduce.pl bib === id = cord-023346-8sqbqjm1 author = nan title = MONDAY: POSTERS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130043 sentences = 7330 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023346-8sqbqjm1.txt txt = ./txt/cord-023346-8sqbqjm1.txt === reduce.pl bib === id = cord-254713-ghcwfcx2 author = Razanajatovo, Norosoa H title = Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date = 2015-03-12 pages = extension = .txt mime = text/plain words = 4163 sentences = 200 flesch = 49 summary = RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species. cache = ./cache/cord-254713-ghcwfcx2.txt txt = ./txt/cord-254713-ghcwfcx2.txt === reduce.pl bib === id = cord-254903-g9ropt9c author = Xu, Xiaofeng title = Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data date = 2020-09-16 pages = extension = .txt mime = text/plain words = 3280 sentences = 179 flesch = 61 summary = RESULTS: In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China's Yunnan Province in 2016. In the present study, we identified a new MGTV strain Yunnan2016 detected in Amblyomma testudinarium ticks [17] and aimed to achieve the following research goals: (1) establish a method to generate the full-length genome sequence of an RNA virus using sRNA-seq data; (2) determine the feasibility of using the sRNA-seq based method in the detection of viruses in a small tick; and (3) provide a high-quality and well-curated reference genome for future studies on MGTV, JMTV, KITV and GXTV. cache = ./cache/cord-254903-g9ropt9c.txt txt = ./txt/cord-254903-g9ropt9c.txt === reduce.pl bib === id = cord-254596-wsmnlnlk author = Grädel, Carole title = Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing date = 2020-07-31 pages = extension = .txt mime = text/plain words = 6911 sentences = 334 flesch = 51 summary = In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains. In order to confirm genotype identification obtained via DRS and to obtain a highly accurate whole-genome enterovirus sequence, we also subjected sample E590 to cDNA sequencing using Illumina MiSeq. MiSeq sequencing library preparation was performed with stool material and following the routine diagnostic pre-treatment (as opposed to chloroform/bead treatment) given that low amount of patient stool sample was available (Figure 1 ). cache = ./cache/cord-254596-wsmnlnlk.txt txt = ./txt/cord-254596-wsmnlnlk.txt === reduce.pl bib === id = cord-023364-ut56gczm author = nan title = EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date = 2005-06-08 pages = extension = .txt mime = text/plain words = 130049 sentences = 7334 flesch = 54 summary = • enhancement of automation/computerisation; • process control to provide an 'error-free pathway'; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody 'combi' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas' disease infection (for retrieval of otherwise wasted blood); • European Union's in vitro diagnostics directive: this has caused some problems and reduced flexibility. cache = ./cache/cord-023364-ut56gczm.txt txt = ./txt/cord-023364-ut56gczm.txt === reduce.pl bib === id = cord-254963-cnvxlv6h author = Paskey, Adrian C. title = Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date = 2019-02-26 pages = extension = .txt mime = text/plain words = 6201 sentences = 267 flesch = 45 summary = In order to test this newly expanded probe panel and to specifically assess the effect of hybridization-based viral enrichment on the sensitivity of HTS for detection of a single virus within a complex environmental sample, commercial bat guano was spiked with increasing concentrations of Influenza virus (IFV). As expected, a dose-dependent effect in the proportion of sequencing reads derived from IFV was observed as the number of spiked genome copies increased ( Fig. 1a and Additional file 1: Table S1 ), in both the unbiased shotgun sequence data as well as the virus enriched sequence data. Such limitations have been of particular concern for U.S. Department of Defense (DoD) laboratories tasked with biosurveillance and biodefense activities in regions with limited material resources and human We demonstrate here that hybridization-based viral target enrichment yields robust coverage of small genomes from clinical samples, even yielding full-length, deeply covered genomes at concentrations whereby Fig. 3 Detection of close relative viruses irrespective of extensive multiplexing. cache = ./cache/cord-254963-cnvxlv6h.txt txt = ./txt/cord-254963-cnvxlv6h.txt === reduce.pl bib === id = cord-255576-738khdwv author = Van Duyne, Rachel title = Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery date = 2012-07-10 pages = extension = .txt mime = text/plain words = 9845 sentences = 517 flesch = 56 summary = We have previously shown that Tax interacts directly with the cellular Rb (Retinoblastoma) protein and targets Rb for degradation via the proteasome pathway, resulting in a decrease in Rb protein expression in HTLV-1 infected cells and a dysregulation of the cell cycle [47] . Collectively, these data indicate that the Drosha in Tax-containing and HTLV-1 infected cells is mostly functionally inactive and the functional suppression of Drosha is dependent on its interaction with a small region of the N-terminus of Tax. We have shown above that Drosha is downregulated, degraded, and mostly inactive in HTLV-1 infected cells, however, it was not clear what effect this dysregulation of Drosha would have on viral replication. Collectively, these data indicate that proteins, such as IKK-b, among others, may directly be regulated by the Tax/Drosha interaction in HTLV infected cells. cache = ./cache/cord-255576-738khdwv.txt txt = ./txt/cord-255576-738khdwv.txt === reduce.pl bib === id = cord-254895-ym0jsir5 author = Eisenächer, Katharina title = The role of viral nucleic acid recognition in dendritic cells for innate and adaptive antiviral immunity date = 2008-01-18 pages = extension = .txt mime = text/plain words = 9040 sentences = 465 flesch = 47 summary = Dendritic cell subpopulations express specific nucleic acid recognition receptors belonging to the Toll-like receptor family (TLR3, 7, 8, 9) and the cytosolic RNA helicase family (RIG-I, MDA5, LGP2). Apart from activating the NFkB and MAPK signaling pathways leading to inflammatory cytokine and chemokine production as well as costimulatory molecule expression, the intracellularly localized nucleic acid recognition receptors TLR3, 7, 8 and 9 specifically trigger type I interferon production via MyD88-and TRIF-dependent signaling pathways. Thus, TRAF6 seems to be required for NFkB activation but not IFN-b induction downstream of IPS-1 which is mainly mediated by TBK1/IKKe. In vitro studies performed with primary cells obtained from RIG-I knockout mice confirmed that RIG-I plays an essential role in eliciting immune responses against specific negative strand and positive strand RNA viruses such as NDV, SeV, VSV, Japanese encephalitis virus (JEV) and Influenza virus in various cell types with the exception of pDCs . cache = ./cache/cord-254895-ym0jsir5.txt txt = ./txt/cord-254895-ym0jsir5.txt === reduce.pl bib === id = cord-255252-md0avnqg author = Tang, Julian W. title = Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date = 2007-07-02 pages = extension = .txt mime = text/plain words = 5317 sentences = 326 flesch = 70 summary = SARS‐CoV viral load and SARS‐CoV/GAPDH RNA ratio for each organ type were related to four time durations: onset of illness to death, death to post‐mortem tissue sampling, and total durations of treatment with ribavirin and hydrocortisone. Post-mortem tissues were collected with great care from the major organs including heart, kidney, liver, spleen, lung, small bowel, psoas (skeletal) muscle, and bone marrow. Figures 1-6 show the results, using semi-log plots, for each organ: heart, kidney, liver, spleen, lung, and small bowel, respectively, for SARS-CoV, GAPDH and the SARS-CoV/GAPDH RNA ratio. In the organspecific viral load results, the overall picture made up from the data points from the seven different patients with different durations of SARS illness, generally, the SARS-CoV/GAPDH RNA ratio never reached above one in heart, kidney, liver, and spleen tissue for all x-axis parameters analyzed. cache = ./cache/cord-255252-md0avnqg.txt txt = ./txt/cord-255252-md0avnqg.txt === reduce.pl bib === id = cord-255607-dbexsugq author = Wu, Yang title = Porcine Epidemic Diarrhea Virus nsp15 Antagonizes Interferon Signaling by RNA Degradation of TBK1 and IRF3 date = 2020-05-31 pages = extension = .txt mime = text/plain words = 6410 sentences = 357 flesch = 48 summary = Our preliminary results revealed that endogenous TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3), the key components in the IFN signaling pathway were downregulated in PEDV infected IPEC-J2 cells by iTRAQ analysis. Moreover, PEDV nsp15 can directly degrade the RNA levels of TBK1 and IRF3 dependent on its EndoU activity to suppress IFN production and constrain the induction of IFN stimulated genes (ISGs), by which PEDV antagonizes the host innate response to facilitate its replication. Previous studies suggest that PEDV can restrain host innate immune response by different strategies, such as by degradation or cleavage of key factors essential the IFN signaling pathway [25, 26] , competitive interaction between viral encoded proteins and modulators for IFN production [27, 28] , or localization changes of antiviral components [29] . cache = ./cache/cord-255607-dbexsugq.txt txt = ./txt/cord-255607-dbexsugq.txt === reduce.pl bib === id = cord-255090-2gpsu1y4 author = Lv, Ke title = Transient inhibition of foot-and-mouth disease virus replication by siRNAs silencing VP1 protein coding region date = 2009-06-30 pages = extension = .txt mime = text/plain words = 6335 sentences = 318 flesch = 52 summary = In addition, variations within multiple regions of the quasispecies of FMDV were retrospectively revealed by sequencing of FMDV genes, and a single nucleotide substitution was identified as the main factor in resistance to RNAi. Our data demonstrated that the three siRNA molecules synthesized with T7 RNA polymerase could have transient inhibitory effects on the replication of FMDV. Recently, several laboratories used RNAi to inhibit foot-and-mouth virus infection in cell culture or in animals taking forms of chemically synthesized siRNA, plasmid encoding shRNA, and adenovirus encoding shRNA (Chen et al., 2004 (Chen et al., , 2006 de los Santos et al., 2005; Kahana et al., 2004; Mohapatra et al., 2005) , showing rapid decrease of FMDV replication. Furthermore, among the five siRNAs candidates, three siRNAs were confirmed efficacious to transiently inhibit the replication of FMDV in BHK-21 cells by determining the relative viral amount within infected cells and the virus titers in supernatants as well as the observation of the emergence of CPE. cache = ./cache/cord-255090-2gpsu1y4.txt txt = ./txt/cord-255090-2gpsu1y4.txt === reduce.pl bib === id = cord-255619-5h3l6nh6 author = Kuo, Shu-Ming title = Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date = 2013-03-23 pages = extension = .txt mime = text/plain words = 6329 sentences = 326 flesch = 55 summary = title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNAbinding capacity of the N protein. In this study, we showed that substituting either of the positively selected residues with the amino acid present in most CH IBVs dramatically reduced the binding capacity of the N protein for synthetic TRS repeats (Fig. 4) . cache = ./cache/cord-255619-5h3l6nh6.txt txt = ./txt/cord-255619-5h3l6nh6.txt === reduce.pl bib === id = cord-256036-gd53s4dv author = Sandmann, Lisa title = Barriers of hepatitis C virus interspecies transmission date = 2013-01-01 pages = extension = .txt mime = text/plain words = 7894 sentences = 373 flesch = 40 summary = In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease cache = ./cache/cord-256036-gd53s4dv.txt txt = ./txt/cord-256036-gd53s4dv.txt === reduce.pl bib === id = cord-255499-31xmue1g author = Bujarski, J.J. title = Recombination date = 2008-07-30 pages = extension = .txt mime = text/plain words = 4852 sentences = 253 flesch = 41 summary = In general, homologous recombination events occur much more often and they are most commonly known as genetic crossing-over that happens in every DNA-based organism during meiosis. The mechanism may involve either homologous crossing-over events or copy-choice processes that rely on template switching by DNA replicase. Aberrant homologous recombination involves crossovers between related RNAs, but the crosses occur at not-corresponding sites leading to sequences insertions or deletions. A double-stranded RNA Pseudomonas phage Phi6 was hypothesized to recombine its RNA based on a copy-choice template switching mechanism, where the crossovers would have occurred inside the virus capsid structures at regions with almost no sequence similarity. In some cases, the base pairing between a partial nascent strand and the acceptor template can lead to the appearance of the rearranged regions in DI RNAs. In addition to rearranged DI RNAs, some RNA viruses accumulate defective RNAs due to a single internal deletion in the genomic RNA of the helper virus. cache = ./cache/cord-255499-31xmue1g.txt txt = ./txt/cord-255499-31xmue1g.txt === reduce.pl bib === id = cord-255545-nycdhdsd author = Schoenike, Barry title = Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date = 1999-03-10 pages = extension = .txt mime = text/plain words = 6170 sentences = 265 flesch = 48 summary = In theory, sense-specific measurement of viral RNAs may be achieved by reverse transcription polymerase chain reaction (RT-PCR) assays which utilize primers of defined polarity during the RT step. Key RT-PCR parameters which were optimized include the design of tagged primers, DNase treatment of in vitro transcribed RNA standards, specification of temperature differences between RT and PCR annealing steps, and use of competitive RNA templates for quantitative assays. In fact, several studies have demonstrated that RT-PCR assays based on specific RNA template recognition by RT primers of defined polarity will not reliably distinguish between viral RNAs of positive or negative sense. Despite the findings above, many published research reports are based on conventional RT-PCR assays, relying on the polarity of primers added to the RT step in putative sense-specific measurements of viral RNAs; rarely are control reactions performed to rigorously show that this method is in fact sense-specific. cache = ./cache/cord-255545-nycdhdsd.txt txt = ./txt/cord-255545-nycdhdsd.txt === reduce.pl bib === id = cord-255495-xnoppq3y author = Elrashdy, Fatma title = On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date = 2020-07-09 pages = extension = .txt mime = text/plain words = 7523 sentences = 353 flesch = 47 summary = It is possible that this "Trojan horse" strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this "silence" time period and then started to re-spread again. The fact that SARS-CoV-2 can be present within the vacuoles or double membrane vesicles (DMVs) within the host cells was proven by the careful post-mortem histopathological analysis of the renal samples of patients with COVID-19 by light microscopy, electron microscopic examination, and immunostaining (Farkash et al., 2020; Su et al., 2020) . Is this "Trojan horse" strategy of the release of the SARS-CoV-2-loaded exosomes or EDMVs represent a reasonable explanation for the appearance of the viral RNA in the recovered COVID-19 patients 7-14 day post discharge? cache = ./cache/cord-255495-xnoppq3y.txt txt = ./txt/cord-255495-xnoppq3y.txt === reduce.pl bib === id = cord-255738-r8zfdsix author = Ge, Feng title = Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date = 2007-03-30 pages = extension = .txt mime = text/plain words = 5103 sentences = 242 flesch = 49 summary = Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric's group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel's group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates. cache = ./cache/cord-255738-r8zfdsix.txt txt = ./txt/cord-255738-r8zfdsix.txt === reduce.pl bib === id = cord-256325-q70rky3r author = Stewart, Cameron R. title = A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date = 2017-07-04 pages = extension = .txt mime = text/plain words = 8310 sentences = 409 flesch = 43 summary = title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease Here we largely focus on findings from two recent RNAi screens to identify protein-coding genes and host-encoded microRNAs impacting the henipavirus infection cycle in human cells. X-ray data have suggested that the methylation of rRNA requires the formation of this complex with involvement of four fibrillarin molecules interacting with different regions of the target rRNAs. The yeast equivalent of fibrillarin, NOP1, has been more extensively studied than the human counterpart but fibrillarin is a well-conserved protein in most organisms, reinforcing the notion that all post-transcriptional processes involving fibrillarin such as chemical modification (methylation) of rRNA, pre-rRNA cleavage and ribosome assembly are essential for proper cellular functioning (Rodriguez-Corona et al. Deffrasnes and colleagues showed that siRNA-mediated knockdown of fibrillarin expression dramatically reduced HeV protein production and viral genome replication but did not impact viral fusion, and that fibrillarin catalytic activity was essential to henipavirus infection. cache = ./cache/cord-256325-q70rky3r.txt txt = ./txt/cord-256325-q70rky3r.txt === reduce.pl bib === id = cord-255795-su7f5ges author = Yelin, Idan title = Evaluation of COVID-19 RT-qPCR test in multi-sample pools date = 2020-03-27 pages = extension = .txt mime = text/plain words = 2262 sentences = 113 flesch = 55 summary = Here, testing a pooling approach for the standard RT-qPCR test, we find that a single positive sample can be detected even in pools of up to 32 samples, with an estimated false negative rate of 10%. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close integral groups, such as hospital departments, army units, or factory shifts. Here, we test the ability of the standard RT-qPCR test for detecting a single positive sample within a pool of negative samples. Pooling clinical RNA samples, we tested previously confirmed positive samples alone and combined with an increasing number of previously confirmed negative samples and found that positive samples can still be well observed in pools of up to 32 samples, and possibly even 64 with additional PCR cycles. We found that a single clinical sample with SARS-CoV-2 RNA can be consistently detected in a pool of up to 32 samples. cache = ./cache/cord-255795-su7f5ges.txt txt = ./txt/cord-255795-su7f5ges.txt === reduce.pl bib === id = cord-256370-cz88t29n author = Jansen van Vuren, Petrus title = Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date = 2016-02-29 pages = extension = .txt mime = text/plain words = 5529 sentences = 263 flesch = 49 summary = This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. Maximum Likelihood trees were prepared using amino acid sequences of all open reading frames from all segments, showing the placement of Mahlapitsi virus (MAHLV) in the Orthoreovirus genus relative to other viruses in this genus for which sequence is available on Genbank. A Maximum Likelihood tree, constructed with nucleic acid sequence data for the RNA-dependent RNA polymerase (RdRp) encoding segments of representative viruses from the different genera within Reoviridae (Figure 7) shows the placement of both isolates amongst other orthoreoviruses in the family. Maximum Likelihood trees were prepared using the deduced amino acid sequences from the open reading frames (ORF's) of all the virus' segments and those of other viruses in the Orthoreovirus genus (Figures 8-10) . cache = ./cache/cord-256370-cz88t29n.txt txt = ./txt/cord-256370-cz88t29n.txt === reduce.pl bib === id = cord-255883-mz6nyisw author = Asif, Muhammad title = COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date = 2020-08-14 pages = extension = .txt mime = text/plain words = 5273 sentences = 283 flesch = 44 summary = Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. An in vitro study conducted by Hoffmann and colleagues revealed that SARC-CoV-2 depends on cellular serine protease (TMPRSS2) for S proteins priming which are known to interact with human ACE2 receptors in the lungs and facilitate entry into the cells. The authors opted the following keywords to find relevant studies: "essential oils", "antiviral", "COVID-19", "SARC-CoV-2", "bronchodilation", "immunomodulatory'', "anti-inflammatory'', "corona virus''. Thus, on the basis of these docking and in vitro studies, it is proposed that garlic essential oils and their isolated constituents, especially DAS, have potential to prevent the entry of virus into host cells as well as to activate molecular antioxidant pathways that decrease the secretions of culprit pro-inflammatory cytokines. Essential oils have long been known to have anti-inflammatory, antioxidant, immunomodulatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2. cache = ./cache/cord-255883-mz6nyisw.txt txt = ./txt/cord-255883-mz6nyisw.txt === reduce.pl bib === id = cord-022888-dnsdg04n author = nan title = Poster Sessions date = 2009-08-19 pages = extension = .txt mime = text/plain words = 188640 sentences = 9313 flesch = 45 summary = Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. cache = ./cache/cord-022888-dnsdg04n.txt txt = ./txt/cord-022888-dnsdg04n.txt === reduce.pl bib === id = cord-256444-grw5s2pf author = Lai, Michael M.C. title = The Molecular Biology of Coronaviruses date = 1997-12-31 pages = extension = .txt mime = text/plain words = 35222 sentences = 1753 flesch = 51 summary = Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. This decade has seen the manipulation of these clones, and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs, to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The species and tissue specificity of a coronavirus infection is a t least partially dictated by the nature and distribution of cellular receptors and other related molecules that regulate virus entry, as evidenced by the viral replication that results when viral RNA is directly introduced into cell types of other animal species. cache = ./cache/cord-256444-grw5s2pf.txt txt = ./txt/cord-256444-grw5s2pf.txt === reduce.pl bib === id = cord-256508-ce59ovan author = Asselah, Tarik title = COVID-19: discovery, diagnostics and drug development date = 2020-10-08 pages = extension = .txt mime = text/plain words = 9214 sentences = 556 flesch = 46 summary = To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The current diagnostic strategy to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of SARS-CoV-2 specific nucleic acid targets [47] . The neutralization assay is a laboratory-based test that uses live virus and cell culture methods to determine if patient antibodies can prevent viral infection in vitro [72] . A randomized, controlled, openlabel trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection and severe respiratory illness COVID-19 was performed [126] . Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals cache = ./cache/cord-256508-ce59ovan.txt txt = ./txt/cord-256508-ce59ovan.txt === reduce.pl bib === id = cord-256510-orr2roxz author = de Castro, Isabel Fernández title = Virus factories: biogenesis and structural design date = 2012-10-04 pages = extension = .txt mime = text/plain words = 5188 sentences = 259 flesch = 43 summary = For example, transmission electron microscopy (TEM) of cells infected with coxsackievirus showed intracellular organized lattices (Fig. 1E) , very similar to those assembled by the viral RNA polymerase in vitro (Kemball et al., 2010) close relationship between self-interaction and replication activity is reported for viral polymerases of other viruses such as FHV (Dye et al., 2005) , hepatitis C virus (Qin et al., 2002) and RUBV (Risco et al., 2012) . For viral genome replication, the virus first assembles cytoplasmic mini-nuclei with attached mitochondria (Tolonen et al., 2001) ; virus morphogenesis then starts an aggresome-like structure (Risco et al., 2002) , where immature viruses assemble using an atypical membrane remodelling mechanism that has been characterized by ET (Chlanda et al., 2009) . Although we are beginning to understand how replication organelles are assembled, information is still limited about how cell organelles are recruited, about the mechanisms of macromolecular transport between compartments, and about the signals that regulate the major structural changes in the factory during distinct stages in the virus life cycle. cache = ./cache/cord-256510-orr2roxz.txt txt = ./txt/cord-256510-orr2roxz.txt === reduce.pl bib === id = cord-256561-fnh2do4z author = Barik, Sailen title = Therapy of Respiratory Viral Infections with Intranasal siRNAs date = 2014-09-23 pages = extension = .txt mime = text/plain words = 2605 sentences = 181 flesch = 60 summary = Based on these results, we propose the following consensus for designing intranasal antiviral siRNAs: (a) modified 19–27 nt-long double-stranded siRNAs are functional in the lung, (b) excessive 2′-OMe and 2′-F modifications in either or both strands of these siRNAs reduce efficacy, (c) limited modifications in the sense strand are beneficial, although their precise efficacy may be position-dependent, (d) cocktail of multiple siRNAs can be highly effective against multiple viral strains and subtypes. Therefore, enhancement of the intracellular and extracellular stability of synthetic siRNAs while increasing (or without compromising) their RNAi activity is a continuing goal for therapeutic translation of RNAi. A variety of chemical modifi cations, including terminal and internal ones, have been added to the fi rst-generation siRNA sequences to improve stability and delivery, leading to what we call "second-generation" siRNAs. Advantage has been taken of the free 2′-OH group of the ribose moiety of RNA (in contrast to DNA that lacks this OH group), to which various substituents were added. cache = ./cache/cord-256561-fnh2do4z.txt txt = ./txt/cord-256561-fnh2do4z.txt === reduce.pl bib === id = cord-257456-15bm9psj author = Arumugam, Arunkumar title = A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date = 2020-09-24 pages = extension = .txt mime = text/plain words = 5286 sentences = 294 flesch = 59 summary = Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. To further improve the speed of a diagnostic assay, we and others tested using untreated or heat-inactivated samples added directly to one-step RT-PCR master mixes without an RNA extraction step [6, [13] [14] [15] [16] [17] [18] [19] . Prior to COVID-19 emerged as a global pandemic, we have tested the feasibility of circumventing the sample preparation steps by adding a few microliters of the unprocessed sample (in VTM) directly into the RT-qPCR assay master mix targeting InfA, InfB, and RSV. cache = ./cache/cord-257456-15bm9psj.txt txt = ./txt/cord-257456-15bm9psj.txt === reduce.pl bib === id = cord-256940-yuja99jg author = Wei, Bo title = Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date = 2020-07-20 pages = extension = .txt mime = text/plain words = 1994 sentences = 136 flesch = 56 summary = title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. However, some COVID-19 patients have been reported to have long-term positivity for SARS-CoV-2 ribonucleic acid (RNA). On April 5, after three consecutive negative nucleic acid test results, he was discharged and transferred to another hospital for further treatment of comorbidities. Thus, DNVr may be a potential antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. cache = ./cache/cord-256940-yuja99jg.txt txt = ./txt/cord-256940-yuja99jg.txt === reduce.pl bib === id = cord-256918-mauzesor author = Domingo, Esteban title = Quasispecies and the implications for virus persistence and escape date = 1998-07-15 pages = extension = .txt mime = text/plain words = 2093 sentences = 112 flesch = 38 summary = Objectives: To discuss indeterminations inherent to a quasispecies structure and to the analytical procedures to define it, biological implications of quasispecies, and the need to take into account this type of population structure, in order to design effective strategies to prevent and control diseases caused by highly variable viruses. Results: Quasispecies have many biological implications, extending from viral pathogenesis to the emergence of new pathogens, rapid antigenic variation, and alterations in cell tropism, virulence, host range and viral gene expression. Since adaptability of RNA viruses is key to viral pathogenesis and strategies for disease control, it would seem obvious that quasispecies should have been regarded as highly relevant to these questions (Domingo, 1989 (Domingo, , 1996 Domingo and Holland, 1992; Duarte et al., 1994; Novella et al., 1995) . The evolution of an RNA virus may be rapid or slow, but mutant swarms are always hidden in their replicating genome populations. cache = ./cache/cord-256918-mauzesor.txt txt = ./txt/cord-256918-mauzesor.txt === reduce.pl bib === id = cord-256615-gvq8uyfk author = Rosenberg, Ronald title = Detecting the emergence of novel, zoonotic viruses pathogenic to humans date = 2014-11-22 pages = extension = .txt mime = text/plain words = 6688 sentences = 306 flesch = 45 summary = RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. Despite the differences in clinical presentation and geographical location, these three pathogens share three characteristics: all were unknown before found infecting humans, all are RNA viruses, and all have proven or putative non-human, animal sources. A single subtropical bat species hardly represents all mammal species and indeed many viruses are known to infect more than one species; they tested for only 9 of the 25 virus families pathogenic to humans. cache = ./cache/cord-256615-gvq8uyfk.txt txt = ./txt/cord-256615-gvq8uyfk.txt === reduce.pl bib === id = cord-257652-ndt8f812 author = Zhang, Yong-Zhen title = The diversity, evolution and origins of vertebrate RNA viruses date = 2018-08-13 pages = extension = .txt mime = text/plain words = 4249 sentences = 171 flesch = 40 summary = In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. However, following the extensive use of PCR and the Sanger sequencing methods for virus identification over the past decade, the number of RNA viruses sampled from lower vertebrates has steadily increased [28] , with notable examples being arenavirus and paramyxoviruses in reptiles [29] , and novirhabdoviruses and other RNA viruses from fish [30] , although these numbers were still very limited compared to the viruses described in birds and mammals. cache = ./cache/cord-257652-ndt8f812.txt txt = ./txt/cord-257652-ndt8f812.txt === reduce.pl bib === id = cord-257693-rnchfjbe author = Wang, Yeming title = Factors Associated With Prolonged Viral Shedding in Patients With Avian Influenza A(H7N9) Virus Infection date = 2018-04-10 pages = extension = .txt mime = text/plain words = 3987 sentences = 212 flesch = 42 summary = Observational studies have reported that prolonged influenza viral shedding in the respiratory tract is associated with severe outcomes of patients with seasonal influenza [10] and that early initiation of antiviral treatment with neuraminidase inhibitors (NAIs) for patients infected with 2009 pandemic influenza A(H1N1) virus (A[H1N1] pdm09) has a survival benefit [11] [12] [13] [14] [15] [16] [17] . We conducted a retrospective, multicenter study of 478 hospitalized patients with laboratory-confirmed A(H7N9) infection who were identified during April 2013-March 2017 to assess the impact of different NAI treatment strategies and corticosteroid treatment on the duration of A(H7N9) shedding. In a multivariable model that included available data from 478 patients, the time from illness onset to antiviral treatment (HR, 0.90 [95% CI, .91-.96]) and systemic corticosteroid administration (HR, 0.62 [95% CI, .50-.77]) were independent factors associated with the duration of A(H7N9) RNA shedding (Table 2 and Figure 4 ). cache = ./cache/cord-257693-rnchfjbe.txt txt = ./txt/cord-257693-rnchfjbe.txt === reduce.pl bib === id = cord-257569-36qx1sy9 author = Hanada, Kousuke title = A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date = 2004-06-17 pages = extension = .txt mime = text/plain words = 3460 sentences = 156 flesch = 43 summary = title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes. First, we estimated the rates of synonymous substitution for 46 different species of RNA viruses except Puumala virus, human T-lymphotropic virus 1 (HTLV-1) and GB virus C/hepatitis G virus (HGV), using the time-serial sample data. This indicated that the transmission mode affected the replication frequency and that differences in the replication frequencies contributed to the variation of the rate of synonymous substitution for RNA viruses. Moreover, in the present study, we proved that the variation in the synonymous substitution rates among RNA viruses was caused by variation of the replication frequency, and that differences in the infection and transmission modes affected the variation of replication frequencies. cache = ./cache/cord-257569-36qx1sy9.txt txt = ./txt/cord-257569-36qx1sy9.txt === reduce.pl bib === id = cord-258035-2tk7maqk author = DeFilippis, Victor title = Functional genomics in virology and antiviral drug discovery date = 2003-10-31 pages = extension = .txt mime = text/plain words = 4769 sentences = 255 flesch = 39 summary = Given that virus replication involves use and manipulation of multiple host proteins and molecular processes, cellular pathways related to transcription and translation, signal transduction, metabolism, host defense and cell cycle control are Review commonly altered in response to, or as a result of, infection with diverse virus types. A special case of virus modulation of host cell gene expression in which functional genomics will reveal novel targets and treatments is viral oncogenesis. The most recent method for analyzing gene inhibition studies has been RNAi or siRNA, where small 21 -23-nucleotide (nt) RNA duplexes interfere with the transcription program by directing degradation of homologous mRNA [34] [35] [36] [37] . Both new-generation antisense oligomers and siRNA can be used to knockdown expression of genes that were found by DNA microarrays to be upregulated in virally infected cells or organisms. RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type 1 replication cache = ./cache/cord-258035-2tk7maqk.txt txt = ./txt/cord-258035-2tk7maqk.txt === reduce.pl bib === id = cord-258547-47cyyetb author = Asasi, Keramat title = Changes of several acute phase factors in broiler chickens in response to infectious bronchitis virus infection date = 2013-08-01 pages = extension = .txt mime = text/plain words = 3588 sentences = 217 flesch = 54 summary = In the serum the acute phase proteins (haptoglobin and serum amyloid A), pro-inflammatory cytokines (interferon-γ and tumor necrosis factor-α), and serum sialic acid (total, TSA; lipid-bound, LBSA; and protein-bound, PBSA) concentrations were measured using validated standard procedures. Based on this evidence, the present study was undertaken to evaluate alteration in concentrations of the acute phase proteins [haptoglobin (Hp) and serum amyloid A (SAA)], pro-inflammatory cytokines (TNF-α and IFN-γ), and the serum level of total sialic acid (TSA), lipid-bound sialic acid (LBSA), and protein-bound sialic acid (PBSA) in experimentally infected chicks by IBV isolate IRFIBV32 compared with healthy chicks. The serum concentrations of IFN-γ, TNF-α, Hp, SAA, TSA, LBSA, and PBSA were increased significantly 2.50, 1.98, 1.82, 3.33, 2.25, 2.44, and 1.77 times, respectively, during experimental infection with IBV in chickens. cache = ./cache/cord-258547-47cyyetb.txt txt = ./txt/cord-258547-47cyyetb.txt === reduce.pl bib === id = cord-259152-pwvcwlh8 author = Ji, Wei title = Cross‐species transmission of the newly identified coronavirus 2019‐nCoV date = 2020-02-19 pages = extension = .txt mime = text/plain words = 1674 sentences = 114 flesch = 51 summary = The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019‐nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019‐nCoV sequence. 4 On 10 January, it was reported that a novel coronavirus designated 2019-nCoV by the World Health Organization (WHO) 5 was identified by high-throughput sequencing of the viral RNA genome, which was released through virological.org. Highthroughput sequencing of viral RNA from patients' samples has identified a novel coronavirus designated 2019-nCoV by the World Health Organization. 10, 11 Results from our analysis suggest that 2019-nCoV has most similar genetic information with bat coronovirus and has most similar codon usage bias with snake. cache = ./cache/cord-259152-pwvcwlh8.txt txt = ./txt/cord-259152-pwvcwlh8.txt === reduce.pl bib === id = cord-258286-lodjcj8c author = Zhang, Xuming title = Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date = 1997-07-07 pages = extension = .txt mime = text/plain words = 5866 sentences = 296 flesch = 54 summary = Previous studies have shown that immunocoma large plaque variant derived from the parental JHM petent mice infected with MHV exhibited increased exstrain (Stohlman et al., 1982) ; the small plaque variant pression of a number of cytokines, including IL-1, IL-6, DS (Stohlman et al., 1982) ; the neutralization-escape mu-TNF-a, and IFN-g, in the CNS at the time of viral cleartant 2.2-V-1 (Fleming et al., 1987; Wang et al., 1992) , and ance (Pearce et al., 1994) . The expressed IFNg exhibited antiviral activity, prevented virus spread in layers of DBT cells grown at approximately 70% confluence in 60-mm petri dishes were infected with MHV at vitro, and altered viral pathogenesis in mice. Expression of IFN-g using an MHV DI RNA vector cell metabolism prior to infection or it may be that interferon acts at an early stage of viral replication. cache = ./cache/cord-258286-lodjcj8c.txt txt = ./txt/cord-258286-lodjcj8c.txt === reduce.pl bib === id = cord-258696-01wj76es author = Decaro, Nicola title = Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia date = 2008-04-30 pages = extension = .txt mime = text/plain words = 3428 sentences = 177 flesch = 61 summary = The dogs, three 2.5-month-old and two 6-month-old pups, were successfully infected, shedding viral RNA with their faeces for the entire observation period (21 days) and displaying systemic clinical signs resembling those observed during the course of natural infection. At postmortem examination, remarkable lesions were observed in the internal organs of the euthanized pups, that tested positive for CCoV by real-time RT-PCR and virus isolation on cell cultures. Unexpectedly, CCoV type II RNA was detected at very high titres in the internal organs of the dead pups and the virus (strain CB/05) was isolated on canine cell cultures. (last day of observation) reaching the maximal mean value of 6.79  10 5 RNA copy numbers/ml of template at day 10 p.i. Surprisingly, CCoV RNA was never detected in the blood of the 6-month-old pups, as well as in the euthanized animals, in whose organs remarkable viral RNA titres were found. cache = ./cache/cord-258696-01wj76es.txt txt = ./txt/cord-258696-01wj76es.txt === reduce.pl bib === id = cord-258172-p54j4zzo author = Barker, Harlan title = Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date = 2020-10-28 pages = extension = .txt mime = text/plain words = 8453 sentences = 409 flesch = 48 summary = Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https:// github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: all cell types aggregated and merged human ATAC-Seq data from ENCODE [43] , transcription start sites and expression data from FANTOM5 [44] , expression quantitative trail loci from GTEx [39] , TFBS metacluster data from GTRD [45] , TFBS binding profile data from JASPAR [46] , and sequence and conservation data from Ensembl [47] . cache = ./cache/cord-258172-p54j4zzo.txt txt = ./txt/cord-258172-p54j4zzo.txt === reduce.pl bib === id = cord-259500-ndjbrtrv author = Satyanarayana, Tatineni title = Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date = 2003-09-01 pages = extension = .txt mime = text/plain words = 6465 sentences = 322 flesch = 60 summary = title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli These data demonstrate that, when hosts are sufficiently susceptible for infection by transcripts of reduced specific infectivity, introduction of frameshift mutations at "slippery sequences" near toxic regions of viral cDNAs can be used as an additional strategy to clone recalcitrant viral sequences in high-copy-number plasmids for reverse genetics. A similar frameshift mutation was also found in the derivative replicon pCTV-⌬Cla. However, the sequence of the progeny virion RNA of CTV9 from infected protoplasts or citrus plants did not contain the additional nt at position 3732 that occurred in the cDNA clones, suggesting that the frameshift mutation present in the original cDNA clone was repaired either during the in vitro transcription or during replication in the protoplasts. cache = ./cache/cord-259500-ndjbrtrv.txt txt = ./txt/cord-259500-ndjbrtrv.txt === reduce.pl bib === id = cord-259916-gr6v098c author = Wang, Hongliang title = Mechanisms of Cellular Membrane Reorganization to Support Hepatitis C Virus Replication date = 2016-05-20 pages = extension = .txt mime = text/plain words = 6186 sentences = 252 flesch = 33 summary = Like all positive-sense RNA viruses, hepatitis C virus (HCV) induces host membrane alterations for its replication termed the membranous web (MW). This review will summarize the recent studies that have led to our current knowledge of the role of viral and host factors in the biogenesis of the MWs and discuss how HCV uses this specialized membrane structure for its replication. A later study of cells containing a subgenomic HCV replicon reported that the membrane alterations induced by HCV replication consisted in part of double-membrane vesicles (DMVs; Figure 1 ) with a diameter around 200 nm that were also positive on immunoelectron microscopy with antibodies against NS5A and double-stranded RNA (dsRNA) [15] . [10] first showed that expression of viral nonstructural proteins resulted in membrane alterations that morphologically resemble those observed in replicon cells, demonstrating that viral RNA replication is not required for membranous web formation. Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex cache = ./cache/cord-259916-gr6v098c.txt txt = ./txt/cord-259916-gr6v098c.txt === reduce.pl bib === id = cord-258678-0atfsivf author = Liu, Hong Yan title = A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date = 2013-11-07 pages = extension = .txt mime = text/plain words = 4788 sentences = 282 flesch = 51 summary = Here, we report the development of a small and simple protein tag that complements the therapeutic and targeting functionalities of chimera with two functional domains: a dsRNA binding domain (dsRBD) for siRNA docking and a pH-dependent polyhistidine to disrupt endosomal membrane. Therefore, it is of critical importance to design a delivery system that is simple for potential regulatory approval and mass production, universal for all siRNAaptamer chimera, neutral and siRNA-binding specific to ensure aptamer targeting, and small to avoid major alteration of chimera's biodistribution profile. To assess their dsRNA binding activity, siRNA-aptamer chimera labeled with fluorophore FAM were incubated with the protein tags and probed with gel electrophoresis (1% agarose). To evaluate the targeting specificity of the aptamer block, PSMA-positive LNCaP cells and PSMA-negative PC3 cells were treated with complex of chimera and dsRBD-His 18 (chimera/protein tag molar ratio at 152, 100 nM chimera) in serum free medium for 2 hours, followed by incubation in complete medium for another 12 h. cache = ./cache/cord-258678-0atfsivf.txt txt = ./txt/cord-258678-0atfsivf.txt === reduce.pl bib === id = cord-259710-qrht9tq3 author = Burimuah, Vitus title = Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana date = 2020-10-27 pages = extension = .txt mime = text/plain words = 3538 sentences = 212 flesch = 59 summary = title: Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana Conclusions: Given that Ghana predominantly practices the extensive and semi-intensive systems of animal rearing, our study highlights the potential for spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species. In this study, we employed a molecular-based detection method to investigate the presence of BCoVs in rectal samples of cattle, sheep and goats from four major regions in Ghana. In a prior study, we reported a high seroprevalence, cross-species infection and serological determinants of BCoV in cattle, sheep and goats in Ghana [19] . In this study, we sought to investigate the presence of BCoVs in rectal samples of cattle, sheep and goats from four major regions in Ghana using molecular-based detection method. cache = ./cache/cord-259710-qrht9tq3.txt txt = ./txt/cord-259710-qrht9tq3.txt === reduce.pl bib === id = cord-259246-azt5sr9w author = Peng, Qi title = Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir date = 2020-10-19 pages = extension = .txt mime = text/plain words = 3216 sentences = 158 flesch = 50 summary = This structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase, and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues which may explain its capacity for mimicking both adenine and guanine nucleotides. Recently, we and other groups have determined the structures of SARS-CoV-2 core polymerase complex in both apo and RNA-bound states 26-30 , providing important information for structure-based antiviral drug design. Similar observations were also reported recently that SARS-CoV-2 polymerase is more tolerant for mismatches between template and product residues than other viral RdRps 5 , which further highlights the requirement for the proofreading nuclease nsp14 to maintain the integrity of viral genome. Interestingly, Favipiravir could be incorporated into the RNA product with similar efficiencies to those of ATP or GTP substrates guided by U or C template residues, respectively (Fig. 1c) . cache = ./cache/cord-259246-azt5sr9w.txt txt = ./txt/cord-259246-azt5sr9w.txt === reduce.pl bib === id = cord-258595-bk35vxlr author = Westhaus, Sandra title = Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date = 2020-08-18 pages = extension = .txt mime = text/plain words = 4965 sentences = 305 flesch = 57 summary = Inoculation of differentiated Caco-2 cells for ten days with purified and concentrated wastewater (P2, P5, P11, and P12) did not result in the production of infectious SARS-CoV-2 particles (data not shown), which suggests that treated sewage appears to be non-infectious even though viral RNA fragments can be detected. Inter-comparing these nine catchment areas, we plotted the estimated cumulative and the acute prevalence against the measured SARS-CoV-2 load (Figure 8 ), the latter calculated from RT-qPCR measured M-gene copy concentration ( Figure 4 ) and the actual wastewater flow Q actual on the day of sampling (Table 2) . In contrast, plotting the incidence against SARS-CoV-2 concentration did not yield a conclusive correlation (not shown), likely because the precision of the qPCR employed was not sufficient to discriminate relatively minor differences in the incidence prevailing in the studied catchment areas at the time of sampling, ranging from 30 to 174 cases per 100,000 residents (less than an order of magnitude, Figure 8C and D). cache = ./cache/cord-258595-bk35vxlr.txt txt = ./txt/cord-258595-bk35vxlr.txt === reduce.pl bib === id = cord-259593-shrd1s7r author = Qin, Zhao-ling title = siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date = 2007-06-27 pages = extension = .txt mime = text/plain words = 4603 sentences = 255 flesch = 56 summary = title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA To study M protein function, three candidate small interfering RNAs (siRNAs) corresponding to M gene sequences were designed, transcribed in vitro, and then tested for their ability to silence M protein expression. The results showed that the mean green fluorescence intensity and M RNA transcripts were significantly reduced, and that the expression of M glycoprotein was strongly inhibited in those cells co-transfected with M-specific siRNAs. These findings demonstrated that the three M-specific siRNAs were able to specifically and effectively inhibit M glycoprotein expression in cultured cells by blocking the accumulation of mRNA, which provides an approach for studies on the functions of M protein and for the development of novel prophylactic or therapeutic agents for SCoV infection. cache = ./cache/cord-259593-shrd1s7r.txt txt = ./txt/cord-259593-shrd1s7r.txt === reduce.pl bib === id = cord-031907-ilhr3iu5 author = nan title = ISEV2020 Abstract Book date = 2020-07-15 pages = extension = .txt mime = text/plain words = 200999 sentences = 11528 flesch = 44 summary = L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. cache = ./cache/cord-031907-ilhr3iu5.txt txt = ./txt/cord-031907-ilhr3iu5.txt === reduce.pl bib === id = cord-259603-bh198xgl author = Snijder, E.J. title = The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date = 2016-09-14 pages = extension = .txt mime = text/plain words = 24187 sentences = 1090 flesch = 50 summary = Reverse-genetics studies targeting specific residues in SARS-CoV nsp7 confirmed the protein's importance for virus replication (Subissi et al., 2014b) , although the impact of single point mutations was smaller than anticipated on the basis of the biochemical characterization of the RNA-binding properties of nsp7-containing protein complexes in vitro (see later). The large number of viral subunits in these complexes (Subissi et al., 2014a) , the likely requirement for host factors (van Hemert et al., 2008) , and the concept of RNA synthesis occurring in a dedicated microenvironment in the infected cell (Knoops et al., 2008; V'Kovski et al., 2015) complicate the straightforward characterization of the CoV RdRp. To reconstitute the enzyme's activities in vitro, purified recombinant nsp12 is a key reagent but, for many years, such studies were hampered by poor nsp12 expression in Escherichia coli. cache = ./cache/cord-259603-bh198xgl.txt txt = ./txt/cord-259603-bh198xgl.txt === reduce.pl bib === id = cord-261735-03hvi4el author = Rodrigues, R. title = Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date = 2011-06-14 pages = extension = .txt mime = text/plain words = 2637 sentences = 159 flesch = 60 summary = A one-step real time quantitative RT-PCR (qRT-PCR) assay was developed to detect all published Dugbe virus (DUGV) genomes of the Nairovirus genus. Frequently detected in tick-borne virus surveys in Africa (Guilherme et al., 1996) , DUGV is a tri-segmented single-stranded negative RNA enveloped virus and is considered endemic in arid regions (Burt et al., 1996) . The aim of this study was to develop a sensitive, specific and rapid one-step quantitative real time RT-PCR assay (qRT-PCR) to detect DUGV in infected cell supernatants, ticks or serum samples. The specificity was evaluated by using RNA extracted from supernatants from CCHFV, Hazara virus, Coronavirus and Influenza A virus infected cells. Among the 498 captured ticks, one Dugbe virus RNA was detected in one tick using the qRT-PCR assay (0.2%). In conclusion, a sensitive and specific qRT-PCR assay was developed to detect and quantify DUGV RNAs in infected cell supernatants, extracts from ticks and potentially sera. cache = ./cache/cord-261735-03hvi4el.txt txt = ./txt/cord-261735-03hvi4el.txt === reduce.pl bib === id = cord-259927-xh9cw9ao author = Papadopoulos, Nikolaos G. title = Promising approaches for the treatment and prevention of viral respiratory illnesses date = 2017-07-21 pages = extension = .txt mime = text/plain words = 7342 sentences = 400 flesch = 34 summary = When considering prevention or treatment of viral respiratory tract infections, potential targets include the causative pathogens themselves but also the immune response, disease transmission, or even just the symptoms. Here we provide an overview of the options and highlight some of the most promising approaches in vRTI treatment, including symptomatic medication, immunomodulatory drugs, antiviral agents, and natural products, as well as in vRTI prevention, ranging from vaccines to immunostimulators and public health policies. Early in vivo evidence suggested that azithromycin has anti-inflammatory and antiviral effects through induction of interferon-stimulated gene mRNA expression and reduced viral replication and release in patients with asthma and chronic obstructive lung disease. mAb therapies to viral infections, such as EBV (rituximab) or RSV (palivizumab), provide passive immunization and are licensed, whereas similar agents targeting influenza and other viruses are in preclinical development. cache = ./cache/cord-259927-xh9cw9ao.txt txt = ./txt/cord-259927-xh9cw9ao.txt === reduce.pl bib === id = cord-259311-ccx61owl author = Kapitula, D. S. title = Performance & Quality Evaluation of Marketed COVID-19 RNA Detection Kits date = 2020-05-01 pages = extension = .txt mime = text/plain words = 3175 sentences = 187 flesch = 53 summary = In order to provide better understanding of the Quality and performance of COVID-19 RNA detection kits on the market, we designed a system to evaluate the specificity (quantitation), sensitivity (LOD) and robustness of the kits using positive RNA and pseudovirus controls based on COVID-19 genomic sequence. At the time of submission, 23 diagnostic kits have been approved in China, of which 8 are based on quantitative Polymerase Chain Reaction (qPCR) using COVID-19 viral RNA sequence as templates and fluorescence detection. Our study aims at providing objective evaluation and comparison of the quality and performance characteristics of 8 of the currently marketed COVID-19 nucleic acid detection kits in China based on qPCR and fluorescence detection. Our study provides an elegant design to define the most important performance characteristics of the RNA detection kits for COVID-19, which are specificity (quantitative), sensitivity (LOD), and robustness. cache = ./cache/cord-259311-ccx61owl.txt txt = ./txt/cord-259311-ccx61owl.txt === reduce.pl bib === id = cord-261417-4pf5nsw2 author = Harwig, Alex title = The Battle of RNA Synthesis: Virus versus Host date = 2017-10-21 pages = extension = .txt mime = text/plain words = 7864 sentences = 443 flesch = 53 summary = Why the virus prefers to use these snRNAs as targets has yet to be experimentally established, but it has been proposed that the selective de-capping of U1 and U2 RNAs in combination with the binding of the viral NS1 protein to U6 snRNA may serve to inhibit host pre-mRNA splicing [66] . The folding of the TAR hairpin is key to the regulation of HIV-1 transcription [94] as it is used as a scaffold to recruit essential transcription factors, including the 86-101 amino acid (aa) viral trans-activator protein (Tat) [83] ( Figure 3C ). Interestingly, the human T-lymphotropic virus type 1 transcriptional activator Tax also utilizes P-TEFb for viral transcription and displaces P-TEFb from 7SK snRNP through binding CycT1 [101, 102] , suggesting that P-TEFb liberation from 7SK snRNP could be a common theme developed by different viruses to support their replication in host cells. cache = ./cache/cord-261417-4pf5nsw2.txt txt = ./txt/cord-261417-4pf5nsw2.txt === reduce.pl bib === id = cord-261532-q923xxn2 author = Chen, Huihui title = The essential adaptors of innate immune signaling date = 2012-09-21 pages = extension = .txt mime = text/plain words = 7414 sentences = 401 flesch = 45 summary = Microbial components and the endogenous molecules released from damaged cells can stimulate germ-line-encoded pattern recognition receptors (PRRs) to transduce signals to the hub of the innate immune signaling network-the adaptor proteins MyD88/TRIF/MAVS/STING/Caspase-1, where integrated signals relay to the relevant transcription factors IRF3/IRF7/NF-κB/ AP-1 and the signal transducer and activator of transcription 6 (STAT6) to trigger the expression of type I interferons and inflammatory cytokines or the assembly of inflammasomes. These receptors can recruit specific adaptor proteins, like myeloid differentiation primary response gene 88 (MyD88) or Toll/interleukin-1 receptor (TIR) domain-containing adaptor inducing IFN-β (TRIF) in the TLR pathway, mitochondrial antiviral signaling protein (MAVS) downstream of RLRs, stimulator of interferon genes (STING) in the cytosolic DNA response pathway and, cysteine aspartic protease 1 (Caspase-1) as part of the inflammasome, all of which orchestrate the host innate responses, through activation of transcriptional factors such as nuclear factor κB (NF-κB), activator protein 1 (AP-1) and interferon regulatory factors (IRFs), to trigger the production of type І interferons (IFNs), inflammatory cytokines and chemokines. cache = ./cache/cord-261532-q923xxn2.txt txt = ./txt/cord-261532-q923xxn2.txt === reduce.pl bib === id = cord-262592-0rdiosxd author = Cuevas, José M. title = Human norovirus hyper-mutation revealed by ultra-deep sequencing date = 2016-04-17 pages = extension = .txt mime = text/plain words = 5828 sentences = 276 flesch = 54 summary = This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. Based on the sequence context of the observed changes, we propose that NoV hypermutation might be driven by ADAR-mediated editing of the viral genomic RNA of either polarity during replication. We used 16 stool samples from patients acutely infected with NoV GII.4 to amplify by RT-PCR a 386-base region encompassing nucleotides 1 to 386 of the VP1 gene (reference sequence: GenBank JX459908; Fig. 1A ). After 48 h incubation, total RNA was extracted from cells, residual DNA was removed with DNAse I, a specific primer annealing to the minus-strand of the VP1 capsid gene was used for reverse transcription, and high-fidelity PCR amplification of a region encompassing positions 19 to 323 of the VP1 gene (305 bases, although only the 266 bases excluding primer regions Fig. 1 . cache = ./cache/cord-262592-0rdiosxd.txt txt = ./txt/cord-262592-0rdiosxd.txt === reduce.pl bib === id = cord-259233-smmhhroe author = de Armas‐Rillo, Laura title = Membrane dynamics associated with viral infection date = 2016-01-28 pages = extension = .txt mime = text/plain words = 7086 sentences = 374 flesch = 40 summary = Several RNA viruses induce the formation of these autophagosome-like vesicles (also referred to as DMVs) to enhance viral replication and non-lytic egression, such as poliovirus and CVB3, HIV-1 and HCV. Indeed, autophagosome-like vesicles may represent a trafficking pathway for these viruses, connecting to multivesicular bodies (MVBs), and assuring virus assembly and budding at the cell surface while protecting them from intrinsic antiviral factors and immune responses. Trogocytosis involves the exchange of cell surface membrane patches that may contain receptor clusters associated to viral particles, while exosomes are vesicles formed from MVBs that could participate in viral infection and spreading between cells of the Alphavirus group of this family [12] , couple their RNA synthesis to endosome and lysosome membranes modified by the association of virus specific components. It remains unclear how proteins from distinct viruses and host cells use the same intracellular membrane compartments or events (e.g. autophagy) to achieve viral replication, without affecting important cellular processes. cache = ./cache/cord-259233-smmhhroe.txt txt = ./txt/cord-259233-smmhhroe.txt === reduce.pl bib === id = cord-261160-g92zhv19 author = Rowland, Raymond R.R title = Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date = 2003-10-30 pages = extension = .txt mime = text/plain words = 6383 sentences = 322 flesch = 48 summary = title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero Even though PRRSV-specific antibody appears as early as 5 days post-infection and is followed by serum neutralizing activity and cell-mediated immunity Molitor, 1997, 1999; Rowland et al., 1999 Rowland et al., , 2001 persistently infected pigs can continue to shed virus. The purpose of this study was to further understand persistent infection in congenitally infected pigs by characterizing the course of clinical disease, sites of virus replication and the capacity to transmit virus in a group of pigs exposed to PRRSV in utero. Analysis of virus and antibody in blood and/or umbilical cords from the 28 live neonates showed that at least 20 or 74% were virus isolation (VI) or RT-PCR positive for PRRSV at the time of farrowing indicating that in utero infection was successful. cache = ./cache/cord-261160-g92zhv19.txt txt = ./txt/cord-261160-g92zhv19.txt === reduce.pl bib === id = cord-260225-bc1hr0fr author = Sirpilla, Olivia title = SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date = 2020-07-20 pages = extension = .txt mime = text/plain words = 8918 sentences = 582 flesch = 44 summary = Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). cache = ./cache/cord-260225-bc1hr0fr.txt txt = ./txt/cord-260225-bc1hr0fr.txt === reduce.pl bib === id = cord-260042-cs0wp99n author = Khan, Samiullah title = Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date = 2019-04-01 pages = extension = .txt mime = text/plain words = 6931 sentences = 362 flesch = 47 summary = The present study aimed to: a) determine mitochondrial counts in the cells of oviduct segments in laying hens at different time-points of egg formation in relation to the requirement of energy for egg production during IBV challenge; b) to determine the expression of nuclear DNA encoded genes in the shell gland to gain insights into their responses to IBV infection and time-points of egg-shell formation. Based on the lack of significant differences in mitochondrial count in the cells between the challenged and control groups for the magnum and isthmus, we focused further on shell gland tissue and studied the expression level of genes involved in mitochondrial density, biogenesis and fission. The lack of any significant difference in the relative expression levels of all of the genes except SDHA, between the control and IBV T challenged groups, may indicate that mitochondrial function may have been enhanced and thus overall egg quality may not have been affected by fewer mitochondria in the shell gland cells of IBV T infected hens. cache = ./cache/cord-260042-cs0wp99n.txt txt = ./txt/cord-260042-cs0wp99n.txt === reduce.pl bib === id = cord-260168-rb7j94dh author = Gu, Jiang title = H5N1 infection of the respiratory tract and beyond: a molecular pathology study date = 2007-09-27 pages = extension = .txt mime = text/plain words = 6291 sentences = 369 flesch = 51 summary = Negative controls also included an unrelated antisense probe against the fragment of the polymerase gene (R1AB) of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 20 as well as H5N1 in-situ hybridisation probes to tissues (including lung and tracheal) obtained from seven adults who died from infectious lung diseases other than H5N1 infl uenza (four, SARS; one, purulent bronchitis; two, pneumonia), one adult who died from a non-infectious disease (gastric ulcer), one pregnant woman who died from an amniotic embolism, and one aborted fetus. Presence of viral sequences and antigens in the CNS is consistent with the recent isolation of H5N1 virus from cerebrospinal fl uid of a boy who died from encephalitis 6 with neurological symptoms commonly seen in patients with H5N1 infl uenza (Gao Zh, unpublished), including the two cases in this study. cache = ./cache/cord-260168-rb7j94dh.txt txt = ./txt/cord-260168-rb7j94dh.txt === reduce.pl bib === id = cord-262318-qpztmdnw author = Guo, Jingxu title = In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors date = 2020-07-16 pages = extension = .txt mime = text/plain words = 6348 sentences = 319 flesch = 58 summary = In this work we have crystallised the protease in its native form with an unperturbed catalytic triad and have conducted crystal-based fragment screening of 844 compounds with the aim of discovering novel inhibitory functional groups which have the potential to be developed as therapeutic agents, either on their own or through chemical coupling. Interestingly, the β-hairpin formed by β9 and β10, which is involved in binding the N-terminal side of the substrate peptide, adopts an appreciably different conformation from that observed in an earlier inhibitor-complexed structure ( The SV3CP enzyme has approximately 90 % sequence identity with other GI noroviral 3C proteases and an identity of the order of 68 % with the enzyme from the GII genotype. The X-ray structure of the Southampton virus 3CL pro has been determined at 1.3 Å resolution in a crystal form that has allowed fragment-screening for novel inhibitors to be undertaken at similar resolutions. cache = ./cache/cord-262318-qpztmdnw.txt txt = ./txt/cord-262318-qpztmdnw.txt === reduce.pl bib === id = cord-260782-1lm8tzbc author = Giles, Julia title = Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date = 2018-07-14 pages = extension = .txt mime = text/plain words = 6575 sentences = 319 flesch = 43 summary = title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) The aim of the current study was to describe histological lesions and viral RNA levels in tissues from possum experimentally infected with WPDV. Histology of brain, kidney and liver tissue from wobbly possum disease virus (WPDV)-infected possums. Whilst RNA levels in selected tissues (liver, spleen, brain and kidney) from WPD-infected possums have been previously reported (Dunowska et al., 2013) , we have expanded both the number of possums and the tissue types tested to provide a greater understanding of the tissues targeted by the virus in-vivo. Detection of moderate to high levels of viral RNA from the sera of all but one infected possum in this study also supports the use of blood or serum samples for detection of WPDV. cache = ./cache/cord-260782-1lm8tzbc.txt txt = ./txt/cord-260782-1lm8tzbc.txt === reduce.pl bib === id = cord-260250-t48y27wg author = Decaro, Nicola title = Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date = 2004-05-07 pages = extension = .txt mime = text/plain words = 3322 sentences = 157 flesch = 51 summary = A TaqMan(®) fluorogenic reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed for the detection and quantitation of canine coronavirus (CCoV) RNA in the faeces of naturally or experimentally infected dogs. The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. As shown in Table 2 , the detec-tion limit of the TaqMan RT-PCR was 1-2 log higher than that of conventional RT-PCR, ranging around 10 1 copies/l and 10 −1.50 TCID 50 /50 l for standard RNA and CCoV strain, respectively, with a detection rate of 100% for each positive dilution. The results of the conventional amplification and real-time analysis carried out on the faecal samples of the CCoV experimentally infected dog are summarized in Fig. 3 . cache = ./cache/cord-260250-t48y27wg.txt txt = ./txt/cord-260250-t48y27wg.txt === reduce.pl bib === id = cord-259671-7de21oaq author = Madhugiri, Ramakanth title = RNA structure analysis of alphacoronavirus terminal genome regions date = 2014-12-19 pages = extension = .txt mime = text/plain words = 11161 sentences = 568 flesch = 50 summary = Overall, the conservation pattern identified for 5′ and 3′-terminal RNA structural elements in the genomes of alphaand betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements. Other internal cis-acting elements include specific RNA signals required for genome packing, which have been characterized in a small number of coronaviruses Escors et al., 2003; Morales et al., 2013; Penzes et al., 1994) , and a complex RNA pseudoknot structure located in the ORF1a-ORF1b overlap region that mediates a (−1) ribosomal frameshift event and thus controls the expression of the second large ORF on the coronavirus genome RNA (ORF1b) (Brierley et al., 1987 (Brierley et al., , 1989 de Haan et al., 2002; Namy et al., 2006) . cache = ./cache/cord-259671-7de21oaq.txt txt = ./txt/cord-259671-7de21oaq.txt === reduce.pl bib === id = cord-260452-js4nr4d8 author = Yu, Junyang title = Activation and Role of NACHT, LRR, and PYD Domains-Containing Protein 3 Inflammasome in RNA Viral Infection date = 2017-10-31 pages = extension = .txt mime = text/plain words = 4082 sentences = 222 flesch = 34 summary = Both the pathogen-associated molecule pattern derived from virions and intracellular stress molecules involved in the process of viral infection lead to activation of the NLRP3 inflammasome, which in turn triggers inflammatory responses for antiviral defense and tissue healing. IL-1β and IL-18 serve to activate myriad downstream cell responses, and orchestrate innate and adaptive immunity through MyD88/IRAK4/TRAF6-mediated NF-κB signaling and the JNK/p38 mitogen-activated protein kinase pathways (60-63), which may represent key events for the NLRP3 inflammasome-dependent antiviral defense. In BV-2 mouse microglia cells infected by Japanese encephalitis virus, the NLRP3 inflammasome induces production of IL-1β and IL-18 rapidly (within 3 h of exposure) and of TNF-α, CCL2, and IL-6 later (within 6 h after exposure) (40) ; the findings suggest that the NLRP3dependent protective inflammatory response is a very early phase innate immune response against RNA viral infection. cache = ./cache/cord-260452-js4nr4d8.txt txt = ./txt/cord-260452-js4nr4d8.txt === reduce.pl bib === id = cord-261110-cnj0e0s9 author = Debarnot, Claire title = Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date = 2011-02-25 pages = extension = .txt mime = text/plain words = 2656 sentences = 169 flesch = 64 summary = This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. We present X-ray diffraction data from these SARS-CoV nsp10-nsp16 crystals. The purified SARS-CoV nsp10-nsp16 complex was analyzed by 12% SDS-PAGE and stained using Coomassie Blue. Lane MK, molecular-weight markers; lane 1, 2 mg nsp10-nsp16 protein complex eluted from the Strep-Tactin column. The nsp10-nsp16 complex eluted from the Strep-Tactin column was analyzed on a 16/60 S200 gel-filtration column and the elution of protein and nucleic acid was followed by measuring the absorption at 280 nm (blue) and 260 nm (orange), respectively. The purified SARS-CoV nsp10-nsp16 complex was loaded onto a 4-12% NuPAGE gel and stained using Coomassie Blue. We have crystallized a complex of the SARS-CoV nsp10 and nsp16 proteins. cache = ./cache/cord-261110-cnj0e0s9.txt txt = ./txt/cord-261110-cnj0e0s9.txt === reduce.pl bib === id = cord-262923-kgzbd6w3 author = Koo, Bonhan title = CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases date = 2018-11-10 pages = extension = .txt mime = text/plain words = 3628 sentences = 212 flesch = 48 summary = Here, we report the development of an improved molecular diagnostics tool that utilizes CRISPR/dCas9-mediated biosensor that couples a nuclease inactivated Cas9 (dCas9) and single microring resonator biosensor, enables label-free and real-time detection of pathogenic DNA and RNA. In this study, we developed an improved diagnostic tool by combining a CRISPR/dCas9 and an isothermal diagnostic approach based on SMR biosensor for simultaneous nucleic acid (RNA and DNA) amplification and detection with speed as well as high sensitivity and specificity. For simultaneous amplification and detection of nucleic acid, sequence specific primer of target was immobilized to the surface of the SMR biosensor and dCas9 RNP was in reaction chamber with single temperature for isothermal reaction with RPA. To achieve sensitive detection with dCas9 RNP on SMR biosensor, we constructed guide RNAs (gRNAs) targeting two tick-borne pathogens that have substantially overlapping clinical presentations: Orientia tsutsugamushi, the causative agent of scrub typhus (ST), and bunyavirus, the causative agent of severe fever with thrombocytopenia syndrome (SFTS) (Fig. 1B) . cache = ./cache/cord-262923-kgzbd6w3.txt txt = ./txt/cord-262923-kgzbd6w3.txt === reduce.pl bib === id = cord-262841-nr42rs8f author = Li, Lanjuan title = SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date = 2003-12-31 pages = extension = .txt mime = text/plain words = 2124 sentences = 107 flesch = 58 summary = Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, "replicative intermediates") and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR). Although the virus has been identified Abbreviations: BNIBernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany; BSL3biosafety level 3; CoVcoronavirus; MHVmouse hepatitis virus; PCRpolymerase chain reaction; minus -RNAreplicative negative-stranded RNA; plus -RNApositive-stranded genomic RNA; RTreverse transcription; SARSsevere acute respiratory syndrome; SCAsodium citrate anticoagulant. In order to evaluate (i) whether SARS-CoV can infect peripheral blood mononuclear cells (PBMCs) of infected persons, (ii) whether the virus can replicate in their PBMCs, and (iii) to reveal any dynamic changes to the virus during the course of the disease, we carried out follow-up investigations on the plusand minus-RNA forms in SARS patients. cache = ./cache/cord-262841-nr42rs8f.txt txt = ./txt/cord-262841-nr42rs8f.txt === reduce.pl bib === id = cord-260695-qwepi0we author = Postler, Thomas S. title = Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date = 2017-11-01 pages = extension = .txt mime = text/plain words = 6315 sentences = 377 flesch = 55 summary = Of the host-encoded lncRNAs reported to be differentially expressed upon HIV-1 infection, only nuclear enriched abundant transcript 1 (NEAT1) and noncoding repressor of nuclear factor of activated T cells (NRON) have been functionally characterized (Lazar et al., 2016) . In this report, we describe a meta-analysis of two independent RNA-seq studies of HIV-1-infected cells and show that, unexpectedly, only three lncRNAs are differentially expressed in both of these datasets (Chang et al., 2011; Mohammadi et al., 2013) . To obtain an unbiased understanding of any changes in lncRNA expression during HIV-1 infection, we performed a meta-analysis of two independent RNA-seq studies conducted by two different groups using two different virus strains ( Supplementary Fig. S1 ) (Chang et al., 2011; Mohammadi et al., 2013) . To validate the results of the in silico analysis of lnc173 expression, we isolated RNA from 4 human cell lines and probed for the presence of both transcript variants by quantitative RT-PCR (qRT-PCR; Fig. 3A -D). cache = ./cache/cord-260695-qwepi0we.txt txt = ./txt/cord-260695-qwepi0we.txt === reduce.pl bib === id = cord-262753-jld1ygxt author = Neidermyer, William J. title = Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date = 2019-06-21 pages = extension = .txt mime = text/plain words = 9235 sentences = 461 flesch = 46 summary = Analysis of sequence reads in the different fractions shows >60% of total cytoplasmic and polysome-associated reads map to the 5 viral genes by 6 hours post-infection, a time point at which robust host cell translational shut-off is observed. The cellular mRNAs that remain most polysome-associated following infection had longer half-lives, were typically larger, and were more AU rich, features that are shared with the viral mRNAs. Several of those mRNAs encode proteins known to positively affect viral replication, and using chemical inhibition and siRNA depletion we confirm that the host chaperone heat shock protein 90 (hsp90) and eukaryotic translation initiation factor 3A (eIF3A)—encoded by 2 such mRNAs—support viral replication. In the present study, we interrogate global mRNA translation in VSV infected cells using RNAseq analysis of the cytoplasmic mRNA transcriptome, and parallel sequencing of polysome-associated mRNAs. We obtain support for the model that an overabundance of viral mRNA contributes to host shut-off by leading to a re-distribution of cellular ribosomes onto viral mRNA. cache = ./cache/cord-262753-jld1ygxt.txt txt = ./txt/cord-262753-jld1ygxt.txt === reduce.pl bib === id = cord-263699-gosqpg3k author = Martínez, José L. title = Role of the Guanine Nucleotide Exchange Factor GBF1 in the Replication of RNA Viruses date = 2020-06-24 pages = extension = .txt mime = text/plain words = 12329 sentences = 463 flesch = 42 summary = GBF1 has been shown not only to facilitate the intracellular traffic of different viral and cellular elements during infection, but also to modulate the replication of viral RNA, the formation and maturation of viral replication complexes, and the processing of viral proteins through mechanisms that do not depend on its canonical role in intracellular transport. In addition to the role of GBF1 in the transport of cellular and viral proteins relevant for RNA replication and viral assembly, it has also been observed that this factor can regulate the lipid composition of the membranous web induced by HCV. The role of GBF1 has been found, principally, to depend on its ability to activate distinct Arf proteins, to regulate different transport pathways that permit the communication between the viral replication organelles and cellular organelles (ER and LDs) involved in virus infection. cache = ./cache/cord-263699-gosqpg3k.txt txt = ./txt/cord-263699-gosqpg3k.txt === reduce.pl bib === id = cord-260345-ugd8kkor author = Giles, Ian G. title = A compendium of reviews in biochemistry and molecular biology published in the first half of 1992 date = 1992-12-31 pages = extension = .txt mime = text/plain words = 5327 sentences = 701 flesch = 45 summary = 203, sodium dodecyl-sulfate.; ted blood-cells; phosphoenolpyruvate carboxylase activity; nucleotide-linked dehydrogenases; alkaline-phosphatase isoenzymes; pathogenesis-related proteins; cr-L-fucosidase; polyactylamide-gel; produce phosphate; general-method. low-density~l&protein; high-performance liquid; chrcmatogmphy mass spectmmetry; chicken vitellogam gene; thin-layer chmmatography; apolipoprotein-VLDL-II; fatty-acid composition; laying turkey hens; egg-yolk; plasma-lipoproteins. human-skin fibroblests; IGF binding-protein; messenger ribonucleic-acid; cooh-teminal truncation; monoclonal-antibody; endothelial-cells; factor receptoc amniotic-fluid; DNA-synthesis; rat-heart. factor-binding-protein; erythroid colony formation; cultured human-tibroblasts; factor messenger-RNA, N-terminal sequence; fetal bovine serum; IGF-I; somatomedin C, clinical-applicstians; stimulating factors. shon-hved protein; dependent pmteolytic system; ubiquitin-conjugating enzyme; repair gene ra&, Escherichia coli; transfer RNA; Sacclurroqces cercvisiue; endoplasmic-reticulum; cell-cycle; amino-acid. polymense chain-reaction; fragment length polymorphisms; dependent diabetes-mellitus; sickle-cell anemia; factor-M gene; enzymatic AMPlificatiat; genomic DNA; mutations; sequence; diagnosis; predisposition; genetics. T-cell receptor; messenger-RNA degradation; gamma-delta; stress proteins; antigen-receptor, lymphocytes-T; ~ycobactcrium fuberc&arir. Wiskott-Aldrich syndrome; heat-shock proteins; receptor-delta; ataxia telangiectasia; transgenic mice; lymphocytes T; bearing cells; recognition; expression; incmase. human granulocyte-macmphage; protein kinase-c; recombinant human interleukin-3; cell growth-factor, murine bone-marrow; express functional receptors; acute lymphocytic-leukemia; GTPase-activating pm&n; factor-independent growth. cache = ./cache/cord-260345-ugd8kkor.txt txt = ./txt/cord-260345-ugd8kkor.txt === reduce.pl bib === id = cord-263033-4790dhc5 author = Laptev, I. G. title = Posttranscriptional modification of messenger RNAs in eukaryotes date = 2015-12-11 pages = extension = .txt mime = text/plain words = 6792 sentences = 437 flesch = 58 summary = The review considers posttranscriptional modification of eukaryotic mRNA, focusing on the major modified nucleotides, the role they play in the cell, the methods to detect them, and the enzymes responsible for modification. Regions distant from the mRNA ends may contain N6 methyladenosine (m 6 A), 5 methylcytidine (m 5 C), pseudouridine (Ψ), and inosine (I), which were believed to play only a minor role because their pro portion in cell RNA is extremely low as compared with the standard nucleotides. In the case of eukaryotic mRNAs, the method is suitable for probing the adenosine methylation status in a particular site of a particular RNA in various cell growth conditions. A method known as site specific cleavage and radioactive labeling followed by ligation assisted extrac tion and thin layer chromatography (SCARLET) [23] makes it possible to establish whether adenosine is methylated in a given position of a given molecule and to estimate the proportion of modified and unmodi fied nucleotides (Fig. 2) . cache = ./cache/cord-263033-4790dhc5.txt txt = ./txt/cord-263033-4790dhc5.txt === reduce.pl bib === id = cord-263433-oldy0gta author = Barriocanal, Marina title = Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin date = 2015-01-09 pages = extension = .txt mime = text/plain words = 8773 sentences = 497 flesch = 50 summary = As the ISGs described to date are coding genes, we sought to determine whether IFN also regulates the expression of long non-coding ISGs. To this aim, we used RNA sequencing to analyze the transcriptome of control and HuH7 cells treated with IFNα2. To address the issue of whether IFN could also regulate expression of lncRNAs, which may play key roles in the antiviral response, we analyzed the transcriptome of cells treated or not with IFNα2 by RNA sequencing (RNASeq). The results showed that at later times post-infection with the influenza virus lacking NS1, there was increased expression of lncISG15, lncBST2/BISPR, and their neighboring coding transcripts (Figure 3A) . To discriminate whether lncISG15 and lncBST2/BISPR are induced directly by the JAK/STAT signaling pathway or by a secondary wave of the IFN response, we evaluated the expression of these lncRNAs and their coding neighboring genes in HuH7 or A549 cells incubated or not with the JAK/STAT inhibitor ruxolitinib. cache = ./cache/cord-263433-oldy0gta.txt txt = ./txt/cord-263433-oldy0gta.txt === reduce.pl bib === id = cord-262776-6k7tcgfs author = Burnouf, Thierry title = Assessment of the viral safety of antivenoms fractionated from equine plasma date = 2004-09-30 pages = extension = .txt mime = text/plain words = 8211 sentences = 417 flesch = 43 summary = Analysis of production parameters indicate that acid pH treatments and caprylic acid precipitations, which have been validated for the manufacture of some human IgG products, appear to provide the best potential for viral inactivation of antivenoms. Among those, caprylic acid and low pH treatments, both of which are commonly used also for the purification of antivenom IgG, have been shown to contribute to the viral safety of human plasma IgG products as described below. It should be kept in mind that treatment of whole plasma or crude fractions, as is the case for equine antivenoms production, may lead to lower rate and kinetics of viral inactivation, due to the high endogenous lipid content, as found in a study that evaluated the virucidal effect of sodium oleate [85] . However, a comparison with validated manufacturing processes used for human IgG clearly indicates that at least two widely used antivenom production steps, caprylic acid treatment and low-pH incubation, are likely to contribute in a robust manner to viral safety, at least against enveloped viruses. cache = ./cache/cord-262776-6k7tcgfs.txt txt = ./txt/cord-262776-6k7tcgfs.txt === reduce.pl bib === id = cord-261279-6mef38eo author = Chu, Daniel K W title = Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date = 2020-01-31 pages = extension = .txt mime = text/plain words = 2971 sentences = 178 flesch = 54 summary = RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). In this study, we report the development of RT-PCR assays to detect this novel virus in human clinical specimens. Two monoplex real-time RT-PCR assays targeting the ORF1b and N gene regions of 2019-nCoV were designed based on the first publicly available sequence in Genbank (Accession number: MN908947). Viral RNA from cells infected by SARS coronavirus or DNA plasmids containing the target sequences were positive in the assays as expected. In addition, the N gene RT-PCR assay was found to be more sensitive in detecting 2019-nCoV RNA in the studied clinical samples. cache = ./cache/cord-261279-6mef38eo.txt txt = ./txt/cord-261279-6mef38eo.txt === reduce.pl bib === id = cord-263239-andje0wu author = Dorobantu, Cristina M. title = Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus date = 2015-09-25 pages = extension = .txt mime = text/plain words = 8997 sentences = 455 flesch = 45 summary = Here we show that cardioviruses manipulate another PI4K, namely the ER-localized phosphatidylinositol 4-kinase III alpha (PI4KA), to generate PI4P-enriched ROs. By siRNA-mediated knockdown and pharmacological inhibition, we demonstrate that PI4KA is an essential host factor for EMCV genome replication. To corroborate that PI4KA activity is required for the step of viral genome replication, we performed a time-of-addition experiment in which AL-9 was added to the cells at different time points after infection with RLuc-EMCV. The Picornavirus EMCV Converges on the Host Lipid Pathway Used by HCV localized throughout the cytoplasm and at the Golgi, OSBP was mainly found at ROs in infected cells, where it largely colocalized with 3AB ( Fig 6D, Pearson's correlation coefficient = 0.71). Finally, data are presented suggesting that the OSBP-mediated exchange of PI4P and cholesterol at RO-MCSs is critical for EMCV genome replication and the global organization of ROs. Membrane alterations in the cytoplasm of cardiovirus-infected cells were already observed decades ago by electron microscopy [37, 38, 63] . cache = ./cache/cord-263239-andje0wu.txt txt = ./txt/cord-263239-andje0wu.txt === reduce.pl bib === id = cord-262844-qeheeqe3 author = Xia, Xuhua title = Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date = 2020-04-14 pages = extension = .txt mime = text/plain words = 3305 sentences = 204 flesch = 53 summary = The zinc finger antiviral protein (ZAP, known as ZC3HAV1 in mammals or hZAP in human), a key component in mammalian interferon-mediated immune response, binds specifically to CpG dinucleotides in viral RNA genomes via its RNA-binding domain (Meagher et al., 2019) . If a coronavirus infects a different host tissue with different ZAP abundance, then its RNA genome will experience different selection pressure against its CpG. The most striking pattern in Fig. 1 is an isolated but dramatic shift in the lineage leading to BatCoV RaTG13 which was reported (Zhou et al., 2020) (Theys et al., 2018) , but also in experimentally CpG dinucleotide-enriched viral genomes (Antzin-Anduetza et al., 2017; Burns et al., 2009; Fros et al., 2017; Trus et al., 2019; Tulloch et al., 2014; Wasson et al., 2017) . To search for a mammalian host with the potential to select viral lineages with low Poder, 2011; Pratelli, 2006) , have genomic ICpG and GC% values similar to those observed in SARS-CoV-2 and BatCoV RaTG13 (Fig. 3A) . cache = ./cache/cord-262844-qeheeqe3.txt txt = ./txt/cord-262844-qeheeqe3.txt === reduce.pl bib === id = cord-263468-996kl9jz author = Cattaneo, Roberto title = Biased hypermutation and other genetic changes in defective measles viruses in human brain infections date = 1988-10-21 pages = extension = .txt mime = text/plain words = 7642 sentences = 306 flesch = 50 summary = Abstract We assessed the alterations of viral gene expression occurring during persistent infections by cloning full-length transcripts of measles virus (MV) genes from brain autopsies of two subacute sclerosing panencephalitis patients and one measles inclusion body encephalitis (MIBE) patient. One of these nucleotide substitutions and one deletion resulted in alteration of the reading frames of two fusion genes, as confirmed by in vitro translation of synthetic mRNAs. One cluster of mutations was exceptional; in the matrix gene of the MIBE case, 50% of the U residues were changed to C, which might result from a highly biased copying event exclusively affecting this gene. most likely based on one hand on the low fidelity of RNA To assess the variability in strains of lytic viruses, and replication (Domingo et al., 1978; for review see Steinto estimate the number of mutations introduced during hauer and Holland, 1987) and on the other hand on the persistence, we counted the differences of lytic and perlow selective pressure exerted on viral genomes in nonsistent viruses from a consensus as defined above. cache = ./cache/cord-263468-996kl9jz.txt txt = ./txt/cord-263468-996kl9jz.txt === reduce.pl bib === id = cord-262282-9xh51cd1 author = Serwer, Philip title = Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date = 2020-05-15 pages = extension = .txt mime = text/plain words = 4323 sentences = 260 flesch = 57 summary = Without going into details concerning live vaccine production via eukaryotic viruses, I think it reasonable to assume that eukaryotic virus production is more difficult, more expensive and less rapid than the production of phages. However, current efforts to human-engineer improved antigens for anti-RNA virus vaccines have shown that neutralizing antibodies typically react with viral proteins that are in states that are context dependent and unstable [12, 13, 15, 20] . I take the liberty of responding here to the obvious objection that no membrane-covered, single-stranded RNA phage has ever been isolated [21] and that the pandemic viruses include influenza, Zika-type and coronaviruses, all in this category. A non-specialist observer reasonably concludes that DNA and RNA vaccines, when viewed in the context of our overall objective, are examples of type 2 strategy options. Given that eukaryotic viruses have doubling times much greater than those of phages (2-5 min for typical coliphages), meeting this objective implies that a live virus vaccine has to be already present in the environment. cache = ./cache/cord-262282-9xh51cd1.txt txt = ./txt/cord-262282-9xh51cd1.txt === reduce.pl bib === id = cord-260647-7bjhobg7 author = Coudray-Meunier, Coralie title = A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date = 2016-01-29 pages = extension = .txt mime = text/plain words = 5581 sentences = 278 flesch = 48 summary = A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The aim of this study was to develop real time RT-PCR assays for detection of a total of 19 human enteric viruses (including 3 genogroupes of norovirus and 4 coronaviruses) and two control process viruses (mengovirus and murine norovirus) generally used for monitoring the recovery of viral foodstuff extraction methods. The sensitivity of conventional qPCR assays targeting 21 viral genomes was compared to the quantitative digital RT-PCR array and to the qualitative nanofluidic real-time PCR array performed on Fluidigm's BioMark System. Similarly, by testing genomes from viruses in stools and RNA from virus production in cells, the limit of detection (LOD) as determined by RT-dPCR was respectively 1.5 to 3.4 log 10 and 1.6 to 2.1 log 10 lower than the expected copy numbers calculated via the standard curve by RT-qPCR. cache = ./cache/cord-260647-7bjhobg7.txt txt = ./txt/cord-260647-7bjhobg7.txt === reduce.pl bib === === reduce.pl bib === id = cord-266585-jfjrk9gy author = Fang, Shouguo title = An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date = 2007-02-05 pages = extension = .txt mime = text/plain words = 7152 sentences = 356 flesch = 56 summary = During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation blocks the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid (Lys) affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. To further demonstrate that the failure to rescue infectious virus from the G15526C mutant transcripts is due to a defect in subgenomic RNA transcription, the full-length clones with and without the G15526C mutation were used to generate recombinant IBV expressing the enhanced green fluorescent protein (EGFP) by replacing the 5a gene with EGFP. cache = ./cache/cord-266585-jfjrk9gy.txt txt = ./txt/cord-266585-jfjrk9gy.txt === reduce.pl bib === id = cord-263315-g7os15m1 author = Martins-da-Silva, Andrea title = Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date = 2018-01-18 pages = extension = .txt mime = text/plain words = 6975 sentences = 460 flesch = 48 summary = title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. In human and mouse plasmacytoid dendritic cells (pDCs), which are professional interferon-producing cells specialized in recognizing viral RNA and DNA through the endosomal Toll-like receptors (TLRs) TLR7 and TLR9, respectively, PLSCR1 was described as a TLR9-binding protein that plays a significant role in type-1 interferon responses in pDCs by regulating TLR9 expression and trafficking [57] . Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. cache = ./cache/cord-263315-g7os15m1.txt txt = ./txt/cord-263315-g7os15m1.txt === reduce.pl bib === id = cord-264884-ydkigome author = Villarreal, Luis P. title = The Widespread Evolutionary Significance of Viruses date = 2008-07-05 pages = extension = .txt mime = text/plain words = 23138 sentences = 1203 flesch = 47 summary = For example, common structural motifs from phage to eukaryotic DNA viruses (T4 and herpesvirus) suggest very ancient links in virus evolution that span all domains of life (see below). On an evolutionary time-scale, the majority of viral lineages tend to exist as species-specifi c persistent (aka temperate, latent, and chronic) infections in which individual hosts will be colonized by mostly silent (asymptomatic) viruses for the duration of their life . It has distinct genetic, fi tness, and evolutionary characteristics that require intimate, host (tissue)-specifi c viral strategies and precise gene functions to attain stable maintenance in the presence of immunity and to allow biologically controlled reactivation. Thus, the phycodnaviruses appear to represent a basal but diverse viral lineage that has both acute and persistent lifestyle and have some clear relationships to most large eukaryotic DNA viruses and many phage. cache = ./cache/cord-264884-ydkigome.txt txt = ./txt/cord-264884-ydkigome.txt === reduce.pl bib === id = cord-260705-huyyw5z6 author = Moshe, Adi title = Virus-Induced Aggregates in Infected Cells date = 2012-10-17 pages = extension = .txt mime = text/plain words = 5063 sentences = 265 flesch = 39 summary = During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intraand intercellular transportation. In plant cells, both RNA and DNA viruses are associated with large inclusions detected in the cytoplasm and nucleus, however, their role in virus propagation or oppositely in virus restraint is less investigated than in infected mammalian cells. In general, mammalian and plant viruses make use of aggregates as scaffolds for anchoring the replication complex, increasing the local concentration of viral and host components required for replication and assembly, and shielding the process of replication from host defense. cache = ./cache/cord-260705-huyyw5z6.txt txt = ./txt/cord-260705-huyyw5z6.txt === reduce.pl bib === id = cord-260422-z22t57ju author = Godet, Julien title = Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1 date = 2012-06-26 pages = extension = .txt mime = text/plain words = 9180 sentences = 486 flesch = 49 summary = Today's view is that RNA chaperones are nucleic acid binding proteins present in all living organisms, including viruses, where they Abbreviations: HIV-1, human immunodeficiency virus-type I; NCp7, nucleocapsid protein of HIV-1; ZF, zinc finger; NA, nucleic acid; TAR, transactivation response element; PBS, primer binding site; AA, amino acids. The substantial nucleic acid chaperone properties exhibited by Tat may account for its ability to promote the annealing of the primer tRNA to the viral RNA (Kameoka et al., 2002) and intervene in the first strand transfer (Boudier et al., 2010) and by this way, to stimulate RTion as does NCp7 (Harrich et al., 1997; Ulich et al., 1999; Apolloni et al., 2007) . Human immunodeficiency virus Type 1 nucleocapsid protein (NCp7) directs specific initiation of minusstrand DNA synthesis primed by human tRNA(Lys3) in vitro: studies of viral RNA molecules mutated in regions that flank the primer binding site cache = ./cache/cord-260422-z22t57ju.txt txt = ./txt/cord-260422-z22t57ju.txt === reduce.pl bib === id = cord-260708-l9w5jhsw author = Lasecka, Lidia title = The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date = 2013-12-11 pages = extension = .txt mime = text/plain words = 10690 sentences = 446 flesch = 46 summary = The nairoviruses are a rapidly emerging group of tick-borne bunyaviruses that includes pathogens of humans (Crimean-Congo hemorrhagic fever virus [CCHFV]) and livestock (Nairobi sheep disease virus [NSDV], also known as Ganjam virus), as well as a large number of viruses for which the normal vertebrate host has not been established. As several potential cysteine-protease-like cleavage sites have been identified in the L protein sequence of nairoviruses [94] and some viral proteins containing an OTU-like protease domain have also been shown to undergo autoproteolytic cleavage to generate multiple mature proteins, e.g., the replicase of BlScV [98] , it has been suggested that the L proteins of nairoviruses may also be autoproteolytically cleaved into an active RNA polymerase and protein(s) with additional function [85] . Role of actin filaments in targeting of Crimean Congo hemorrhagic fever virus nucleocapsid protein to perinuclear regions of mammalian cells Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin Induction of caspase activation and cleavage of the viral nucleocapsid protein in different cell types during Crimean-Congo hemorrhagic fever virus infection cache = ./cache/cord-260708-l9w5jhsw.txt txt = ./txt/cord-260708-l9w5jhsw.txt === reduce.pl bib === id = cord-262347-ejhz9rra author = Kappes, Matthew A. title = PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity date = 2015-03-07 pages = extension = .txt mime = text/plain words = 10170 sentences = 498 flesch = 42 summary = The nidovirus order constitutes a group of singlestranded positive-sense RNA viruses which share a hallmark replication/transcription strategy, similar genomic organization, and a defining set of genetic elements, but differ in host species and range, disease phenotype, virion morphology, cellular tropism, genomic size and encoded content . It has been shown that the EAV replicase proteins (ORF1a/b) are sufficient to support viral replication (Molenkamp et al., 2000b) , but that infectivity is dependent on the presence of the structural genes encoded at the 3 0 -end of the arterivirus genome Molenkamp et al., 2000b; Verheije et al., 2002) . Leader-body junction sequence of the viral subgenomic mRNAs of porcine reproductive and respiratory syndrome virus isolated in Taiwan Molecular cloning and nucleotide sequencing of the 3 0 -terminal genomic RNA of the porcine reproductive and respiratory syndrome virus Comparison of the 5 0 leader sequences of North American isolates of reference and field strains of porcine reproductive and respiratory syndrome virus (PRRSV) cache = ./cache/cord-262347-ejhz9rra.txt txt = ./txt/cord-262347-ejhz9rra.txt === reduce.pl bib === id = cord-264159-e9071tyv author = Lin, Weikang Nicholas title = The Role of Single-Cell Technology in the Study and Control of Infectious Diseases date = 2020-06-10 pages = extension = .txt mime = text/plain words = 13339 sentences = 580 flesch = 36 summary = In pathophysiological studies of infectious disease, single-cell omics offer excellent spatial-temporal resolution that help to not only reconstruct the uneven subcellular distribution of pathogen across the entire host cell population, but also reveal the sequence of immune events accompanied by the change of immune cell profiles. Moreover, viral mutation can be correlated with host gene expression status at the single-cell level to further investigate their potential mutual effect on one another throughout the course of infection and reveal the dynamic host responses and pathogen adaptations in the progression of infection [32] . Technologies that enable the simultaneous measurement of multiple parameters facilitate high-resolution characterization of transcripts and protein at the single-cell level and boost our understanding of how host immune responses are initiated and orchestrated against infection. As covered earlier in this review, the main applications of scRNA-seq in infectious disease study comprise of the following: (1) studying effect of host cell heterogeneity on infection, (2) identifying host immune responses, and (3) antibody discovery. cache = ./cache/cord-264159-e9071tyv.txt txt = ./txt/cord-264159-e9071tyv.txt === reduce.pl bib === id = cord-263334-wwkdum94 author = Li, Chen title = Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date = 2014-01-20 pages = extension = .txt mime = text/plain words = 7683 sentences = 423 flesch = 54 summary = BHK-21 cells transfected with the DDX3 shRNA were infected with JEV (MOI¼ 0.01) for 48 h, Viral titers determined by plaque formation assay at 48 hpi. (F) BHK-21 cells transfected with different amounts of DDX3 shRNA plasmid were infected with JEV (MOI ¼0.01), 48 h later, the amount of virus released into the medium was determined by plaque formation assay. In order to determine whether cellular DDX3 is involved in virus assembly or release, the BHK-21 cells were transfected with DDX3 shRNA plasmid before being infected with JEV (MOI ¼0.01). The virus titers were detected 2 days later by plaque formation assay, the results showed that overexpression of DDX3r-K230E, DDX3r-S382L and the control plasmid pcDNA3.1 after DDX3 knockdown resulted in the reduction of JEV replication for 13-fold (p o0.01), 12-fold (p o0.01) and 15-fold (p o0.01). The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3′ UTR cache = ./cache/cord-263334-wwkdum94.txt txt = ./txt/cord-263334-wwkdum94.txt === reduce.pl bib === id = cord-265855-zf52vl11 author = Mayor-Ibarguren, Ander title = A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date = 2020-07-10 pages = extension = .txt mime = text/plain words = 5324 sentences = 283 flesch = 47 summary = Zinc deficiency may increase ACE-2 receptor activity on type 2 pneumocytes and other cells that are infected by SARS-COV-2, mainly in the lower respiratory tract. Although there are no specific data regarding zinc in this pathway for SARS-CoV-2, zinc may limit infection through upregulation of IFN-alpha production and an increase in its antiviral activity (77, 78) . Thus, patients with IL-6-174 GG polymorphism (C-carriers) may be susceptible to developing a severe infection due to SARS-CoV-2, leading to an increase in IL-6 levels that produce a cytokine storm related to impaired zinc homeostasis. We believe there is enough evidence to further investigate how zinc status or homeostasis is involved in the pathogenesis of severe illness produced by SARS-CoV-2 infection, and its potential role as an active treatment should be assessed in clinical trials. cache = ./cache/cord-265855-zf52vl11.txt txt = ./txt/cord-265855-zf52vl11.txt === reduce.pl bib === id = cord-263157-8jin6oru author = Martínez, Miguel Angel title = Progress in the Therapeutic Applications of siRNAs Against HIV-1 date = 2008-10-13 pages = extension = .txt mime = text/plain words = 9234 sentences = 466 flesch = 45 summary = Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Importantly, this study made the extraordinary demonstration that cell transfection of synthetic 21 base pairs (bp) short interfering RNA (siRNA) duplexes can mediate RNAi in a sequence-specific manner; this finding enabled the specific regulation of gene expression in a variety of biological systems, including diseased cells. Soon after the demonstration that synthetic siRNAs were able to induce the RNAi mechanism in mammalian cells (15) , several studies reported that HIV-1 gene expression and replication ex vivo could be inhibited by virus-specific synthetic siR-NAs (16 22) or expressed siRNAs (16, 18) that were targeted to early or late phases of virus replication. To counteract this strategic weakness, co-expression of multiple siRNAs or shRNAs that target conserved RNA sequences could reduce the emergence of single siRNA-resistant virus with a comparable effect to that achieved by the multiple anti-HIV drug combination approach employed by HAART. cache = ./cache/cord-263157-8jin6oru.txt txt = ./txt/cord-263157-8jin6oru.txt === reduce.pl bib === id = cord-264944-7xj27r98 author = Koopmans, Marion title = Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date = 1993-07-31 pages = extension = .txt mime = text/plain words = 5182 sentences = 255 flesch = 54 summary = The method was compared to existing extraction techniques by studying the quality of the templates for reverse-transcriptase polymerase chain reaction amplification (RT-PCR), using virus-infected and mock-infected paraffin-embedded cell pellets as a model. The method was compared to existing extraction techniques by studying the quality of the templates for rcvcrsetranscriptase polymerase chain reaction amplification (RT-PCR), using virusinfected and mock-infected paraffin-embedded cell pellets as a model. In the work reported here we used paraffin-embedded torovirus-infected cell pellets to compare the effect of different fixatives and RNA extraction methods on RT-PCR amplification of tissue extracts. cache = ./cache/cord-264944-7xj27r98.txt txt = ./txt/cord-264944-7xj27r98.txt === reduce.pl bib === id = cord-264678-wt0lvhfl author = Wu, Tzong-Yuan title = IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico date = 2009-05-27 pages = extension = .txt mime = text/plain words = 5333 sentences = 306 flesch = 58 summary = To develop the IRES search system, it will be necessary to screen the database of virus sequences by the prediction of secondary structure to identify the candidate IRES element in the virus genome, especially those positive strand viruses with 5' untranslated regions. Enterovirus IRES domain IV [25] , was first selected as a target to compare with the whole genome sequences from four different viruses (Enterovirus 71 (U22521), Bovine Enterovirus (NC_001859), Human Rhinovirus (NC_001617) and Hepatitis C virus (NC_004102) [26] [27] [28] ) were downloaded into IRSS and ran UTR2SQ.pl program to proceed RNA secondary structure prediction (see Figure 1 ). First, the IRSS search capability is evaluated while virus genomes sequences were substituted for the entire UTRdb. The known IRES element which was used for RNA comparison was selected such as HCV IRES domain III structure for example. cache = ./cache/cord-264678-wt0lvhfl.txt txt = ./txt/cord-264678-wt0lvhfl.txt === reduce.pl bib === id = cord-265895-ck7eto16 author = Baric, Ralph S. title = Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date = 1987-02-28 pages = extension = .txt mime = text/plain words = 4507 sentences = 228 flesch = 60 summary = These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription. These data, coupled with the presence of discrete large leader-containing RNAs which range from 84 to 1000 nucleotides in length in MHV-infected cells (Baric et a/., 1985) suggest that discontinuous RNA intermediates may be dissociated and reassert between viral RNA templates to generate recombinant viruses by a copy-choice mechanism (Makino eta/., 1986a). The leader-containing RNAs larger than 1 10 nucleotides in length detected by the leader-specific cDNA probe were more heterogeneous (Fig. 2) (Baric et al., 1985) suggesting that multiple RNA species in this size range were present. cache = ./cache/cord-265895-ck7eto16.txt txt = ./txt/cord-265895-ck7eto16.txt === reduce.pl bib === === reduce.pl bib === id = cord-263987-ff6kor0c author = Holmes, Ian H. title = Solving the master equation for Indels date = 2017-05-12 pages = extension = .txt mime = text/plain words = 7131 sentences = 357 flesch = 44 summary = BACKGROUND: Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. MAIN TEXT: This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees. CONCLUSIONS: While approximations that use finite-state machines (Pair HMMs and transducers) currently represent the most practical approach to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly with the matrix exponential of the underlying continuous-time Markov chain also show promise, especially in view of recent advances. cache = ./cache/cord-263987-ff6kor0c.txt txt = ./txt/cord-263987-ff6kor0c.txt === reduce.pl bib === id = cord-266921-x9q7dwc4 author = Worrall, Jonathan AR title = Information available at cut rates: structure and mechanism of ribonucleases date = 2006-12-26 pages = extension = .txt mime = text/plain words = 4616 sentences = 222 flesch = 49 summary = The exoribonuclease RNase II is representative of an extensive enzyme family found in all three domains of life, whose members play roles in the maturation, turn-Structure and mechanism of ribonucleases Worrall and Luisi 131 Whereas DEAD-box helicases use the free energy of ATP binding and hydrolysis to disrupt secondary structure, RNase R transduces the favourable free energy of RNA backbone hydrolysis into mechanical work that translates the single-stranded substrate further into the catalytic pocket, much like a ratchet. Crystal structures of the core of the exosomes from the archaea Sulfolobus solfataricus and Archaeoglobus fulgidus have recently become available, revealing a hexameric ring comprising two types of RNase-PH-like subunits, known as Rrp41 and Rrp42 (rRNA-processing proteins 41 and 42; see Figure 4a ) [36 ,37 ,38 ] . Structure of Escherichia coli RNase E catalytic domain and its implications for RNA turnover and processing cache = ./cache/cord-266921-x9q7dwc4.txt txt = ./txt/cord-266921-x9q7dwc4.txt === reduce.pl bib === id = cord-266521-vovas81d author = Yokobayashi, Yohei title = Aptamer-based and aptazyme-based riboswitches in mammalian cells date = 2019-06-22 pages = extension = .txt mime = text/plain words = 3228 sentences = 155 flesch = 43 summary = In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. While the ribozyme was not specifically regulated by a small molecule via an aptamer, this work paved the way for the subsequent riboswitches that employ allosterically regulated ribozymes (aptazymes) embedded in the 5 0 and/or 3 0 UTR to chemically regulate gene expression in mammalian cells (Figure 1a ) [13] [14] [15] [16] . A new mode of engineered RNA-based gene regulation in mammalian cells was demonstrated by controlling the accessibility of a miRNA target site by aptamer-ligand interaction cache = ./cache/cord-266521-vovas81d.txt txt = ./txt/cord-266521-vovas81d.txt === reduce.pl bib === id = cord-262076-b5u5hp2r author = Liu, Ying Poi title = Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron date = 2008-03-16 pages = extension = .txt mime = text/plain words = 6881 sentences = 414 flesch = 56 summary = We show that the expression of individual miRNAs is greatly enhanced in multiplex hairpin transcripts that are properly processed into functional miRNAs. HIV-1 replication can be potently inhibited by simultaneous expression of four antiviral miRNAs. These combined results indicate that the multiplex miRNA strategy is a promising therapeutic approach against escape-prone viral pathogens. By repeating this procedure we obtained constructs expressing different combinations of 1, 2, 3, 4 and 6 pri-miRNAs. The RNA structures formed by the transcripts were predicted with the Mfold program (47) at http://frontend.bioinfo.rpi.edu/ applications/mfold/ and found to be similar to the predicted conformation of the wild-type pri-miRNAs. The firefly luciferase (FL) reporters containing HIV-1 target sequences pol47 (Luc-A pol47 ), pol1 (Luc-B pol1 ), gag5 (Luc-C gag5 ), r/t5 (Luc-D r/t5 ), ldr9 (Luc-E ldr9 ) and the anti-HIV shRNAs have been described previously (32) . cache = ./cache/cord-262076-b5u5hp2r.txt txt = ./txt/cord-262076-b5u5hp2r.txt === reduce.pl bib === id = cord-267115-6jqdi417 author = Giobbe, Giovanni Giuseppe title = SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date = 2020-06-24 pages = extension = .txt mime = text/plain words = 8080 sentences = 408 flesch = 47 summary = Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. Principal component analysis (PCA) showed smaller heterogeneity in the organoid groups derived at different stages of fetal and pediatric development with respect to the primary tissues analyzed at the same stages, which may also include some heterogeneity from the surrounding cells as a result of the isolation procedure (Fig. 3a) . In order to validate both fetal and pediatric gastric organoids as functional in vitro models of SARS-CoV-2 infection and replication, we optimized the culture condition for viral infection in a 3D system (Fig. 4a) . cache = ./cache/cord-267115-6jqdi417.txt txt = ./txt/cord-267115-6jqdi417.txt === reduce.pl bib === id = cord-262511-96xp1v0r author = Khabar, Khalid S. A. title = Rapid transit in the immune cells: the role of mRNA turnover regulation date = 2007-03-30 pages = extension = .txt mime = text/plain words = 6542 sentences = 342 flesch = 43 summary = Post-transcriptional regulation contributes significantly to this rapid transit by several mechanisms, including mRNA stability modulation and translational control; collectively, they aim to control the expression of key gene products involved in the immune response. The stabilization of cytokine mRNA and other immune response gene products can occur by the activity of mRNA stabilization-promoting proteins such as human antigen (HuR) protein or by inactivation of RNA decay-promoting proteins such as the zinc finger protein, tristetraprolin (TTP). Traditionally, post-transcriptional regulation in innate immunity has been studied in response to the bacterial endotoxin, LPS, which binds CD14 in a complex with TLR4 on the surface of neutrophils and macrophages and initiates a cascade of signals that causes cell activation, the inflammatory response, and phagocytosis [35] . With the coordinated kinetics model, stabilizing RNA-binding proteins such as HuR can occur initially following immune cell activation, allowing rapid and early response of cytokine production. cache = ./cache/cord-262511-96xp1v0r.txt txt = ./txt/cord-262511-96xp1v0r.txt === reduce.pl bib === id = cord-262609-cssgzvus author = Sivakumaran, K title = RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis date = 1999-12-03 pages = extension = .txt mime = text/plain words = 10580 sentences = 550 flesch = 55 summary = title: RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis In contrast, we find that position-specific changes in the RNA sequence will affect replicase recognition, modulate the polymerization process, and contribute to the differential accumulation of viral RNAs. These functional results are in agreement with the phylogenetic analysis of BMV and related viral sequences and suggest that a similar mechanism of RNA synthesis takes place for members of the alphavirus superfamily. Results herein demonstrate that the endscript directing genomic plus-strand synthesis also interacts with the viral replicase via a mechanism that does not depend on a speci®c preformed RNA structure. An interesting conclusion from our analysis of the BMV genomic minus-strand RNA endscript is that template sequence may regulate the amount of RNA synthesis in a manner independent of replicase-promoter interaction. cache = ./cache/cord-262609-cssgzvus.txt txt = ./txt/cord-262609-cssgzvus.txt === reduce.pl bib === id = cord-267588-ruuzr6l1 author = Garnett, Lauren title = Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date = 2020-08-08 pages = extension = .txt mime = text/plain words = 3093 sentences = 156 flesch = 51 summary = This study aimed to examine the efficacy of six different swabs that are commonly found in hospital settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6" cotton tipped applicators, and HOLOGIC Aptima), along with more readily available alternative transport mediums (DMEM, PBS, 100% ethanol, 0.9% normal saline and VTM) for their use in molecular detection of SARS-CoV-2. Therefore, our results suggest that the cotton and wood For the portion of the study focusing on alternative transport media, we assessed the ability of DMEM, PBS, 0.9% Normal Saline, and 100% ethanol compared to VTM to be used as medium for the preservation and recovery of viral RNA to be quantified by molecular detection. Despite finding similar levels of viral RNA collected using different swabs and transport media, there is variation when evaluating different respiratory clinical samples while testing for SARS-CoV-2. cache = ./cache/cord-267588-ruuzr6l1.txt txt = ./txt/cord-267588-ruuzr6l1.txt === reduce.pl bib === id = cord-266960-kyx6xhvj author = Temple, Mark D. title = Real-time audio and visual display of the Coronavirus genome date = 2020-10-02 pages = extension = .txt mime = text/plain words = 6780 sentences = 360 flesch = 56 summary = The sonification of codons derived from all three reading frames of the viral RNA sequence in combination with sonified metadata provide the framework for this display. CONCLUSION: The auditory display in combination with real-time animation of the process of translation and transcription provide a unique insight into the large body of evidence describing the metabolism of the RNA genome. Audio generated from each of these sequence motifs and metadata were combined to create a complex auditory display to represent either transcription or translation. High resolution analysis of gene expression in Coronavirus genomes has detected ribosome protected fragments which map to non-canonical ORF's, these may be novel protein-coding ORFs and short regulatory uORFs. The tool highlights the occurrence of one such uORF of 30 nucleotides (including the stop codon) in the 5′ untranslated region downstream of TRS1 [35] that is not documented in the GenBank metadata. In the Additional file 4: supplementary example 'Sonification Sub-genomic RNA' the auditory display represents the process of transcription. cache = ./cache/cord-266960-kyx6xhvj.txt txt = ./txt/cord-266960-kyx6xhvj.txt === reduce.pl bib === id = cord-266520-n439dwcx author = Levanova, Alesia A. title = Enzymatically synthesized 2'-fluoro-modified Dicer-substrate siRNA swarms against herpes simplex virus demonstrate enhanced antiviral efficacy and low cytotoxicity date = 2020-08-13 pages = extension = .txt mime = text/plain words = 3615 sentences = 251 flesch = 54 summary = The antiviral efficacy of the 2'-F-siRNA swarms and the elicited cellular innate responses did not correlate suggesting that innate immunity pathways do not significantly contribute to the observed enhanced antiviral activity of the modified siRNAs. The results support further applications of enzymatically produced siRNA molecules with incorporated adenosine nucleotides, carrying fluoro-modification on ribose C2' position, for further antiviral studies in vitro and in vivo. We have previously generated three antiviral siRNA swarms against herpes simplex virus type 1 (HSV-1) mRNAs encoding essential viral proteins, including glycoprotein B (UL27), the infected cell protein 8 (ICP8; UL29), and ICP27 (UL54) (Romanovskaya et al., 2012; Paavilainen et al., 2016) . The siRNA swarm targeting mRNA of HSV single-stranded DNA binding protein ICP8, encoded by the UL29 gene, harbors a most pronounced antiviral effect (Paavilainen et al., 2016) and induces only minimal non-specific cellular responses (Romanovskaya et al., 2012) . cache = ./cache/cord-266520-n439dwcx.txt txt = ./txt/cord-266520-n439dwcx.txt === reduce.pl bib === id = cord-267027-diwm1940 author = Le, Shu-Yun title = Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses date = 1992-12-31 pages = extension = .txt mime = text/plain words = 4348 sentences = 270 flesch = 59 summary = Abstract A combination of comparative sequence analysis and thermodynamic methods reveals the conservation of tertiary structure elements in the 5′ untranslated region (UTR) of human enteroviruses and rhinoviruses. Base pairings between highly conserved 17-nucleotide (nt) and 21-nt sequences in the 5′ UTR of human enteroviruses and rhinoviruses constitute a predicted pseudoknot that is significantly more stable than those that can be formed from a large set of randomly shuffled sequences. The predicted pseudoknots, K2 (tertiary interactions: between the region 497-501 and 550-554) and K3 (579-581 and 600-602) in the RLP of PV2L were found to be totally conserved in all 22 human enteroviruses and rhinoviruses. Based on the common RNA secondary structures (Le and Zuker, 1990 ) of the 5' UTR in 18 human enteroviruses and rhinoviruses, two sequences complementary to the highly conserved polypyrimidine sequence in all picornaviruses were identified in human 18 S rRNA . cache = ./cache/cord-267027-diwm1940.txt txt = ./txt/cord-267027-diwm1940.txt === reduce.pl bib === id = cord-266464-wuf3s8m0 author = Kim, So Yeon title = Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection date = 2016-10-17 pages = extension = .txt mime = text/plain words = 1810 sentences = 100 flesch = 50 summary = title: Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection We evaluated the diagnostic and clinical usefulness of blood specimens to detect Middle East respiratory syndrome coronavirus infection in 21 patients from the 2015 outbreak in South Korea. Respiratory specimens are preferred for viral RNA detection and confirmatory diagnosis of MERS-CoV infection in humans (5) . Our study aimed to evaluate the diagnostic utility of blood specimens for MERS-CoV infection by using large numbers of patients with a single viral origin and to determine the relationship between blood viral detection and clinical characteristics. Between the blood viral RNA-positive and -negative groups, we found no differences in age, duration from symptom onset to diagnosis of MERS-CoV infection, or an invasive procedure before the specimens were obtained (online Technical Appendix Table 3 ). Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission cache = ./cache/cord-266464-wuf3s8m0.txt txt = ./txt/cord-266464-wuf3s8m0.txt === reduce.pl bib === id = cord-265381-ppjohov8 author = Pillai-Nair, Neeta title = Cis-acting Regulatory Elements in the Potato Virus X 3′ Non-translated Region Differentially Affect Minus-strand and Plus-strand RNA Accumulation date = 2003-02-21 pages = extension = .txt mime = text/plain words = 10016 sentences = 521 flesch = 57 summary = 6 -13 Cis-acting elements required for minus-strand RNA accumulation in vivo or RNA synthesis in vitro have been well studied for the plant plus-strand RNA viruses that contain tRNA-like structures in the 3 0 NTR 2 such as brome mosaic virus (BMV), 14 -16 cucumber mosaic virus (CMV), 17 tobacco mosaic virus (TMV) 18 and turnip yellow mosaic virus (TYMV), 19, 20 and for several other viruses such as alfalfa mosaic virus (AlMV), 21, 22 barley stripe mosaic virus (BSMV), 23 cymbidium ringspot virus (CymRSV), 24 red clover necrotic mosaic virus (RCNMV) 25 and turnip crinkle virus (TCV). The role of the 3 0 NTR cis-acting sequences and/ or structures in PVX RNA accumulation was studied by solution structure probing and by introducing wild-type (w.t.) and mutant transcripts into tobacco protoplasts for analysis of minus and plusstrand RNA accumulation by S 1 nuclease protection assays. cache = ./cache/cord-265381-ppjohov8.txt txt = ./txt/cord-265381-ppjohov8.txt === reduce.pl bib === id = cord-263645-wupre5uj author = Morgan, Brittany S title = Insights into the development of chemical probes for RNA date = 2018-09-19 pages = extension = .txt mime = text/plain words = 7104 sentences = 341 flesch = 43 summary = One important example is the development of chemical probes, which has greatly progressed the study of proteins and related diseases (11, 12) but has been challenging for non-ribosomal RNAs. This powerful chemical tool requires small molecules with well-defined biological activity, cell permeability, and selectivity to accurately and reliably probe specific mechanistic and phenotypic questions (11, 12) . While ligands that bind non-ribosomal RNA in vitro have been reported for decades, the development of chemical probes with evidence of specific small molecule:RNA engagement in cell or animal models has dramatically increased in the last four years. Recent studies report several drug-like small molecules that target a range of RNAs in animal models, including riboswitches (15) , miRNAs, (16, 17) splice sites (18) , and mature mRNAs (19) , at least one of which is currently in clinical trials (NCT02268552). cache = ./cache/cord-263645-wupre5uj.txt txt = ./txt/cord-263645-wupre5uj.txt === reduce.pl bib === id = cord-267036-llngs3v5 author = Lai, Ming‐Chih title = Functional interplay between viral and cellular SR proteins in control of post‐transcriptional gene regulation date = 2009-02-10 pages = extension = .txt mime = text/plain words = 4460 sentences = 263 flesch = 44 summary = Numerous lines of evidence indicate that cellular SR proteins are important for regulation of viral RNA splicing and participate in other steps of post-transcriptional viral gene expression control. The E2 protein encoded by HPVs primarily regulates the transcription of early promoters by binding to a consensus element within the long control region of the viral genome, and also functions together with the E1 protein in viral DNA replication [16] . It has been shown that reduced activity of SR proteins resulting from viral infection can be recovered by overexpression of SR proteins or by their rephosphorylation in the host cells [74] , and that HIV expression can be greatly increased when SRp75 is phosphorylated by SRPK2 [69] . Cellular SR proteins and their cooperative or antagonistic factors may play a critical role in the life cycle control of viruses, which involves a series of alternative splicing events for expression of viral genome or proteins. HIV-1 infection induces changes in expression of cellular splicing factors that regulate alternative viral splcing and virus production in macrophages cache = ./cache/cord-267036-llngs3v5.txt txt = ./txt/cord-267036-llngs3v5.txt === reduce.pl bib === id = cord-267326-355q6k6k author = Gu, Xiaoqiong title = Geospatial distribution of viromes in tropical freshwater ecosystems date = 2018-06-15 pages = extension = .txt mime = text/plain words = 8426 sentences = 424 flesch = 44 summary = This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. However, up till now, studies of land use impacts on the virome community in freshwater ecosystems are still limited as they mainly rely on traditional methodology (culture-based method or qPCR/RT-qPCR), which focuses on limited human virus targets without considering the whole picture of the viral community in the water environment (Corsi et al., 2014; Lenaker et al., 2017) . Thus, the objectives of this study were to: 1) investigate the overall virome distribution and diversity in diverse freshwater ecosystems (reservoirs/tributaries) in a tropical environment, 2) compare the virome community based on the different land use patterns, 3) assess the extent of human-related pathogenic viruses in surface waters, especially emerging zoonotic and human-related viruses, which may have been undetected before. cache = ./cache/cord-267326-355q6k6k.txt txt = ./txt/cord-267326-355q6k6k.txt === reduce.pl bib === id = cord-267867-q52nvn0n author = Chevalier, Christophe title = Inhibition of Hepatitis C Virus Infection in Cell Culture by Small Interfering RNAs date = 2016-12-14 pages = extension = .txt mime = text/plain words = 8001 sentences = 395 flesch = 48 summary = Several siRNAs dramatically reduced or even abrogated the replication of selectable subgenomic HCV replicons upon cotransfection of human hepatoma cells with viral target and siRNAs, or upon transfection of cells supporting autonomous replication of HCV replicon with siRNAs. Importantly, three siRNAs also proved capable of strongly inhibiting virus production in cell culture. Several siRNAs dramatically reduced or even abrogated the replication of selectable subgenomic HCV replicons upon cotransfection of human hepatoma cells with viral target and siRNAs, or upon transfection of cells supporting autonomous replication of HCV replicon with siRNAs. Importantly, three siRNAs also proved capable of strongly inhibiting virus production in cell culture. We sought to determine whether the siRNAs si240-1a, si244, and si313, shown to be the most efficient in inhibiting the replication of HCV subgenomic replicons both transiently and under selective pressure, are also capable of efficiently blocking virus infection in cell culture. cache = ./cache/cord-267867-q52nvn0n.txt txt = ./txt/cord-267867-q52nvn0n.txt === reduce.pl bib === id = cord-265173-70wyecwj author = Trujillo-Uscanga, Adrian title = Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date = 2020-08-27 pages = extension = .txt mime = text/plain words = 5671 sentences = 282 flesch = 53 summary = title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication Viruses modulate p53 functions in different manners: single-stranded RNA viruses such as the human coronavirus NL63 (HCoV-NL63) induces its degradation of p53 (Yuan et al., 2015) to ensure viral growth in infected cells (Ma-Lauer et al., 2016) , Zika (ZIKV) and West Nile (WNV) activate p53 to facilitate their replication (El Ghouzzi et al., 2016) (Teng et al., 2017) (Yang et al., 2008) while Adenovirus Even though p53 is implicated in the induction of apoptosis and in many viral infections, its role during calicivirus infection has not been studied. Here we found that p53 interacts with FCV dsRNA, the protease-polymerase NS6/7, and VP1 in the RC; moreover, knockdown of p53 resulted in a significant reduction of the NS viral protein synthesis and virus production, indicating its role for efficient viral replication. cache = ./cache/cord-265173-70wyecwj.txt txt = ./txt/cord-265173-70wyecwj.txt === reduce.pl bib === id = cord-267377-wyhsxj6g author = Edwards, Michael C. title = Coat protein expression strategy of oat blue dwarf virus() date = 2014-01-14 pages = extension = .txt mime = text/plain words = 4709 sentences = 231 flesch = 54 summary = The single, large ORF encodes a polyprotein with domains specifying methyltransferase (mtr), protease (pro), helicase/NTpase (hel), and polymerase (pol) activities fused to the sequence encoding the CPs. The major and minor coat proteins map to the same CP sequence and size differences between them are potentially determined by translation initiation at two different start codons (minor, AUG 5581 and major, AUG 5710 ). Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, major CP mutants GH1-7 (premature termination mutant) and KL1-3 (initiation codon mutant), and AB15-25 (marafibox mutant) and incubated for 40 h. Accumulation of viral coat proteins (CPs) and RNA in oat protoplasts inoculated with premature termination and initiation codon mutants of the CP gene. Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, premature termination mutants GH1-7 and EF2-2, and initiation codon mutants IJ4-7 (minor CP), and KL1-3 and KL2-5 (major CP) and incubated for 24 h. cache = ./cache/cord-267377-wyhsxj6g.txt txt = ./txt/cord-267377-wyhsxj6g.txt === reduce.pl bib === id = cord-265508-t1nfyzf5 author = Boursnell, M.E.G. title = Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date = 1984-08-31 pages = extension = .txt mime = text/plain words = 2130 sentences = 125 flesch = 61 summary = authors: Boursnell, M.E.G.; Brown, T.D.K. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. The organisation of the messenger RNAs and in vitro translation studies have led to the hypothesis that the 5'-most sequences of each mRNA, which are not present in the next smallest mRNA, contain the complete coding sequences for the major protein product produced by that messenger species (Stern and Kennedy, 1980b; Lai et al., 1981) . In this paper we report the nucleotide sequence of a cloned cDNA copy of IBV genomic RNA in the region corresponding to the 5' end of mRNA B. The region of the IBV sequence presented in this paper contains the 5' ends, on the viral genome, of mRNAs A and B. cache = ./cache/cord-265508-t1nfyzf5.txt txt = ./txt/cord-265508-t1nfyzf5.txt === reduce.pl bib === id = cord-265139-x7g3jcjm author = Zaiou, Mohamed title = The Emerging Role and Promise of Circular RNAs in Obesity and Related Metabolic Disorders date = 2020-06-16 pages = extension = .txt mime = text/plain words = 8180 sentences = 440 flesch = 41 summary = There is also growing evidence that circRNAs are closely linked to non-alcoholic fatty liver disease (NAFLD), a disorder that is caused by a plethora of factors including hepatic lipid accumulation, adipose tissue and mitochondrial dysfunction, a high-fat diet, obesity, a chronic inflammatory state, insulin resistance (IR), and genetic and epigenetic factors [48, 55] . In addition to classical epigenetic modifications, a variety of ncRNAs have been uncovered in different cells and organs including adipose tissues, many of which are involved in the regulation of adipogenesis and other metabolic processes implying their role in the etiology of obesity [69] . Emerging evidence from in vitro and in vivo animal studies suggest that circRNAs are expressed in adipose tissues and may modulate adipogenesis and lipid metabolism. Collectively, the results from the above studies demonstrate that several circRNAs are differentially expressed in adipose tissue and support a significant role of these RNA species in the regulatory networks of adipogenesis. cache = ./cache/cord-265139-x7g3jcjm.txt txt = ./txt/cord-265139-x7g3jcjm.txt === reduce.pl bib === id = cord-263302-z5uhrta5 author = Zhang, Xuming title = Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date = 2000-12-05 pages = extension = .txt mime = text/plain words = 7944 sentences = 411 flesch = 58 summary = Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). Further sequencing on cDNA clones derived from JHM2c mRNAs by reserve transcription-polymerase chain reaction (RT-PCR) has shown that the leader-body joining sites in subgenomic mRNA2-1 are more heterogeneous . When it was placed in front of the chloramphenicol acetyl-transferase (CAT) gene in the defective-interfering (DI) RNA-CAT reporter plasmid, the IG5-1, which is devoid of any known IRES sequence, can direct the synthesis of a subgenomic CAT-containing mRNA and expression of the CAT activity, thus confirming that the IG5-1 serves as a promoter for transcription of a subgenomic mRNA. To identify the minimal sequence required for subgenomic mRNA transcription, three deletions within the 140-nt sequence were made by PCR, and the deletion fragments were cloned into the DI RNA-CAT reporter vector in place of the wild-type, full-length (140-nt) se, and MHV-1 (F), respectively. cache = ./cache/cord-263302-z5uhrta5.txt txt = ./txt/cord-263302-z5uhrta5.txt === reduce.pl bib === id = cord-264746-gfn312aa author = Muse, Spencer title = GENOMICS AND BIOINFORMATICS date = 2012-03-29 pages = extension = .txt mime = text/plain words = 10976 sentences = 583 flesch = 58 summary = The success of this project (it came in almost 3 years ahead of time and 10% under budget, while at the same time providing more data than originally planned) depended on innovations in a variety of areas: breakthroughs in basic molecular biology to allow manipulation of DNA and other compounds; improved engineering and manufacturing technology to produce equipment for reading the sequences of DNA; advances in robotics and laboratory automation; development of statistical methods to interpret data from sequencing projects; and the creation of specialized computing hardware and software systems to circumvent massive computational barriers that faced genome scientists. Although the list of important biotechnologies changes on an almost daily basis, there are three prominent data types in today's environment: (1) genome sequences provide the starting point that allows scientists to begin understanding the genetic underpinnings of an organism; (2) measurements of gene expression levels facilitate studies of gene regulation, which, among other things, help us to understand how an organism's genome interacts with its environment; and (3) genetic polymorphisms are variations from individual to individual within species, and understanding how these variations correlate with phenotypes such as disease susceptibility is a crucial element of modern biomedical research. cache = ./cache/cord-264746-gfn312aa.txt txt = ./txt/cord-264746-gfn312aa.txt === reduce.pl bib === id = cord-263357-krvei97r author = Holmes, Kathryn V. title = The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia date = 2013-01-08 pages = extension = .txt mime = text/plain words = 2076 sentences = 83 flesch = 43 summary = Sequencing and bioinformatic analysis of the viral genomic RNA showed that it is a novel virus not previously detected in any other species and that its closest relatives are two Asian bat coronaviruses. demonstrated how state-of-the-art sequencing technology and bioinformatic analysis can quickly provide critical insight into the viral genome sequence, phylogeny, replication strategy, and potential drug and vaccine targets and generate tools to evaluate the possible epidemic risk associated with this novel human virus. In June 2012, a novel coronavirus, tentatively named HCoV-EMC (for Erasmus Medical Center where the initial genome sequence was done), was isolated in a monkey kidney cell line from a sputum specimen from a 60-year-old man from the Kingdom of Saudi Arabia who died of acute severe pneumonia and renal failure. The genomic analysis suggests that HCoV-EMC may be a zoonotic virus that spilled over to infect the 9 laboratory confirmed patients, either directly or indirectly, from an unknown reservoir, possibly a bat. cache = ./cache/cord-263357-krvei97r.txt txt = ./txt/cord-263357-krvei97r.txt === reduce.pl bib === id = cord-266127-phv08xe2 author = Mukhopadhyay, Urbi title = Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date = 2019-08-26 pages = extension = .txt mime = text/plain words = 7600 sentences = 432 flesch = 46 summary = Consistent to our previous results, Rbx1 expression was successfully knocked down in response to Rbx1 siRNA in RV-SA11-infected cells lysed at 9 hpi as well as in mock-infected control but not in RV-SA11-infected cells harvested FIGURE 1 Host RNA interference is blocked during early hours of RV-SA11 infection. Together, the data suggest that actively replicating RV-SA11 triggers attenuation in protein levels of AGO2 leading to functional blocking of RNAi during early time points (2-6 hpi) of infection. Sensitivity of ectopic GFP (pEGFP-N1) expression to siGFP was also reduced in RV-NSP1overexpressing cells ( Figure S4A ), indicating that RV-NSP1 might FIGURE 3 Rotaviral nonstructural protein 1 triggers ubiquitination and proteasomal degradation of AGO2. Rotavirus nonstructural protein 1 suppresses virus-induced cellular apoptosis to facilitate viral growth by activating the cell survival pathways during early stages of infection cache = ./cache/cord-266127-phv08xe2.txt txt = ./txt/cord-266127-phv08xe2.txt === reduce.pl bib === id = cord-263580-zxnmylkw author = Pyle, Anna Marie title = RNA helicases and remodeling proteins date = 2011-08-20 pages = extension = .txt mime = text/plain words = 2650 sentences = 131 flesch = 50 summary = New studies have revealed molecular mechanisms for coupling between ATP hydrolysis and unwinding, the physical basis for regulatory control by cofactors, and novel functions for RNA remodeling proteins. For DEAD-box proteins where the mechanochemical cycle has been studied, ATP hydrolysis (specifically, at the stage of Pi release) stimulates the dissociation of bound RNA molecules [46 ,47] , allowing recycling of these 'single-use' proteins [7] . Like many DEAD-box proteins, Mss116 is capable of unwinding short RNA duplexes [46 ,52,53] , however, studies of Mss116 mutants in vivo and in vitro show that its role in splicing is not necessarily dependent on helicase activity [52, 54 ] . This structure reveals the Dbp5 export motor imbedded within the complex containing other proteins involved in its function, revealing roles for small molecule activators and a conserved mechanism for ATP hydrolysis in RNA release cache = ./cache/cord-263580-zxnmylkw.txt txt = ./txt/cord-263580-zxnmylkw.txt === reduce.pl bib === id = cord-267533-nmgtan4e author = Hu, Zhigang title = Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date = 2020-10-29 pages = extension = .txt mime = text/plain words = 3605 sentences = 214 flesch = 46 summary = By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. The study of Xu and colleagues [5] estimated the risk factors of delayed viral shedding (≥ 15 days after illness onset) and found that male, delayed hospital admission, and invasive mechanical ventilation were positively associated with prolonged SARS-CoV-2 RNA detection duration. Delayed hospital admission, hypokalemia, and subpleural lesion were still the independent risk factors of long-term SARS-CoV-2 RNA detection in multivariate binomial logistic regression analysis with a generalized additive model. LASSO analysis with Cox regression model found six independent risk factors of prolonged SARS-CoV-2 RNA detection duration, including cough, dyspnea, delayed hospital admission, subpleural lesion, the use of methylprednisolone, and the use of thymosin. cache = ./cache/cord-267533-nmgtan4e.txt txt = ./txt/cord-267533-nmgtan4e.txt === reduce.pl bib === id = cord-268071-ow2aijmj author = Pachetti, Maria title = Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date = 2020-04-22 pages = extension = .txt mime = text/plain words = 4449 sentences = 236 flesch = 53 summary = Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. Naturally occurring mutations in critical residues for drug efficacy can lead to drug resistance phenomena, with a significant loss in the binding affinity of these molecules to the RdRp. We focused our study on SARS-CoV-2 mutations in order to assess if new viral variants were spreading across the Countries. Among all mutation sites analyzed, RdRp mutant is particularly interesting given that the enzyme is directly involved in viral replication and its fidelity determines the mutagenic capabilities of SARS-CoV-2. In the present work we have compared the SARS-CoV-2 reference genome to those exported from the GISAID database with the aim of gaining important insights into virus mutations, their occurrence over time and within different geographic areas. cache = ./cache/cord-268071-ow2aijmj.txt txt = ./txt/cord-268071-ow2aijmj.txt === reduce.pl bib === id = cord-266634-bww62vx8 author = Gopinath, M. title = Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus date = 2015-10-07 pages = extension = .txt mime = text/plain words = 2304 sentences = 104 flesch = 53 summary = In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Considering the presence of both KDKE tetrad, responsible for 2 0 -O-methyl transferase as well as GXGXG motif for SAM substrate binding, domain III could likely represent the methyl transfer module (both N 7 -guanine and 2 0 -Omethyl) of RPV L protein. Consensus sequence between the viral mRNAs is given in bold the capped RNA with the partially purified L-P complex from insect cells resulted in a concentration dependent N 7 guanine methylation of 6 bp substrate (Fig. 2b , marked as rL) which was not detected in a mock-purified high-density fraction from insect cells infected with non-recombinant baculovirus (Fig. 2b, mock) . Further, to functionally validate the methyl transferase activity of domain III (aa 1717-2183, LD3) of RPV L protein, LD3 was purified from insect cells using metal chelate affinity chromatography as described earlier [8] . cache = ./cache/cord-266634-bww62vx8.txt txt = ./txt/cord-266634-bww62vx8.txt === reduce.pl bib === id = cord-265461-hj2b1wc4 author = Decroly, Etienne title = Biochemical principles and inhibitors to interfere with viral capping pathways date = 2017-05-18 pages = extension = .txt mime = text/plain words = 5089 sentences = 262 flesch = 46 summary = Some virus families code for two different MTase domains carrying a cap-binding site (e.g., poxviruses [11] , coronaviruses [ Structure of inhibitors targeting enzymes involved in viral RNA capping pathways. Cap analogues exemplified here with m7 GTP, and several inhibitors of cap-binding protein have been identified through X-ray structure analysis of the influenza virus PB2-CBD in complex with the corresponding ligands. The X-ray structure of influenza A or B virus PB2 in complex with m7 GTP [49, 50] reveals a conserved cap-recognition mechanism in which the methylated guanosine is stacked between two aromatic residues similar to its binding mode with the eukaryotic initiation factor (eIF4E). However, the past research decade has a contrario unveiled that RNA capping is essential for virus replication, and is in fact a most interesting target for the design of potent antivirals due to two main reasons: (i) incomplete/inhibited RNA capping triggers a potent host immune response adding up to direct inhibition of viral gene expression, and (ii) structural and functional studies of viral capping enzymes have revealed a profound uniqueness of the viral enzymes involved, which shows promises to achieve high drug selectivity. cache = ./cache/cord-265461-hj2b1wc4.txt txt = ./txt/cord-265461-hj2b1wc4.txt === reduce.pl bib === id = cord-267124-8efdzlc0 author = Wichmann, Dominic title = Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date = 2020-05-06 pages = extension = .txt mime = text/plain words = 4062 sentences = 240 flesch = 50 summary = In response to the pandemic spread of SARS-CoV-2, the authorities of the German federal state of Hamburg ordered mandatory autopsies in all patients dying with a diagnosis of COVID-19 confirmed by polymerase chain reaction (PCR). During autopsy, tissue samples for histology were taken from the following organs: heart, lungs, liver, kidneys, spleen, pancreas, brain, prostate and testes (in males), ovaries (in females), small bowel, saphenous vein, common carotid artery, pharynx, and muscle. In this autopsy study of 12 consecutive patients who died of COVID-19, we found a high incidence of deep venous thrombosis (58%). In studies that examined deceased patients with COVID-19 without relying on autopsy, no increased rates of pulmonary embolism were observed clinically. To our knowledge, only 3 case reports have been published on patients with COVID-19 who have undergone complete autopsy and a few more in which only lung tissue was examined (7, 8) . cache = ./cache/cord-267124-8efdzlc0.txt txt = ./txt/cord-267124-8efdzlc0.txt === reduce.pl bib === id = cord-264488-989t9ld1 author = Park, Il-Hyun title = Inhibition of hepatitis B virus replication by ligand-mediated activation of RNase L date = 2014-02-06 pages = extension = .txt mime = text/plain words = 5320 sentences = 269 flesch = 54 summary = In the present study, the potential antiviral activity of RNase L against hepatitis B virus (HBV) was explored utilizing the recently reported infection protocol based on human hepatoma HepG2 cells stably complemented with the virus entry factor NTCP. These results suggest that HBV replication can be regulated through interferon-mediated RNA decay pathways and that activation of these host antiviral factors may represent a novel therapeutic strategy for HBV infection. Our data indicate that ligand-mediated activation of these enzymes results in a marked inhibition of HBV replication in both infected and transfected cells. With the newly established HepG2-NTCP cell culture system, which permits HBV infection, we showed that viral gene expression and replication can be profoundly reduced by 2-5Aor poly(I:C)-mediated activation of RNase L. In HBV1.2-transfected Huh-7 cells, it was further confirmed that this type of inhibition occurred mostly through viral RNA degradation via the ribonuclease function of RNase L. cache = ./cache/cord-264488-989t9ld1.txt txt = ./txt/cord-264488-989t9ld1.txt === reduce.pl bib === id = cord-268337-o6lo55o8 author = Lloyd, Richard E. title = Translational control by viral proteinases date = 2005-11-21 pages = extension = .txt mime = text/plain words = 9416 sentences = 495 flesch = 49 summary = Human immunodeficiency virus-1 (HIV-1) infection of cells resulted in partial cleavages of eIF4GI that was mapped to three sites in two regions on either side of the eIF3-binding domain ( Fig. 1) (Ohlmann et al., 2002; Ventoso et al., 2001) . Translation assays based on luciferase reporter constructs in cells indicated that expression of HIV protease (HIV PR) primarily inhibited translation of capped mRNAs. Interestingly, comparison of translation function of eIF4GI C-terminal cleavage products produced by L pro and HIV PR revealed that the slightly shorter HIV PR-derived fragment was defective in supporting translation of the PV-IRES but not the EMCV IRES. Demonstration in vitro that eucaryotic initiation factor 3 is active but a cap-binding protein complex is inactive in poliovirus-infected HeLa cells Eukaryotic initiation factor 4GII (eIF4GII), but not eIF4GI, cleavage correlates with inhibition of host cell protein synthesis after human rhinovirus infection Cleavage of eukaryotic initiation factor eIF4G and inhibition of host-cell protein synthesis during feline calicivirus infection cache = ./cache/cord-268337-o6lo55o8.txt txt = ./txt/cord-268337-o6lo55o8.txt === reduce.pl bib === id = cord-265410-khwzdi79 author = Bartlett, Stuart title = Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars date = 2020-04-16 pages = extension = .txt mime = text/plain words = 9439 sentences = 470 flesch = 47 summary = Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. Hence, in the search for extraterrestrial life, we must consider that: (1) Life exactly as we know it may be rare in the universe, but a more general class of phenomena with life-like characteristics may be far more common; (2) There may be systems, yet to be discovered or even imagined, that more successfully satisfy the living criteria than even earthly life does; (3) By loosening our constraints on the definition of life, we open ourselves up to exploring the full parameter space of physical and chemical interactions that may create life. Lyfe is any hypothetical phenomenon that maintains a low-entropy state via dissipation and disequilibria conversions, utilizes autocatalytic networks to achieve nonlinear growth and proliferation, employs homeostatic regulatory mechanisms to maintain stability and mitigate external perturbations, and acquires and processes functional information about its environment. cache = ./cache/cord-265410-khwzdi79.txt txt = ./txt/cord-265410-khwzdi79.txt === reduce.pl bib === id = cord-266985-9qwttt2y author = Gale, P. title = Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date = 2014-11-04 pages = extension = .txt mime = text/plain words = 8073 sentences = 341 flesch = 43 summary = At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. The binding of NoV capsid protein to its HBGA receptor Table 1 Breakdown of the initial infection process into four steps for building a mechanistic dose-response relationship for RNA viruses through the oral route: information needs Host glycans play a central role in the pathogen infection process including binding of virus to specific receptors in steps 1 and 2 and also in the immune system. cache = ./cache/cord-266985-9qwttt2y.txt txt = ./txt/cord-266985-9qwttt2y.txt === reduce.pl bib === id = cord-015394-uj7fe5y6 author = nan title = Scientific Abstracts date = 2008-12-23 pages = extension = .txt mime = text/plain words = 242330 sentences = 15267 flesch = 52 summary = Studies involving immunohistochemical analysis of normal ovaries have shown that granulosa cells express significantly higher levels of the activator protein-1 (AP-1) transcription factor, cFos compared to theca cells, where cFos expression is virtually absent. Following acute hypoxia (0.5% O2) for one to six hours, RhoA mRNA, total protein and activation (RhoA-GTP) levels were analysed, using semi-quantitative PCRs and western blot, and compared to normoxic non-pregnant human uterine smooth muscle control cells. Since there is an urgent need for non-invasive methods for determination of fetal (F) and placental (P) function, this study was designed to evaluate the genes differently and commonly expressed in P tissue and leukocytes in maternal (M) and F circulation.Material and Methods. The current study: 1) localized IL-6 mRNA levels in preeclamptic versus normal decidual sections; 2) evaluated mechanisms regulating IL-6 synthesis by targeting intracellular signaling pathways with specific inhibitors; 3) identified potential IL-6 targets by immunolocalizing the IL-6 receptor (IL-6R) to specific cell types in placental bed biopsies. cache = ./cache/cord-015394-uj7fe5y6.txt txt = ./txt/cord-015394-uj7fe5y6.txt === reduce.pl bib === id = cord-267475-6f4h3cck author = Kozak, Marilyn title = Pushing the limits of the scanning mechanism for initiation of translation date = 2002-10-16 pages = extension = .txt mime = text/plain words = 24538 sentences = 1234 flesch = 50 summary = This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG(START) codon. (Whether the second AUG codon resides in a strong or weak context is not relevant; the ribosome reads the mRNA linearly and thus the decision to stop or to bypass the first AUG is not influenced by whether there is a better initiation site downstream.) The large number of genes that employ leaky scanning precludes discussion of the biological significance of the proteins thereby produced, but it merits noting that, for many of the viruses in Table 3 , replication requires production of both listed proteins. cache = ./cache/cord-267475-6f4h3cck.txt txt = ./txt/cord-267475-6f4h3cck.txt === reduce.pl bib === id = cord-269496-tnw7sxlh author = Sen Gupta, Parth Sarthi title = Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date = 2020-10-28 pages = extension = .txt mime = text/plain words = 4910 sentences = 246 flesch = 53 summary = Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of −187.3 kJ/mol, almost twice that of Helicase (−94.6 kJ/mol) and even lower than that of Importin-α (−156.7 kJ/mol). Together, being conserved and a necessary component for the replication of coronavirus, a multi-functional protein, Nsp13-helicase, is another vital SARS-COV-2 target (Jia et al., 2019) , which can be considered further for antiviral drug discovery provided a very small number of Nsp13 inhibitors reported to date . Molecular docking of Ivermectin with twelve SARS-COV-2's targets along with Importin-a was carried out, followed by binding mechanism exploration and structural stability analysis using molecular dynamics (MD) simulation through the root-meansquare deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (R g ), and binding free energy of the complexes of Ivermectin with the best targets. cache = ./cache/cord-269496-tnw7sxlh.txt txt = ./txt/cord-269496-tnw7sxlh.txt === reduce.pl bib === id = cord-268206-ino9srb6 author = Hamed, Manal A. title = An overview on COVID-19: reality and expectation date = 2020-06-01 pages = extension = .txt mime = text/plain words = 6067 sentences = 330 flesch = 46 summary = Recently, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), commonly known as coronavirus disease-2019 (COVID-19) has rapidly spread across China and around the world. In the current SARS-COV-2 pandemic, Wu and McGoogan (2020) showed that patients with chronic diseases, including diabetes, were at higher risk for severe COVID-19 infection and mortality. The former (S) is the wild type which is milder while the latter (L) is the novel one which resulted in high binding affinity between SARS-COV-2 virus with angiotensin-converting enzyme 2 receptor in human cells. The use of convalescent plasma was recommended before as an important treatment during outbreaks of Ebola virus, Middle East respiratory syndrome coronavirus, SARS-COV-1, H5N1 avian influenza, and H1N1 influenza (Zhou et al. In a study involving patients with pandemic influenza (H1N1) and SARS virus, treatment of severe infection with convalescent plasma was associated with reduced respiratory viral load, serum cytokine response, and mortality (Cheng et al. cache = ./cache/cord-268206-ino9srb6.txt txt = ./txt/cord-268206-ino9srb6.txt === reduce.pl bib === id = cord-268122-74nj66vb author = Xie, Na title = NAD(+) metabolism: pathophysiologic mechanisms and therapeutic potential date = 2020-10-07 pages = extension = .txt mime = text/plain words = 32037 sentences = 1955 flesch = 39 summary = The NAD + decline during normal aging results in oxidative damage, metabolic disorder, circadian rhythm abnormalities, and mitochondrial dysfunction through regulating signaling pathways, such as p53, NF-κB, PGC-1α and HIF-1α, by sirtuins and PARPs. NAD + and its metabolites function as crucial regulators to maintain cellular redox homeostasis through replenishing the reducing power or modulating the activity of NAD + -consuming enzymes including sirtuins and PARPs. However, disequilibrium of NAD + metabolism could disturb physiological processes, including mitochondria function, circadian rhythm, inflammation, DNA repair and metabolism, leading to aging-associated dysfunction and cancer. c The deduced NAD + levels in kidney are attributed to the decreased expression of enzymes in NAD + de novo synthesis and increased consumption by DNA damage activated PARPs. NAD + depletion inhibits the SIRT1/PGC1α mediated mitochondrial quality control, ATP production and NAD + de novo biosynthesis. cache = ./cache/cord-268122-74nj66vb.txt txt = ./txt/cord-268122-74nj66vb.txt === reduce.pl bib === id = cord-267532-5rnqd9mb author = Zhang, Xuming title = Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date = 1998-03-01 pages = extension = .txt mime = text/plain words = 6892 sentences = 357 flesch = 55 summary = HEor CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. In the present study, we used this DI RNA vector system to express the viral HE gene in the CNS of mice in the presence of an HE-deficient helper virus. To determine the basis for the reduction in mortality following A59-DE-HE infection compared to other viruses ( Fig. 2) , virus titers in the brains of mice infected with A59-DE-HE were initially compared to mice infected with the parental A59 or A59-DE-CAT at 6 days p.i. Based on the survival of most mice infected with A59-DE-HE, reduced viral replication in the CNS was anticipated. IL-6 mRNA was also increased in the CNS of mice infected with A59-DE-HE virus (Fig. 5B) ; however, no differences were detected in the liver between the two groups. cache = ./cache/cord-267532-5rnqd9mb.txt txt = ./txt/cord-267532-5rnqd9mb.txt === reduce.pl bib === id = cord-269193-a647hwu9 author = Lin, Debby A. title = Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date = 1991-05-31 pages = extension = .txt mime = text/plain words = 2946 sentences = 152 flesch = 57 summary = Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) . cache = ./cache/cord-269193-a647hwu9.txt txt = ./txt/cord-269193-a647hwu9.txt === reduce.pl bib === id = cord-268763-s16n7f17 author = Williams, J. G. title = Identification of Three Endotypes in Pediatric Acute Respiratory Distress Syndrome by Nasal Transcriptomic Profiling date = 2020-05-02 pages = extension = .txt mime = text/plain words = 4791 sentences = 270 flesch = 48 summary = The sequences from these specimens was used for downstream analysis (Figure 1) Assessing Nasal Specimen Similarity 64 nasal brushing specimens from 15 PARDS and 10 control subjects collected on study days 1, 3, 7, and 14, were analyzed by DESeq2. In comparing Group A, B, and C subjects, only disease severity (PELOD2) was statistically significant (Supplemental Table 1 ), and for individual specimens, PARDS classification (None, Mild, Moderate, or Severe), and the presence of direct lung injury, a viral or combined viral/bacterial cause of ARDS were significantly different between groups A, B, and C (Supplemental Table 2 ). Interferon-γ and tumor necrosis factor-related signaling were notable in Group B ( in conjunction with our findings that the only clinical variables that differentiated specimens from groups B and C from A were severity of lung injury and a viral cause of ARDS, and that viruses were the most common trigger of ARDS in both groups B and C, these data demonstrate that nasal epithelial transcriptomics can identify three distinct endotypes in PARDS: Endotypes A, B, and C. cache = ./cache/cord-268763-s16n7f17.txt txt = ./txt/cord-268763-s16n7f17.txt === reduce.pl bib === id = cord-268565-2sg1tlrg author = Clarke, David K. title = Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector date = 2006-09-15 pages = extension = .txt mime = text/plain words = 8286 sentences = 338 flesch = 34 summary = However, because durable neutralizing antibodies are usually elicited against the VSV surface glycoprotein after a single vaccination with replication-competent rVSV vectors, glycoprotein exchange vectors were designed to allow more effective boosting of immune responses to target antigens. In these pioneering studies, rhesus macaques were immunized with a combination of two prototypic rVSV vectors expressing a HIV-1 89.6 Env gp160/VSV-G fusion polypeptide and simian immunodeficiency virus (SIV) Gag p55 protein. Vaccine vector administration by a combination of intramuscular and intranasal routes clearly demonstrated the ability of rVSV vectors to elicit potent antigen-specific cellmediated immune responses in NHPs. In addition, this study also clearly demonstrated for the first time the ability of rVSV vectors expressing Env and Gag proteins to provide highly significant protection from AIDS after an intravenous heterologous SIV/HIV (SHIV) 89 .6P challenge [89] . Immunogenicity of attenuated vesicular stomatitis virus vectors expressing HIV type 1 Env and SIV Gag proteins: comparison of intranasal and intramuscular vaccination routes cache = ./cache/cord-268565-2sg1tlrg.txt txt = ./txt/cord-268565-2sg1tlrg.txt === reduce.pl bib === id = cord-269726-z0frgm7s author = Gidari, Anna title = Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date = 2020-10-10 pages = extension = .txt mime = text/plain words = 6678 sentences = 441 flesch = 54 summary = Criteria for patients' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) . cache = ./cache/cord-269726-z0frgm7s.txt txt = ./txt/cord-269726-z0frgm7s.txt === reduce.pl bib === id = cord-268718-tt07cwrf author = Tan, Heng Wee title = Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date = 2020-06-30 pages = extension = .txt mime = text/plain words = 6346 sentences = 400 flesch = 52 summary = 54 Virus infectivity study has indicated that the SARS-CoV-2 is able to utilize ACE2 of human, Chinese horseshoe bats, civet, and pig but was not able to use mouse ACE2. The roles of ACE2 expression in SARS-CoV-2 pathogenesis and human COVID-19 susceptibility are largely unknown. B, ACE2 expression in lung cancer patients with different smoking histories analyzed using similar methods as described previously 106 other symptoms in addition to respiratory symptoms, suggesting that SARS-CoV-2 could perhaps infect other organs (Figure 3 ). 118 In addition to sputum, SARS-CoV-2 RNA has been detected in the stools of a COVID-19 patient, 119 F I G U R E 3 Tissue distribution of angiotensin-converting enzyme 2 (ACE2) expression and potential COVID-19 susceptibility. Expression of elevated levels of proinflammatory cytokines in SARS-CoV-infected ACE2 + cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS cache = ./cache/cord-268718-tt07cwrf.txt txt = ./txt/cord-268718-tt07cwrf.txt === reduce.pl bib === id = cord-268139-tgpsu4qz author = Brockway, Sarah M. title = Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication date = 2005-09-30 pages = extension = .txt mime = text/plain words = 10127 sentences = 558 flesch = 54 summary = title: Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication In the current study, a reverse genetic approach was used to define the role of the 28-kDa amino-terminal product (nsp1) of the gene 1 polyprotein during replication of the coronavirus murine hepatitis virus (MHV) in cell culture. To determine whether nsp1 is required for MHV replication and to identify residues critical for protein function, mutant viruses that contained deletions or point mutations within the nsp1-coding region were generated and assayed for defects in viral replication, viral protein expression, protein localization, and RNA synthesis. Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication Experiments were next performed to determine if viral gene expression occurred in cells electroporated with RNA for mutants that did not produce infectious virus (VUSB5, VUSB6, nsp1DFL, and nsp1DMid). cache = ./cache/cord-268139-tgpsu4qz.txt txt = ./txt/cord-268139-tgpsu4qz.txt === reduce.pl bib === id = cord-269011-230p8rsf author = de Haan, Cornelis A.M. title = Molecular Interactions in the Assembly of Coronaviruses date = 2005-08-31 pages = extension = .txt mime = text/plain words = 22956 sentences = 1052 flesch = 46 summary = Biochemical and theoretical studies led to a topological model for the MHV M protein Rottier et al., 1984 Rottier et al., , 1986 , in which the polypeptide spans the lipid bilayer three times, leaving a small amino-terminal domain (15-35 residues) in the lumen of intracellular organelles (or outside the virus), whereas the carboxyterminal half of the protein is located on the cytoplasmic side of the membrane (or inside the virion). Using a mutational approach including deletions, insertions, and substitutions, both the transmembrane domain and the cysteine-rich region immediately downstream thereof, but not the carboxy-terminal part of the cytoplasmic tail, were shown to be important for MHV S protein-induced cell-cell fusion (Bos et al., 1995; Chang and Gombold, 2001; Chang et al., 2000) The cleavage requirements of the S proteins for the biological activities of the coronavirus spike remain enigmatic. cache = ./cache/cord-269011-230p8rsf.txt txt = ./txt/cord-269011-230p8rsf.txt === reduce.pl bib === id = cord-269771-hffxb7bm author = Cheung, Ka Shing title = Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date = 2020-04-03 pages = extension = .txt mime = text/plain words = 4797 sentences = 263 flesch = 51 summary = title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool, and also summarized data from a cohort of patients with COVID-19 in Hong Kong. The proportion of patients with detectable stool viral RNA was higher among those with diarrhea than those without diarrhea Table 2 including the hospital admission period, places in which the patients were recruited, sample size, age, sex, disease severity, non-gastrointestinal symptoms (fever and respiratory symptoms) on presentation, and gastrointestinal symptoms (anorexia, nausea/vomiting, diarrhea and abdominal pain/discomfort). In this meta-analysis of 4,243 COVID-19 patients from six countries, the pooled prevalence of all gastrointestinal symptoms (including anorexia, nausea/vomiting, diarrhea or abdominal pain) was 17.6%. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series cache = ./cache/cord-269771-hffxb7bm.txt txt = ./txt/cord-269771-hffxb7bm.txt === reduce.pl bib === id = cord-269194-b1wlr3t7 author = Engstrom-Melnyk, Julia title = Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date = 2015-12-31 pages = extension = .txt mime = text/plain words = 12542 sentences = 501 flesch = 36 summary = Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. cache = ./cache/cord-269194-b1wlr3t7.txt txt = ./txt/cord-269194-b1wlr3t7.txt === reduce.pl bib === id = cord-268970-uz7q6z2f author = Ott, Isabel M. title = Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date = 2020-08-04 pages = extension = .txt mime = text/plain words = 2790 sentences = 181 flesch = 58 summary = Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. To explore the viability of broadly deploying affordable saliva-based surveillance approaches 8 , we characterized SARS-CoV-2 RNA stability and virus infectivity from saliva samples stored in widely available, sterile, nuclease-free laboratory plastic (polypropylene) tubes. Following RNA extraction 9 and RT-qPCR 10 testing for SARS-CoV-2 on the day of saliva collection 2 , the remaining sample volumes (n=20) were aliquoted and stored at -80°C, room temperature (recorded as ~19°C) and 30°C. Moreover, SARS-CoV-2 RNA remained relatively stable in saliva samples left for up to 25 days at room temperature (~19°C; Ct increase of 0.027, 95% CI: -0.019, 0.071) ( Figure 1B) . cache = ./cache/cord-268970-uz7q6z2f.txt txt = ./txt/cord-268970-uz7q6z2f.txt === reduce.pl bib === id = cord-268467-btfz6ye8 author = Schreiber, Steven S. title = Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E date = 1989-03-31 pages = extension = .txt mime = text/plain words = 5035 sentences = 343 flesch = 59 summary = The 3′-noncoding region of the genome contains an 11-nucleotide sequence, which is relatively conserved throughout the Coronavirus family and lends support to the theory that this region is important for the replication of negative-strand RNA. This result suggested that the HCV229E subgenomic mRNAs possess a nested-set structure similar to other coronaviruses and that A34 represented a cDNA clone of either the 3'-end of the genomic RNA or the leader sequence. The 3'-noncoding region contains the sequence TGGAAGAGCCA, 75 nucleotides from the 3'-end (Fig. 4) which is relatively conserved among coronaviruses and is found at approximately the same location in all of these viral genomes (Kapke and Brian, 1986; Skinner and Siddell, 1984; Armstrong et a/., 1983; Lapps et al., 1987; Kamahora et a/., 1988; Boursnell et al., 1985) ( Table 1) . Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3'end of the viral mRNA leader sequence cache = ./cache/cord-268467-btfz6ye8.txt txt = ./txt/cord-268467-btfz6ye8.txt === reduce.pl bib === id = cord-269150-d1sgnxc0 author = Tan, Yong Wah title = Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date = 2012-02-22 pages = extension = .txt mime = text/plain words = 6977 sentences = 346 flesch = 53 summary = In a screen based on a yeast three-hybrid system using the 5′-untranslated region (5′-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. In this study, we describe the interaction of a cellular protein, MADP1 (zinc finger CCHC-type and RNA binding motif 1) with the 5 0 -UTR of IBV and SARS-CoV, using yeast-based three hybrid screen (34) and RNA-binding assays. Using indirect immunofluorescence, we confirmed that MADP1, despite being reported as a nuclear protein (35) , was detected in the cytoplasm of virus-infected cells and partially co-localized with the RTCs. Upon silencing of MADP1 using siRNA, viral RNA synthesis on general has been affected, resulting in a lower replication efficiency and infectivity. cache = ./cache/cord-269150-d1sgnxc0.txt txt = ./txt/cord-269150-d1sgnxc0.txt === reduce.pl bib === id = cord-269466-9hnal9ad author = Agbeci, Maxime title = Contribution of Host Intracellular Transport Machineries to Intercellular Movement of Turnip Mosaic Virus date = 2013-10-03 pages = extension = .txt mime = text/plain words = 7184 sentences = 391 flesch = 49 summary = In this study, we used a novel dual gene cassette construct that differentiated primary infected cells from cells infected after virus intercellular movement to show that the early as well as the late secretory pathway, but not endocytosis, was important for TuMV transport. By using a dual cassette of genes encoding fluorescent proteins that can differentiate between primary infected cells and cells infected after intercellular transport, we provide evidence that turnip mosaic virus (TuMV) needs a functional secretory pathway where pre-and post-Golgi trafficking and the actomyosin network are important for its movement. Fig. 2E shows that that there was no significant difference in the ratio of red over green fluorescence during BFA and CMA treatments compared with the no inhibitor treatment (TuMV alone) at 4 dpinf, indicating that viral protein production in the primary infected cells was not affected by the drug treatments. cache = ./cache/cord-269466-9hnal9ad.txt txt = ./txt/cord-269466-9hnal9ad.txt === reduce.pl bib === id = cord-270550-if748w2n author = Bailey, Adam L. title = SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date = 2020-11-05 pages = extension = .txt mime = text/plain words = 5808 sentences = 440 flesch = 49 summary = To ascertain whether human pluripotent stem cell-derived cardiomyocytes (hPSC-derived 150 CMs) can serve as an appropriate model to study cardiac SARS-CoV-2 infection, we measured 151 ACE2 mRNA expression in hPSC-derived CMs. Quantitative RT-PCR revealed that hPSC-152 derived CMs abundantly expressed ACE2 mRNA. We identified numerous host genes that were differentially 226 regulated upon SARS-CoV-2 infection in each of the examined cell types and two-dimensional 227 tissues (Fig. 3c) . 236 GO pathway analysis revealed that infected hPSC-derived CMs and two-dimensional co-237 culture tissues showed upregulation of genes associated with immune cell activation, stress-238 induced transcription, and responses to pathogens including viruses. Consistent with the 343 possibility that disrupted sarcomere gene expression might contribute to reduced EHT 344 contractility, immunostaining of hPSC-derived CMs infected with SARS-CoV-2 revealed evidence 345 of sarcomere loss 3 days following infection (Fig. 6c) , a time point that preceded cell death. cache = ./cache/cord-270550-if748w2n.txt txt = ./txt/cord-270550-if748w2n.txt === reduce.pl bib === id = cord-270143-muxrxvyo author = Markotter, Wanda title = Paramyxo- and Coronaviruses in Rwandan Bats date = 2019-07-02 pages = extension = .txt mime = text/plain words = 4897 sentences = 254 flesch = 49 summary = A high diversity of coronaand paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of coronaand paramyxoviral RNA using reverse transcription PCR assays. Although several surveillance studies have been implemented to detect potential zoonotic viruses in bats, including from countries in the Congo basin and East Africa, limited information is available for Rwanda. Confirmation of species identification of bats, in which viral RNA was detected, was performed by amplifying the cytochrome b (cyt b) or cytochrome oxidase one (COI) gene region and determining the DNA sequence. aegyptiacus-derived viral sequence (BatPV/Rou_aeg/UP438/RWA/2008) grouped within a Henipavirus-related clade and was near identical to a paramyxoviral sequence detected in the same host species previously reported from Kenya [36] . cache = ./cache/cord-270143-muxrxvyo.txt txt = ./txt/cord-270143-muxrxvyo.txt === reduce.pl bib === id = cord-269294-vx7xr80t author = Kwong, Ann D. title = Viral and cellular RNA helicases as antiviral targets date = 2005-09-23 pages = extension = .txt mime = text/plain words = 6378 sentences = 398 flesch = 55 summary = Here, we discuss the role of these enzymes, factors affecting their potential as drug targets and progress in the development of agents that inhibit their activity using the hepatitis C virus-encoded helicase NS3 and the cellular helicase DDX3 adopted for use by HIV-1 as examples. The solution of the crystal structure of HCV helicase complexed with oligonucleotide, as well as mutagenesis studies, have identified key residues that are essential for enzyme activity or translocation of the RNA substrate 13, 72 . Theoretically, an unwinding assay should increase the odds of finding an inhibitor because inhibition of any of the potential mechanisms of action listed above, except those requiring a cellular environment (for example, turnover and replicase-complex formation), should result in 'hits' (for example, low-potency chemical starting points for medicinal chemistry optimization). Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding cache = ./cache/cord-269294-vx7xr80t.txt txt = ./txt/cord-269294-vx7xr80t.txt === reduce.pl bib === id = cord-270243-moxleyjg author = Cholleti, Harindranath title = Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date = 2018-05-28 pages = extension = .txt mime = text/plain words = 3245 sentences = 190 flesch = 50 summary = Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Different studies have shown that viral pathogens, such as Thogoto viruses, Wad Medani virus, Nairobi sheep disease virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus and Tick-borne encephalitis virus [1, [6] [7] [8] , can be found in Rhipicephalus ticks. Numerous studies have used metagenomics to explore viral communities in different arthropod species and have in these identified viruses associated with a broad range of animals, plants and insects. However, the identified ORFs exhibit high genetic diversity to known quaranjavirus genomes, with an amino acid identity of only 32-55%, indicating that these represent novel viral sequences belonging to the Quaranjavirus genus. The parvovirus sequences identified in the current study had closest similarity to non-structural protein 1 of different densoviruses, which were shown previously to integrate into tick genomes such as in Ixodes, Amblyomma and Rhipicephalus genera [28, 29] . cache = ./cache/cord-270243-moxleyjg.txt txt = ./txt/cord-270243-moxleyjg.txt === reduce.pl bib === id = cord-269766-arjoemla author = Dutescu, R. Michael title = Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date = 2020-09-08 pages = extension = .txt mime = text/plain words = 2141 sentences = 124 flesch = 57 summary = title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS: We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. CONCLUSIONS: Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. To clarify this, we tested the tear fluid of confirmed hospitalized SARS-CoV-2 patients by PCR using a method not previously used for the collection of tear samples. In this study, we could confirm SARS-CoV-2 RNA positive tear samples by PCR in as many as 28% of determined SARS-CoV-2 patients by oropharyngeal swabs. 13 In a more recent cross-sectional study, only 1 (1.38%) conjunctival swab of 72 confirmed SARS-CoV-2 cases was tested positive. cache = ./cache/cord-269766-arjoemla.txt txt = ./txt/cord-269766-arjoemla.txt === reduce.pl bib === id = cord-271648-m2c5bvuj author = Ashour, Hossam M. title = Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date = 2020-03-04 pages = extension = .txt mime = text/plain words = 7536 sentences = 401 flesch = 56 summary = Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. However, unlike SARS-CoV, human-to-human transmission of MERS-CoV is not easy and has not been confirmed except in cases of very close contact with infected patients in health care settings [67] . Similar to the adaptation of SARS-CoV to human host, MERSr-CoVs that are circulating in bats had to undergo several amino acid changes in RBD of S protein to become capable of infecting camels and humans ( Figure 2 ) [74] . S protein of severe acute respiratory syndrome-associated coronavirus mediates entry into hepatoma cell lines and is targeted by neutralizing antibodies in infected patients Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) coronavirus S protein neutralizes the virus in a rhesus macaque SARS model cache = ./cache/cord-271648-m2c5bvuj.txt txt = ./txt/cord-271648-m2c5bvuj.txt === reduce.pl bib === id = cord-270594-62xotol3 author = He, Lei title = Identification and characterization of vp7 gene in Bombyx mori cytoplasmic polyhedrosis virus date = 2017-09-05 pages = extension = .txt mime = text/plain words = 4444 sentences = 266 flesch = 55 summary = In this study, the viral structural protein 7 (VP7) polyclonal antibody was prepared with immunized mouse to explore the presence of small VP7 gene-encoded proteins in Bombyx mori cytoplasmic polyhedrosis virus. The replication of BmCPV genome in the cultured cells and midgut of silkworm was decreased by reducing the expression level of vp7 gene using RNA interference. In immunoprecipitation experiments, using a polyclonal antiserum directed against the VP7, one additional shorter band in BmCPV infected midguts was detected, and then the band was analyzed with mass spectrum (MS), the MS results showed thatone candidate interacted protein (VP7 voltage-dependent anion-selective channel-like isoform, VDAC) was identified from silkworm. A novel protein was detected from the overexpression of vp7 gene in the BmCPV infected cultured cells, with VP7 antibody. Total proteins from the BmCPV infected silkworm midguts (from the first day to the twelfth day) were also extracted, and detected with VP7 antibody. cache = ./cache/cord-270594-62xotol3.txt txt = ./txt/cord-270594-62xotol3.txt === reduce.pl bib === id = cord-270940-acwkh6ed author = Kallio-Kokko, Hannimari title = Viral zoonoses in Europe date = 2005-06-29 pages = extension = .txt mime = text/plain words = 14695 sentences = 733 flesch = 46 summary = Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans. cache = ./cache/cord-270940-acwkh6ed.txt txt = ./txt/cord-270940-acwkh6ed.txt === reduce.pl bib === id = cord-269720-o81j3d1j author = Page, Kevin W. title = Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus date = 1990 pages = extension = .txt mime = text/plain words = 3553 sentences = 172 flesch = 59 summary = Primer extension, of a synthetic oligonucleotide complementary to the 5′ end of the nucleoprotein gene of TGEV was used to produce a single-stranded DNA copy of the leader RNA from the nucleoprotein mRNA species from TGEV and PRCV, the sequences of which were determined by Maxam and Gilbert cleavage. Comparison of the leader RNAs of TGEV and PRCV with published leader RNAs of other coronaviruses was used to identify areas of conserved sequence and potential secondary structure that may be involved in the transcription of coronavirus subgenomic mRNA species. The site, ACTAAAC, is seven nucleotides upstream of the nucleoprotein initiation codon and has also been found to precede all the TGEV structural protein genes and two of the three potential genes shown to be at the 5' end of mRNA species (15) (16) (17) . The two porcine coronavirus leader sequences were identical, indicating that the two viruses probably use the same RNA polymerase-leader complex binding site, ACTAAAC, for the synthesis of subgenomic mRNA species. cache = ./cache/cord-269720-o81j3d1j.txt txt = ./txt/cord-269720-o81j3d1j.txt === reduce.pl bib === id = cord-270604-u62437dh author = Cuthill, Jennifer Hoyal title = A SIMPLE MODEL EXPLAINS THE DYNAMICS OF PREFERENTIAL HOST SWITCHING AMONG MAMMAL RNA VIRUSES date = 2013-02-19 pages = extension = .txt mime = text/plain words = 7441 sentences = 322 flesch = 42 summary = We present an empirical test of two theoretical models of preferential host switching, using observed phylogenetic distributions of host species for RNA viruses of three mammal orders (primates, carnivores, and ungulates). To overcome the above complications, this study takes an alternative approach, and reconstructs the dynamics of preferential host switching among 38 recorded "multihost" RNA viruses of mammals, on phylogenies of their primate, carnivore, and ungulate hosts. To achieve this, approximate Bayesian computation (ABC) is used to test the fit of the two models of preferential host switching to the observed distributions of multihost RNA viruses on the phylogenies of their mammal hosts (primates, carnivores, and terrestrial ungulates). This indicates that ABC model selection was effective with each of the three sample sizes used for calculation of the HSD summary statistics (which corresponded to the number of observed host-virus associations, of 22 for primates, 12 for carnivores, and 4 for ungulates). cache = ./cache/cord-270604-u62437dh.txt txt = ./txt/cord-270604-u62437dh.txt === reduce.pl bib === id = cord-270670-cubh9jxc author = Domingo, E. title = Viruses as Quasispecies: Biological Implications date = 2006 pages = extension = .txt mime = text/plain words = 10489 sentences = 453 flesch = 39 summary = a Upon infection with an RNA virus (even with a single particle, as depicted here, enlarged about 10 6 times), viral replication leads to a mutant spectrum of related genomes, termed viral quasispecies. As further discussed in the text, in real infections multiple mutant spectra that can amount to a large number of replicating (or potentially replicating) genomes (up to 10 9 or even 10 12 per infected individual) provide highly dynamic mutant repertoire viral yields in cell culture, have been immensely powerful in characterizing the population dynamics of RNA viruses (see references in the reviews by Domingo and Holland 1997; Quiñones-Mateu and Arts 2002; Novella 2003; and the chapters by Quiñones-Mateu and Arts and Escarmís et al., this volume) . Despite these limitations, determination of nucleotide sequence heterogeneities in virus populations using correct reagents and adequate controls has consistently documented that most RNA viruses (and also some DNA viruses) consist of complex mutant spectra, with an average number of 1-100 mutations per genome (Sect. cache = ./cache/cord-270670-cubh9jxc.txt txt = ./txt/cord-270670-cubh9jxc.txt === reduce.pl bib === id = cord-269975-1ebmq7t8 author = Duplantier, Allen J. title = Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date = 2020-05-27 pages = extension = .txt mime = text/plain words = 12963 sentences = 580 flesch = 32 summary = None of the filoviruses or henipaviruses has any FDA-approved therapeutics or vaccines available for prevention or treatment of human disease, and while ribavirin is sometimes used to treat Lassa fever, it is not a terribly effective drug against this viral infection [28] . Many of the therapeutics that are in different stages of either preclinical or clinical development for select biothreat pathogens include small molecule antivirals (Tables 7.3 and 7.4), antibody (or antibody cocktails) against viruses or bacteria/virulence factors (Table 7 .5), and combination drug therapy (Table 7 .6). Although no FDA-approved HDT therapies are yet available for treating infectious diseases, we have summarized in this section the antimicrobial Primary screening of small molecule chemical libraries in the phenotypic HCI assay will identify compounds that inhibit pathogen infection as well as those that may contribute to cellular toxicity. cache = ./cache/cord-269975-1ebmq7t8.txt txt = ./txt/cord-269975-1ebmq7t8.txt === reduce.pl bib === id = cord-270473-5tok4mqk author = Nanda, S. K. title = Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome date = 2003-09-19 pages = extension = .txt mime = text/plain words = 7102 sentences = 384 flesch = 53 summary = We have previously shown that mitochondrial-aconitase binds specifically to the 3′ terminal 42 nucleotides of the Murine hepatitis virus (MHV) RNA along with three additional proteins of 70, 58 and 40 kDa to form a stable RNA-protein complex. The assays were done essentially as previously described [22] except that the partially purified post-mitochondrial lysates (approximately 3 µg total protein) were incubated at 22 • C with purified m-apo-aconitase (8-10 µg, graciously supplied by M.C. Kennedy, Gannon University, Erie, PA) and MHV-JHM 3 UTR RNA in ATPase buffer (20 mM Hepes, pH 7.4, 100 mM KCl, 5 mM MgCl 2 , 0.1% NP-40, 1 mM DTT, 1 mM ATP containing 2 µCi [γ-32 P]ATP plus cocktails of protease and phosphatase inhibitors). Gel supershift assays with anti-phosphotyrosine antibodies (Fig. 2B ) demonstrate that at least one of the proteins in the complex formed with MHV 3 (+)42 containing RNAs and m-aconitase, mtHSP70, HSP60, and HSP40 is tyrosine phosphorylated. cache = ./cache/cord-270473-5tok4mqk.txt txt = ./txt/cord-270473-5tok4mqk.txt === reduce.pl bib === id = cord-271972-qhr6iir6 author = Gaglia, Marta Maria title = Viruses and the cellular RNA decay machinery date = 2010-05-06 pages = extension = .txt mime = text/plain words = 6580 sentences = 393 flesch = 48 summary = [10] [11] [12] [13] [14] While the role of the Lsm proteins in eukaryotes is closely linked to mRNA degradation, several viruses use this complex instead to facilitate viral replication and, surprisingly, to enhance viral RNA stability. 25 It is notable that the virus-associated roles of the Lsm complex in mRNA stabilization, enhanced translation, and replication are at odds with its established cellular function in activating mRNA decapping to facilitate message degradation. However, the zinc-finger antiviral protein (ZAP), an important mediator of cellular response to retroviruses, 39 alphaviruses, 40 and filoviruses, 41 has been shown to bind the hRrp46 component of the exosome and to recruit the complex to viral mRNAs to promote their degradation. Nonetheless, given the widespread roles for the exosome in RNA quality control and turnover, viruses presumably activate this complex at least indirectly when triggering turnover of cellular mRNAs. For example, infection by select herpes and coronaviruses results in a global destruction of host messages. cache = ./cache/cord-271972-qhr6iir6.txt txt = ./txt/cord-271972-qhr6iir6.txt === reduce.pl bib === id = cord-272378-umvi0veu author = Subramanian, Subbaya title = Special Issue: MicroRNA Regulation in Health and Disease date = 2019-06-15 pages = extension = .txt mime = text/plain words = 2126 sentences = 120 flesch = 47 summary = MicroRNAs are single-stranded non-coding RNAs that are typically 18-25 nucleotides (nts) in length and are best known for their role in the post-transcriptional regulation of gene expression. However, it is possible that the frequency of MREs in the entire transcriptome of a given cell contributes to the dynamic gene regulatory process by acting as a sponge for mature miRNAs, thus regulating their functional availability. Thus, gene expression regulation is a complex process involving the dynamic interactions between miRNA-mRNA-lncRNA-circRNA. This Special Issue of Genes, entitled "MicroRNA Regulation in Health and Disease" consists of a series of articles spanning the clinical realm from colorectal cancer to pulmonary fibrosis. Somatostatin (SST) analogues were used to control the proliferation and symptoms of neuroendocrine tumors (NETs) in an article by Døssing et al., entitled "Somatostatin Analogue Treatment Primarily Induce miRNA Expression Changes and Up-Regulates Growth Inhibitory miR-7 and miR-148a in Neuroendocrine Cells" [15] . cache = ./cache/cord-272378-umvi0veu.txt txt = ./txt/cord-272378-umvi0veu.txt === reduce.pl bib === id = cord-271091-ffn59sgf author = Galao, Rui P title = Saccharomyces cerevisiae: a versatile eukaryotic system in virology date = 2007-10-10 pages = extension = .txt mime = text/plain words = 6539 sentences = 318 flesch = 42 summary = These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. Although the expression of viral proteins in yeast not always necessarily reflects their role in higher eukaryotes, here we selected some examples in which the analysis in yeast of their effect on highly conserved cellular processes such as cell cycle control, apoptosis or mRNA degradation have contributed to the current understanding of the pathogenesis of important viral pathogens such as HIV-1 and HCV. The identification of the host factors involved in viral RNA replication is a priority area of research in virology because it can provide new targets for antiviral drug development. cache = ./cache/cord-271091-ffn59sgf.txt txt = ./txt/cord-271091-ffn59sgf.txt === reduce.pl bib === id = cord-271127-l9bxqtqs author = Renault, Sylvaine title = Commensal and mutualistic relationships of reoviruses with their parasitoid wasp hosts date = 2005-02-28 pages = extension = .txt mime = text/plain words = 6784 sentences = 376 flesch = 54 summary = (2) Putative mutualistic virus: a reovirus present routinely in a wasp population in association with others viruses, but which does not appear to play a major role in the host/parasitoid relationship. DpAV-4 has been shown to be essential in the host/parasitoid relationship, as it is able to inhibit melanization, and to interfere with the cytolysis of host tissues in lepidopteran pupae parasitized by the wasp (Bigot et al., 1997b; Renault et al., 2002) . The occurrence of this domain in the protein coded by the DpRV-1 4.3 kb genomic fragment might be correlated with a possible role of this virus in its interaction with the ascovirus DpAV-4 in its lepidopteran and wasp hosts. Owing to the apparent absence of DpAV-1 virions or RNA within the egg, the transmission of DpRV-1 to the wasp larva during their development in host pupae was investigated. cache = ./cache/cord-271127-l9bxqtqs.txt txt = ./txt/cord-271127-l9bxqtqs.txt === reduce.pl bib === id = cord-271526-14nfqusv author = Molenkamp, Richard title = Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal date = 1997-12-08 pages = extension = .txt mime = text/plain words = 5535 sentences = 341 flesch = 56 summary = To determine the specificity of the nucleocapsid pro-RNA-protein complexes (Fig. 3, lanes 8-10 and 12) , tein-Ps180 RNA interaction in UV cross-linking assays, clearly indicating that the observed supershift was not competition experiments were performed. This interaction was studied by gel retardation and UV Lysates were prepared from the virus peak fractions (pcross-linking assays using an RNA probe containing the lysate) and from the gradient bottom fractions (b-lysate; 69-nt Ps and the N protein from MHV-A59 infected cell negative control). A structural model for coronaviruses was flanked by non-MHV sequences could confer specific proposed, in which a spherical core, composed of a combination of N and M proteins, was present in addition to encapsidation to a heterologous RNA in MHV infected INTERACTION BETWEEN NUCLEOCAPSID PROTEIN AND PACKAGING SIGNAL of a murine coronavirus in the absence of helper virus. cache = ./cache/cord-271526-14nfqusv.txt txt = ./txt/cord-271526-14nfqusv.txt === reduce.pl bib === id = cord-269866-3tpyj04y author = Liu, D. X. title = Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus date = 1992-01-31 pages = extension = .txt mime = text/plain words = 3164 sentences = 137 flesch = 50 summary = We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. cache = ./cache/cord-269866-3tpyj04y.txt txt = ./txt/cord-269866-3tpyj04y.txt === reduce.pl bib === id = cord-271504-t3y1w9ef author = Luo, Zichao title = Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date = 2020-06-16 pages = extension = .txt mime = text/plain words = 14361 sentences = 795 flesch = 42 summary = A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] . cache = ./cache/cord-271504-t3y1w9ef.txt txt = ./txt/cord-271504-t3y1w9ef.txt === reduce.pl bib === id = cord-272050-0u62j7nj author = Okamoto, Kimiyuki title = cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1 date = 2008-05-25 pages = extension = .txt mime = text/plain words = 5335 sentences = 262 flesch = 50 summary = In contrast, cis-preferential function of the viral encoded proteins or a coupling between translation and replication has been reported for several viruses, including Alfalfa mosaic virus (AMV) (Neeleman and Bol, 1999; van Rossum et al., 1996) , Clover yellow mosaic virus (CYMV) (White et al., 1992) , Bovine coronavirus (Chang et al., 1994) , Cowpea mosaic virus (van Bokhoven et al., 1993) , Poliovirus (Hagino-Yamagishi and Nomoto, 1989; Johnson and Sarnow, 1991; Novak and Kirkegaard, 1994) , Turnip crinkle virus (TCV) (White et al., 1995) , Tobacco etch virus (Mahajan et al., 1996; Schaad et al., 1996) , Tobacco mosaic virus (TMV) (Lewandowski and Dawson, 2000) , Tomato bushy stunt virus (TBSV) (Oster et al., 1998) , Turnip yellow mosaic virus (TYMV) (Weiland and Dreher, 1993) , and Rubella virus (Liang and Gillam, 2001) . cis-Acting core RNA elements required for negative-strand RNA synthesis and cap-independent translation are separated in the 3¢-untranslated region of Red clover necrotic mosaic virus RNA1 cache = ./cache/cord-272050-0u62j7nj.txt txt = ./txt/cord-272050-0u62j7nj.txt === reduce.pl bib === id = cord-271130-6s79q1c1 author = Filoni, Claudia title = Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date = 2017-11-17 pages = extension = .txt mime = text/plain words = 6584 sentences = 337 flesch = 47 summary = title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) Thus, the aim of this study was to perform additional serological and molecular tests and monitor the population of jaguarundis at FPZSP for FeLV infection and development of FeLV-related diseases for 5 years (2003) (2004) (2005) (2006) (2007) . Two captive-born male jaguarundis, the geriatric #1 and the mature adult #4, presented serological and molecular FeLV test results similar to the progressive FeLV infection outcome in domestic cats [25] . Moreover, consistent with findings in domestic cats with a progressive FeLV infection, no antibodies to FeLV antigens were detected in jaguarundis #1 and #4. Two captive-born jaguarundis, #2 and #22, presented test results similar to those reported for domestic cats with abortive FeLV infection and seroconversion as the only marker of FeLV exposure [28] . cache = ./cache/cord-271130-6s79q1c1.txt txt = ./txt/cord-271130-6s79q1c1.txt === reduce.pl bib === id = cord-271701-tx0lqgff author = te Velthuis, Aartjan J.W. title = The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date = 2011-10-29 pages = extension = .txt mime = text/plain words = 7357 sentences = 367 flesch = 56 summary = Commonly, its core subunit is a single RNA-dependent RNA polymerase (RdRp) that drives the production of template strands for replication, new genome molecules, and-in many RNA virus groupsalso subgenomic (sg) mRNAs. This canonical RdRp is structurally conserved among RNA viruses and widely accepted to drive catalysis of phosphodiester bond formation via a well-established reaction mechanism involving two metal ions that are coordinated by aspartate residues in its motifs A and C (3) (4) (5) . Interestingly, both nsp8 and nsp(7+8) are able to extend the RNA primers beyond template length in the presence of heparin ( Figure 4D and Supplementary Figure S2B ), suggesting that these extensions result from terminal transferase activity and not from template switching, as was previously observed for poliovirus 3D pol (20) . Subsequent alanine substitution of the N-terminal D/ ExD/E motif, composed of D50 and D52 in SARS-CoV, greatly affected primer extension activity on the CU 10 template as shown in Figure 5C . cache = ./cache/cord-271701-tx0lqgff.txt txt = ./txt/cord-271701-tx0lqgff.txt === reduce.pl bib === id = cord-273487-nfgjz6f9 author = Xu, Zaikun title = The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles date = 2012-11-10 pages = extension = .txt mime = text/plain words = 5354 sentences = 286 flesch = 56 summary = Loss of DDX56 helicase activity did not affect expression of WNV capsid protein (Fig. 4A ) nor its secretion from infected cells in the form of virus particles (Fig. 5A ). Data in Fig. 5B show that virus particles isolated from infected cells expressing helicase dead mutants D166N and E167Q contained 3-4 times less genomic RNA than those isolated from non-silencing cells or cells expressing RNAi-resistant wild type DDX56. Data in Fig. 6 show that in transfected or infected cells, the WNV capsid does not bind to the DEAD box helicase-containing region of DDX56 (DDX56-NT-myc), but rather, the C-terminal part of the protein, which was produced in cells expressing DDX56-CT-myc. The helicase activity of DDX56 is not essential for replication or assembly of WNV virions per se but our data indicate that it is critical for infectivity of virus particles. cache = ./cache/cord-273487-nfgjz6f9.txt txt = ./txt/cord-273487-nfgjz6f9.txt === reduce.pl bib === id = cord-274110-nyyunoha author = Orlinger, Klaus K. title = An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system date = 2010-04-26 pages = extension = .txt mime = text/plain words = 5113 sentences = 271 flesch = 50 summary = A cDNA comprising the complete genome of West Nile Virus (WNV) was generated by chemical synthesis using published sequence data, independent of any preformed viral components. The synthetic WNV, produced by transfection of in vitro transcribed RNA into cell culture, exhibited undistinguishable biological properties compared to the corresponding animal-derived wild-type virus. Taking advantage of the rapid progression of gene synthesis technology (for review [24] ), we intended to adopt such a synthetic approach to produce a flavivirus cDNA system for the generation of a synthetic WNV seed virus for use in vaccine development. The production and characterization of the resulting West Nile Virus, which fully matched the sequence of the in silico designed viral genome, confirms the feasibility and accuracy of the synthetic flavivirus reverse genetic system. Cover slips with fixed cells were dried, rehydrated with phosphate-buffered saline and treated with a polyclonal mouse anti-WNV serum (1:50 dilution) obtained after immunization of mice with a formalin-inactivated whole virus vaccine preparation. cache = ./cache/cord-274110-nyyunoha.txt txt = ./txt/cord-274110-nyyunoha.txt === reduce.pl bib === id = cord-271434-30nh2gc7 author = Tian, Fei title = A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing date = 2020-07-27 pages = extension = .txt mime = text/plain words = 4323 sentences = 209 flesch = 49 summary = In this work, we develop an automated centrifugal microfluidic system (Figure 1 ) consisting of a microfluidic disc and a customized instrument for rapid sample-to-answer detection of SARS-CoV-2 armored RNA particles with high sensitivity and specificity. Virus lysis buffer, RT-LAMP reagents, and mineral oil were sequentially injected into the microfluidic disc for on-chip release of viral nucleic acids, amplification of target RNA, and sealing of reaction unit. To demonstrate the automated detection of viral nucleic acids by the centrifugal microfluidic system, we loaded different concentrations of SARS-CoV-2 armored RNA particles with N gene (0.5, 1, 10, 10 2 , 10 3 copies/μL) into five reaction units of the microfluidic disc, and used the instrument to carry out on-chip release of viral nuclei acids, RT-LAMP, and realtime fluorescence signal detection. cache = ./cache/cord-271434-30nh2gc7.txt txt = ./txt/cord-271434-30nh2gc7.txt === reduce.pl bib === id = cord-271781-cfv0ta10 author = Patel, Kishan P. title = Transmission of SARS-CoV-2: an update of current literature date = 2020-07-07 pages = extension = .txt mime = text/plain words = 4469 sentences = 232 flesch = 47 summary = To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Additionally, studies have noted that its fecal-oral transmission potential may lie in the fact that prolonged viral shedding can occur in fecal matter-one case reported an asymptomatic COVID-19 patient experiencing viral detection in the stool for up to 42 days, while nasopharyngeal sampling was negative [31] . To oppose, in a retrospective review of nine COVID-19 pregnant mothers who underwent cesarean section, six patients had samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples tested for SARS-CoV-2, and all were negative [43] . cache = ./cache/cord-271781-cfv0ta10.txt txt = ./txt/cord-271781-cfv0ta10.txt === reduce.pl bib === id = cord-270892-ycc3csyh author = Rollinger, Judith M. title = The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date = 2010-12-13 pages = extension = .txt mime = text/plain words = 19628 sentences = 1166 flesch = 41 summary = [79] [80] [81] [82] Taken together, the results of natural cold studies as well as of experimental infection in human volunteers clearly demonstrate that HRV are able to replicate in the upper as well as in the lower airways. Such an anti-HRV drug would have to be (i) with broad spectrum activity because of the high number of HRV serotypes, (ii) administered very early in infection to demonstrate a good antiviral effect because of the fast infection kinetics, (iii) very safe because of the broad application by millions of people, and (iv) directed against a highly conserved target with low risk of resistance development. The HRV-induced CPE, infectious virus titers, viral protein expression, and RNA synthesis can be chosen as parameters to evaluate the anti-HRV activity of compounds in cell-culture based assays. Due to the lack of a small-animal model for HRV infection until 2008, the experimental human challenge model has to be used to approve effects of potential antiviral drugs under controlled conditions in preclinical studies. cache = ./cache/cord-270892-ycc3csyh.txt txt = ./txt/cord-270892-ycc3csyh.txt === reduce.pl bib === id = cord-271188-ewlxy5po author = Liu, Wei title = Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date = 2020-04-20 pages = extension = .txt mime = text/plain words = 4237 sentences = 245 flesch = 42 summary = Abbreviations 311, 2-hydroxy-1-naphthylaldehyde benzoyl hydrazine; 3CL pro , 3C-like protease; ABCE1, ATP binding cassette subfamily E member 1; ACE, angiotensin-converting enzyme 2; ADK, aryl diketoacids; AIDS, acquired immunodeficiency syndrome; APN, aminopeptidase N; AT2, small population of type II alveolar cells; BMP, bone morphogenetic proteins; Bp4aT, 2-benzoylpyridine 4-allyl-3thiosemicarbazone; Bp4eT, 2-benzoylpyridine 4-ethyl-3thiosemicarbazone; COVID-19, novel coronavirus pneumonia; CoVs, coronaviruses; DFO, deferoxamine; DFP, deferiprone; DPP4, dipeptidyl-peptidase 4.; E, envelope; EPDTC, Nethyl-Nphenyldithiocarbamic acid zinc; ER, endoplasmic reticulum; HCMV, human cytomegalovirus; HFE, homeostatic iron regulator protein; HIV, human immunodeficiency virus; HSA, human serum albumin; IP10, interferon-inducible protein 10; M, membrane; MBD, metal-binding domain; MCP1, monocyte chemotactic protein 1; MERS, Middle East respiratory syndrome; N, nucleocapsid; PBMC, peripheral blood mononuclear cells; PL pro , papain-like protease; PMA, phenylmercuric acetate; PPY, phenyl-1-pyridin-2yl-ethanone; RdRp, RNA-dependent RNA polymerase; ROS, reactive oxygen species; S, spike; SARS, severe acute respiratory syndrome; SARS-CoV-2, the 2019 novel coronavirus; SCD, sickle cell disease; TDT, toluene-3,4-dithiolato zinc; TfR1, transferrin receptor1 cache = ./cache/cord-271188-ewlxy5po.txt txt = ./txt/cord-271188-ewlxy5po.txt === reduce.pl bib === id = cord-274049-3gw65kpu author = Zhang, Han title = CRISPR Editing in Biological and Biomedical Investigation date = 2017-05-31 pages = extension = .txt mime = text/plain words = 6583 sentences = 333 flesch = 40 summary = © 2017 Wiley Periodicals, Inc. nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), have enabled the manipulation of genes by targeting DNA double-stranded breaks (DSBs) via non-homologous end-joining (NHEJ) or homology-directed repair (HDR) pathways [Rudin et al., 1989; Rouet et al., 1994; Choulika et al., 1995; Bibikova et al., 2002; Moscou and Bogdanove, 2009 ]. Overall, these studies empower a broader range of disease modeling applications via CRISPR-Cas9-mediated genome engineering, allowing researchers to uncover fundamental mechanisms in disease initiation, maintenance and procession, and explore the therapeutic potential of the CRISPR-Cas9 system to correct disease-causing mutations. Owing to its ability to completely disrupt target genes and the simplicity of designing potent sgRNAs, the CRISPR-Cas9 system has been extended to large-scale loss-of-function (LOF) genome screens in human cells [Koike-Yusa et al., 2014; Shalem et al., 2014; Wang et al., 2014; Zhou et al., 2014] . Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease cache = ./cache/cord-274049-3gw65kpu.txt txt = ./txt/cord-274049-3gw65kpu.txt === reduce.pl bib === id = cord-273326-gmw8gl2r author = Saiz, Juan-Carlos title = Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date = 2018-08-24 pages = extension = .txt mime = text/plain words = 7111 sentences = 293 flesch = 34 summary = In this line, and contrary to above mentioned report [73] , CQ, an FDA-approved anti-inflammatory 4-aminoquinoline and an autophagy inhibitor widely used as an anti-malaria drug that is administered to pregnant women at risk of exposure to Plasmodium parasites, was shown to have anti-ZIKV activity in different cell types (Vero cells, human brain microvascular endothelial cells (hBMECs), and human neural stem cells (NSCs)), affecting early stages of the viral life cycle, possibly by raising the endosomal pH and inhibiting the fusion of the envelope protein to the endosomal membrane [74, 75] . Similarly, by using a drug repurposing screening of over 6000 molecules, it was found that emricasan, a pan-caspase inhibitor that restrains ZIKV-induced increases in caspase-3 activity and is currently in phase 2 clinical trials in chronic hepatitis C virus (HCV)-infected patients, protected human cortical neural progenitor cells (NPC) in both monolayer and three-dimensional organoid cultures, showing neuroprotective activity without suppression of viral replication [82] . cache = ./cache/cord-273326-gmw8gl2r.txt txt = ./txt/cord-273326-gmw8gl2r.txt === reduce.pl bib === id = cord-272871-gu9ptt9y author = White, K.Andrew title = Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products date = 1991-08-31 pages = extension = .txt mime = text/plain words = 4609 sentences = 241 flesch = 60 summary = Abstract A small group of 1.2-kb RNAs present on polyribosoes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Figure 2 shows Northern blots of polyribosomal RNA extracted from CYMV-infected tissue containing the 1.2-kb RNAs. The 7.0-kb gRNA is identified by all probes (Fig. 2 , lanes a, c, e, g, i, and k; probes 1 to 6), but the 1 .O-kb sgRNA encoding coat protein hybridizes only to probes corresponding to the 3' region of the gRNA (Fig. 2 , lanes i and k; probes 5 and 6). The majority of the sequence of the prototype 1.2-kb RNA (Fig. 4) and of additional 1.2-kb RNAs is identical WHITE, BANCROFT, AND MACKIE with the corresponding region of CYMV gRNA reported by Sit et al. cache = ./cache/cord-272871-gu9ptt9y.txt txt = ./txt/cord-272871-gu9ptt9y.txt === reduce.pl bib === id = cord-271241-w1q46y63 author = Ruggiero, Emanuela title = Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy date = 2020-05-18 pages = extension = .txt mime = text/plain words = 8912 sentences = 495 flesch = 45 summary = Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. 1 In the past few decades, pharmaceutical and biotechnological advance has succeeded in developing new therapeutics for the management of different viral diseases: for example, anti-retroviral therapy against the human immunodeficiency virus (HIV), or the pan-genotypic direct-acting antiviral drugs used for hepatitis C (HCV) management. In addition, such PQSs are highly conserved, despite the high recombination rates that characterize viruses, suggesting a crucial role for G4s in viral evolution and replication, and corroborating their targeting as a valid pharmacological approach for antiviral therapy. cache = ./cache/cord-271241-w1q46y63.txt txt = ./txt/cord-271241-w1q46y63.txt === reduce.pl bib === id = cord-274080-884x48on author = Rumlová, Michaela title = In vitro methods for testing antiviral drugs date = 2018-06-30 pages = extension = .txt mime = text/plain words = 17989 sentences = 941 flesch = 41 summary = For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. cache = ./cache/cord-274080-884x48on.txt txt = ./txt/cord-274080-884x48on.txt === reduce.pl bib === id = cord-272268-8vrcwwll author = Kedersha, Nancy title = Chapter 4 Regulation of Translation by Stress Granules and Processing Bodies date = 2009-10-27 pages = extension = .txt mime = text/plain words = 8598 sentences = 456 flesch = 45 summary = Cytoplasmic stress granules (SGs) and processing bodies (PBs) are dynamic structures that form in response to stress-induced translational arrest. Critical components of the ''cell biology'' of protein translation are mRNP granules known as processing bodies (PBs) and stress granules (SGs). These transient cytoplasmic ''structures'' are actively assembled from untranslated mRNA by a host of RNA-binding proteins, which determine whether specific transcripts will be reinitiated, degraded, or stored. In 1999, it was noted that stress-induced translational arrest causes untranslated mRNPs to assemble into large cytoplasmic ''SGs,'' whose formation is triggered by, and dependent upon, the phosphorylation of eIF2a. Virus infection also induces the assembly of SGs and PBs suggesting that RNA granules play a role in reprogramming mRNA translation/decay during viral infection. RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2a to the assembly of mammalian stress granules cache = ./cache/cord-272268-8vrcwwll.txt txt = ./txt/cord-272268-8vrcwwll.txt === reduce.pl bib === id = cord-274353-tzlcpx7q author = McDermott, Amy title = Inner Workings: Molecular biologists offer “wartime service” in the effort to test for COVID-19 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1987 sentences = 99 flesch = 46 summary = In order to legally perform diagnostic work on human samples in the United States, a lab needs certification from the Centers for Medicare & Medicaid Services, through its Clinical Laboratory Improvement Amendments (CLIA) program (2) . On March 12, for example, California Governor Gavin Newsom issued an executive order suspending certification and licensure requirements for any researcher with relevant skills who meets CLIA requirements to run the COVID-19 test; such a person may now temporarily run the assays under the supervision of a medical laboratory scientist in a CLIA-certified lab (4). To get around its limitations, UC Berkeley is temporarily extending the clinical lab's CLIA certificate into the larger Innovative Genomics Institute on campus, and will staff it with volunteer researchers who have the relevant skills to run the assay, supervised by a licensed medical laboratory scientist. cache = ./cache/cord-274353-tzlcpx7q.txt txt = ./txt/cord-274353-tzlcpx7q.txt === reduce.pl bib === id = cord-272579-aenuyht0 author = Emmett, Stevan R. title = The Cell Cycle and Virus Infection date = 2005 pages = extension = .txt mime = text/plain words = 6456 sentences = 388 flesch = 60 summary = A number of different viruses interact with the cell cycle in order to subvert host-cell function and increase the efficiency of virus replication; examples can be found from DNA, retro, and RNA viruses. The majority of studies have been conducted on DNA and retroviruses whose primary site of replication is the nucleus, but increasingly a number of researchers are demonstrating that RNA viruses, whose primary site of replication is normally the cytoplasm, also interfere with the cell cycle. Viral interference with the cell cycle can have a myriad of different effects to improve virus infection, for example to promote replication of viral DNA genomes, or to delay the cell cycle to allow sufficient time for RNA virus assembly. Increasingly we have found that proteomic approaches allow the rapid analysis of a whole plethora of cell cycle proteins that may be affected by virus infection. cache = ./cache/cord-272579-aenuyht0.txt txt = ./txt/cord-272579-aenuyht0.txt === reduce.pl bib === id = cord-272573-wxqly479 author = Maia Chagas, Andre title = Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date = 2020-04-24 pages = extension = .txt mime = text/plain words = 5074 sentences = 317 flesch = 55 summary = Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics. Community and commercial open source efforts in diagnostic technology to date have focused on four areas: i) open platforms for scaling reactions as exemplified by Opentrons ( Fig 3A) [28] , an open source lab automation platform that has been working with BP Genomics and the Open Medicine Institute to automate up to 2,400 tests per day and achieve US FDA EUA approval and is now automating COVID-19 testing at the Biomedical Diagnostic Center (CBD) of Hospital Clinic of Barcelona; ii) trying to fill gaps where less attention is being paid by clinical diagnostics companies, such as Chia Bio's Open qPCR (Fig 3B) environmental test kit for surveillance via surface swabs [111] ; iii) distributed reproduction of rapidly-published, lab-scale protocols, seen within the OpenCOVID initiative hosted by Just One Giant Lab [39] which involves many community labs worldwide; iv) initiatives such as the Open Enzyme Collection [93] , Free Genes [94] and Biomaker Challenge [112] which are investigating new approaches to foundational technologies such as reagents and instrumentation, with a view to building capacity and resources or global science and medicine to face a future pandemic. cache = ./cache/cord-272573-wxqly479.txt txt = ./txt/cord-272573-wxqly479.txt === reduce.pl bib === id = cord-275720-kf9m4zho author = Cho, Won Kyong title = Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date = 2012-05-06 pages = extension = .txt mime = text/plain words = 7132 sentences = 390 flesch = 47 summary = At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. This is the first report of a genome-wide fungal gene expression analysis during mycovirus infection using a 3′ tiling microarray, and our findings show global differences in host cellular pathways in F. For example, according to the qRT-PCR and microarray results, the transcript levels for three genes, including FGSG_01379, FGSG_03143, and FGSG_03911, were highly reduced at both 36 h and 120 h, whereas FGSG_03788, FGSG_00023, FGSG_07804, FGSG_07801, and FGSG_13222 were strongly induced regardless of the time point ( Figure 3A -C). graminearum harboring FgV1-DK21 in detail, samples were harvested at two different time points, thus providing lists of differentially expressed genes early and late in the host containing FgV1-DK21 as compared to an uninfected strain. cache = ./cache/cord-275720-kf9m4zho.txt txt = ./txt/cord-275720-kf9m4zho.txt === reduce.pl bib === id = cord-273609-whm2ce4u author = Li, Qingdi Quentin title = Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment date = 2012-06-29 pages = extension = .txt mime = text/plain words = 8166 sentences = 373 flesch = 47 summary = title: Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment BACKGROUND: The selection of stable and suitable reference genes for real-time quantitative PCR (RT-qPCR) is a crucial prerequisite for reliable gene expression analysis under different experimental conditions. The most commonly used reference genes, including β-actin, cyclophilin, GAPDH, tubulin, and 18S and 28S ribosomal RNAs, have shown variable expression levels in different cells and tissues under different conditions, and therefore they are unsuitable for normalization purposes owing to large measurement error [6, . As seen in Table 7 , normalization of the RT-qPCR data against the reference genes suggested as optimal by the four software packages (hkgFinder, geNorm, BestKeeper, and NormFinder) or the 2 -ΔΔCT method, gave comparable relative expression levels of the target genes under fluconazole treatment in C. cache = ./cache/cord-273609-whm2ce4u.txt txt = ./txt/cord-273609-whm2ce4u.txt === reduce.pl bib === id = cord-274536-fv7mltj7 author = Tong, Yongqing title = Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3120 sentences = 188 flesch = 59 summary = RESULTS: Of the enrolled 1008 severe patients, the nasopharyngeal swab specimens showed the highest positive rate of SARS-CoV-2 RNA (71.06%), followed by alveolar lavage fluid (66.67%), oropharyngeal swab (30.77%), sputum (28.53%), urine (16.30%), blood (12.5%), stool (12.21%), anal swab (11.22%) and corneal secretion (2.99%), and SARS-CoV-2 RNA couldn't be detected in other types of specimen in this study. Firstly, we analyzed the possible sites of infection in hospitalized patients with COVID-19 by detecting viral RNA with 12 different types of specimens, including nasopharyngeal swab, oropharyngeal swab, sputum, bronchoalveolar lavage fluid (BALF), stool, anal swab, urine, peritoneal dialysis fluid (PDF), blood, sweat, cerebrospinal fluid (CSF) and corneal secretion. The 20 discharged cases of COVID-19, the criteria [12] for which was the SARS-CoV-2 virus RNA detection negative in two consecutive respiratory specimens (at least 1 day of time interval of sampling) for patients who have reached the standards of isolation period (14 days) after clinical cured, during the isolation period were selected to detect SARS-CoV-2 RNA with multiple specimens including nasopharyngeal swab, oropharyngeal swab, sputum, stool, anal swab, urine and blood. cache = ./cache/cord-274536-fv7mltj7.txt txt = ./txt/cord-274536-fv7mltj7.txt === reduce.pl bib === id = cord-275225-fvq8hezk author = Hornyák, Ákos title = Detection of subgenomic mRNA of feline coronavirus by real-time polymerase chain reaction based on primer-probe energy transfer (P-sg-QPCR) date = 2012-02-18 pages = extension = .txt mime = text/plain words = 7138 sentences = 337 flesch = 50 summary = The quantitative sg-mRNA detection method revealed more than 10-50,000 times increase of the M gene sg-mRNA in organ materials of feline infectious peritonitis cases, compared to those of the enteric FCoV variants present in the faeces of normal, healthy cats. The quantitative sg-mRNA detection method revealed more than 10-50,000 times increase of the M gene sg-mRNA in organ materials of feline infectious peritonitis cases, compared to those of the enteric FCoV variants present in the faeces of normal, healthy cats. These results indicate the applicability of the new P-sg-QPCR test as a powerful novel tool for the better detection and quantitation of FCoV and for the improved diagnosis of feline infectious peritonitis, this important disease of the Felidae, causing serious losses in the cat populations at a global scale. The detailed analysis of the feline infectious peritonitis positive cat samples by SYBR-Green QPCR method revealed that the following organs harbour FCoV most frequently: lungs 6/6 (100%), liver 6/6 (100%), kidney 10/11 (90.9%), mesenteric lymph node 18/20 (90%), spleen 16/20 (80%) and gut 15/10 (66.7%). cache = ./cache/cord-275225-fvq8hezk.txt txt = ./txt/cord-275225-fvq8hezk.txt === reduce.pl bib === id = cord-271419-v6dfel3l author = Adachi, Shun title = Commentary: Origin and evolution of pathogenic coronaviruses date = 2020-04-21 pages = extension = .txt mime = text/plain words = 1211 sentences = 77 flesch = 51 summary = Among viruses, some coronaviruses (CoVs) are notorious for causing the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The said article has successfully predicted today's COVID-19 outbreak by pointing out that novel pathogenic variants will readily emerge from very diversified severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs) of the bat origin through their close coexistence and high genetic recombination ability (Figure 1) . Since RNA viruses are easy to mutate and coronaviruses have high potentials for recombination, we can easily see the track of mutations and evolutions of the viruses, especially for SARS-CoV and MERS-CoV. Thus, to consider the origin of new pathogens and the prevention of their transmission to humans, and control of the viruses, not only studies on SARS-CoV, MERS-CoV, and SARS-CoV-2, but also those on their relatives SARSr-CoVs and MERSr-CoVs are recommendable for bats tracked for the ecology and evolution. cache = ./cache/cord-271419-v6dfel3l.txt txt = ./txt/cord-271419-v6dfel3l.txt === reduce.pl bib === id = cord-273019-hbpfz8rt author = Glingston, R. Sahaya title = Organelle dynamics and viral infections: at cross roads date = 2018-06-25 pages = extension = .txt mime = text/plain words = 9513 sentences = 486 flesch = 35 summary = Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host's fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . cache = ./cache/cord-273019-hbpfz8rt.txt txt = ./txt/cord-273019-hbpfz8rt.txt === reduce.pl bib === id = cord-275683-1qj9ri18 author = Roux, Simon title = Metagenomics in Virology date = 2019-06-12 pages = extension = .txt mime = text/plain words = 5891 sentences = 225 flesch = 37 summary = Against the background of an extensive viral diversity revealed by metagenomics across many environments, new sequence assembly approaches that reconstruct complete genome sequences from metagenomes have recently revealed surprisingly cosmopolitan viruses in specific ecological niches. However, these techniques can only detect previously known viruses, and often require Box 1 Use of complementary methods to target different types of viruses A number of approaches have been developed to specifically select and survey the genetic material contained by virus particles in a given sample. Virus sequences obtained from "bulk" metagenomes will typically reflect viruses infecting their host cell at the time of sampling, either actively replicating or not, while viromes enables a deeper and more focused exploration of the virus diversity in a specific site or sample. With viral metagenomics being applied to a larger set of samples and environments, and with bioinformatic analyses including genome assembly and interpretation constantly improving, novel groups of dominant and widespread viruses may thus be progressively revealed across many environments. cache = ./cache/cord-275683-1qj9ri18.txt txt = ./txt/cord-275683-1qj9ri18.txt === reduce.pl bib === id = cord-276988-bvsz5q6d author = Neu, Carolin T. title = Post-Transcriptional Expression Control in Platelet Biogenesis and Function date = 2020-10-15 pages = extension = .txt mime = text/plain words = 11394 sentences = 581 flesch = 38 summary = Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs. Blood platelets-the major players in hemostasis-are small anucleate cell fragments with a characteristic discoid shape and a diameter of 1 to 3 µm that originate from megakaryocytes (MKs). The m 7 G cap and poly(A) tail promote mRNA translation and stability, while the UTRs expose sequences for RNA-binding proteins (RBPs) and regulatory sites for microRNA (miRNA)-mediated translational and degradation control [45, [52] [53] [54] . Moreover, RNA-Seq analysis of platelet miRNAs in patients with myocardial infarction revealed nine differentially expressed platelet miRNAs compared to healthy controls, which were released upon platelet aggregation and taken up by endothelial cells via a vesicle-dependent mechanism [80] . Megakaryopoiesis, megakaryocyte maturation, as well as platelet formation, were shown to be highly complex processes that are regulated on multiple levels including epigenetic, transcriptional as well as post-transcriptional gene expression control mechanisms. cache = ./cache/cord-276988-bvsz5q6d.txt txt = ./txt/cord-276988-bvsz5q6d.txt === reduce.pl bib === id = cord-274569-jh0dyyz7 author = Alenquer, Marta title = Exosome Biogenesis, Regulation, and Function in Viral Infection date = 2015-09-17 pages = extension = .txt mime = text/plain words = 7844 sentences = 447 flesch = 43 summary = These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. This mechanism was recently reported for HCV [113] , where exosomes derived from infected human hepatoma cells containing full-length viral RNA, along with core and envelope proteins [115] , were shown to be infectious and a major route of transmission. demonstrated that B lymphocytes infected with Epstein-Barr virus (EBV), a human gammaherpesvirus associated with a variety of lymphoblastoid and epithelial cancers, released exosomes containing MHC II molecules, and that these vesicles were capable of activating specific CD4 + T cell clones in vitro [122] . cache = ./cache/cord-274569-jh0dyyz7.txt txt = ./txt/cord-274569-jh0dyyz7.txt === reduce.pl bib === id = cord-275602-cog4nma0 author = Watkins, Kevin title = Emerging Infectious Diseases: a Review date = 2018-06-22 pages = extension = .txt mime = text/plain words = 4672 sentences = 278 flesch = 49 summary = SUMMARY: In addition to the aforementioned pathogens, the Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, Nipah virus, New Delhi metallo-ß-lactamase-1 Enterobacteriaceae, Rift Valley Fever virus, and Crimean-Congo Hemorrhagic Fever virus are reviewed. In 1992, an expert committee that produced the Institute of Medicine report on emerging infections defined them as "new, reemerging, or drug-resistant infections whose incidence in humans has increased within the past two decades or whose incidence threatens to increase in the near future." Additionally, six major contributors to these diseases were presented and included changes in human demographics and behavior, advances in technology and changes in industry practices, economic development and changes in land-use patterns, dramatic increases in volume and speed of international travel and commerce, microbial adaptation and change, and breakdown of public health capacity [1] . The World Health Organization has prioritized a number of infectious diseases as requiring urgent need for research and development given the concern for potential of severe outbreaks. cache = ./cache/cord-275602-cog4nma0.txt txt = ./txt/cord-275602-cog4nma0.txt === reduce.pl bib === id = cord-274401-pjyvg53w author = Hrkach, Jeff title = From micro to nano: evolution and impact of drug delivery in treating disease date = 2020-05-08 pages = extension = .txt mime = text/plain words = 2055 sentences = 100 flesch = 38 summary = An early wave featured injectable (i.e., intramuscular, subcutaneous) biodegradable polymeric microspheres to control drug release profiles for peptides and small molecules (e.g., Lupron Depot®, Risperdal Consta®). With these early successes for microspheres, research shifted to exploring systemic delivery by intravenous injection, which required smaller particle sizes and modified surface properties (e.g., PEGylation) to enable long circulation times. These new innovations resulted in the nanoparticle medicines Doxil® and Abraxane®, designed to improve the therapeutic index of cytotoxic cancer agents by decreasing systemic exposure and delivering more drug to tumors. In 2003, the FDA approved Risperdal Consta®, a controlled release form of risperidone encapsulated in PLG microspheres that enabled dosing once every 2 weeks by intramuscular injection. The many successes of controlled release microsphere-based medicines led innovators to explore the potential of drug delivery for systemic administration to reach specific sites of disease, with particular interest in targeting tumors for treating cancer. cache = ./cache/cord-274401-pjyvg53w.txt txt = ./txt/cord-274401-pjyvg53w.txt === reduce.pl bib === id = cord-273379-w8vy5rl8 author = Mizutani, Tetsuya title = Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA date = 2000-09-30 pages = extension = .txt mime = text/plain words = 4033 sentences = 184 flesch = 48 summary = RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5′ 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. We purified genome-length RI without contamination of any detectable level of MHV subgenomic mRNAs. We used RNase protection assays to look for nascent subgenomic mRNAs containing the leader sequence in the genome-length RI. If leader-sequence-containing subgenomic mRNA 6 elongates on the genome-length RI, then the RNase protection assay using probe 1 and purified radiolabeled genome-length RI should produce a radiolabeled 300-nt-long RNA fragment (300-nt fragment) that corresponds to the 5Ј-end 300 nt of nascent mRNA 6 (see Fig. 3A ). RNase A treatment of the gel-purified genome-length RI produced RF 1 (Fig. 2B) , and the RNase protection assay demonstrated the presence of nascent leader-sequence-containing subgenomic mRNAs in the genome-length RI. cache = ./cache/cord-273379-w8vy5rl8.txt txt = ./txt/cord-273379-w8vy5rl8.txt === reduce.pl bib === id = cord-275403-g4rohhtt author = Bautista, Elida M. title = Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus date = 2002-07-05 pages = extension = .txt mime = text/plain words = 7432 sentences = 401 flesch = 48 summary = To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. As initial proof of helicase-like activity, experiments were performed to test the ability of purified PRRSV-14 nsp10 protein to hydrolyze radiolabeled ribonucleotides in the presence or absence of polyribonucleotides. To further analyze the predicted helicase activity of the PRRSV nsp10 protein, experiments were performed using duplex substrates prepared with synthetic oligonucleotides containing single-strand regions at the 3Ј or 5Ј ends and short duplex regions (21 and 24 bp). The 5Ј-to-3Ј orientation of the unwinding activity of the PRRSV helicase was further confirmed in experiments using substrates prepared with in vitro transcribed RNA that contained singlestrand regions at the 5Ј end of both strands and duplex regions of 67 bp (5Ј5ЈDuplex #1) and 85 bp (5Ј5ЈDuplex #2), as shown in Fig. 9B . cache = ./cache/cord-275403-g4rohhtt.txt txt = ./txt/cord-275403-g4rohhtt.txt === reduce.pl bib === id = cord-272702-7uc4ozjy author = Graham, T. G. W. title = Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date = 2020-09-18 pages = extension = .txt mime = text/plain words = 8061 sentences = 483 flesch = 59 summary = We therefore tested whether we could detect SARS-CoV-2 RNA by adding 1 μ l of each swab sample to 20 μ l TaqPath reactions containing the N1, N2, and RNase P (RP) probes ( Fig 2A) . Taken together, these results show that RT-qPCR with BEARmix can detect SARS-CoV-2 in clinical samples, either using purified RNA or by direct addition of swab samples, albeit with somewhat less sensitivity than commercial TaqPath master mix. To evaluate a complete protocol in which swab samples are collected into PK solution and then added directly to BEARmix RT-PCRs, we prepared contrived swab samples in which live virus was mixed with pathogenfree human nasal fluid prior to dilution into either DNA/RNA Shield, VCM containing 0.4 mg/ml proteinase K, or a solution of 0.4 mg/ml proteinase K in water (Fig 6) . Here we have developed simple, academic laboratory-derived methods for RNA extraction, direct sample addition, and RT-PCR detection that provide low-cost alternatives to the use of commercial kits (Fig 8) . cache = ./cache/cord-272702-7uc4ozjy.txt txt = ./txt/cord-272702-7uc4ozjy.txt === reduce.pl bib === id = cord-275252-4e3cn50u author = Rad SM, Ali Hosseini title = Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date = 2020-05-16 pages = extension = .txt mime = text/plain words = 4368 sentences = 302 flesch = 53 summary = In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. A common primary focus of mutational analysis of emerging viruses is the alteration in amino acid sequence of viral proteins that may provide enhanced or new functions for virus replication, immune avoidance, or spread. However, the potential of these mutations to impact upon RNA structure and miRNA recognition provides a basis for ongoing monitoring of viral evolution at these sites in the SARS-CoV-2 genome. cache = ./cache/cord-275252-4e3cn50u.txt txt = ./txt/cord-275252-4e3cn50u.txt === reduce.pl bib === id = cord-277355-si3g5dih author = He, Yu title = The role of capsid in the flaviviral life cycle and perspectives for vaccine development date = 2020-09-17 pages = extension = .txt mime = text/plain words = 6885 sentences = 319 flesch = 45 summary = Although current studies on flaviviruses have shown that the flaviviral assembly process does not exhibit a necessary step occurring in the cell nucleus, it has been well demonstrated that many mosquito-borne flavivirus CPs partially localize in the cell nucleus [44] [45] [46] [47] [48] ; in the cytoplasm, in addition to localizing in the ER, DENV CP and ZIKV CP have also been demonstrated to accumulate on LDs [13, 16] , but the link between the functional importance and the subcellular distribution of CPs is still unclear. Interestingly, a study showed that a CD61-71 mutant had abolished ZIKV infectious virion production that was then restored by adaptive mutations (prM-E21K and NS2B-E27G) only in BHK21 cells but not in other cell lines (indicate complex interactions that apparently occur between structural and non-structural proteins during virus replication and/or assembly), making this live virus function like a single-round infectious particle (SRIP) in vivo and safely inducing strong immunity protection against vertical transmission in mice [33] . cache = ./cache/cord-277355-si3g5dih.txt txt = ./txt/cord-277355-si3g5dih.txt === reduce.pl bib === id = cord-272729-nbgdmavr author = Kim, Youngnam title = Ribavirin efficiently suppresses porcine nidovirus replication date = 2012-10-27 pages = extension = .txt mime = text/plain words = 6654 sentences = 296 flesch = 44 summary = Investigations into the mechanism of action of ribavirin against PRRSV and PEDV revealed that the addition of guanosine to the ribavirin treatment significantly reversed the antiviral effects, suggesting that depletion of the intracellular GTP pool by inhibiting IMP dehydrogenase may be essential for ribavirin activity. Further experiments revealed that suppression of ribavirin affects post-entry steps of the replication cycle of PRRSV and PEDV, including viral genomic and sg RNA synthesis, viral protein expression, and virus production. Several mechanisms of action for the antiviral activity of ribavirin have been suggested, including a reduction in cellular GTP pools via inosine monophosphate dehydrogenase (IMPDH) inhibition and increased mutation frequency on the virus genome leading to error catastrophe (Graci and Cameron, 2006) . Treatment of cells with ribavirin resulted in significant attenuation of postentry steps during the replication of porcine nidovirus, as determined by lower progeny production, diminished viral protein expression, and decreased synthesis of genomic RNA and sg mRNA. cache = ./cache/cord-272729-nbgdmavr.txt txt = ./txt/cord-272729-nbgdmavr.txt === reduce.pl bib === id = cord-275859-ix8du1er author = Mouzakis, Kathryn D. title = HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date = 2012-12-15 pages = extension = .txt mime = text/plain words = 6721 sentences = 322 flesch = 50 summary = In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Here, we investigate the role of the HIV-1 RNA structure in frameshifting, focusing on elucidating the relationships between frameshift efficiency and (i) the downstream RNA stem-loop thermodynamic stability, (ii) spacer length and (iii) surrounding genomic secondary structure. Our data further indicate that the base pairs important for frameshifting are located at a distance of 8 nt from the slippery site, which corresponds to the length of the spacer and is consistent with a structural model of the ribosome paused at the frameshift site. Instead, we observe a strong correlation (R 2 = 0.88) between frameshift efficiency and local stability of the first 3 bp at the base of the stem-loop using a one-phase exponential decay function ( Figure 3C and Supplementary Table S3 ). cache = ./cache/cord-275859-ix8du1er.txt txt = ./txt/cord-275859-ix8du1er.txt === reduce.pl bib === id = cord-273910-fna7s9te author = Bochud, Pierre-Yves title = Innate immunogenetics: a tool for exploring new frontiers of host defence date = 2007-07-20 pages = extension = .txt mime = text/plain words = 7063 sentences = 391 flesch = 39 summary = Recent immunogenetic studies have associated polymorphisms of the genes encoding TLRs, NLRs, and key signal-transducing molecules, such as interleukin-1 receptor-associated kinase 4 (IRAK4), with increased susceptibility to, or outcome of, infectious diseases. With the availability of high-throughput genotyping techniques, it is becoming increasingly evident that analyses of genetic polymorphisms of innate immune genes will further improve our knowledge of the host antimicrobial defence response and help in identifying individuals who are at increased risk of life-threatening infections. Since the innate immune system senses only a limited number of highly conserved microbial-associated molecular patterns 23 via a limited number of receptors and signalling molecules, as anticipated, several polymorphisms have been found to confer an increased susceptibility to specifi c pathogens (table 2, table 3 , and fi gure 4). [36] [37] [38] Taken together, these data clearly show that mutations in the genes encoding TLRs and downstream signal-transducing molecules infl uence innate immune responses and increase susceptibility to many infectious diseases. cache = ./cache/cord-273910-fna7s9te.txt txt = ./txt/cord-273910-fna7s9te.txt === reduce.pl bib === id = cord-010092-uftc8inx author = nan title = Abstract of 29th Regional Congress of the ISBT date = 2019-06-07 pages = extension = .txt mime = text/plain words = 233304 sentences = 13171 flesch = 54 summary = Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. cache = ./cache/cord-010092-uftc8inx.txt txt = ./txt/cord-010092-uftc8inx.txt === reduce.pl bib === id = cord-276739-84vf5bts author = Sakurai, Akira title = Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date = 2011-08-22 pages = extension = .txt mime = text/plain words = 3311 sentences = 182 flesch = 54 summary = Using SHRT-PCR, 86 strains of influenza viruses isolated by the Tokyo Metropolitan Institute of Public Health were tested; the results showed 100% sensitivity and specificity for each influenza A and B virus, and swine-origin influenza virus. This method offers high sensitivity and selectivity, but generally requires approximately 2 h per run; therefore, qRT-PCR is not appropriate for rapid virus detection or subtyping in outbreaks of fast-spreading and/or highly pathogenic viruses at public health centers, hospitals, airports, and other public transportation hubs. The commercial reaction mixture was from the qRT-PCR kit, RNA-Direct TM SYBR ® Green Real-time PCR Master Mix (Toyobo, Osaka, Japan; http://www.toyobo.co.jp/e/). The SHRT-PCR system detects the highly conserved sequence of the corresponding viral genome, and the newly designed primer sets targeted for typing MP segments do not exhibit any cross reactions among other influenza viruses (Table 5 ). cache = ./cache/cord-276739-84vf5bts.txt txt = ./txt/cord-276739-84vf5bts.txt === reduce.pl bib === id = cord-273723-srfypn7j author = Omar, Sarah title = Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date = 2020-07-30 pages = extension = .txt mime = text/plain words = 2932 sentences = 135 flesch = 46 summary = title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis As far as we are aware, there are currently no published data on the duration of RNA positivity in the upper respiratory of patients with mild COVID-19 that could inform a public health assessment of RT-qPCR as a tool for monitoring home isolation. At 14 days after onset, the earliest moment to discontinue home isolation currently recommended in Germany [18] , 53.5% of COVID-19 patients still had detectable SARS-CoV-2 RNA (Figure 2) . Duration of SARS-CoV-2-RNA positivity in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 (n = 537) For cases where laboratory monitoring is indispensable, knowledge of the RT-qPCR threshold cycle may improve our judgement on whether a positive result indicates infectiousness or not [20] . cache = ./cache/cord-273723-srfypn7j.txt txt = ./txt/cord-273723-srfypn7j.txt === reduce.pl bib === id = cord-274773-3jhka8wl author = Zhang, Jialin title = Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date = 2019-09-30 pages = extension = .txt mime = text/plain words = 3943 sentences = 207 flesch = 51 summary = title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge High levels of IgG antibodies and NA were also detected in the serum of neonatal piglets born to immunized sows, which suggests that the antibodies were successfully transferred through the colostrum and milk. The protective efficacy of passive immunity elicited by the inactivated PDCoV vaccine against challenge with a highly pathogenic virulent strain in neonatal piglets born to immunized sows was investigated. These results suggest that within the first week, IgG antibodies in colostrum and milk of immunized sows could provide protection for piglets against TGEV virulent challenge. Moreover, high levels of IgG antibodies and NA responses were detected in serum, which protected the piglets against virulent PDCoV challenge. Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5-day-old neonatal piglets from virulent challenge cache = ./cache/cord-274773-3jhka8wl.txt txt = ./txt/cord-274773-3jhka8wl.txt === reduce.pl bib === id = cord-272666-3uidpr79 author = Doyle, Nicole title = Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date = 2018-09-06 pages = extension = .txt mime = text/plain words = 7472 sentences = 358 flesch = 52 summary = In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. In a subsequent study by others, it was shown that expression of only nsp3 and 4 from either MERS-CoV or SARS-CoV was able to induce DMV formation, and furthermore, addition of nsp6 made no difference to their shape or size, and did not induce the spherule-like structures seen following infection with whole virus [26] . cache = ./cache/cord-272666-3uidpr79.txt txt = ./txt/cord-272666-3uidpr79.txt === reduce.pl bib === id = cord-272576-ez731lif author = Wada, Yoshiko title = Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count date = 2016-11-03 pages = extension = .txt mime = text/plain words = 5641 sentences = 273 flesch = 50 summary = To face the world-wide threats caused by zoonotic RNA viruses, which suddenly cause serious outbreaks by invasion from nonhuman hosts and mutate rapidly, we must understand the molecular evolutionary changes in their genome sequences extensively by innovating various technologies, including those used in big data analyses, e.g., large-scale word count. The present time-series analysis on influenza A genomes showed that the 20-mers exhibiting the most evident directional changes observed in common for three different subtypes corresponded to several influenza A siRNAs, which were experimentally validated. The present study focused on time-series changes, but not on data variations caused largely by random mutations and sequencing uncertainty, and therefore, average characteristics of strains isolated in a similar period were analyzed, summing up the sequences isolated in one month and calculating an averaged mononucleotide composition for each month (Fig. 1b) . cache = ./cache/cord-272576-ez731lif.txt txt = ./txt/cord-272576-ez731lif.txt === reduce.pl bib === id = cord-275565-xerr4vki author = Kumar, Manish title = Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date = 2020-09-15 pages = extension = .txt mime = text/plain words = 3456 sentences = 230 flesch = 58 summary = For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and filtration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. Thus, there still remains questions pertaining to: i) capability of conventional WWTPs to reduce the abundance of SARS-CoV-2 RNA, ii) better understanding of the protocol, virus J o u r n a l P r e -p r o o f Journal Pre-proof precipitation through PEG and filtration which one is better methods for concentrating the samples before RNA isolation. Appraising the genetic loading reduction through Upflow Anaerobic Sludge Blanket (UASB) systems, and iii) Comparing the performances between PEG and filtration as virus concentration methods in terms of SARS-CoV-2 RNA sensitivity and inhibition removal. cache = ./cache/cord-275565-xerr4vki.txt txt = ./txt/cord-275565-xerr4vki.txt === reduce.pl bib === id = cord-273711-bxijla09 author = Zhao, Zhixun title = RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells date = 2012-02-17 pages = extension = .txt mime = text/plain words = 4172 sentences = 242 flesch = 53 summary = title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells When Vero cells were transfected with shRNA expression vectors (p61/GFP, p70/GFP, p165/GFP and p296/GFP) and then infected with GTPV, GTPV-ORF095-70 was found to be the most effective inhibition site in decreasing cytopathic effect (CPE) induced by GTPV. These results suggest that the siRNA generated by in vitro transcription effectively and specifically inhibit the expression of GTPV ORF095 conserved regions in BHK-21 cells. To investigate whether or not knockout of ORF095 relieves cytopathic effect (CPE) induced by GTPV, Vero cells were transfected by plasmids expressing ORF095 protein-targeted shRNAs (p61/GFP, p70/GFP, p165/GFP and p296/GFP), respectively. Therefore, ORF095 gene is a good target to suppress GTPV replication by RNAi. In conclusion, this study demonstrates that vector-based shRNA methodology can effectively inhibit GTPV replication on Vero cells. RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells cache = ./cache/cord-273711-bxijla09.txt txt = ./txt/cord-273711-bxijla09.txt === reduce.pl bib === id = cord-276185-ysspkbj7 author = Milewska, Aleksandra title = APOBEC3-mediated restriction of RNA virus replication date = 2018-04-13 pages = extension = .txt mime = text/plain words = 5507 sentences = 317 flesch = 54 summary = In experiments in vitro, three human APOBEC3 proteins (A3C, A3F and A3H) inhibited HCoV-NL63 infection and limited production of progeny virus, but did not cause hypermutation of the coronaviral genome. Although the precise molecular mechanism of deaminase-dependent inhibition of coronavirus replication remains elusive, our results further our understanding of APOBEC-mediated restriction of RNA virus infections. HCoV-NL63 infection resulted in upregulation of expression of A3A, A3C, A3D and A3F and A3C, A3F and A3H all inhibited HCoV-NL63 replication, we tested whether this inhibition was the result of the catalytic activity of the APOBECs. Plasmids encoding variants of A3C, A3F and A3H with Glu → Gln substitutions in the catalytic site were prepared 31 and mRNAs encoding active or inactive proteins were transfected into LLC-Mk2 cells, which were infected with HCoV-NL63 and cultured prior to visualisation of viral proteins with specific antibodies. cache = ./cache/cord-276185-ysspkbj7.txt txt = ./txt/cord-276185-ysspkbj7.txt === reduce.pl bib === id = cord-275307-d7htyfcl author = Gaglia, Marta Maria title = Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date = 2015-12-08 pages = extension = .txt mime = text/plain words = 10860 sentences = 537 flesch = 57 summary = Development of a novel bioinformatics pipeline to detect highconfidence SOX cleavage sites across the transcriptome following PARE Prior analyses of individual mRNAs indicated that the KSHV RNase SOX cuts at specific locations within the RNA, in a manner dependent on the sequence surrounding the cleavage site [5] . This example shows the expected distribution for a cut site followed by exonucleolytic degradation due PARE libraries from two replicates of SOX-expressing or GFP control cells and extracted the 5' end of each mapped read, which represents the cleavage site (S1 Table) . Indeed, the sequences flanking the set of reproducible SOX cut sites (identified with a confidence level of 99.99%) were a closer match to the motif compared to those surrounding GFP-specific fragment ends, as shown by the distribution of the log likelihood scores (Fig 6A) . cache = ./cache/cord-275307-d7htyfcl.txt txt = ./txt/cord-275307-d7htyfcl.txt === reduce.pl bib === id = cord-276908-9jthjf24 author = Gupta, Akanksha title = COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date = 2020-07-06 pages = extension = .txt mime = text/plain words = 5174 sentences = 385 flesch = 57 summary = In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. cache = ./cache/cord-276908-9jthjf24.txt txt = ./txt/cord-276908-9jthjf24.txt === reduce.pl bib === id = cord-273367-gl266pvt author = Gunawardana, M. title = Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints date = 2020-07-28 pages = extension = .txt mime = text/plain words = 5731 sentences = 417 flesch = 59 summary = Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples collected at three timepoints. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic participants. Subject 557 18, a self-quarantined employee who had just recovered from suspected COVID-19 (based on 558 symptomology) at the start of the study, repeatedly tested negative for SARS-CoV-2 RNA, but 559 tested positive for IgM antibodies that rapidly declined (τ1/2 = 8.8 d, Fig. 4A) . cache = ./cache/cord-273367-gl266pvt.txt txt = ./txt/cord-273367-gl266pvt.txt === reduce.pl bib === id = cord-274463-0nvw2egm author = Sánchez-Navarro, Jesús A. title = Plant tissue distribution and chemical inactivation of six carnation viruses date = 2006-12-11 pages = extension = .txt mime = text/plain words = 2940 sentences = 203 flesch = 55 summary = Viral RNA or DNA accumulation on root, stem, leaf, sepal, petal, stamen, pistil and ovary tissues of infected carnation or Saponaria vaccaria plants was analysed by non-isotopic molecular hybridisation. A negative hybridisation signal was also observed in root tissue of CVMV infected carnation plants (Fig. 1B) whereas the viral RNA accumulation was determined to be 625 ng g À1 of infected pistil tissue (dilution 5 À3 ) followed by petal, stamen and pistil with 125 ng (dilution 5 À2 ) and sepal with 25 ng (5 À1 ) ( Table 1 ). The viral distribution results showed two patterns for the six carnation viruses: high titres of CarMV, CRSV, CIRV, and CLV accumulated with small differences among the plant tissue analysed whereas there were low amounts of CERV and CVMV irregularly distributed over the infected plant. cache = ./cache/cord-274463-0nvw2egm.txt txt = ./txt/cord-274463-0nvw2egm.txt === reduce.pl bib === id = cord-273366-xd84f8ct author = Brownsword, Matthew J. title = Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling date = 2020-05-14 pages = extension = .txt mime = text/plain words = 8910 sentences = 520 flesch = 47 summary = Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. Vero cells were infected with IBV and at the indicated time points, cells were fixed and labelled with anti-dsRNA to detect virus infection and with anti-G3BP1 to detect SG. Following identification of SG in IBV infected cells, the requirement for active virus replication in induction of granules was assessed. At 24 hpi, cells were fixed and labelled with anti-G3BP1 (red) to detect stress granules (SG) and IBV infected cells were detected with an anti-dsRNA antibody (green). Junin virus infection impairs stress-granule formation in Vero cells treated with arsenite via inhibition of eIF2alpha phosphorylation cache = ./cache/cord-273366-xd84f8ct.txt txt = ./txt/cord-273366-xd84f8ct.txt === reduce.pl bib === id = cord-274663-zyzgk2z3 author = Chang, Stewart T. title = Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line date = 2011-09-20 pages = extension = .txt mime = text/plain words = 6991 sentences = 358 flesch = 48 summary = Using NGS, we detected small but significant changes in host gene expression affecting T cell function that coincided with the initiation of viral RNA production at 12 h postinfection (hpi). In addition, by using NGS, we observed the dramatic expansion of viral mRNA expression and detected new viral splice events occurring during viral replication and differential expression of noncoding RNA species, including microRNA host genes. In our data set, we observed no change in the expression of the Crm1-encoding gene XPO1, but several members of the Ran signaling pathway were downregulated, suggesting that the overall export of unspliced viral RNA was suppressed (see Fig. S5B in the supplemental material; data not shown for XPO1). The regulation of these and transcription factors specific for other functions (e.g., EGR1, KLF13, and MYC) may explain how HIV initiated replication with minimal disruption to host gene expression at 12 hpi but elicited larger-scale changes later in infection. cache = ./cache/cord-274663-zyzgk2z3.txt txt = ./txt/cord-274663-zyzgk2z3.txt === reduce.pl bib === id = cord-278099-ypov9ha3 author = Kumar, Surender title = Molecular characterization of a novel cryptic virus infecting pigeonpea plants date = 2017-08-03 pages = extension = .txt mime = text/plain words = 11403 sentences = 622 flesch = 55 summary = The four dsRNAs eluted from the agarose gel were purified and have been used as templates for RT-PCR amplification employed in SISPA to generate fulllength cDNAs. It is of interest to examine if ArCV-1 RNA dependent RNA polymerase (RdRp) structurally resembles the known RdRp of the dsRNA bacteriophage Փ-6, reovirus, or with other viruses like calciviruses and picornaviruses [12] [13] [14] [15] [16] . We report here the results of elaborated computer-assisted analysis of ArCV-1 replicase which revealed the presence of conserved sequence motifs (A to G) present in the fingers and palm subdomains of the polymerase that are shared in most of the RdRps. Interestingly, ArCV-1 replicase has more structural resemblances with several members of ssRNA (+) mono-partite Picornaviruses (viral replication by primer-dependent initiation), than the de novo dsRNA bacteriophage Փ-6 and reovirus polymerases. Possible functions of the residues of the A to G motifs described for identical RdRps was conserved with respect to the ArCV-1 3Dpol structure and was discussed in structural analysis of ArCVTable 1 ) and the 3' terminus contained the sequence "GCA CCCATATTC". cache = ./cache/cord-278099-ypov9ha3.txt txt = ./txt/cord-278099-ypov9ha3.txt === reduce.pl bib === id = cord-276997-hbovh7s9 author = Alsved, Malin title = Aerosolization and recovery of viable murine norovirus in an experimental setup date = 2020-09-29 pages = extension = .txt mime = text/plain words = 6031 sentences = 297 flesch = 46 summary = However, the infectivity of airborne human noroviruses has not been possible to assess in real-world environments, nor in laboratory experiments, since there is no well-established cell culturing system for these viruses working at the low concentrations obtained in air samples 6 . SLAG: Sparging liquid aerosol generator; HEPA filter: high efficiency particulate air filter; nsRNA: negative sense RNA; psRNA: positive sense RNA; MNV: murine norovirus; qRT-PCR: quantitative reverse transcriptase polymerase chain reaction. Taken together, as compared to the atomizer, a smaller amount of SLAG aerosol is collected by the BioSampler (i.e., higher physical dilution), but these particles contain more MNV psRNA copies (lower viral dilution relative the physical dilution). The experimental setup described here highlights some difficulties in studies on aerosolized viruses: (1) the lack of standards in how to generate bioaerosol that results in significant differences in aerosol particle size and concentration, (2) the necessity to determine both physical and viral dilution factors, and (3) www.nature.com/scientificreports/ during airborne transport due to the low-solute solution and dilution in the setup. cache = ./cache/cord-276997-hbovh7s9.txt txt = ./txt/cord-276997-hbovh7s9.txt === reduce.pl bib === id = cord-274097-11hvriqy author = Katz, Louis M. title = Is SARS‐CoV‐2 transfusion transmitted? date = 2020-06-16 pages = extension = .txt mime = text/plain words = 2023 sentences = 132 flesch = 51 summary = The few studies of SARS-CoV-2 RNA in donors or of donors developing COVID-19 after giving blood are a mix of small series wherein prospectively test-positive units were quarantined and not transfused or involved units quarantined after donation to permit the donor time to get ill before units are distributed. In a lookback to recipients of 17 transfused components from seven South Korean donors who developed COVID-19 6 to 15 days after donation, there was no associated clinical morbidity in the recipients; however, archived samples tested by PCR after the donors reported their illnesses were negative. 21 Precise estimates of the prevalence of asymptomatic/presymptomatic infection and especially of whether RNA-emia or, more germane to this topic, viremia occur in the absence of illness (especially in healthy donors or the larger well population who might be qualified to donate) are among the key missing data needed to inform our debate about any risk of TTI and subsequent TTD. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations cache = ./cache/cord-274097-11hvriqy.txt txt = ./txt/cord-274097-11hvriqy.txt === reduce.pl bib === id = cord-274567-xd37wxxf author = Monpoeho, S. title = Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date = 2002-07-13 pages = extension = .txt mime = text/plain words = 3284 sentences = 161 flesch = 47 summary = title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. Detection of EVs by amplification of viral RNA from CSF using reverse transcriptase-polymerase chain reaction (RT-PCR) assay has already been reported [4, 5, 6 ]. The fluorogenic RT-PCR was applied to detection of EVs in the CSF of 104 patients presenting with signs of meningitis. Amplicor enterovirus polymerase chain reaction in patients with aseptic meningitis: a sensitive test limited by amplification inhibitors Comparison of use of cerebrospinal fluid, serum, and throat swab specimens in diagnosis of enteroviral acute neurological infection by a rapid RNA detection PCR assay cache = ./cache/cord-274567-xd37wxxf.txt txt = ./txt/cord-274567-xd37wxxf.txt === reduce.pl bib === id = cord-274785-9jgg8ukr author = Zhang, Qiang title = Viral Regulation of RNA Granules in Infected Cells date = 2019-04-29 pages = extension = .txt mime = text/plain words = 7384 sentences = 458 flesch = 47 summary = TIA/G3BP/PABP-specific stress granules (SG) and GW182/DCP-specific RNA processing bodies (PB) are two major distinguishable RNA granules in somatic cells and contain various ribosomal subunits, translation factors, scaffold proteins, RNA-binding proteins, RNA decay enzymes and helicases to exclude mRNAs from the cellular active translational pool. The process of SG formation can be artificially divided into the following steps ( Fig. 2) : (1) accumulation of stalled translation initiation complexes ) in response to various types of stress; (2) the RNA-binding proteins such as RAS-GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and T cell-restricted intracellular antigen 1 (TIA1) bind mRNAs and aggregate to nucleate SG formation. SG proteins (eIF4G, eIF3, PABP) are selectively sequestered within Ebola virus inclusion bodies and co-localize with viral RNA to form inclusion body-bound granules, which are functionally and structurally different from canonical SG, probably leading to inhibit the antiviral role of SG (Nelson et al. Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly cache = ./cache/cord-274785-9jgg8ukr.txt txt = ./txt/cord-274785-9jgg8ukr.txt === reduce.pl bib === id = cord-276364-zyw5aukk author = Wong, Ho Him title = Manipulation of autophagy by (+) RNA viruses date = 2019-08-08 pages = extension = .txt mime = text/plain words = 6884 sentences = 360 flesch = 33 summary = Over the past few decades, a growing body of research has defined the critical role of this pathway in facilitating infection by numerous +RNA RNA viruses, including poliovirus (PV) [7, 8] , Coxsackievirus B3 (CVB3) [9, 10] , CVB4 [11] , Enterovirus 71 (EV71) [12] , Human rhinovirus (HRV) [13] , Foot-and-mouth disease virus (FMDV) [14] , encephalomyocarditis virus (EMCV) [15] , Dengue virus (DENV) [16, 17] , Zika virus (ZIKV) [18, 19] , Hepatitis C virus (HCV) [20] , Mouse hepatitic virus (MHV), Newcastle disease virus (NDV) [21] , Severe and acute respiratory syndrome coronavirus (SARS-CoV) [22] , Chikungunya virus (ChikV) [23] , and Japanese encephalitis virus (JEV) [24] . Delineating the process of viral assembly from replication is technically challenging, especially since both processes would very likely Induces formation of autophagosome-like double-membrane liposomes [112] Summary of Interactions between proteins from positive strand RNA viruses and host autophagy machinery. cache = ./cache/cord-276364-zyw5aukk.txt txt = ./txt/cord-276364-zyw5aukk.txt === reduce.pl bib === id = cord-277318-cwuls6xs author = Visscher, Koen title = −1 Programmed Ribosomal Frameshifting as a Force-Dependent Process date = 2016-02-02 pages = extension = .txt mime = text/plain words = 8568 sentences = 455 flesch = 48 summary = 13 A recent single-molecule experiment indicates that ribosome helicase action during the translational elongation cycle may be twofold: it destabilizes the helical junction at the mRNA entry site favoring an open conformation, and it appears to pull mRNA strands apart during the translocation step when relatively large structural rearrangements occur on the ribosome. 26 We will review methods and experiments that apply force to the single molecules to determine the mechanical properties of codon-anticodon interaction at the slippery site, the stability of downstream mRNA structure motifs that give rise to −1 PRF, and elastic properties of the ssRNA elasticity bridging those elements. 104, 105 Single-molecule assays that probe the codon-anticodon dynamics at the slippery sequence and investigate the force dependence of the translation elongational cycle (discussed later in the chapter; see Fig. 8 ) should be fit to answer these questions and allow unfolding of −1 PRF mRNA structure motifs held at the ribosome's entry site. cache = ./cache/cord-277318-cwuls6xs.txt txt = ./txt/cord-277318-cwuls6xs.txt === reduce.pl bib === id = cord-276493-hoaxv5e0 author = Jeong, Gi Uk title = Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date = 2020-07-14 pages = extension = .txt mime = text/plain words = 5687 sentences = 363 flesch = 56 summary = With increasing structural data of key proteins in both SARS-CoV-2 and the host, such as the spike glycoprotein (S), the main protease (M pro ), RNA-dependent RNA polymerase (RdRp), and human angiotensin-converting enzyme 2 (hACE2), the structure-based design of new drugs has emerged as the most promising antiviral strategy. Several structure-based drug discovery studies have investigated the interaction of inhibitors in the substrate-binding pockets of SARS-CoV-2 M pro ( Figure 3C ) (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . Because most inhibitors occupy the substrate binding pocket of SARS-CoV-2 FIGURE 4 | CryoEM structure of RdRp in complex with cofactors (nsp7 and nsp8), RNA template, and remdesivir. In addition, we provided structural insights into the mechanism of action of well-characterized drugs targeting the interaction between hACE2 and the spike protein of SARS-CoV-2 for viral entry, as well as M pro and RdRp for viral replication. cache = ./cache/cord-276493-hoaxv5e0.txt txt = ./txt/cord-276493-hoaxv5e0.txt === reduce.pl bib === id = cord-277841-7sp8ftbc author = Kumari, Pratibha title = Potential diagnostics and therapeutic approaches in COVID-19 date = 2020-08-12 pages = extension = .txt mime = text/plain words = 4873 sentences = 279 flesch = 45 summary = Molecular diagnostic tests target the detection of any of the following markers such as the specific region of the viral genome, certain enzyme, RNA-dependent RNA polymerase, the structural proteins such as surface spike glycoprotein, nucleocapsid protein, envelope protein, or membrane protein of SARS-CoV-2. COVID-19 is a contagious disease, caused by a novel severe acute respiratory syndrome Coronavirus (SARS-CoV-2). In this article, we evaluated literature for reports informing various diagnostic methods, potential antiviral chemical therapeutics, and effective treatment strategies towards clinical management of COVID-19 patients. Molecular diagnostic methods target to detect either specific regions of the viral genome or RNA-dependent RNA polymerase (RdRP) and/or structural proteins of SARS-CoV-2 (Table 1) . Like most immunological diagnostic protocols, Enzyme-Linked Immunosorbent Assay (ELISA) for COVID-19 detection uses IgM and IgG antibody against nucleocapsid (N) and receptor binding domain spike proteins (S) of SARS-CoV-2. Table 2: Primers and probes for targeting SARS-Cov-2 genes in an RT-PCR test for COVID-19 diagnosis. cache = ./cache/cord-277841-7sp8ftbc.txt txt = ./txt/cord-277841-7sp8ftbc.txt === reduce.pl bib === id = cord-277687-u3q36o3e author = Shean, Ryan C. title = VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank date = 2019-01-23 pages = extension = .txt mime = text/plain words = 4071 sentences = 212 flesch = 49 summary = title: VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank In order to accept submitted viral genomic data, NCBI GenBank requires 1) viral sequence complete with at least one protein annotation, 2) author/depositor metadata, and 3) viral sequence metadata, such as strain, collection date, collection location, and coverage. VAPiD handles batch submissions of multiple viruses of different types without prior knowledge of the viral species, correctly annotates RNA editing and ribosomal slippage, performs spellchecking on annotations, handles batch or individual submission of metadata, runs with a simple one-line command, and creates annotated viral sequence files for GenBank submission. This first example is the task that the authors originally wrote VAPiD for -annotating large numbers of genomes from different viral species, which mirrors the type of data that many clinical and public health laboratories may encounter. cache = ./cache/cord-277687-u3q36o3e.txt txt = ./txt/cord-277687-u3q36o3e.txt === reduce.pl bib === id = cord-275795-ee7qyw5h author = Monette, Anne title = T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date = 2018-10-24 pages = extension = .txt mime = text/plain words = 28265 sentences = 1205 flesch = 38 summary = We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. Since that time, the occurrence of epidemics and outbreaks are now at lower risk, following the introduction of massive vaccination programs able to induce immune system targeting of viruses causing severe disorders affecting distinct geographical locations, and with many epidemiological reports demonstrating long-term efficacy of viral control of non-naïve populations. This approach is being developed to use virus-infected cell-killing antibodies that produce an antiviral environment; these termed antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies, which are predicted to link innate and adaptive immune responses, and is becoming possible due to new technologies for rapid isolation and characterization of monoclonal antibodies targeting conserved regions of influenza virus, reviewed in Jegaskanda et al. cache = ./cache/cord-275795-ee7qyw5h.txt txt = ./txt/cord-275795-ee7qyw5h.txt === reduce.pl bib === id = cord-276198-psjua913 author = V’kovski, Philip title = New insights on the role of paired membrane structures in coronavirus replication date = 2015-04-16 pages = extension = .txt mime = text/plain words = 6083 sentences = 303 flesch = 44 summary = Many nidovirus and all coronavirus TM1 proteins contain one or more ubiquitin-like domains which may help to anchor the viral RNA to the membranes where replication takes place (Hurst et al., 2013) . The maze-like paired-membrane structures that resulted from coexpression of SARS-CoV TM1 and TM2 have not ever been reported in coronavirus-infected cells, suggesting that this should be interpreted as a conditional, or perhaps partial phenotype, that is not observed when the full viral replicase polyprotein is expressed. Since DMVs are reminiscent of the double-membranes of autophagosomes, several lines of controversial evidence hypothesized a diversion of Atg (autophagyrelated) proteins and autophagosome function during coronavirus replication, as it is the case for other +RNA viruses (Prentice et al., 2004; Snijder et al., 2006; Zhao et al., 2007; Maier and Britton, 2012; Richards and Jackson, 2013) . Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex cache = ./cache/cord-276198-psjua913.txt txt = ./txt/cord-276198-psjua913.txt === reduce.pl bib === id = cord-276541-u9ebql5a author = Lan, Yungang title = Inhibition of porcine hemagglutinating encephalomyelitis virus replication by short hairpin RNAs targeting of the nucleocapsid gene in a porcine kidney cell line date = 2011-11-25 pages = extension = .txt mime = text/plain words = 3067 sentences = 172 flesch = 56 summary = title: Inhibition of porcine hemagglutinating encephalomyelitis virus replication by short hairpin RNAs targeting of the nucleocapsid gene in a porcine kidney cell line Here, we constructed a single short hairpin RNA (shRNA) plasmid expression system that targeted the N gene and investigated whether shRNAmediated RNA interference could inhibit PHEV replication in PK-15 cells. To study the inhibitory effects of RNA interference on PHEV replication, the level of viral antigen produced in the PK-15 cells after shRNA transfection and viral infection was examined 48 h post-infection by an indirect immunofluorescence assay (IFA) using anti-PHEV serum. To quantify the effect of shRNA on viral replication at 48 h postviral infection, the viral genome copy number was determined by real-time PCR, using the serially diluted plasmid pT-N as a standard. It is clear from this study that the DNA vector-based shRNA approach, that is, the use of RNAi expression plasmids directed against the PHEV N gene, could effectively block expression of the viral target gene and inhibit viral replication. cache = ./cache/cord-276541-u9ebql5a.txt txt = ./txt/cord-276541-u9ebql5a.txt === reduce.pl bib === id = cord-279070-cy049zbi author = Hewson, I. title = Description of viral assemblages associated with the Gorgonia ventalina holobiont date = 2011-12-29 pages = extension = .txt mime = text/plain words = 2569 sentences = 152 flesch = 52 summary = DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Ten samples of sea fans (5 each of visually 'healthy' and 'diseased' tissues) were used to generate metagenomic libraries of the viral fraction following protocols for tissues in Thurber et al. Contigs [ 100 bp that did not match protein databases by BLASTx against nr at e-values \ 10 -5 were further characterized by tBLASTx analysis against all viral genomes in GenBank. The proportion of annotated sequence reads (BLASTx against nr databse) and contigs was highest for DNA virus libraries and least for the RNA viral reads (Fig. 1) . The majority of matches for both DNA and RNA viral contigs and reads were to bacterial and metazoan proteins. In contrast to the RNA metaviromes, DNA viruses were well annotated, where *50% of contigs [ 100 bp matched proteins in the nr database. cache = ./cache/cord-279070-cy049zbi.txt txt = ./txt/cord-279070-cy049zbi.txt === reduce.pl bib === id = cord-277306-r8jki3x4 author = Osborne, Christina title = Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans date = 2011-05-12 pages = extension = .txt mime = text/plain words = 5186 sentences = 223 flesch = 56 summary = At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. To increase the sensitivity of RNA detection, based on our previously published bat CoV sequences [17] and new data from this study, we designed specific primers within the amplicons of alphacoronaviruses from bats of several species in the genus Myotis and big brown bats (Table S1 ). Although the number of big brown bats sampled at site #5 was small (4 in 2008 and 14 in 2009), the prevalence of CoV RNA in these bats during these two summers was high (29% to 100%) ( Table 2) . cache = ./cache/cord-277306-r8jki3x4.txt txt = ./txt/cord-277306-r8jki3x4.txt === reduce.pl bib === id = cord-276575-jfug80yu author = Aigner, Achim title = Applications of RNA interference: current state and prospects for siRNA-based strategies in vivo date = 2007-04-25 pages = extension = .txt mime = text/plain words = 5251 sentences = 325 flesch = 47 summary = From the mechanism, it becomes clear that small interfering RNAs (siRNAs) play a pivotal role in triggering RNAi. Thus, the efficient delivery of target gene-specific siRNAs is one major challenge in the establishment of therapeutic RNAi. Numerous studies, based on different modes of administration and various siRNA formulations and/or modifications, have already accumulated promising results. While the inhibition of the activity of (aberrant) gene products, e.g., through small molecule inhibitors or inhibitory antibodies is one major focus in therapy, much attention has now shifted to an earlier step, i.e., the initial knockdown of the specific gene of interest through RNAi. However, for the in vivo application of RNAi in mammals as a therapeutic approach for reversing a pathological condition as well as for the study of particular gene functions, sophisticated strategies for the induction of RNAi are needed. RNAi-mediated gene-targeting through systemic application of polyethylenimine (PEI)-complexed siRNA in vivo cache = ./cache/cord-276575-jfug80yu.txt txt = ./txt/cord-276575-jfug80yu.txt === reduce.pl bib === id = cord-277566-j3ehiwn9 author = Verheije, Monique H. title = Mouse Hepatitis Coronavirus RNA Replication Depends on GBF1-Mediated ARF1 Activation date = 2008-06-13 pages = extension = .txt mime = text/plain words = 8918 sentences = 449 flesch = 49 summary = Here, we study the involvement of the secretory pathway in mouse hepatitis coronavirus (MHV) replication by using the drug brefeldin A (BFA), which is known to interfere with ER-Golgi membrane traffic by inhibiting the activation of ADP-ribosylation factor (ARF) small GTPases. Therefore, LR7 cells infected with MHV-A59 were treated with BFA for 30 minutes starting 5.5 h p.i. They were subsequently fixed and processed for immunofluorescence using antibodies both against nsp8, which served as a protein marker for the MHV replication sites [50, 51] , and against the viral structural protein M, known to reside in the Golgi [52] . In complete agreement with the luciferase expression data shown above, this result demonstrates that BFA inhibits, but does not completely block, the formation of RCs. To study the effects of BFA on the DMVs at an ultrastructural level, MHV-infected LR7 cells were fixed at 6 h p.i. and embedded in Epon resin in order to be analyzed by electron microscopy. cache = ./cache/cord-277566-j3ehiwn9.txt txt = ./txt/cord-277566-j3ehiwn9.txt === reduce.pl bib === id = cord-278123-mq56em3z author = Hasan, Mohammad Rubayet title = Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date = 2020-07-24 pages = extension = .txt mime = text/plain words = 3924 sentences = 259 flesch = 58 summary = Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. Standard approach for detection of SARS-CoV-2 RNA from nasopharyngeal specimens in our laboratory involves extraction of total nucleic acids from specimens in an IVD-labeled, automated extraction platform followed by RT-qPCR, based on one of the assays (Table 1) suggested by World Health Organization (WHO) [11] . Based on these results, the optimal pre-treatment and reaction conditions for the direct approach were: i) transfer and dilute (4-fold) 10 μl of NPFS specimen in NFW; ii) incubate at 65˚C for 10 min; and iii) test 8 μl of heat lysed specimen in a 20 μl reaction using TaqPath™ 1-Step RT-qPCR Master Mix. The analytical sensitivity of the direct RT-qPCR assay using specimens prepared in this manner was determined by serially diluting a specimen positive for SARS-CoV-2 with a negative specimen as a diluent. cache = ./cache/cord-278123-mq56em3z.txt txt = ./txt/cord-278123-mq56em3z.txt === reduce.pl bib === id = cord-279841-oq25o4qr author = Ahlquist, Paul title = Viral and host determinants of RNA virus vector replication and expression date = 2005-03-07 pages = extension = .txt mime = text/plain words = 2269 sentences = 99 flesch = 36 summary = Further insights into RNA virus vector design and optimization are emerging from recent advances on the function of viral RNA replication factors, the nature of the viral RNA replication complex as a membrane-bounded compartment sequestering replication components from competing processes and host defenses, and identification of surprisingly diverse host genes contributing to many virus replication steps. An unusual feature of BMV for identifying and characterizing host functions in viral replication is that BMV directs RNA replication, gene expression and virion formation in the genetic model yeast, Saccharomyces cerevisiae [13] . In recent years, classical yeast genetics have been used to identify host genes that function in controlling BMV translation [14, 15] , selecting BMV RNAs as replication templates [16] , activating the viral RNA replication complex [17] , maintaining a lipid composition required for membrane-associated RNA replication [18, 19] , and other steps. cache = ./cache/cord-279841-oq25o4qr.txt txt = ./txt/cord-279841-oq25o4qr.txt === reduce.pl bib === id = cord-276006-mjjnkqv6 author = Jarach, Natanel title = Polymers in the Medical Antiviral Front-Line date = 2020-07-31 pages = extension = .txt mime = text/plain words = 12573 sentences = 738 flesch = 41 summary = Those anions show antiviral properties by affecting Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. cache = ./cache/cord-276006-mjjnkqv6.txt txt = ./txt/cord-276006-mjjnkqv6.txt === reduce.pl bib === id = cord-278436-job4854r author = Xie, Mao-Hua title = A phage RNA-binding protein binds to a non-cognate structured RNA and stabilizes its core structure date = 2009-01-09 pages = extension = .txt mime = text/plain words = 3380 sentences = 196 flesch = 60 summary = Recent studies suggest that some RNA-binding proteins facilitate the folding of non-cognate RNAs. Here, we report that bacteriophage MS2 coat protein (MS2 CP) bound and promoted the catalytic activity of Candida group I ribozyme. This mechanism is similar to that of the yeast mitochondrial tyrosyl-tRNA synthetase on other group I introns, suggesting that different RNA-binding proteins may use common mechanisms to support RNA structures. Interestingly, CYT 18 also stimulates the activity of several non-cognate group I introns [12] , questioning the specificity of the action of RNA-binding proteins. In this study, the protein-protected RNA cloning (PRC) method has been developed to successfully identify the MS2-binding site on the Candida group I ribozyme RNA. In summary, the finding of MS2 CP binding of the P5ab-P5 structure of the Candida group I ribozyme suggests that this phage protein can interact with a bulged RNA paired region connected to an asymmetric internal loop containing three adenines. cache = ./cache/cord-278436-job4854r.txt txt = ./txt/cord-278436-job4854r.txt === reduce.pl bib === id = cord-278482-j5zlismf author = Taylor, Raymond title = BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date = 2016-06-30 pages = extension = .txt mime = text/plain words = 2543 sentences = 131 flesch = 47 summary = Summary The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. In a study in cynomolgus macaques infected with MARV [5] , 0/6 controls survived compared to 17/18 animals treated with a 15 mg/kg BD dose of The maximum viral load, as measured by quantitation of viral RNA copies in the peripheral blood, was reduced by ∼600-fold (geometric mean 0.008 × 10 9 compared to 4.79 × 10 9 copies/mL, p < 0.0005). The slope of the relationship of the dose of BCX4430 to both antiviral effect and survival in nonclinical models of lethal viral infections is steep. cache = ./cache/cord-278482-j5zlismf.txt txt = ./txt/cord-278482-j5zlismf.txt === reduce.pl bib === id = cord-280272-mn596x1p author = Akhrymuk, Ivan title = Magnetic Nanotrap Particles Preserve the Stability of Venezuelan Equine Encephalitis Virus in Blood for Laboratory Detection date = 2020-01-28 pages = extension = .txt mime = text/plain words = 6551 sentences = 300 flesch = 51 summary = We have tested the ability of magnetic Nanotrap® (NT) particles to improve stability and detection of Venezuelan equine encephalitis virus (VEEV), viral capsid protein, and viral genomic RNA in whole human blood at elevated temperature and prolonged storage conditions. We have tested the ability of magnetic Nanotrap ® (NT) particles to improve stability and detection of Venezuelan equine encephalitis virus (VEEV), viral capsid protein, and viral genomic RNA in whole human blood at elevated temperature and prolonged storage conditions. In this study, we sought to apply new magnetic NT particles that consist of NIPAm copolymers functionalized with reactive red 120 to evaluate the efficacy of preservation of infectious VEEV, viral RNA, and VEEV capsid protein in whole blood samples at ambient and elevated temperature as well as at low and high humidity conditions. cache = ./cache/cord-280272-mn596x1p.txt txt = ./txt/cord-280272-mn596x1p.txt === reduce.pl bib === id = cord-278684-txlvla0j author = Gonzalez–Dunia, Daniel title = Borna Disease Virus and the Brain date = 1998-01-30 pages = extension = .txt mime = text/plain words = 13952 sentences = 784 flesch = 43 summary = The BDV paradigm is amenable to study virus–cell interactions in the CNS that can lead to neurodevelopmental abnormalities, immune-mediated damage, as well as alterations in cell differentiated functions that affect brain homeostasis. Evidence provided by epidemiological and clinical data, together with virological studies, have led to the hypothesis that chronic viral infections of the CNS contribute to human mental disorders of unknown etiology. Therefore, neuronal damage seen in BD appears to be mediated by the cytotoxic activity of CD8 ϩ T-cells present in the brain parenchyma of BDV-infected rats. Studies on PTI-NB rats may provide valuable information regarding the contribution of CNS resident cells to disturbances in cytokine gene expression caused by BDV. Borna disease virus replicates in astrocytes, Schwann cells and ependymal cells in persistently infected rats: Location of viral genomic and messenger RNAs by in situ hybridization Expression of tissue factor is increased in astrocytes within the central nervous system during persistent infection with Borna disease virus cache = ./cache/cord-278684-txlvla0j.txt txt = ./txt/cord-278684-txlvla0j.txt === reduce.pl bib === id = cord-279418-3r1ijafm author = Nevers, Quentin title = Negri bodies and other virus membrane-less replication compartments() date = 2020-08-21 pages = extension = .txt mime = text/plain words = 6437 sentences = 406 flesch = 44 summary = We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. With the rapid identification of cellular membraneless compartments and proteins that undergo LLPS in vitro, a major challenge in the field is to demonstrate unambiguously that a specific structure is indeed a phase-separated liquid body in the cellular context. Until now, only a few specific cellular factors, which directly interact with viral proteins such as the nucleoproteins and phosphoproteins of MNV, have been shown to concentrate in these structures. Upon Infection, Cellular WD Repeat-Containing Protein 5 (WDR5) Localizes to Cytoplasmic Inclusion Bodies and Enhances Measles Virus Replication The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression The Cellular Protein CAD is Recruited into Ebola Virus Inclusion Bodies by the Nucleoprotein NP to Facilitate Genome Replication and Transcription cache = ./cache/cord-279418-3r1ijafm.txt txt = ./txt/cord-279418-3r1ijafm.txt === reduce.pl bib === id = cord-280795-wtrt13ij author = Han, Yu-Tsung title = Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus date = 2007-10-10 pages = extension = .txt mime = text/plain words = 5813 sentences = 300 flesch = 52 summary = As a step toward better understanding the relationship between activities and structures of the helicase-like domain of BaMV replicase, we set out to investigate the importance of each signature motif to its NTPase and RNA 5′-triphosphatase activities by mutational and kinetic analyses. The apparent K i value of AMPPNP in inhibiting RNA 5′-triphosphatase activity The enzymatic activity was determined at 20°C by enzyme-coupled assay in 1 ml solution that contained 10 pmol enzyme, 0.1 to 3 mM NTP and other buffer components as described under Materials and methods except that the amounts of pyruvate kinase were increased up to 50, 75 and 300 U for GTPase, UTPase and CTPase assay, respectively, to assure the rate of NTP hydrolysis being the limiting step within the coupling reaction. The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5′ cap structure by exhibiting RNA 5′-triphosphatase activity cache = ./cache/cord-280795-wtrt13ij.txt txt = ./txt/cord-280795-wtrt13ij.txt === reduce.pl bib === id = cord-279404-u0fs6xcj author = Carrington, Christine V.F. title = Detection and Phylogenetic Analysis of Group 1 Coronaviruses in South American Bats date = 2008-12-17 pages = extension = .txt mime = text/plain words = 1761 sentences = 126 flesch = 66 summary = The search for the animal reservoir of the severe acute respiratory syndrome coronavirus (SARS-CoV) led to extensive surveys of coronaviruses in wild and domestic animal populations in China, resulting in the detection of a wide variety of novel bat coronaviruses (Bt-CoVs) (2) (3) (4) (5) . Our detection of RNA from group 1 CoVs in Trinidadian bats shows that Bt-CoVs have a wider distribution than previously suspected and is added support for bats as the original host species for these viruses. Despite the geographic proximity of the bats from which the Trinidadian Bt-CoV sequences were derived-Couva and Fyzabad are 28 km (17 miles) apart, and Trinidad has an area of only 4,769 km 2 (1,864 square miles)-they are relatively highly divergent. Trinidadian bat coronavirus (Bt-CoV) sequences are highlighted in red and North American Bt-CoV in blue. Detection of group 1 coronaviruses in bats in North America cache = ./cache/cord-279404-u0fs6xcj.txt txt = ./txt/cord-279404-u0fs6xcj.txt === reduce.pl bib === id = cord-280003-ndpuezpo author = Lou, Bin title = Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date = 2020-03-27 pages = extension = .txt mime = text/plain words = 3024 sentences = 190 flesch = 57 summary = Serial sera of COVID-19 patients were collected and total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 were detected. The first detectible serology marker is total antibody and followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 day post exposure (d.p.e) or 9, 10 and 12 days post onset, separately. In order to answer some of the questions, we investigated the characteristics of antibody responses in 80 Covid-19 patients during their hospitalization periods, through detecting total antibody, IgM and IgG using immunoassays. A total of 80 Covid-19 patients and 100 to 300 healthy people were tested for antibodies against SARS-CoV-2 using different immunoassays. The present data showed that the sensitivity of total antibody detection was higher than that of IgM and IgG (p<0.001) while the specificities are overall comparable when the same testing technic (ELISA, CLMA or LFIA) is used. cache = ./cache/cord-280003-ndpuezpo.txt txt = ./txt/cord-280003-ndpuezpo.txt === reduce.pl bib === id = cord-277547-2vim1wno author = Zandi, Keivan title = Antiviral activity of four types of bioflavonoid against dengue virus type-2 date = 2011-12-28 pages = extension = .txt mime = text/plain words = 4381 sentences = 247 flesch = 52 summary = In the present study, antiviral activity of four types of bioflavonoid against dengue virus type -2 (DENV-2) in Vero cell was evaluated. Daidzein showed a weak anti-dengue activity with IC(50 )= 142.6 μg mL(-1 )when the DENV-2 infected cells were treated after virus adsorption. Although there was no significant direct virucidal activity against DENV-2 by quercetin, continuous treatment of cells from 5 h before virus infection up to 4 days post-infection exhibited anti-dengue activity with IC 50 = 28.9 μg mL -1 (Figure 3a) . There was no significant change in the antiviral activity of daidzein when cells were treated continuously from 5 h before virus infection up to 4 days post infection comparing to its anti-dengue activity for postadsorption treatment (Figure 1 ). To investigate which of the many flavonoids could affect DENV infection, in the present study, we examined the potential effects of quercetin, naringin, hesperetin and daidzein on dengue virus infection of Vero cells. cache = ./cache/cord-277547-2vim1wno.txt txt = ./txt/cord-277547-2vim1wno.txt === reduce.pl bib === id = cord-281020-g1muealp author = Belov, George A title = (+)RNA viruses rewire cellular pathways to build replication organelles date = 2012-10-01 pages = extension = .txt mime = text/plain words = 3965 sentences = 202 flesch = 30 summary = The universal requirement of (+)RNA viruses for cellular membranes for genome replication, and the formation of membranous replication organelles with similar architecture, suggest that they target essential control mechanisms of membrane metabolism conserved among eukaryotes. These viruses universally require cellular membranes for assembly of their replication complexescontaining viral proteins, RNA, and host factorsto amplify their genome. Expression of poliovirus and HCV proteins in the presence of BFA resulted in the appearance of new membrane structures that are indistinguishable from those observed without the drug, indicating that GBF1 is more probably involved in the function of replication organelles than in their formation [41, 45] . For HCV, the absence of PI4KIIIa activity induced a dramatic change in the ultrastructural morphology of the membranous replication complex, suggesting a role of PI4P in recruiting specific membrane-shaping proteins [51 ] . cache = ./cache/cord-281020-g1muealp.txt txt = ./txt/cord-281020-g1muealp.txt === reduce.pl bib === id = cord-280048-b4dz1lnn author = Domingo, Esteban title = Viral quasispecies date = 2019-10-17 pages = extension = .txt mime = text/plain words = 7955 sentences = 411 flesch = 36 summary = Research on quasispecies has proceeded through several theoretical and experimental avenues that include continuing studies on evolutionary optimization and the origin of life, RNA-RNA interactions and replicator networks, the error threshold in variable fitness landscapes, consideration of chemical mutagenesis and proofreading mechanisms, evolution of tumor cells, bacterial populations or stem cells, chromosomal instability, drug resistance, and conformation distributions in prions (a class of proteins with conformation-dependent pathogenic potential; in this case the quasispecies is defined by a distribution of conformations) [16, 20] . Adaptability of RNA viruses is linked to parameters that facilitate exploration of sequence space: genome size (1.8 to 33 Kb), population size (variable but that can attain an impressive 10 12 individual genomes in an infected host at a given time), replication rate, mutation rate, fecundity (yield of viral particles per cell), and number of mutations required for a phenotypic change (surprisingly low for several relevant traits) (see [49] ). cache = ./cache/cord-280048-b4dz1lnn.txt txt = ./txt/cord-280048-b4dz1lnn.txt === reduce.pl bib === id = cord-276914-44ji0g78 author = Chen, Weilie title = Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity date = 2020-02-26 pages = extension = .txt mime = text/plain words = 2479 sentences = 126 flesch = 58 summary = However, the concentration of viral RNA in the anal swab (Ct value = 24 + 39) was higher than in the blood (Ct value = 34 + 39) from patient 2, suggesting that the virus might replicate in the digestive tract. Patient 3 (Figure 3(A) ) was transferred to the ICU directly on illness day 11 because of his severe condition, the 2019-nCoV virus was laboratory detected both in pharyngeal (Ct = 30 + 30) and blood samples (Ct = 37 + 39) on day 12, And his infection was confirmed by CDC on day 13. His disease advanced pretty fast and became severe on day 7 and he was transferred to ICU after his blood sample was detected to be virus-positive (Ct = 32 + 37). For patient 1, a high concentration of viral RNA (Ct = 23 + 27, on day 13) was detected in anal swab but not in pharyngeal (the same day) and blood (1 d ahead). cache = ./cache/cord-276914-44ji0g78.txt txt = ./txt/cord-276914-44ji0g78.txt === reduce.pl bib === id = cord-279985-de0b27nq author = Anraku, Itaru title = Kunjin replicon-based simian immunodeficiency virus gag vaccines date = 2008-06-19 pages = extension = .txt mime = text/plain words = 6392 sentences = 325 flesch = 53 summary = Kunjin replicon VLP vaccines encoding HIV-1 gag have also been shown to induce CD8 T cell immunity comparable to that seen after immunisation with recombinant vaccinia [11] . Here we describe the behaviour of four different Kunjin replicon VLP vaccines encoding SIV gag and show that only the Gag-pol vaccine (i) induced good levels of both effector memory and central memory T cell responses 10 weeks post-vaccination, comparable to those induced by the previously described HIV-1 gag Kunjin replicon VLP vaccine [11] , (ii) showed good levels of protection against challenge with A20 cells expressing SIV Gag ≈9 months post-vaccination, and (iii) displayed high levels of insert stability. In summary we describe here a Kunjin replicon SIV Gag-pol VLP vaccine, which showed high insert stability, good induction of effector and central memory responses, and good protection against a model challenge. cache = ./cache/cord-279985-de0b27nq.txt txt = ./txt/cord-279985-de0b27nq.txt === reduce.pl bib === id = cord-277874-cr53ycrm author = Neault, N. title = SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date = 2020-09-03 pages = extension = .txt mime = text/plain words = 7079 sentences = 372 flesch = 49 summary = We believe MPAD based SARS-CoV-2 protein quantitation represents a promising epidemiological tool with a sensitivity sufficiently superior to viral RNA measurement that, in addition to enabling early detection and population tracking of COVID-19 load, will also open the way to effective infection surveillance of specific facilities, schools and residences. Primary sludge and PEG precipitated influent fractions, collected from the contiguous cities of Ottawa and Gatineau in April through June 2020, were analysed for the presence of four SARS-CoV-2 structural proteins, N (nucleocapsid), M (membrane), S (spike), and E (envelope), by western blot. Next, in order to assure specificity for detection of SARS-CoV-2 proteins, we used MPAD with an expanded panel to simultaneously measure three viral proteins, N, S and M, along with six fecal content control proteins in PEG precipitated "influent solids" samples drawn from the Ottawa WRRF during the study period ( Fig 5) . cache = ./cache/cord-277874-cr53ycrm.txt txt = ./txt/cord-277874-cr53ycrm.txt === reduce.pl bib === id = cord-022940-atbjwpo5 author = nan title = Poster Sessions date = 2016-09-07 pages = extension = .txt mime = text/plain words = 241182 sentences = 12746 flesch = 47 summary = We have studied the effect of inhibition of IRE1 (inositol requiring enzyme 1), which is a central mediator of endoplasmic reticulum stress and controls cell proliferation and tumor growth, on hypoxic regulation of the expression of different proliferation related genes in U87 glioma cells. Transient inhibition of Akt and mTOR protein kinase activation in tumor cells followed by reactivation of signaling pathway did not result in a time-dependent difference on EGFR, HER2 and HER3 expression levels. In our study we aimed to determine cytotoxic effect of RES in K562 human CML cell line and to evaluate the expressions of miRNAs that are associated with genetics of leukemia after treatment with RES; to investigate target genes of miRNAs which show significant expression alterations and molecular mechanisms of RES treatment. cache = ./cache/cord-022940-atbjwpo5.txt txt = ./txt/cord-022940-atbjwpo5.txt === reduce.pl bib === id = cord-280001-y7pvj2l1 author = Patel, Robin title = Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date = 2020-03-26 pages = extension = .txt mime = text/plain words = 1785 sentences = 77 flesch = 46 summary = If the test is positive though, the result is most likely correct, although stray viral RNA that makes its way into the testing process (for example, as the specimen is being collected or as a result of specimen cross-contamination or testing performed by a laboratory worker who is infected with SARS-CoV-2 [these are just some examples]) could conceivably result in a falsely positive result. Testing patients for SARS-CoV-2 helps identify those who are infected, which is useful for individual patient management, as well as for implementation of mitigation strategies to prevent spread in health care facilities and in the community alike (Fig. 1) . Given that SARS-CoV-2 can infect anyone and result in transmission prior to the onset of symptoms or even possibly without individuals ever developing symptoms, testing asymptomatic patients could even be considered. Finally, serologic testing can possibly be used diagnostically to test viral RNA-negative individuals presenting late in their illness. cache = ./cache/cord-280001-y7pvj2l1.txt txt = ./txt/cord-280001-y7pvj2l1.txt === reduce.pl bib === id = cord-280130-ewqe9edq author = Weber, Friedemann title = Viral suppression of the interferon system date = 2007-01-27 pages = extension = .txt mime = text/plain words = 4298 sentences = 224 flesch = 39 summary = In most nucleated body cells, viral infections activate transcription of the ''classic'' IFN-b gene [1] by a signaling chain which is initiated by the RNA sensors RIG-I and MDA-5, which in turn act trough the adaptor IPS-1 and the kinases TBK-1 and IKK-3 to activate the transcription factor IRF-3 (see reviews by P. Many RNA and DNA viruses therefore express proteins which bind this key molecule to avoid both IFN induction and activation of dsRNA-dependent antiviral enzymes [7, 8] . Binding of the influenza virus NS1 protein to double-stranded RNA inhibits the activation of the protein kinase that phosphorylates the elF-2 translation initiation factor Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Double-stranded RNA binding of influenza B virus nonstructural NS1 protein inhibits protein kinase R but is not essential to antagonize production of alpha/beta interferon cache = ./cache/cord-280130-ewqe9edq.txt txt = ./txt/cord-280130-ewqe9edq.txt === reduce.pl bib === id = cord-281124-4nhy35xn author = Soowannayan, Chumporn title = RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date = 2011-08-03 pages = extension = .txt mime = text/plain words = 5596 sentences = 259 flesch = 53 summary = To examine this domain in more detail, the 18 aa peptide (M(11)PVRRPLPPQPPRNARLI(29)) encompassing this sequence was synthesized and found to bind nucleic acids similarly to the full-length N protein in EMSAs. The data indicate a fundamental role for the GAV N protein proline/arginine-rich domain in nucleating genomic ssRNA to form nucleocapsids. In a preliminary attempt to identify an RNA packaging signal in the GAV genome, EMSAs were performed using ssRNAs synthesized to various genome regions including (i) an ORF1b gene 39-region spanning the relative position to the genome packaging signal identified in MHV [28] , (ii) a 39-terminal genome region corresponding in position to the region in the infectious bronchitis virus (IBV) genome reported to contain an RNA binding domain [29] and (iii) the 59-genomic RNA terminus which, in coronaviruses, has also been reported to interact specifically with N protein [30] . cache = ./cache/cord-281124-4nhy35xn.txt txt = ./txt/cord-281124-4nhy35xn.txt === reduce.pl bib === id = cord-278635-vwdxr1bl author = Świętoń, Edyta title = Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date = 2020-08-28 pages = extension = .txt mime = text/plain words = 5432 sentences = 295 flesch = 48 summary = In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). cache = ./cache/cord-278635-vwdxr1bl.txt txt = ./txt/cord-278635-vwdxr1bl.txt === reduce.pl bib === id = cord-279623-ezax8c1u author = Huang, Yong title = Regulatory long non-coding RNA and its functions date = 2012-04-26 pages = extension = .txt mime = text/plain words = 3564 sentences = 201 flesch = 47 summary = (CCND1) promoter can produce low-copy transcript lncRNAs in human cell lines which can be combined to the 5 ′end regulatory region of the CCND1 that are induced in response to DNA damage signals for the recruitment of the translocated-in-liposarcoma protein to the CCND1 promoter to cause gene-specific Fig. 1 Paradigms for functions of lncRNAs expression inhibiting the CREB-binding protein and p300 histone acetyltransferase activities [59] . The results directly implicate long non-coding RNAmediated transcriptional regulation of gene expression as a fundamental control mechanism for physiologic processes, such as vascular development [32] . To sum up, intense investigation of the lncRNA transcription will likely expand our understanding of both the cell biology and functions of lncRNAs. Non-coding RNAs revealed during identification of genes involved in chicken immune responses Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells cache = ./cache/cord-279623-ezax8c1u.txt txt = ./txt/cord-279623-ezax8c1u.txt === reduce.pl bib === id = cord-280941-ds6x0yym author = Kim, Young-Seok title = Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date = 2018-05-17 pages = extension = .txt mime = text/plain words = 9411 sentences = 491 flesch = 51 summary = The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic "pace-keeping" role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections. Taken together, the results confirmed the immunologically relevant conformation of the MERS-CoV RBD displayed on the hybrid ferritin particles, and the crucial role of RNA in controlling the kinetic pathway for the assembly of viral antigen monomers into stable NPs. To evaluate the immunogenicity of ferritin-based NPs, BALB/c mice (n = 5) were immunized with RBD, RBD-FR, and RBD-[SSG]-FR NPs antigens. cache = ./cache/cord-280941-ds6x0yym.txt txt = ./txt/cord-280941-ds6x0yym.txt === reduce.pl bib === id = cord-281174-3c1vue0y author = Greene, Shermalyn R title = Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date = 2003-01-16 pages = extension = .txt mime = text/plain words = 5250 sentences = 248 flesch = 48 summary = The application of a rapid nucleic acid sequence-based amplification (NASBA) assay for the detection of NLV RNA in stool is described using the NucliSens® Basic Kit. Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate. Despite the specificity of the NASBA primer/probe sequences for NV, other representatives from both NLV genogroups I and II could be detected by the Basic Kit assay in outbreak stool specimens, although the results were inconsistent. In this study, we report the application of a rapid NASBA assay for the detection of NV RNA in stool using the NucliSens † Basic Kit. This assay was compared directly with RT-PCR and used for the detection of NV and other NLVs in fecal specimens obtained from human challenge studies and NLV outbreaks. cache = ./cache/cord-281174-3c1vue0y.txt txt = ./txt/cord-281174-3c1vue0y.txt === reduce.pl bib === id = cord-278186-t3izmz6n author = Le Naour, Julie title = Trial watch: TLR3 agonists in cancer therapy date = 2020-06-02 pages = extension = .txt mime = text/plain words = 7615 sentences = 473 flesch = 40 summary = ABBREVIATIONS: cDC, conventional dendritic cell; CMT, cytokine modulating treatment; CRC, colorectal carcinoma; CTL, cytotoxic T lymphocyte; DC, dendritic cell; dsRNA, double-stranded RNA; FLT3LG, fms-related receptor tyrosine kinase 3 ligand; HNSCC, head and neck squamous cell carcinoma; IFN, interferon; IL, interleukin; ISV, in situ vaccine; MUC1, mucin 1, cell surface associated; PD-1, programmed cell death 1; PD-L1, programmed death-ligand 1; polyA:U, polyadenylic:polyuridylic acid; polyI:C, polyriboinosinic:polyribocytidylic acid; TLR, Toll-like receptor Alongside, a pilot study on patients with metastatic HNSCC and melanoma who received intratumoral or intramuscular Hiltonol™ reported clinical benefits for at least one of the 8 individuals enrolled in this trial, coupled to moderate side effects (such as inflammation at the injection site and fatigue) as well as increased levels of CD4, CD8, PD-1, and PD-L1 in tumors, confirming the activation of systemic immunity. cache = ./cache/cord-278186-t3izmz6n.txt txt = ./txt/cord-278186-t3izmz6n.txt === reduce.pl bib === id = cord-277830-6fsz9iy7 author = Saikatendu, Kumar Singh title = Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date = 2005-11-08 pages = extension = .txt mime = text/plain words = 6555 sentences = 344 flesch = 56 summary = The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p. One of its sequence homologs, Poa1p (YBR022) from Saccharomyces cerevisiae, was recently functionally characterized as a highly specific phosphatase that removes the 1 00 phosphate group of ADP-ribose-1 00 -phosphate (Appr-1 00 -p) in the latter half of the tRNA splicing pathway in yeast (Shull et al., 2005) , hinting at a similar substrate specificity for SARS ADRP. A view of the proposed active site of SARS ADRP along with the superimposed structures of AF1521 and yeast Ymx7 are shown in Figure 4B , highlighting the interactions that are likely between residues of the protein with the ligand. cache = ./cache/cord-277830-6fsz9iy7.txt txt = ./txt/cord-277830-6fsz9iy7.txt === reduce.pl bib === id = cord-282372-nmii30mc author = Youk, Jeonghwan title = Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date = 2020-07-10 pages = extension = .txt mime = text/plain words = 5124 sentences = 294 flesch = 53 summary = Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Although basic molecular mechanisms in SARS-CoV-2 infection have been identified [5] [6] [7] [8] , most findings have been obtained from experiments using non-physiological cell lines 9 , model animals, such as transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) 10 , ferrets 11 and golden hamsters 12 , or from observation in clinical cohorts 13 and/or inference from in-silico computational methods [14] [15] [16] . Immunostaining for double-stranded viral RNA (dsRNA) and nucleocapsid protein (NP) of SARS-CoV-2 identified widespread viral infection in hAT2 cells co-expressing pro-SFTPC and ACE2 in hAOs ( Fig. 2a and 2b; Extended Data Fig. 3) . cache = ./cache/cord-282372-nmii30mc.txt txt = ./txt/cord-282372-nmii30mc.txt === reduce.pl bib === id = cord-278081-tk7vn1v1 author = Brooks, Wesley H. title = Viral Impact in Autoimmune Diseases: Expanding the “X Chromosome–Nucleolus Nexus” Hypothesis date = 2017-11-28 pages = extension = .txt mime = text/plain words = 9823 sentences = 457 flesch = 42 summary = Here is presented new details to the hypothesis, explaining how the disrupted chromatin can lead to subsequent disruption of the nucleolus, even nucleolar fragmentation, which results in ineffective nucleolar functioning, misfolded RNAs, misassembled or incompletely assembled ribonucleoprotein (RNP) complexes, and stabilization of nucleolar components in autoantigenic conformations. For now there is no direct connection between viruses and the "X chromosome-nucleolus nexus" hypothesis to the increased risk of cancers among autoimmune disease patients but we can consider the induction by viruses of increased polyamine levels and the possible reactivation of X-linked polyamine genes as means by which competition for the cellular methyl donor, SAM, could reduce DNA methylation and open oncogenes for overexpression in proliferation competent cells. A disrupted Barr body could generate an abundance of polyamines and Alu RNA from X-linked genes and elements that further stress and damage the nucleolus, making it very inefficient in its functions, even fragmenting it and possibly leading to cell death. cache = ./cache/cord-278081-tk7vn1v1.txt txt = ./txt/cord-278081-tk7vn1v1.txt === reduce.pl bib === id = cord-279691-v5kpmk0b author = Hagemeijer, Marne C. title = Biogenesis and Dynamics of the Coronavirus Replicative Structures date = 2012-11-21 pages = extension = .txt mime = text/plain words = 9036 sentences = 483 flesch = 43 summary = Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). cache = ./cache/cord-279691-v5kpmk0b.txt txt = ./txt/cord-279691-v5kpmk0b.txt === reduce.pl bib === id = cord-279346-7del8d2p author = Callendret, Benoît title = Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date = 2007-07-05 pages = extension = .txt mime = text/plain words = 10731 sentences = 471 flesch = 49 summary = title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. The influence of SS, MPMV-CTE or WPRE on expression of S protein in transfected cells and on induction of a protective SARS-CoV-specific immunity in mice after naked DNA immunization are compared. cache = ./cache/cord-279346-7del8d2p.txt txt = ./txt/cord-279346-7del8d2p.txt === reduce.pl bib === id = cord-278250-dwok857k author = Li, Heng title = The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date = 2019-08-19 pages = extension = .txt mime = text/plain words = 7452 sentences = 379 flesch = 44 summary = We performed metagenomic sequencing of fecal samples to detect the bacterial microbiome and virome composition of healthy one-year-old rhesus monkeys housed at the IMBCAMS (Fig. 1) . We comprehensively analyzed the interactions among the gut virome, bacterial microbiome and metabolomes based on the above results there were noticeable differences in bacterial β-diversity between control and experimental animals, as determined using principal component analysis (PCA), and the results showed good repeatability within a single group (Additional file 2: Figure S2F ). Briefly, the fecal virome composition was noticeably altered after depletion of the bacterial microbiome, and the abundances of many DNA viruses, bacteriophages and RNA viruses in the gut were clearly decreased. As expected, the whole gut bacterial microbiome, including gram-positive and gram-negative bacteria (Additional file 2: Figure S2E ), was depleted after treatment with the antibiotic cocktail, except for Escherichia-Shigella species belonging to Proteobacteria, which were resistant to the cocktail. cache = ./cache/cord-278250-dwok857k.txt txt = ./txt/cord-278250-dwok857k.txt === reduce.pl bib === id = cord-278647-krh63hqp author = Carter, Robert W title = A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918 date = 2012-10-12 pages = extension = .txt mime = text/plain words = 8413 sentences = 425 flesch = 52 summary = At the time of its disappearance in 2009, the human H1N1 lineage had accumulated over 1400 point mutations (more than 10% of the genome), including approximately 330 non-synonymous changes (7.4% of all codons). This process may play a role in natural pandemic cessation and has apparently contributed to the exponential decline in mortality rates over time, as seen in all major human influenza strains. Given this large body of data, it becomes feasible to test the attenuation model using mutation accumulation rates, non-synonymous amino acid changes, changing dN/dS ratios, changing transition/transversions ratios, and changes in codon specificity over time. Using the amended 1918 Brevig Mission virus as a reference and including all human and porcine viruses in the database, we calculated SNPs, indels, transitions, transversions, non-synonymous amino acid changes, dN/dS ratios, predicted protein lengths (for all 11 proteins), the normalized codon scores (NCS) and relative synonymous codon usage (RSCU) [51] score for each predicted protein of each genome. cache = ./cache/cord-278647-krh63hqp.txt txt = ./txt/cord-278647-krh63hqp.txt === reduce.pl bib === id = cord-280616-9mwr6a4x author = Yang, Ying title = Small non-coding RNAs-based bone regulation and targeting therapeutic strategies date = 2017-11-15 pages = extension = .txt mime = text/plain words = 16961 sentences = 828 flesch = 36 summary = reported a mechanosensitive miRNA, hsa-miR-103a-3p, that exhibited negative effects on Runx2 during cyclic mechanical stretch (CMS)induced osteoblastogenesis, leading to decreased bone formation both in vitro and in vivo (Zuo et al., 2015) . To understand whether other effective paracrine pathways exist in the interaction between the two cell types, Li and colleagues conducted miRNA-mediated osteoclast-directed osteoblastic bone formation in ovariectomized (OVX) mice, indicating that inhibition of osteoclast-derived exosomal mmu-miR-214-3p induced significantly suppressed osteoclastogenesis (Li et al., 2016b) . In addition, Krzeszinski and colleagues found that mmu-miR-34a-5p knockout and heterozygous mice exhibited elevated bone resorption and reduced bone mass by targeting transforming growth factor-b-induced factor 2 (Tgif2), indicating that miR-34a-5p was a critical osteoclast suppressor and a potential therapeutic strategy to combat osteoporosis, and could exert both anti-catabolic and anabolic effects compared to current drugs that are solely anticatabolic (Krzeszinski et al., 2014) . cache = ./cache/cord-280616-9mwr6a4x.txt txt = ./txt/cord-280616-9mwr6a4x.txt === reduce.pl bib === id = cord-278055-v2ed3tei author = Sia, Sin Fun title = Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date = 2020-05-14 pages = extension = .txt mime = text/plain words = 5396 sentences = 292 flesch = 56 summary = Previous study of SARS-CoV (Urbani strain) in 5-weeks-old golden Syrian hamsters showed robust viral replication with peak viral titers detected in the lungs on 2 dpi, followed by rapid viral clearance by 7 dpi, but without weight loss or evidence of disease in the inoculated animals 20 . Our results indicate that the golden Syrian hamster is a suitable experimental animal model for SARS-CoV-2, as there is apparent weight loss in the inoculated and naturally-infected hamsters and evidence of efficient viral replication in the nasal mucosa and lower respiratory epithelial cells. c, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one inoculated donor on 1 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. e, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one donor on 6 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. cache = ./cache/cord-278055-v2ed3tei.txt txt = ./txt/cord-278055-v2ed3tei.txt === reduce.pl bib === id = cord-283132-rfw8njpo author = Olsen, Christopher W. title = A review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination date = 1993-07-31 pages = extension = .txt mime = text/plain words = 13945 sentences = 687 flesch = 42 summary = List of abbreviations: ADE=antibody-dependent enhancement; BCV=bovine coronavirus; C' =complement; C'-ADE=complement-mediated antibody-dependent enhancement; CCV=canine coronavirus; CNS=central nervous system; CR=complement receptor; CVLP=coronavirus-like particle; ds=double-stranded; DTH=delayed-type hypersensitivity; EAV=equine arteritis virus; FcR = Fc receptor; FECV = feline enteric coronavirus; FeLV = feline leukemia virus; FIP = feline infectious peritonitis; FIPV = feline infectious peritonitis virus; HCV-229E = human coronavirus 229E; HCV-OC43=human coronavirus OC43; HE=hemagglutinating esterase; HEV=hemagglutinating encephalomyelitis virus; HIV=human immunodeficiency virus; HRSV=human respiratory syncytial virus; IBV = infectious bronchitis virus; kB = kilobases; kDa = kilodaltons; LDHV = lactate dehydrogenase virus; M = membrane (protein); mAb = monoclonal antibody; MHC = major histocompatability; MHV=mouse hepatitis virus; mRNA=messenger RNA; N=nucleocapsid (protein); Nlinked = asparagine-linked (glycosylation); NS = nonstructural (protein); O-linked = serine-or th reonine-linked (glycosylation); ORF--open reading frame; Pol = polymerase (protein); PRCV = porcine respiratory coronavirus; RCV = rat coronavirus; RECV = rabbit enteric coronaivirus; RI = replicative intermediate; rHuIFN~ =recombinant human interferon alpha; S= spike (protein); SDAV = sialodacryoadenitis virus; SIV = simian immunodeficiency virus; SPF = specific-pathogen-free; TCIDs0=tissue culture infectious dose 50%; TCV=turkey coronavirus; TGEV=transmissible gastroenteritis virus; ts=temperature-sensitive; VN=virus neutralization (-izing). cache = ./cache/cord-283132-rfw8njpo.txt txt = ./txt/cord-283132-rfw8njpo.txt === reduce.pl bib === id = cord-280994-w8dtfjel author = Peng, Qi title = Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date = 2020-04-23 pages = extension = .txt mime = text/plain words = 2105 sentences = 135 flesch = 55 summary = Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. Simultaneous 193 replacement of the nsp7 and nsp8 cofactors further enhanced the efficiency for RNA synthesis 194 to ~2.2 times of that for the SARS-CoV-2 homologous complex ( Figure 4B ). After 3 rounds of extensive 2D classification, ~924,000 particles 437 were selected for 3D classification with the density map of SARS-CoV nsp12-nsp7-nsp8 438 complex (EMDB-0520) as the reference which was low-pass filtered to 60 Å resolution. One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities cache = ./cache/cord-280994-w8dtfjel.txt txt = ./txt/cord-280994-w8dtfjel.txt === reduce.pl bib === id = cord-286332-cdg4im5h author = van Beurden, Steven J. title = A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination date = 2017-06-12 pages = extension = .txt mime = text/plain words = 6995 sentences = 350 flesch = 54 summary = Herein, the genomic part coding for the spike glycoprotein ectodomain was replaced by that of the coronavirus mouse hepatitis virus (MHV), allowing for the selection and propagation of recombinant mIBV in murine cells. This problem was solved by transfecting IBV genomic RNA into otherwise non-susceptible cells, exchanging the IBV spike gene by that of the mouse hepatitis virus (MHV) provided as part of a synthetic RNA, and by subsequently rescuing recombinant IBV from infected/ transfected cells in embryonated eggs (Fig. 1) . b Stage 1 in targeted RNA recombination: an interspecies chimeric murinized IBV with a MHV spike ectodomain (mIBV) is generated by a single recombination event of IBV genomic RNA with synthetic RNA transcribed from donor plasmid p-mIBV in the 3′-end region of the 1b gene (indicated by a black curved line). Upon transfection of synthetic rIBV donor RNA into mIBV-infected murine LR7 cells, subsequent infectious IBV virus particles could be rescued in ECE. cache = ./cache/cord-286332-cdg4im5h.txt txt = ./txt/cord-286332-cdg4im5h.txt === reduce.pl bib === id = cord-281385-oxohdfpu author = Noble, Christian G. title = Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine date = 2014-09-19 pages = extension = .txt mime = text/plain words = 2621 sentences = 152 flesch = 58 summary = Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. The SAM-depleted and SAM-containing MTases exhibited comparable enzymatic activities (N-7 MTase, 2 0 -O MTase, and covalent GMP-MTase complex formation the natural product Sinefungin, showing that this is a viable approach to identify novel small molecules that bind to the same pocket. This conclusion was supported by two complementary structural and functional approaches: (i) the crystal structure unequivocally shows that absence of SAM does not affect the overall conformation of DENV MTase, including the SAM-binding pocket; (ii) depletion of SAM from the recombinant MTase did not change the activities of cap methylations and GMP-MTase complex formation. Structural and functional analysis of methylation and 5 0 -RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5 cache = ./cache/cord-281385-oxohdfpu.txt txt = ./txt/cord-281385-oxohdfpu.txt === reduce.pl bib === id = cord-281717-kzd9vvci author = Digard, Paul title = Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date = 2020-05-08 pages = extension = .txt mime = text/plain words = 4473 sentences = 266 flesch = 53 summary = CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. 79 SARS-CoV-2 was recently reported to have a CpG composition lower than other members of the 80 betacoronavirus genus, comparable to certain canine alphacoronaviruses; an observation used to draw 81 inferences over its origin and/or epizootic potential (Xia 2020 in GC content (from ~ 0.32 -0.47) was seen across the Coronaviridae, and as expected, all viruses 97 exhibited some degree of CpG suppression, with CpG O:E ratios ranging from 0.37 to 0.74 (Fig 2A) . cache = ./cache/cord-281717-kzd9vvci.txt txt = ./txt/cord-281717-kzd9vvci.txt === reduce.pl bib === id = cord-282764-d9x1wii6 author = Chang, Chia-Yin title = Influence of intron and exon splicing enhancers on mammalian cell expression of a truncated spike protein of SARS-CoV and its implication for subunit vaccine development date = 2006-02-20 pages = extension = .txt mime = text/plain words = 4812 sentences = 231 flesch = 52 summary = title: Influence of intron and exon splicing enhancers on mammalian cell expression of a truncated spike protein of SARS-CoV and its implication for subunit vaccine development A truncated S protein of the TW1 strain, S(TR2) (88 kDa), carrying three S fragments (S74–253, S294–739, and S1129–1255) was investigated to study the influences of intron and exon splicing enhancers to improve S(TR2) protein expression in mammalian cells. Therefore, several different strategies for improving S TR2 protein expression in mammalian cells were investigated in this report, including intron addition and the application of exon splicing enhancers. The intron-dependent enhancement of S TR2 protein expression in CHO/dhFr− cells was further investigated by measuring total RNA level, in vivo RNA stability, and RNA elongation rate in this study. The results indicated that the intron-dependent S TR2 protein expression in mammalian cells correlated with a higher level of total RNA accumulation as determined by quantitative RT-PCR (Fig. 4A) . cache = ./cache/cord-282764-d9x1wii6.txt txt = ./txt/cord-282764-d9x1wii6.txt === reduce.pl bib === id = cord-280427-smqc23vr author = Singla, Rubal title = Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date = 2020-09-14 pages = extension = .txt mime = text/plain words = 7194 sentences = 381 flesch = 58 summary = The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. cache = ./cache/cord-280427-smqc23vr.txt txt = ./txt/cord-280427-smqc23vr.txt === reduce.pl bib === id = cord-285290-l7mnq4yb author = Warner, Katherine Deigan title = Principles for targeting RNA with drug-like small molecules date = 2018-07-06 pages = extension = .txt mime = text/plain words = 7564 sentences = 400 flesch = 49 summary = Here, we discuss principles for discovering small-molecule drugs that target RNA and argue that the overarching challenge is to identify appropriate target structures – namely in disease-causing RNAs that have high information content, and consequently appropriate ligand binding pockets. In our view, successful targeting of RNA in therapeutically useful ways with small molecules requires three distinct components: (1) identification of RNAs and RNA motifs with disease-related function, (2) use of screening approaches and libraries likely to identify drug-like molecules with appropriate pharmacological properties and (3) identification of and focus on RNA motifs with sufficient structural sophistication that make it likely that high affinity and specificity in small-molecule binding can be achieved. (1) a therapeutically compelling RNA target, (2) a screening approach that will identify drug-like lead molecules with appropriate pharmacological properties and (3) the identification of RNA motifs with sufficient information content such that high-specificity and high-potency binding to a high-quality pocket is achieved. cache = ./cache/cord-285290-l7mnq4yb.txt txt = ./txt/cord-285290-l7mnq4yb.txt === reduce.pl bib === id = cord-286298-pn9nwl64 author = Helmy, Yosra A. title = The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date = 2020-04-24 pages = extension = .txt mime = text/plain words = 9290 sentences = 516 flesch = 51 summary = Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. cache = ./cache/cord-286298-pn9nwl64.txt txt = ./txt/cord-286298-pn9nwl64.txt === reduce.pl bib === id = cord-284549-edliu3it author = Zhou, Hui title = Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells date = 2019-11-27 pages = extension = .txt mime = text/plain words = 4697 sentences = 289 flesch = 62 summary = In this study, we screened all the nonstructural proteins of HCV and found that HCV NS2 could suppress RNAi induced either by small hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) in mammalian cells. In this study, we uncovered that HCV nonstructural NS2 protein possessed a potent in vitro VSR activity that suppressed the RNAi induced by short hairpin RNA (shRNA) and siRNA in mammalian cells. Our results showed that the reversal effect of EGFP silencing could be observed at 48 hpt (Fig. 2C) , indicating that the VSR activity was dependent on the expression level of HCV NS2 protein. To investigate whether HCV NS2 can inhibit this step, small RNAs harvested from HEK293T cells co-expressing EGFP-specific shRNA together with NS2 were subjected to Northern blotting with a DIG-labeled RNA probe targeting EGFP siRNA produced from shRNA by Dicer. cache = ./cache/cord-284549-edliu3it.txt txt = ./txt/cord-284549-edliu3it.txt === reduce.pl bib === id = cord-281254-x7ivjvti author = Chang, Zhijie title = Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date = 2012-08-16 pages = extension = .txt mime = text/plain words = 3803 sentences = 256 flesch = 56 summary = The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. Since SARS-CoV rep-To address the issue related to delivery of siRNAs into cells or lication also requires certain host proteins, genes from host cells living organisms, researchers have used several approaches, ininvolved in viral replication can also be selected as targets. Therefore, RNA interference this coronavirus family), siRNAs targeting different genes of can be a tool for down-regulation of gene expression in cultured SARS-CoV were used by various groups to inhibit virus gene cells as well as in living organisms. cache = ./cache/cord-281254-x7ivjvti.txt txt = ./txt/cord-281254-x7ivjvti.txt === reduce.pl bib === id = cord-281285-5g1rw202 author = Simonis, Alexander title = A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date = 2020-11-03 pages = extension = .txt mime = text/plain words = 9501 sentences = 504 flesch = 46 summary = Based on its MOA, repurposed drugs with anti-SARS-CoV-2 activity can be divided into substances that prevent viral entry into host cells (1-2) and inhibit viral proteases (3) and inhibitors of viral replicase (4). The disappointing clinical results might be related to sub-therapeutic levels for inhibition of SARS-COV-2 because application of 400/100 mg of lopinavir/ritonavir twice daily was shown to yield median serum concentrations of 7.2 mg/l (11.5 µM) in patients with HIV (van der Lugt et al, 2009), which is significantly lower than the observed EC 50 in the in vitro studies. In this comparative review, we focus on repurposed drugs with antiviral effects against SARS-CoV-2 in cell-based assays as those substances offer great opportunities for a treatment early in the course of COVID-19 by inhibition of viral replication and might be even suitable for preventive strategies as shown for neuraminidase inhibitors in case of influenza (Jefferson et al, 2014) . cache = ./cache/cord-281285-5g1rw202.txt txt = ./txt/cord-281285-5g1rw202.txt === reduce.pl bib === id = cord-285935-5rsk6g7l author = Kinast, Volker title = Hepatitis E Virus Drug Development date = 2019-05-28 pages = extension = .txt mime = text/plain words = 6638 sentences = 364 flesch = 46 summary = Cyclic peptides (CP) that had been developed to abrogate interaction of p6Gag and TSG101 and inhibited viral release of HIV Virus like particles (VLPs) [76] were tested for their activity against HEV [77] . The compounds RBV and mycophenolic acid (MPA), both of which target enzymes involved in nucleotide synthesis, are either already used as treatment against HEV or have been reported for their potential to inhibit the virus. So far, the antiviral activity against HEV of only four drugs (Sofosbuvir, pegIFN-α, Ribavirin and silvestrol) was approved in experimental settings beyond in vitro cell culture systems. Sofosbuvir Inhibits Hepatitis E Virus Replication In Vitro and Results in an Additive Effect When Combined With Ribavirin Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo cache = ./cache/cord-285935-5rsk6g7l.txt txt = ./txt/cord-285935-5rsk6g7l.txt === reduce.pl bib === id = cord-284941-wfn0pnev author = Samal, S.K. title = Paramyxoviruses of Animals date = 2008-07-30 pages = extension = .txt mime = text/plain words = 4948 sentences = 251 flesch = 41 summary = The members of this virus family are enveloped and have genomes consisting of a single segment of negative-sense RNA that contains 6–10 genes encoding up to 12 proteins. The family Paramyxoviridae contains a large number of viruses of animals (Table 1) , including a number of major animal pathogens (such as Newcastle disease virus (NDV), canine distemper virus, and rinderpest virus), zoonotic pathogens (such as Hendra and Nipah viruses), and a number of somewhat obscure viruses whose natural histories are poorly understood. A number of animal paramyxoviruses have been recovered from cDNAs using reverse genetics, including simian virus 5, NDV, bovine parainfluenza virus 3, Sendai virus, canine distemper virus, rinderpest virus, bovine respiratory syncytial virus, and avian metapneumovirus. Infection occurs by several different routes, including aerosols (NDV, bovine respiratory syncytial virus, avian metapneumovirus) and contaminated feed and water (Newcastle disease, canine distemper, and rinderpest viruses). cache = ./cache/cord-284941-wfn0pnev.txt txt = ./txt/cord-284941-wfn0pnev.txt === reduce.pl bib === id = cord-286352-uftl1mx5 author = Baril, Martin title = The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot date = 2003-08-15 pages = extension = .txt mime = text/plain words = 5666 sentences = 254 flesch = 57 summary = Since the region downstream of the stem-loop increases frameshifting in the presence of this stem-loop, as shown in Figure 3 , these results also support our suggestion that the frameshift stimulatory signal in MVP5180 is more complex than a simple stemloop and could correspond to a pseudoknot structure. The frameshift efficiencies of the constructs containing these mutations were assessed in vitro and in cultured cells and are presented in Figure 4 (b) (see also Table 1 To provide an independent support for the pseudoknot structure in subtype MVP5180 of HIV-1 group O frameshift stimulatory signal, we made a structural probing analysis of an RNA fragment encompassing the gag/pol frameshift region of this subtype. Our results show that the frameshift stimulatory signal of subtype MVP5180 of HIV-1 group O is a pseudoknot, where 8 nt of a 10-nt loop capping an 8-bp stem base-pair with a downstream complementary sequence. cache = ./cache/cord-286352-uftl1mx5.txt txt = ./txt/cord-286352-uftl1mx5.txt === reduce.pl bib === id = cord-286232-jo24ia4s author = Hasebe, Rie title = Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways date = 2009-10-25 pages = extension = .txt mime = text/plain words = 6962 sentences = 364 flesch = 51 summary = Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. In HeLa and receptor-expressing CHO cells, infectious entry of HSV requires trafficking of the virus to an acidic intracellular compartment, phosphatidylinositol 3-kinase activity, glycoprotein D (gD) receptors, as well as viral gB, gD, and gH-gL (Nicola et al., 2003; Nicola and Straus, 2004) . With the use of ultrastructural analysis, we have previously suggested that EHV-1 enters equine brain microvascular endothelial cells (EBMECs) via endocytosis (Hasebe et al., 2006) . Localization of EHV-1 and caveolae during viral internalization Caveolar endocytosis has emerged as a route of entry for several viruses including simian virus 40 (SV40) (Anderson et al., 1996) , mouse polyomavirus (Richterová et al., 2001; Gilbert et al., 2003; Gilbert and Benjamin, 2004) , echovirus (Marjomäki et al., 2002) , human papillomavirus type 31 (Bousarghin et al., 2003; Smith et al., 2007) , human polyomavirus BK (BKV) (Eash et al., 2004) , and species C human adenovirus (Colin et al., 2005) . cache = ./cache/cord-286232-jo24ia4s.txt txt = ./txt/cord-286232-jo24ia4s.txt === reduce.pl bib === id = cord-284076-087oltss author = Patel, Deendayal title = Peptide-conjugated morpholino oligomers inhibit porcine reproductive and respiratory syndrome virus replication date = 2007-10-04 pages = extension = .txt mime = text/plain words = 7761 sentences = 411 flesch = 56 summary = Of 12 peptide-conjugated PMO (PPMO), four were found to be highly effective at inhibiting PRRSV replication in cell culture in a dose-dependant and sequence-specific manner. In a previous study (Zhang et al., 2006) , we tested six PPMO and found one of them (5UP1), designed to target the 5 terminal region of the PRRSV genome, to be a highly effective inhibitor of PRRSV replication in a sequence-specific and dose-dependent manner. Confirmation of the CPE observations and PRRSV yield titration was obtained by IFA on CRL11171 cells after virus inoculation and PPMO treatment (Fig. 2B ). demonstrated that PPMO generated little cytotoxicity in both CRL11171 and PAM cells, further indicating that the suppression of virus replication observed in the antiviral experiments above was due to sequence-specific effects. Treatment of cells with PPMO 5UP2 or 5HP led to suppression of PRRSV replication of all North American strains, producing virus yields not detectable (ND) in this assay. cache = ./cache/cord-284076-087oltss.txt txt = ./txt/cord-284076-087oltss.txt === reduce.pl bib === id = cord-286149-awhnjwyc author = Hoon‐Hanks, L.L. title = Metagenomic Investigation of Idiopathic Meningoencephalomyelitis in Dogs date = 2017-12-02 pages = extension = .txt mime = text/plain words = 5441 sentences = 289 flesch = 51 summary = In previous investigations of MUO in dogs, only brain samples were tested for infectious agents; however, CSF is a common sample utilized in the clinical evaluation of neurologic disease for the detection of infectious agent nucleic acids, especially by PCR. Additionally, RNA was extracted from postmortem brain samples from a mule deer (Odocoileus hemionus), green tree python (Morelia viridis), American crow (Corvus brachyrhynchos), and American robin (Turdus migratorius), all of which had previously been tested by PCR, metagenomic sequencing, or both, and were found to be infected with specific known infectious agents. There are several possible biological and technical explanations for our study's inability to identify a candidate etiologic agent for MUO, including the underlying pathogenesis of the disease, sample type and collection methods, case inclusion criteria, sensitivity of diagnostics, and database limitations. cache = ./cache/cord-286149-awhnjwyc.txt txt = ./txt/cord-286149-awhnjwyc.txt === reduce.pl bib === id = cord-285159-gytebbua author = Eydoux, Cecilia title = A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date = 2020-07-07 pages = extension = .txt mime = text/plain words = 3603 sentences = 215 flesch = 59 summary = Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights A new SARS-CoV non radioactive RNA polymerase assay is described The robotized assay is suitable to identify RdRp inhibitors based on HTS -A new SARS-CoV non radioactive RNA polymerase assay is described -The robotized assay is suitable to identify RdRp inhibitors based on HTS the RdRp core nsp12 and shown to confer full activity and processivity to nsp12 (Subissi et al., 2014) . Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). cache = ./cache/cord-285159-gytebbua.txt txt = ./txt/cord-285159-gytebbua.txt === reduce.pl bib === id = cord-283168-kl1hoa1x author = Farkas, Tibor title = Molecular detection of novel picornaviruses in chickens and turkeys date = 2011-12-13 pages = extension = .txt mime = text/plain words = 4034 sentences = 196 flesch = 52 summary = Fecal specimens, including swabs and litter extracts, collected from chickens, domestic ducks, turkeys, and Canadian geese were tested using degenerate primers targeting regions encoding for conserved amino acid motifs (YGDD and DY(T/S)(R/K/G)WDST) in calicivirus RNA-dependent RNA polymerases. Analysis of 2.2–3.2 kb extended genome sequences including the partial P2 (2C) and complete P3 (3A, 3B (VPg), 3C(pro), and 3D(pol)) regions of selected strains indicated that viruses yielding the 280/283 bp amplicons represent a putative new genus of Picornaviridae. This study utilized a broadly reactive primer set targeting conserved amino acid motifs encoding regions present in calicivirus RNA-dependent RNA polymerases (RdRp) and are partially also present in other viral RdRps. As part of the study here we report the serendipitous detection of novel picornaviruses in chicken and turkey samples that included diagnostic cases with runting-stunting syndrome (RSS). cache = ./cache/cord-283168-kl1hoa1x.txt txt = ./txt/cord-283168-kl1hoa1x.txt === reduce.pl bib === id = cord-283439-hqdq2qrh author = Rahman, Mohammad Tariqur title = Can Zn Be a Critical Element in COVID-19 Treatment? date = 2020-05-26 pages = extension = .txt mime = text/plain words = 5248 sentences = 315 flesch = 50 summary = The suggested treatments for COVID-19 are, but not limited to, the use of (i) convalescent plasma for COVID-19 treatment [63] [64] [65] ; (ii) ribavirin, a nucleoside analogue in combination with recombinant interferon showed inhibition of MERS-CoV replication [66] ; (iii) lopinavir/ritonavir-a combination of a protease inhibitor and a booster used for the treatment of human immunodeficiency virus infection [67] ; (iv) remdesivir, a nucleotide analogue that inhibit RNA polymerase with a broad spectrum of anti-viral activities; in inhibition of human and zoonotic coronavirus [15, 68, 69] ; (v) favipiravir (also known as T-705, Avigan or favilavir) is a pyrazinecarboxamide derivative known to inhibit RNA polymerase [70] . In the current pandemic of SARS-CoV-2, Zn supplement could play an important role to treat COVID-19 patients such as (i) added immune boosting effects with anti-viral drugs and (ii) stopping SARS-CoV-2 replication in infected cells, if combined with chloroquine. cache = ./cache/cord-283439-hqdq2qrh.txt txt = ./txt/cord-283439-hqdq2qrh.txt === reduce.pl bib === id = cord-287093-9mertwj7 author = Netherton, Christopher L title = Virus factories, double membrane vesicles and viroplasm generated in animal cells date = 2011-10-12 pages = extension = .txt mime = text/plain words = 4308 sentences = 227 flesch = 39 summary = In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses. In this review, we discuss how three supergroups of (+)strand RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses (NCLDV). The RNA-dependent RNA polymerases (RdRp) of the (+)strand RNA viruses are targeted to the cytoplasmic face of membrane-bound organelles and subsequent assembly of the replicase complex induces membrane curvature and the formation of densely packed membrane vesicles (reviewed in [1, 2] ) ( Figure 1 ). This suggests that replication may take place on CM and that genomes are transferred to vesicular packets for envelopment and budding, while excess viral RNA may be stored in DMVs. Picornaviruses generate densely packed DMVs between 200 and 400 nm in diameter, a series of single membraned vesicles resulting from fragmentation of the Golgi, and autophagosomes possibly generated as a bystander response to infection [11 ,12-16] . cache = ./cache/cord-287093-9mertwj7.txt txt = ./txt/cord-287093-9mertwj7.txt === reduce.pl bib === id = cord-283097-rlf5nv5q author = Ganar, Ketan title = Newcastle disease virus: Current status and our understanding date = 2014-05-12 pages = extension = .txt mime = text/plain words = 8613 sentences = 415 flesch = 46 summary = Newcastle disease virus-vectored vaccines expressing the hemagglutinin or neuraminidase protein of H5N1 highly pathogenic avian influenza virus protect against virus challenge in monkeys Quantitative basic residue requirements in the cleavage-activation site of the fusion glycoprotein as a determinant of virulence for Newcastle disease virus Role of C596 in the Cterminal extension of the haemagglutinin-neuraminidase protein in replication and pathogenicity of a highly virulent Indonesian strain of Newcastle disease virus Role of the cytoplasmic tail amino acid sequences of Newcastle disease virus hemagglutinin-neuraminidase protein in virion incorporation, cell fusion, and pathogenicity Evaluation of the Newcastle disease virus F and HN proteins in protective immunity by using a recombinant avian paramyxovirus type 3 vector in chickens Role of fusion protein cleavage site in the virulence of Newcastle disease virus A single amino acid change, Q114R, in the cleavage-site sequence of Newcastle disease virus fusion protein attenuates viral replication and pathogenicity cache = ./cache/cord-283097-rlf5nv5q.txt txt = ./txt/cord-283097-rlf5nv5q.txt === reduce.pl bib === id = cord-287501-7it4kh0e author = Roh, Changhyun title = A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date = 2012-05-03 pages = extension = .txt mime = text/plain words = 2964 sentences = 153 flesch = 45 summary = We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. 33 In this study, we report a novel approach for the inhibitor screening of SARS-CoV N protein using a quantum dots (QDs)-conjugated oligonucleotide system with wide applicability for facile and sensitive imaging analysis on a biochip. To the best of our knowledge, this is the first report on the inhibition effects of (-)-catechin gallate and (-)-gallocatechin gallate on SARS-CoV N protein using an optical nanoparticle-based RNA oligonucleotide platform. Among the polyphenolic compounds screened, (-)-catechin gallate and (-)-gallocatechin gallate showed high anti-SARS-CoV N protein activity. At a concentration of 0.05 µg mL -1 , (-)-catechin gallate and (-)-gallocatechin gallate showed more than 40% inhibition activity on a QDs-RNA oligonucleotide biochip platform. cache = ./cache/cord-287501-7it4kh0e.txt txt = ./txt/cord-287501-7it4kh0e.txt === reduce.pl bib === id = cord-283895-1p5uog38 author = Trottier, J. title = Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date = 2020-07-09 pages = extension = .txt mime = text/plain words = 1925 sentences = 125 flesch = 61 summary = Indeed, several reports indicate that SARS-CoV-2 RNA was readily detected in wastewater, and it is proposed that such approach could anticipate the occurrence of novel COVID-19 outbreaks in low prevalence regions , La Rosa et al., 2020 , Medema et al., 2020 , Orive et al., 2020 , Randazzo et al., 2020 . First, we showed that the Ebola standard (Ebo Std) primer/probe set was not detecting RNA from SARS-CoV-2-infected Vero E6 cells (Table 1) . . https://doi.org/10.1101/2020.07.08.20148882 doi: medRxiv preprint Next, we measured the SARS-CoV-2 RNA levels using N1 and N3 primer/probe sets in wastewater collected upstream of the main WWTP of the Montpellier metropolitan area on May 7 th , 18 th , 26 th , June 4 th , 15 th and 25 th (Figure 2A ). This intriguing result is reminiscent of a recent Spanish study, in which the authors could detect SARS-CoV-2 RNA in wastewater weeks before the first COVID-19 cases were reported (Randazzo et al., 2020) . cache = ./cache/cord-283895-1p5uog38.txt txt = ./txt/cord-283895-1p5uog38.txt === reduce.pl bib === id = cord-281281-knelqmzx author = Villas-Boas, Gustavo R. title = The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date = 2020-09-07 pages = extension = .txt mime = text/plain words = 15780 sentences = 708 flesch = 42 summary = The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. cache = ./cache/cord-281281-knelqmzx.txt txt = ./txt/cord-281281-knelqmzx.txt === reduce.pl bib === id = cord-286416-8eu6wp9b author = Valiente-Echeverría, Fernando title = Viral modulation of stress granules date = 2012-06-14 pages = extension = .txt mime = text/plain words = 5570 sentences = 290 flesch = 49 summary = If deadenylation (e.g., CCR4/Not1), destabilization (e.g., TTP/XRN1) and decapping (e.g., DCP1/DCP2) complex; and even RISC (Ago) complex are recruited to mRNA, these will be targeted to PBs. Conversely, if TIA-1/TIAR or proteins such as G3BP/USP10 are recruited to the stalled initiation complexes, these will be directed to SGs. Different pathways in SG assembly are described (in red): (i) phosphorylation of eIF2␣ induced by the exposure to different stress inducers (e.g., arsenite and thapsigargin) (Fig. 1) ; (ii) Hippuristanol and Pateamine A, drugs that inhibit the helicase activity of eIF4A altering ATP binding or ATPase activity; and (iii) the overexpression of SG markers, such as G3BP or TIA-1. West Nile virus infections suppress early viral RNA synthesis and avoid inducing the cell stress granule response Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly cache = ./cache/cord-286416-8eu6wp9b.txt txt = ./txt/cord-286416-8eu6wp9b.txt === reduce.pl bib === id = cord-281565-v8s2ski3 author = Belmonte-Reche, Efres title = Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2 date = 2020-08-20 pages = extension = .txt mime = text/plain words = 4545 sentences = 253 flesch = 53 summary = These PQS and PiMS have been assessed according to their potential to form, uniqueness, frequency of appearance, conservation rates between 3297 different 2019-nCoV clinical cases, confirmed quadruplex-forming sequence presence and localization within the genome. Then, these PQS and PiMS were evaluated by their frequency of appearance in the corresponding genome, the presence of known-to-form quadruplex structures sequences within and their probability of quadruplex-formation score (as the mean of G4Hunter (52) and the adaptation of the PQSfinder algorithm (53) ). A flexible configuration of quadruplex definitions will detect larger amounts of candidates at the expense of requiring more computing power and accepting sequences that are more ambiguous in forming quadruplex structures in vitro (as determined by their score; with longer loops, smaller runs, more bulges and more complementary G/C %, Figure 1 , B). Expanding the search for common candidates to the entire virus realm, we matched one PQS and PiMS from the 2019-nCoV with the potential quadruplexes found in four viruses from cache = ./cache/cord-281565-v8s2ski3.txt txt = ./txt/cord-281565-v8s2ski3.txt === reduce.pl bib === id = cord-282618-tjvjlyn9 author = Luke, J M title = Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers date = 2010-11-25 pages = extension = .txt mime = text/plain words = 6241 sentences = 336 flesch = 43 summary = To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. A neomycin resistance gene (NeoR) without an upstream Kozak sequence was cloned downstream of an enhanced green fluorescent protein (EGFP) transgene in different configurations similar to that used with PREs. Quantifiable neoR translation products were present in all tested configurations, as was biologically active neoR protein after plasmid transfection into both HEK293 and CHO cell lines (Supplementary Table S1 ). The assay was in the same format as in (a), except for the fact that Pol III inhibitor-treated cells were transfected with EGFP plasmids containing the CMV-HTLV-I R promoter with or without VA1; (c) Inhibition of PKR, not of adenosine deaminase acting on RNA (ADAR) or RNA interference (RNAI), was required for VA1 expression enhancement effect. cache = ./cache/cord-282618-tjvjlyn9.txt txt = ./txt/cord-282618-tjvjlyn9.txt === reduce.pl bib === id = cord-287228-0qm939ve author = Hong, Ke title = Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date = 2020-10-27 pages = extension = .txt mime = text/plain words = 3616 sentences = 192 flesch = 51 summary = In one study including 70 patients with COVID-19, 21% clinically recovered patients with two consecutive negative results of nucleic acid detection experienced a later positive testing for SARS-CoV-2, and the longest duration of viral RNA positivity in this study was 45 days following infection [4] . A total of 2860 COVID-19 patients were hospitalized and followed in this hospital since the epidemic, and those with persistent or intermittent viral RNA positivity in respiratory samples (including the nasopharyngeal, oropharyngeal and sputum samples) for at least 4 weeks were included in our study, regardless of the age and their clinical status. However, in most of these studies, PCR testing was used as a marker to indicate the existence of virus, and patients with positive viral RNA was considered infectious though they have been infected for months without further clinical symptoms. cache = ./cache/cord-287228-0qm939ve.txt txt = ./txt/cord-287228-0qm939ve.txt === reduce.pl bib === id = cord-287153-jbuuph6w author = Lund, Morten title = Experimental Piscine orthoreovirus infection mediates protection against pancreas disease in Atlantic salmon (Salmo salar) date = 2016-10-21 pages = extension = .txt mime = text/plain words = 7435 sentences = 399 flesch = 54 summary = The most prevalent viral diseases in Norwegian salmon aquaculture are heart and skeletal muscle inflammation (HSMI) caused by Piscine orthoreovirus (PRV), and pancreas disease (PD) caused by Salmonid alphavirus (SAV). The SAV RNA level in heart was significantly lower in the co-infected fish at 4 and 6 WPC-SAV compared to the SAV3 controls (p < 0.05). Using a non-parametric rank test of the ordinal histopathological score, changes in pancreas were found to be significantly lower at 4 and 6 WPC-SAV in both early and late co-infection compared to the SAV control groups (p < 0.05), except at 4 WPC-SAV in the PRV-SAV3-late group (Figures 6 and 7) . Microarray analysis was performed on hearts sampled at 4 and 6 WPC-SAV from the late co-infection and differences between the SAV3 control and PRV-SAV3-late group were analyzed (Table 2) . SAV RNA levels in heart were significantly lower 6 WPC-SAV in the early co-infected groups compared to the SAV controls. cache = ./cache/cord-287153-jbuuph6w.txt txt = ./txt/cord-287153-jbuuph6w.txt === reduce.pl bib === id = cord-287396-18p171nr author = Schroyen, Martine title = Current transcriptomics in pig immunity research date = 2014-11-15 pages = extension = .txt mime = text/plain words = 9824 sentences = 467 flesch = 44 summary = Other meta-analysis studies, examining the immune response to Salmonella typhimurium, combine microarray information with data such as serum cytokine measurements or microbiota differences. typhimurium will be discussed in the section ''Overall value of transcriptomics in important infectious swine diseases.'' In addition, whole genome microarrays were used to study pig response to Haemophilus parasuis infection by Zhao et al. In 2010, Xiao and collaborators performed a 3' tag digital gene expression (DGE) analysis of the porcine lung transcriptome on pigs infected with the PRRS virus (Xiao et al. Most pig immune studies conducted to identify host response to common porcine pathogens or to immune response stimulators such as LPS or PMA/ionomycin described in this review provide gene expression data from a single tissue or isolated cell type, and this at a limited number of times post-infection/stimulation. Recently, such a meta-analysis was performed by combining results of several microarray-based pig immune studies to find PRRS-specific responses (Badaoui et al. cache = ./cache/cord-287396-18p171nr.txt txt = ./txt/cord-287396-18p171nr.txt === reduce.pl bib === id = cord-287275-vwyny1vt author = Zhang, Meng-Jia title = Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China date = 2018-10-30 pages = extension = .txt mime = text/plain words = 5181 sentences = 267 flesch = 56 summary = In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. In addition, it has been reported that newborn piglets inoculated with two recent Chinese PDCoV isolates, named CHN-HN-2014 and CHN-GD-2016, developed clear clinical signs, including severe diarrhea, vomiting, and dehydration [21, 22] . Analysis of the genomic sequence suggested that CHN-HG-2017 is a potential recombinant virus derived from Chinese and Vietnam PDCoV strains. To confirm that virus propagation had occurred, the infectivity of the plaque-purified CHN-HG-2017 strain in LLC-PK1 cells was tested by IFA and western blot with an mAb against the PDCoV N protein. Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014 cache = ./cache/cord-287275-vwyny1vt.txt txt = ./txt/cord-287275-vwyny1vt.txt === reduce.pl bib === id = cord-282742-eyukbot7 author = Diosa-Toro, Mayra title = Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date = 2013-02-20 pages = extension = .txt mime = text/plain words = 6493 sentences = 364 flesch = 48 summary = Geiss, Pierson, and Diamond (2005) observed that siRNAs targeting the C gene had no effect on virus replication when transfected into cells 10 h after WNV infection using lipid-based reagents. In addition, no significant reduction in viral protein or RNA levels was seen in WNV replicon-expressing cells transfected with siRNAs targeting the NS3 gene using lipid-based reagents. Also, a recent report showed that siRNA toward the TNF-a gene reduced cytokine response in DENV-infected DCs, highlighting the potential of targeted RNAi-based approaches to simultaneously decrease viral replication and the detrimental host immune response (Subramanya et al., 2010) . In addition, it has been shown that WNV (Chotkowski et al., 2008) and DENV (Mukherjee & Hanley, 2010) infection (Mukherjee & Hanley, 2010) of Drosophila cell lines induce functional virus-specific siRNAs that promote a protective RNAi response. So far we have described the antiviral effect of the RNAi mechanism induced by exogenous delivery of siRNA or precursors, and how cellular miRNA can target sequences artificially introduced within the genome of flaviviruses. cache = ./cache/cord-282742-eyukbot7.txt txt = ./txt/cord-282742-eyukbot7.txt === reduce.pl bib === id = cord-287324-ecpicv5v author = Qiu, Yuan title = Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods date = 2017-06-02 pages = extension = .txt mime = text/plain words = 3736 sentences = 194 flesch = 55 summary = In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. In this study, we detected the viromes of RNA viruses of one mock sample and two pooled authentic samples, using the libraries prepared by the three methods on the Personal Genome Machine (PGM) platform, with the aim to generate data of significance for virome detection of RNA viruses and characterize the viromes of RNA viruses in ducks and minks. In the future, it is of significance to compare methods 2 and 3 in detecting viromes of RNA viruses in some clinical samples containing limited viral RNA. Detection of viromes of ducks and minks increases our understanding of the viral diversity in the animals, and provides novel clues for further studies regarding diagnosis of infectious diseases, identification of novel viruses and research of host-virus relationships. cache = ./cache/cord-287324-ecpicv5v.txt txt = ./txt/cord-287324-ecpicv5v.txt === reduce.pl bib === id = cord-287372-ya5uvoki author = Böszörményi, Kinga P. title = Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date = 2020-11-05 pages = extension = .txt mime = text/plain words = 3973 sentences = 249 flesch = 58 summary = This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. Rhesus macaques have also been applied 116 in COVID-19 pathogenesis studies [22, 24, 32, 33] , and to test the efficacy of remdesivir in the 117 treatment of SARS-CoV-2 infection [34] . we compared SARS-CoV-2 replication in rhesus and cynomolgus macaque species and 129 monitored signs of COVID-19-like disease symptoms for three weeks after infection. The animals from this study were not 342 euthanized to be able to perform re-infection studies or to monitor them for late clinical signs, 343 or co-morbidities related to We conclude that the course of SARS-CoV-2 infection of both macaque species is highly 345 similar, indicating that they are equally suitable models to test vaccines and antivirals in a 346 preclinical setting for safety and efficacy. cache = ./cache/cord-287372-ya5uvoki.txt txt = ./txt/cord-287372-ya5uvoki.txt === reduce.pl bib === id = cord-287488-h102xn29 author = Araujo, Danielle Bastos title = SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date = 2020-10-23 pages = extension = .txt mime = text/plain words = 3927 sentences = 223 flesch = 53 summary = BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. METHODS: After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS: The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks viable (titre 2.11 × 10(6) TCID50/mL, titre 1.5 × 10(6) PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. cache = ./cache/cord-287488-h102xn29.txt txt = ./txt/cord-287488-h102xn29.txt === reduce.pl bib === id = cord-286877-0h5vgi5c author = Dahiya, Shyam S. title = Immunogenicity of a DNA-launched replicon-based canine parvovirus DNA vaccine expressing VP2 antigen in dogs date = 2012-10-31 pages = extension = .txt mime = text/plain words = 5260 sentences = 261 flesch = 43 summary = When the pAlpha-CPV-VP2 was injected intradermal as DNA-launched replicon-based DNA vaccine in dogs, it induced CPV-specific humoral and cell mediated immune responses. To increase antigen production and immunogenicity with DNA vaccines, a new strategy has been developed to express the target heterologous antigen under the control of replicon from positive-strand RNA viruses with the promise of using the ability of these viruses to produce large amounts of viral proteins in infected cells. The replicon-based CPV DNA vaccine plasmid (pAlpha-CPV-VP2) encoding CPV-VP2 was constructed and evaluated to express CPV-VP2 protein in transfected cells in SDS-PAGE and Western blot (data not shown). To assess the protective efficacy of different CPV vaccines, sera collected from all immunized and control dogs were analyzed for presence of virus neutralizing (VN) antibody. CD8 + lymphocytes in dogs immunized with replicon-based CPV DNA vaccine compared to controls (Fig. 7) . There were over 24 thousand times more CPV-VP2 mRNA transcripts in pAlpha-CPV-VP2-transfected BHK-21 cells compared to respective non-replicating control indicating the self-replicating ability of replicon-based CPV-VP2 DNA vaccine. cache = ./cache/cord-286877-0h5vgi5c.txt txt = ./txt/cord-286877-0h5vgi5c.txt === reduce.pl bib === id = cord-284609-1q75zw6b author = King, Andrew M.Q. title = Recombination in RNA date = 1982-07-31 pages = extension = .txt mime = text/plain words = 4067 sentences = 198 flesch = 50 summary = RNAase Tl fingerprints of virus RNA, prepared from representatives of each recombinant type, confirmed the approximate crossover sites that had been deduced from the inheritance of proteins. The possibility of genetic recombination in such viruses was first suggested many years ago by Hirst (1962) and Ledinko (1963) , who showed that infection of cells with a mixture of inhibitor-sensitive variants of poliovirus resulted in an enhanced yield of resistant progeny that were genetically stable. Second, we have obtained biochemical evidence of genetic recombination by crossing temperature-sensitive mutants of aphthovirus that possess second-site mutations affecting polypeptide charge. This paper describes a cross between two subtype strains of aphthovirus that has provided the first biochemical demonstration of genetic recombination at the level of RNA. Several spontaneous temperature-sensitive mutants of subtype OS were isolated and screened by electrofocusing polypeptides induced in virus-infected cells. cache = ./cache/cord-284609-1q75zw6b.txt txt = ./txt/cord-284609-1q75zw6b.txt === reduce.pl bib === id = cord-284933-flbibrcm author = Kim, Jong-Oh title = Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection date = 2017-01-13 pages = extension = .txt mime = text/plain words = 4259 sentences = 266 flesch = 54 summary = title: Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection Ubiquitin-like protein 4a (UBL4a), C-C motif chemokine 2 (CCL2), lysozyme g (LYG_EPICO) and two novel genes (ID: SGU016297, SGU008676) were highly expressed in the NNV-infected group compared to that in the mock group. In this study, we performed a transcriptome analysis of the brain tissue of sevenband grouper infected with NNV compared to mock brain tissue using a RNA-Seq. The total number of unigenes and the average length of the unigenes were 104,348 and 845 bp, respectively. In this study, we performed a transcriptome analysis of the brain tissue of sevenband grouper infected with NNV compared to mock brain tissue using a RNA-Seq. The total number of unigenes and the average length of the unigenes were 104,348 and 845 bp, respectively. In this study, we identified innate immune response relevant genes of sevenband grouper involved in NNV infection. cache = ./cache/cord-284933-flbibrcm.txt txt = ./txt/cord-284933-flbibrcm.txt === reduce.pl bib === id = cord-287487-qeltdch7 author = Graepel, Kevin W. title = Proofreading-Deficient Coronaviruses Adapt for Increased Fitness over Long-Term Passage without Reversion of Exoribonuclease-Inactivating Mutations date = 2017-11-07 pages = extension = .txt mime = text/plain words = 7470 sentences = 467 flesch = 49 summary = Alanine substitution of ExoN catalytic residues [ExoN(-)] in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and murine hepatitis virus (MHV) disrupts ExoN activity, yielding viable mutant viruses with defective replication, up to 20-fold-decreased fidelity, and increased susceptibility to nucleoside analogues. High-or low-fidelity variants are described for many RNA viruses infecting animals, including the coronaviruses (CoVs) murine hepatitis virus (MHV-A59) and severe acute respiratory syndrome-associated coronavirus (SARS-CoV) (13) (14) (15) (16) (17) , as well as foot-and-mouth disease virus (18) (19) (20) (21) (22) , poliovirus (23) (24) (25) (26) (27) (28) (29) , Chikungunya virus (30, 31) , influenza virus (32) , coxsackievirus B3 (33, 34) , and human enterovirus 71 (35) (36) (37) . The evolved mutations in MHV-ExoN(-) nsp14 and nsp12, which encodes the RdRp, accounted for only part of the increased nucleoside analogue resistance of MHV-ExoN(-) P250, implicating multiple replicase proteins in adaptation for viral fitness. cache = ./cache/cord-287487-qeltdch7.txt txt = ./txt/cord-287487-qeltdch7.txt === reduce.pl bib === id = cord-287466-ag5y781z author = Cowley, J.A. title = Nidoviruses of Fish and Crustaceans date = 2016-09-09 pages = extension = .txt mime = text/plain words = 17715 sentences = 760 flesch = 47 summary = As evidenced by the presence of genomic-length and sgmRNA-length replicativeintermediate double-stranded (ds)RNAs in shrimp cells infected with gill-associated virus (GAV) (Cowley et al., 2002a) , the type species okavirus (Cowley et al., 2012) , it is speculated that transcription termination of the antisense RNAs might occur at precise positions, resulting in common 3′-termini, and that these then act directly as promoters for transcription initiation of the genomic and sgmRNAs. In all other nidoviruses, however, and for the longest of the sgmRNAs transcribed by toroviruses, the (−) and (+) strand sgmRNAs are transcribed using a far more complex discontinuous process involving the splicing of a common "anti-leader" sequence derived from the genome 5′-terminus to each (−) strand sgmRNA that then acts as a universal promoter for transcribing each (+) strand sgmRNA (Pasternak et al., 2006; Sawicki et al., 2007; Smits et al., 2005; van Vliet et al., 2002) . Nidoviruses of aquatic species include the rod-shaped okaviruses GAV and yellow head virus (YHV) that primarily infect Penaeid shrimp (Longyant et al., 2005; Flegel, 2012; Flegel et al., 1997a; Cowley et al., 2000a Cowley et al., , 2002a Cowley and Walker, 2002; Sittidilokratna et al., 2008) and a morphologically similar virus with a ~22 kb ssRNA genome detected in diseased Chinese mitten crabs (Zhang and Bonami, 2007) . cache = ./cache/cord-287466-ag5y781z.txt txt = ./txt/cord-287466-ag5y781z.txt === reduce.pl bib === id = cord-287349-1zcq7kzx author = Chen, James title = Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2959 sentences = 215 flesch = 53 summary = title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. The analogous structural 234 arrangement leads us to propose that the SARS-CoV-2 RdRp may backtrack, generating a single-235 stranded RNA segment at the 3'-end that would extrude out the RdRp secondary channel 236 Table S1 ; Video S1). This aspect of helicase function could provide the NTP-296 dependent motor activity necessary to backtrack the RdRp. In cellular organisms, DdRp 297 backtracking plays important roles in many processes, including the control of pausing during 298 transcription elongation, termination, DNA repair, and fidelity (Nudler, 2012) . Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase cache = ./cache/cord-287349-1zcq7kzx.txt txt = ./txt/cord-287349-1zcq7kzx.txt === reduce.pl bib === id = cord-283411-40ojqv1y author = Ben-Shmuel, Amir title = Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date = 2020-09-10 pages = extension = .txt mime = text/plain words = 1174 sentences = 91 flesch = 56 summary = title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit. cache = ./cache/cord-283411-40ojqv1y.txt txt = ./txt/cord-283411-40ojqv1y.txt === reduce.pl bib === id = cord-284118-z8zwjvbu author = Baczko, Knut title = Measles virus gene expression in subacute sclerosing panencephalitis date = 1984-10-31 pages = extension = .txt mime = text/plain words = 3140 sentences = 166 flesch = 57 summary = Measles virus-specific mRNAs were present, but the amount of matrix (M) protein mRNA was greatly reduced in comparison to lytically infected cells and phospho-(P) protein mRNA was hardly detectable whereas the level of the corresponding intermediate-sized (is-) RNA was greatly increased. Measles virus-specific mRNAs were present, but the amount of matrix (M) protein mRNA was greatly reduced in comparison to lytically infected cells and phospho-(P) protein mRNA was hardly detectable whereas the level of the corresponding intermediate-sized (is-) RNA was greatly increased. This interpretation is further supported by studies of non-productive cell lines which, although persistently infected with SSPE viruses, do not express measles virus M protein (Lin and Thormar, 1980; Machamer et al., 1981; Carter et al., 1983a) . This failure could result from an alteration of this specific mRNA which would prevent correct function in translation reactions, as studies of non-productive cell lines persistently infected with SSPE virus indicate (Carter et al., 1983a) . cache = ./cache/cord-284118-z8zwjvbu.txt txt = ./txt/cord-284118-z8zwjvbu.txt === reduce.pl bib === id = cord-288167-976qxja2 author = Park, Wan Beom title = Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date = 2018-05-09 pages = extension = .txt mime = text/plain words = 1373 sentences = 87 flesch = 52 summary = title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection BACKGROUND: Information on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. In the present study, replicative MERS-CoV was detected in sputum or transtracheal aspirate for up to 4 weeks after symptom development in MERS-CoV-infected patients with severe pneumonia. In conclusion, replicative MERS-CoV was detected in lower respiratory tract specimens for up to 4 weeks after symptom development, which was well correlated with the detection of genomic RNA. In upper respiratory tract specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. Middle East respiratory syndrome coronavirus (MERS-CoV) genomic RNA (upE) titers in sputum and transtracheal aspirates with vs. cache = ./cache/cord-288167-976qxja2.txt txt = ./txt/cord-288167-976qxja2.txt === reduce.pl bib === id = cord-283880-lrrkuist author = Kumar, Arvind title = Evolution of selective-sequencing approaches for virus discovery and virome analysis date = 2017-07-15 pages = extension = .txt mime = text/plain words = 5934 sentences = 286 flesch = 38 summary = Use of sequence dependent (i.e; generic PCR assays and microarray) and sequence independent (i.e; single primer amplification (SISPA) and random priming) approaches for nucleic acid amplification combined with Sanger sequencing or HTS allowed the rapid identification of new viruses after 1980 (Bishop-Lilly et al., 2010; Chang et al., 1994; Day et al., 2010; Grard et al., 2012; Kapoor et al., 2015; Ladner et al., 2016; Linnen et al., 1996; Matsui et al., 1991; Mokili et al., 2012; Muerhoff et al., 1997; Nichol et al., 1993; Qin et al., 2014; Quan et al., 2010; Simons et al., 1995b) (Fig. 1) . For the virome analysis of clinical samples with an abundance of host cells, like blood or tissues, pre-extraction based enrichment is not appropriate as the virus genome itself can be present in its non-capsidated or transcribed form. In positive selection methods, samples are enriched for viral nucleic acids directly using probes targeting the viruses like in PCR assays, microarray or virus capture (in solution based hybridization) approaches. cache = ./cache/cord-283880-lrrkuist.txt txt = ./txt/cord-283880-lrrkuist.txt === reduce.pl bib === id = cord-288962-jgtoehcr author = Andréoletti, Laurent title = Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date = 2000-06-06 pages = extension = .txt mime = text/plain words = 3704 sentences = 186 flesch = 36 summary = To define the role of enteroviruses and human rhinoviruses as etiological agents in childhood bronchiolitis, clinical aspirates from 84 infants admitted to hospital with symptoms of obstructive bronchiolitis were tested by picornavirus RT‐PCR assay, adenovirus PCR assay and classical immunofluorescence antigen detection of common respiratory viral agents. In summary, combination of molecular and classical detection assays of common viruses can be used to demonstrate enterovirus and human rhinovirus respiratory infection in childhood bronchiolitis, and provides an improved approach to obtain new insights into concomitant viral respiratory tract infection in infants. To investigate the role of enteroviruses and human rhinoviruses as etiological agent in bronchiolitis, 84 nasopharyngeal aspirates were tested by picornavirus RT-PCR assay, classical immunofluorescence antigens detection of respiratory syncytial viruses, influenza viruses, parainfluenza viruses, coronaviruses, and adenovirus PCR assay. cache = ./cache/cord-288962-jgtoehcr.txt txt = ./txt/cord-288962-jgtoehcr.txt === reduce.pl bib === id = cord-286243-ddpemgqt author = Whitaker, Amy M. title = APE1: A skilled nucleic acid surgeon date = 2018-11-30 pages = extension = .txt mime = text/plain words = 5842 sentences = 274 flesch = 41 summary = One such factor is the multifunctional enzyme human apurinic/apyrimidinic endonuclease 1 (APE1), known best for its DNA backbone cleavage activity at AP sites during base excision repair (BER). Abbreviations: 1-nt, 1-nucleotide; 5OHU, 5-hydroxy-2′-deoxyuridine; 8-oxoG, 8-oxoGuanine; AP, apurinic/apyrimidinic; APE1, human apurinic/apyrimidinic endonuclease 1; APE2, apurinic/apyrimidinic endonuclease 2; BER, base excision repair; DHT, 5,6-dihydrothymidine; DHU, 5,6-dihydro-2′-deoxyuridine; dRP, deoxyribonucleotide-phosphate; IR, ionizing radiation; NIR, nucleotide incision repair; pBQ-C, benzetheno exocyclic adduct of cytosine; PG, phosphoglycolate; PNK, polynucleotide kinase; PUA, α,β-unsaturated aldehyde; ROS, reactive oxygen species; THF, tetrahydrofuran; Tdp1, tyrosyl-DNA phosphodiesterase 1; XRCC1, X-ray repair cross-complementing protein 1 ⁎ Corresponding author. The BER pathway requires the coordinated activity of at least five enzymes including: (1) a DNA glycosylase capable of excising the modified base; (2) an AP-endonuclease, such as APE1, to generate a nick at the lesion site; (3) DNA polymerase β, which performs both lyase and DNA synthesis activities to remove the 5′ dRP (deoxyribonucleotide-phosphate) and fill the resulting gap; and, finally (4) DNA ligase III and (5) XRCC1 (X-ray repair cross-complementing protein 1) scaffolding to seal the nick and complete the repair, (Fig. 1) . cache = ./cache/cord-286243-ddpemgqt.txt txt = ./txt/cord-286243-ddpemgqt.txt === reduce.pl bib === id = cord-283998-whwksoxt author = Tannock, Gregory A. title = The RNA of human coronavirus OC-43 date = 1977-12-31 pages = extension = .txt mime = text/plain words = 3978 sentences = 213 flesch = 57 summary = Abstract A homogeneous RNA complex with a sedimentation coefficient of 70 S and an apparent molecular weight of approximately 6.1 × 106 was released from purified 32P-labeled, mouse-brain-derived OC-43 virus after treatment with 1% sodium dodecyl sulfate (SDS) for 15 min at 23°. This suggests that (a) extensive nicking of a large RNA molecule has occurred during viral growth, due to ribonucleases which are inactivated during phenol extractions; (b) heterogeneity for OC-43 RNA is not due to internal ribonuclease activity and fragments are held together by noncovalent linkages much weaker than those present in the 70 S retroviral RNA complex, or by small proteins; or, most probably, (c) a combination of extensive nicking and weak noncovalent linkages results in the heterogeneous denaturation products. The RNA of avian infectious bronchitis virus (IBV) was first described by Tannock (1973) , who obtained from purified virions a highly heterogeneous array of RNA fragments using a phenol-sodium dodecyl sulfate (SDS) extraction procedure. cache = ./cache/cord-283998-whwksoxt.txt txt = ./txt/cord-283998-whwksoxt.txt === reduce.pl bib === id = cord-288093-012ipcdr author = Bouvette, Jonathan title = High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date = 2018-12-06 pages = extension = .txt mime = text/plain words = 7258 sentences = 382 flesch = 54 summary = Moreover, high-throughput studies have identified additional non-coding RNAs that are likely processed by Dicer [9] as well as several pre-miRNA binding proteins that may regulate its cleavage activity [10] [11] [12] . The structure and activity of the purified Dicer were assessed by size-exclusion chromatography coupled to multi-angle light-scattering and refractive index (SEC-MALS/RI), negative stain transmission electron microscopy (TEM), binding assay and steady-state kinetics. Our kinetic analysis for Dicer cleavage of the pre-let-7a-1 substrate were performed under strict steady state conditions and reveals k cat and K M values that are much higher than previously reported. Moreover, SEC -MALS/RI analysis of a purified Dicer sample stored for 6 months at − 80°C in sucrose/DDM-containing buffer shows that the purified protein remains almost exclusively monomeric ( ≥ 94%), indicating that the protein is intact after long-term storage (Additional file 1: Figure S1 ). cache = ./cache/cord-288093-012ipcdr.txt txt = ./txt/cord-288093-012ipcdr.txt === reduce.pl bib === id = cord-283590-xvnv17zy author = Chen, Dabiao title = Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date = 2020-03-05 pages = extension = .txt mime = text/plain words = 1499 sentences = 96 flesch = 48 summary = Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People's Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). cache = ./cache/cord-283590-xvnv17zy.txt txt = ./txt/cord-283590-xvnv17zy.txt === reduce.pl bib === id = cord-285868-fz5utxss author = Jheng, Jia-Rong title = ER stress, autophagy, and RNA viruses date = 2014-08-05 pages = extension = .txt mime = text/plain words = 9345 sentences = 480 flesch = 38 summary = In addition to regulation of cell death, it is reported that HCV induces the expression of CHOP at mRNA and protein levels and is correlated with autophagy induction; knockdown of CHOP not only increases HCV PAMP-mediated innate immune activation, but also elevates its inhibitory effect on virus replication (Ke and Chen, 2011) . Overexpression of HCV E1 and/or E2 induces the expression of CHOP in a PERK-dependent manner (Chan and Egan, 2005) ; while upon HCV infection, CHOP protein is upregulated by PERK, activating transcription factor (ATF6), and inositol-requiring transmembrane kinase/endonuclease 1 (IRE1) collectively. It was reported that rotavirus NSP4 viroporin initiates autophagy to transport viral proteins to sites of virus replication for assembly of mature particles, which involves an increase of cytoplasmic calcium and subsequent activation of the CaMKK-β-AMPK pathway. Regulated IRE1-dependent decay pathway is activated during Japanese encephalitis virus-induced unfolded protein response and benefits viral replication cache = ./cache/cord-285868-fz5utxss.txt txt = ./txt/cord-285868-fz5utxss.txt === reduce.pl bib === id = cord-283346-0v4b6do2 author = Ansari, Abdul Wahid title = Host chemokine (C-C motif) ligand-2 (CCL2) is differentially regulated in HIV type 1 (HIV-1)-infected individuals date = 2006-08-17 pages = extension = .txt mime = text/plain words = 4326 sentences = 220 flesch = 48 summary = CCL2 was the most strongly regulated gene at mRNA level and its serum concentration was significantly elevated in viremic compared with aviremic and HIV-1 seronegative controls, indicating a positive correlation between viremia and CCL2. For example, the C-C chemokines macrophage inflammatory protein (MIP)-1a/CCL3, MIP-1b/CCL4 and regulated upon activation, normal T cell expressed and secreted (RANTES)/ CCL5 inhibit M-tropic HIV-1 infection by competing with the virus for its binding to the co-receptor CCR5 (11) (12) (13) (14) (15) (16) (17) . To investigate the impact of HIV-1 viremia on the host inflammatory cytokine/chemokine network, more specifically on CCL2, we utilized DNA microarray approach on PBMC RNA derived from HIV-1-infected viremic and aviremic individuals. In this study, we report that HIV-1 viremic patients show an altered expression of key inflammatory cytokines and chemokines as compared with aviremic individuals. Furthermore, increased mRNA transcripts were again detected in CCL2, CXCL10 and IFN-c when more RNA samples derived from additional aviremic and viremic patients were analyzed individually. cache = ./cache/cord-283346-0v4b6do2.txt txt = ./txt/cord-283346-0v4b6do2.txt === reduce.pl bib === id = cord-288390-p1q3v1ie author = Habjan, Matthias title = Cytoplasmic sensing of viral nucleic acids date = 2015-02-07 pages = extension = .txt mime = text/plain words = 4040 sentences = 252 flesch = 48 summary = These sensors induce expression of cytokines, affect cellular functions required for virus replication and directly target viral nucleic acids through degradation or sequestration. These sensors induce expression of cytokines, affect cellular functions required for virus replication and directly target viral nucleic acids through degradation or sequestration. In this review we concentrate on intracellular nucleic acid sensors and effector proteins that evolved to mediate specialised tasks including, firstly, expression of cytokines such as type I interferons (IFN-a/b); secondly, modulation of cellular machineries required for virus replication and thirdly, direct inhibition of virus growth ( Figure 1 ). Among the best characterised cytoplasmic proteins involved in virus sensing are RIG-I-like receptors (RLRs), a family of DExD/H-box helicases which specifically identify viral RNAs and have the ability to stimulate expression of IFN-a/b and other cytokines (Figure 3 ) [4, 17] . Virus infection activates a restricted set of sensor and effector proteins that modulate cellular pathways and directly target viral nucleic acid, thereby shaping the innate immune response. cache = ./cache/cord-288390-p1q3v1ie.txt txt = ./txt/cord-288390-p1q3v1ie.txt === reduce.pl bib === id = cord-289038-15yp9uqy author = Chow, Jonathan Tak-Sum title = Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date = 2020-08-26 pages = extension = .txt mime = text/plain words = 5312 sentences = 445 flesch = 62 summary = The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection. Another recent study used a high-throughput reporter screen of miRNA from human and mouse respiratory epithelial cells to identify hsa-miR-127-3p, hsa-miR-486-5p, and hsa-miR-593-5p as contributors to the antiviral defence against influenza A virus by targeting the genomes of the H3N2 and attenuated PR8 (H1N1) viral strains [16] . Given the wealth of evidence supporting a role for miRNA in host cell antiviral defence mechanisms, we sought to identify human miRNA that have the potential to target the SARS-CoV-2 genome. DEA of Calu3 cells infected with SARS-CoV revealed that only hsa-miR-155-3p (upregulated) and hsa-let-7a-3p (downregulated) out of the 128 miRNA we identified in this study, were differentially expressed ( Figure 4B ). cache = ./cache/cord-289038-15yp9uqy.txt txt = ./txt/cord-289038-15yp9uqy.txt === reduce.pl bib === id = cord-285330-td4vr0zv author = Mohammadi, Ali title = Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date = 2015-11-12 pages = extension = .txt mime = text/plain words = 3157 sentences = 180 flesch = 56 summary = title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. In this study, we identified IBV load in different tissues of experimentally infected broilers to clarify the replication strength of IRFIBV32 Isolate at intervals post challenge. Gross lesions were recorded and their trachea, lungs, kidneys, caecal tonsils, testes and ovaries were aseptically collected separately for the virus detection, titration and histopathological evaluations. We detected the viral RNA in the caecal tonsils of infected chicken from 1 to 20 dpi and the maximal loads of the virus were on 5 dpi. Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens cache = ./cache/cord-285330-td4vr0zv.txt txt = ./txt/cord-285330-td4vr0zv.txt === reduce.pl bib === id = cord-288701-nx9fg4yn author = Mari, Viviana title = Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date = 2015-12-17 pages = extension = .txt mime = text/plain words = 4827 sentences = 227 flesch = 53 summary = The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. To overcome these limitations, we have developed a multiplex real-time RT-PCR assay for simultaneous detection of the different species of bovine pestiviruses, including the emerging HoBi-like group, allowing a rapid, sensitive and specific diagnosis of pestivirus infection and characterisation of the viral species. cache = ./cache/cord-288701-nx9fg4yn.txt txt = ./txt/cord-288701-nx9fg4yn.txt === reduce.pl bib === id = cord-285262-690kpupt author = Imre, Gergely title = The involvement of regulated cell death forms in modulating the bacterial and viral pathogenesis date = 2020-01-27 pages = extension = .txt mime = text/plain words = 13203 sentences = 714 flesch = 38 summary = Apoptosis, necroptosis and pyroptosis represent three distinct types of regulated cell death forms, which play significant roles in response to viral and bacterial infections. Abstract Apoptosis, necroptosis and pyroptosis represent three distinct types of regulated cell death forms, which play significant roles in response to viral and bacterial infections. In this chapter, based on the current advances in the research, we give a detailed description about the key cell death modalities, including apoptosis, necroptosis and pyroptosis emerging in response to pathogenic insults, and we discuss how bacterial and viral infections can modulate these signaling pathways. The components of the bacterial T3SS trigger inflammasome formation and pyroptotic cell death in Shigella infected macrophages through the activation of the NLR family CARD domain containing protein 4 (NLRC4) (Fig. 3) . Macrophage activation redirects yersinia-infected host cell death from apoptosis to caspase-1-dependent pyroptosis cache = ./cache/cord-285262-690kpupt.txt txt = ./txt/cord-285262-690kpupt.txt === reduce.pl bib === id = cord-289093-si8btsab author = Beard, Philippa M. title = A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date = 2014-06-05 pages = extension = .txt mime = text/plain words = 6578 sentences = 310 flesch = 49 summary = To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. The methodology in the previously published VACV screens varied considerably; Mercer et al [32] measured the growth of a thymidine-kinase-deficient VACV (strain Western Reserve) after only 8 h of infection, thereby identifying cellular proteins involved in the initial stages of virus replication but excluding analysis of viral spread. cache = ./cache/cord-289093-si8btsab.txt txt = ./txt/cord-289093-si8btsab.txt === reduce.pl bib === id = cord-288651-bgo8istm author = SHI, Yi title = Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date = 2005-03-17 pages = extension = .txt mime = text/plain words = 3062 sentences = 242 flesch = 62 summary = RNA interference (RNAi) is triggered by the presence of a double-stranded RNA (dsRNA), and results in the silencing of homologous gene expression through the specific degradation of an mRNA containing the same sequence. Here, we studied the effects of synthetic siRNA duplexes targeted to SARS coronavirus structural proteins E, M, and N in a cell culture system. Specific inhibition of cellular mRNA by RNAi can be triggered in mammalian cells by the introduction of synthetic 21-to 23-nucleotide duplexes of RNA N genes of SARS-CoV and evaluated their effects on viral genes expression in Vero E6 cells. The results show that all siRNA duplexes specifically reduced SARS-CoV genes expression to different extents compared with the control (Fig. 1) . Kinetic study results (Fig. 2B ) revealed a continuous increase in the specific inhibition of SARS-CoV genes expression by No. 5, No. 6, and No. 16 siRNA from 24 to 72 h after transfection. cache = ./cache/cord-288651-bgo8istm.txt txt = ./txt/cord-288651-bgo8istm.txt === reduce.pl bib === id = cord-289192-1ecr16a3 author = Fujita, Motomichi title = Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA date = 2019-02-01 pages = extension = .txt mime = text/plain words = 2374 sentences = 160 flesch = 54 summary = title: Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA Here, we describe a simple, rapid, cost-effective, high-throughput method using a homogeneous time-resolved fluorescence (HTRF) assay [2] focusing on viral dsRNA. The dsRNA-HTRF assay may be a useful method for screening of antiviral agents against (+) ssRNA viruses. Moreover, we determined whether the dsRNA-HTRF assay could detect the concentration-and time-dependent signals. Therefore, to evaluate whether the dsRNA-HTRF assay can detect (+) ssRNA viruses, we focused on infection by picornaviruses represented by HRV. Schematic diagram of the double-stranded RNA (dsRNA) -homogeneous time-resolved fluorescence (HTRF)-based assay. In addition, we examined whether the dsRNA-HTRF assay could detect a single cycle of viral replication. H1-HeLa cells were infected with HRV-B14 at MOI of 10 to achieve single-cycle growth, and viral dsRNA was detected at 6 h post-infection using the dsRNA-HTRF assay ( Supplementary Fig. 2) , indicating that this assay could evaluate the single-cycle growth of HRV-B14. cache = ./cache/cord-289192-1ecr16a3.txt txt = ./txt/cord-289192-1ecr16a3.txt === reduce.pl bib === id = cord-288960-v6l6o5va author = Li, Yang title = Regulating STING in health and disease date = 2017-06-07 pages = extension = .txt mime = text/plain words = 12297 sentences = 689 flesch = 41 summary = Possibly via RIG-I -dependent RNA detection which may in turn induce STING [6] Vesicular stomatitis virus Negative strand ssRNA virus Unknown [6] Human immunodeficiency virus Negative strand ssRNA virus dsDNA reverse transcribed from viral RNA induces cGAS-STING pathway [28] Influenza A virus Negative strand ssRNA virus Possibly via membrane fusion or unknown mechanism independent of DNA recognition [29] Mycobacteria tuberculosis Bacteria producing c-di-GMP c-di-GMP [30, 31] Streptococcus pneumoniae Bacteria dsDNA Bacterial dsDNA [32] Streptococcus pyrogenes Bacteria dsDNA Bacterial dsDNA [33] Staphylococcus aureus Bacteria producing c-di-AMP c-di-AMP [34] Listeria monocytogenes Bacteria producing c-di-AMP c-di-AMP [35] Vibrio cholera Bacteria producing 3′-3′ cGAMP 3′-3′ cGAMP [36, 37] Abbreviations: dsDNA double-stranded DNA, ssRNA single-stranded RNA The type I interferon signal adaptor protein STING is responsible for mediating double-stranded DNA sensing responses and the detection of bacterial cyclic dinucleotides c-di-AMP, c-di-GMP, and 3′-3′ cGAMP. cache = ./cache/cord-288960-v6l6o5va.txt txt = ./txt/cord-288960-v6l6o5va.txt === reduce.pl bib === id = cord-289321-ahl46ql9 author = van Buuren, Nicholas title = Transmission genetics of drug-resistant hepatitis C virus date = 2018-03-28 pages = extension = .txt mime = text/plain words = 7817 sentences = 394 flesch = 48 summary = Differential visualization of drug-resistant and -susceptible RNA genomes within cells revealed that resistant variants of NS3/4A protease and NS5A phosphoprotein are cis-dominant, ensuring their direct selection from complex environments. Our goal was to screen the HCV-encoded viral proteins that are current targets of antiviral compounds to determine the intracellular dominance relationships between drug-resistant and drug-susceptible genomes. To test whether susceptibility to NS5A inhibitors was dominant in the context of viral infections, we analyzed U, S, S + R and R cell populations by flow cytometry as previously performed for the NS3/4A inhibitor in Figure 3 . To test whether exogenously expressed drug-susceptible NS5A proteins could co-assemble with drug-resistant NS5A, we utilized the previously described HCV plasmid that expresses HA-tagged and GFP-tagged NS5A within the same polyprotein but does not support genome replication ( Figure 5A) . Failure of NS5A proteins to mix during infection is a likely explanation for the cis-dominance of drug resistance observed in cultured cells (Figure 4) . cache = ./cache/cord-289321-ahl46ql9.txt txt = ./txt/cord-289321-ahl46ql9.txt === reduce.pl bib === id = cord-286711-nr6vnl9h author = nan title = Other viruses causing gastroenteritis date = 2003-12-31 pages = extension = .txt mime = text/plain words = 2186 sentences = 125 flesch = 48 summary = Some of these viruses discussed in this chapter are toroviruses, picobirnaviruses, enteroviruses, human immunodeficiency virus (HIV), herpesviruses, and coronaviruses. Cytomegalovirus (CMV) and herpes simplex viruses, members of the Herpesviridae family, are found as the cause of colitis and esophagitis, mainly in HIV-infected patients. Besides the viruses producing the majority of human viral gastroenteritis (Sections II-V), other viruses infect more rarely, but are sometimes able to cause epidemics. HIV, the causative agent of the Acquired Immunodeficiency Syndrome (AIDS), is a member of the Lentivirus genus of the Retroviridae family. HIV, the causative agent of the Acquired Immunodeficiency Syndrome (AIDS), is a member of the Lentivirus genus of the Retroviridae family. Cytomegalovirus (CMV) and herpes simplex viruses, members of the Herpesviridae family, are found as the cause of colitis and oesophagitis, mainly in HIV-infected patients (Levinson and Bennets, 1985; Jacobson and Mills, 1988; Dieterich and Robinson, 1991; Theise et al. Enteric viruses and diarrhoea in HIV-infected patients cache = ./cache/cord-286711-nr6vnl9h.txt txt = ./txt/cord-286711-nr6vnl9h.txt === reduce.pl bib === id = cord-288879-rj03dsib author = Schein, Catherine H. title = Polyglutamine Repeats in Viruses date = 2018-09-04 pages = extension = .txt mime = text/plain words = 6195 sentences = 301 flesch = 45 summary = While the mechanisms for the function and toxicity of extended polyQ segments (or the nucleic regions that encode them) in eukaryotic proteins continue to be actively studied [16] , there has been little exploration of their occurrence and possible roles, even in neurovirulent viruses. At the start of this work, the ViPR database [29] , which allows rapid access to the published sequences of over 75,000 viral genomes or genome segments, was used to determine which RNA and DNA viruses contain polyQ repeats. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses). Under growth conditions allowing the virus to resume lytic growth, where the enzyme activity is required to ensure efficient replication, the region Fig. 2 Soluble polyQ segments (of cell or viral origin) may prevent beclin-1-induced autophagy, which depends on the DNA binding ability of the polyQ segment of wt-ataxin-3 (based on [2, 67] ). cache = ./cache/cord-288879-rj03dsib.txt txt = ./txt/cord-288879-rj03dsib.txt === reduce.pl bib === id = cord-284707-72vx11aq author = Leibowitz, Julian L. title = Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells date = 1988-09-30 pages = extension = .txt mime = text/plain words = 5498 sentences = 316 flesch = 53 summary = For mouse hepatitis virus (MHV), one of the most extensively studied coronaviruses, there are seven species of MHV-specific mRNA present in infected cells, the largest of which is indistinguishable from virion RNA (Leibowitz et a/., 1981; Lai et a/., 1981; Spaan et a/., 1981) . In this paper we report the characteristics of a permeabilized cell system and demonstrate that it incorporates ribonucle-otide triphosphates into RNA molecules which appear identical to the virus-specific mRNAs synthesized in MHV-infected cells. Protease inhibitors and RNase inhibitors have both been reported to increase the RNA-dependent RNA polymerase activity present in extracts of West Nile virus-infected cells (Grun and Brinton, 1986) . The kinetics of the development of the MHV-specific RNA polymerase activity over the course of infection was determined in permeabilized cells. In this work we report the development and characterization of a permeabilized cell system for assaying MHV-specific RNA polymerase activity. cache = ./cache/cord-284707-72vx11aq.txt txt = ./txt/cord-284707-72vx11aq.txt === reduce.pl bib === id = cord-284156-btb4oodz author = Liu, Yiliu title = Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date = 2017-01-03 pages = extension = .txt mime = text/plain words = 7021 sentences = 397 flesch = 38 summary = Retinoic acid-inducible gene-I (RIG-I) is critical in triggering antiviral and inflammatory responses for the control of viral replication in response to cytoplasmic virus-specific RNA structures. They function as cytoplasmic sensors for the recognition of a variety of RNA viruses and subsequent activation of downstream signaling to drive type I IFN production and antiviral gene expressions. (c) Interactions between RIG-I-TRIM25 complex and 14-3-3ϵ promote RIG-I translocation to mitochondrial mitochondrial antiviral signaling protein (MAVS) for downstream signaling, leading to interferon production. Protein purification and mass spectrometry analysis identified that phosphorylation of Thr170 in the CARDs antagonizes RIG-I signaling by inhibiting TRIM25-mediated Lys172 ubiquitination and MAVS binding (68) . Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Inhibition of dengue and chikungunya virus infections by RIG-I-mediated type I interferon-independent stimulation of the innate antiviral response cache = ./cache/cord-284156-btb4oodz.txt txt = ./txt/cord-284156-btb4oodz.txt === reduce.pl bib === id = cord-289407-8fje16z1 author = Moore, G. title = Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date = 2020-09-25 pages = extension = .txt mime = text/plain words = 4720 sentences = 328 flesch = 59 summary = Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. 6 Air samples taken during tracheostomy procedures, high flow nasal oxygen treatment, non-invasive ventilation and nebulisation have not contained SARS-CoV-2 RNA 7 and HCWs exposed to unrecognised COVID-19 patients undergoing similar high-risk AGPs have not become infected. . https://doi.org/10.1101/2020.09.24.20191411 doi: medRxiv preprint Several studies, utilising a range of air and surface sampling methods, have been carried out to determine the presence and prevalence of SARS-CoV-2 in the healthcare environment. [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] The detection of viral RNA in air samples differs with study with some reporting widespread airborne contamination 14, 18, 21 but many reporting low or non-detectable concentrations 13, 15, 16, 19 even in samples collected 10 cm from the face of positive patients. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients cache = ./cache/cord-289407-8fje16z1.txt txt = ./txt/cord-289407-8fje16z1.txt === reduce.pl bib === id = cord-285505-8norumv6 author = Vere Hodge, R. Anthony title = Meeting report: 27th International conference on antiviral research, in Raleigh, NC, USA date = 2014-09-16 pages = extension = .txt mime = text/plain words = 10276 sentences = 566 flesch = 58 summary = The focus of John's presentation was on the research conducted in his own and his collaborators' laboratories that ultimately led to the invention of three compounds which were discovered to have antiviral activity against human cytomegalovirus (HCMV) and which later entered clinical trials: BDCRB pyranoside (GW275175X) (Phase I), maribavir (Phases I, II and III) and cyclopropavir (Phase I). In monotherapy studies after oral dosing with TDF (300 mg) and TAF (25 mg), the plasma TFV AUC is reduced from 1920 to 268 ng.h/ml respectively whereas the reduction in HIV load from baseline is improved, from log 10 0.97 to log 10 1.46 copies/ml, respectively, reflecting the more efficient delivery of TAF to target cells and tissues. David Margolis, University of North Carolina, NC, USA In HIV-infected patients, there is a long-lasting reservoir of HIV in the form of integrated viral DNA in resting CD4+ memory cells of the host immune system. cache = ./cache/cord-285505-8norumv6.txt txt = ./txt/cord-285505-8norumv6.txt === reduce.pl bib === id = cord-290481-i2ppvsh5 author = Dolja, Valerian V. title = Comparative and functional genomics of closteroviruses date = 2006-03-09 pages = extension = .txt mime = text/plain words = 9298 sentences = 455 flesch = 47 summary = It was concluded that, at least in part, viral pathogenicity is due to interference of silencing suppressors with developmental function of plant small RNAs. Despite their mechanistic similarity, p21 and p19 appear to be structurally and evolutionarily unrelated and neither has detectable homologues outside the respective virus genera (Vargason et al., 2003; Ye and Patel, 2005) . Although Citrus tristeza virus (CTV) encodes p20, a p21like suppressor of RNA silencing, screening of the CTV genome revealed an additional suppressor, p23, that has no homologues in other closteroviruses (Fig. 2) (Lu et al., 2004) . A comparison of TMV and BYV, which both evolved from the alphavirus-like ancestors, shows that the large part of the ∼9 kb genomic surplus of BYV is dedicated to facilitating the synthesis of the virion RNA and multiple sgRNAs. The rest of the surplus was invested in the formation of the complex virion tail that empowers virus transport within and transmission between the host plants and in suppression of RNA silencing (Fig. 1) . cache = ./cache/cord-290481-i2ppvsh5.txt txt = ./txt/cord-290481-i2ppvsh5.txt === reduce.pl bib === id = cord-290472-w77cmljm author = Sharon, Donald title = Systems Biology Approaches to Disease Marker Discovery date = 2010-06-09 pages = extension = .txt mime = text/plain words = 8665 sentences = 393 flesch = 39 summary = These markers, such as protein (including autoantibodies, which are antibodies specific to self-antigens [43] ), hormonal markers (such as lack of insulin in Type I diabetic patients [89] ), and genetic/genomic markers (such as BRCA1 mutation in breast cancer patients [52] ), enable clinicians to diagnose the disease while it is still at early stages, to ensure appropriate surgical intervention, efficient drug treat-ment and monitoring, and to predict an individual's risk of developing specific diseases before they experience symptoms. Scientists, such as the group led by Gil Mor at Yale University, recruited proteomics-based approaches using antibody-based protein microarrays to identify new serum biomarkers, which, in combination with CA-125, may enhance the early detection of ovarian cancer [48, 66, 110] . To date, no studies that attempt to identify novel breast cancer markers have been performed using high-density protein microarrays. cache = ./cache/cord-290472-w77cmljm.txt txt = ./txt/cord-290472-w77cmljm.txt === reduce.pl bib === id = cord-285676-4kgy20o9 author = de Vries, Antoine A.F. title = The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses date = 1997-02-28 pages = extension = .txt mime = text/plain words = 7980 sentences = 437 flesch = 53 summary = The overlapping ORFs 1a and b found at the 58 end of the nidoviral genome are frequently referred to as the ''polymerase gene.'' However, there is little doubt that the processing of the encoded polyproteins yields proteins required for RNA synthesis as well as a number of products involved in other aspects of virus replication. The sequence conservation between the more closely related corona-and toroviruses is clustered in six domains, four of which are also found in the arterivirus POL1b: the ''classical'' RNA-dependent RNA polymerase (RdRp) and helicase (H) domains, which are also present in the polymerases of most other viruses, a zinc finger motif (zf), and a short region of 80-100 residues, which has not yet been identified in other viral polymerases and was called the ''coronavirus-like'' (CVL) domain (3) (motif 2 in Fig. 1b) . cache = ./cache/cord-285676-4kgy20o9.txt txt = ./txt/cord-285676-4kgy20o9.txt === reduce.pl bib === id = cord-286103-cgky6ar6 author = Otaki, Momoko title = Inhibition of measles virus and subacute sclerosing panencephalitis virus by RNA interference date = 2006-02-13 pages = extension = .txt mime = text/plain words = 3538 sentences = 228 flesch = 56 summary = In this study, we adopted RNA interference (RNAi) strategy and examined whether small interfering RNAs (siRNAs) can be used to inhibit replication of MeV and SSPE virus. We report here that siRNAs targeted against L mRNA of MeV, either synthetic siRNAs or those generated by pcPUR + U6i-based expression plasmids, effectively and specifically inhibited replication of both MeV and SSPE virus without exhibiting any cytotoxic effect. We report here that siRNAs targeted against L mRNA of MeV, either synthetic ones or those generated by pcPUR + U6i-based expression plasmids, effectively inhibit replication of both MeV and SSPE virus. Indeed, we demonstrated in the present study that siRNAs targeted against selected portions of L mRNA of MeV, especially MV-L2 -L4 and -L5, either synthetic siRNAs or those expressed by pcPUR + U6i-based plasmids, effectively inhibited replication of both MeV and SSPE virus (Figs. cache = ./cache/cord-286103-cgky6ar6.txt txt = ./txt/cord-286103-cgky6ar6.txt === reduce.pl bib === id = cord-291026-99cit4ig author = Lung, O. title = Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date = 2015-01-27 pages = extension = .txt mime = text/plain words = 4566 sentences = 206 flesch = 55 summary = In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Archived viral nucleic acid from 18 laboratory-amplified non-CSF viruses including eight other pestiviruses (BVDV 1-Hastings, Singer and NY1 strains; BVDV 2-Ames 125c, 890, 24515 strains; BDV-Coos Bay; HoBi atypical pestivirus), African swine fever virus-Lisbon, swine vesicular disease virus-ITL 19/92, porcine respiratory and reproductive syndrome virus-YNL, swine influenza virus (H3N2), porcine circovirus 1 (PCV1, derived from infectious clone based on GenBank accession no. The iiRT-PCR assay accurately detected all CSFV RNA samples which represented all three genotypes, and eight of 11 subgenotypes that were available for testing and gave negative results for three BVDV type 1 strains, three BVDV type 2 strains, BDV, HoBi atypical pestivirus, ASFV and nine other viruses that affect livestock. cache = ./cache/cord-291026-99cit4ig.txt txt = ./txt/cord-291026-99cit4ig.txt === reduce.pl bib === id = cord-290550-u8x9drva author = Radford, Alan D. title = Application of next-generation sequencing technologies in virology date = 2012-09-17 pages = extension = .txt mime = text/plain words = 7931 sentences = 382 flesch = 43 summary = Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. Although this review has concentrated on the use of NGS to study viral sequences directly, it is clear that these approaches provide new opportunities to explore the interaction of replicating viruses with their host, particularly their transcriptome, in a non-targeted, hypothesis-generating mode. Viral transcriptome analysis of feline immunodeficiency virus infected cells using second generation sequencing technology cache = ./cache/cord-290550-u8x9drva.txt txt = ./txt/cord-290550-u8x9drva.txt === reduce.pl bib === id = cord-286719-1xjmlwqr author = Draz, Mohamed Shehata title = Applications of gold nanoparticles in virus detection date = 2018-02-15 pages = extension = .txt mime = text/plain words = 18990 sentences = 901 flesch = 37 summary = The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) . cache = ./cache/cord-286719-1xjmlwqr.txt txt = ./txt/cord-286719-1xjmlwqr.txt === reduce.pl bib === id = cord-285785-29ohzeug author = Chen, Xiaolan title = Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System date = 2020-08-12 pages = extension = .txt mime = text/plain words = 9666 sentences = 600 flesch = 46 summary = Expression analysis and bioinformatical functional annotation through RNA sequence by using line 6 3 and line 7 2 showed that lncRNAs were aberrantly expressed and were involved in immune-related pathways that indicate that lncRNAs participate in regulating MDV infection [70] . Although the underlying functional mechanism of ncRNAs has been revealed in many species, it is still beginning to emerge in response to avian disease, except for miRNAs. Researches on circRNAs and lncRNAs are basically performed on the analysis of their expression profile and associated pathways. For lncRNAs and circRNAs, they mainly exhibit their function through lncRNA/circRNA-miRNA-mRNA axis, however, in some cases they could also regulate the immune process by directly interacting with RNA binding proteins or virus gene sequence. Gene expression profile and long non-coding RNA analysis, using RNA-Seq, in chicken embryonic fibroblast cells infected by avian leukosis virus cache = ./cache/cord-285785-29ohzeug.txt txt = ./txt/cord-285785-29ohzeug.txt === reduce.pl bib === id = cord-286343-s8n1ldol author = Martin, Javier title = Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date = 2020-10-09 pages = extension = .txt mime = text/plain words = 5925 sentences = 340 flesch = 53 summary = We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory (data not shown). cache = ./cache/cord-286343-s8n1ldol.txt txt = ./txt/cord-286343-s8n1ldol.txt === reduce.pl bib === id = cord-290744-m0vpizuh author = Kindler, E. title = Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date = 2016-09-09 pages = extension = .txt mime = text/plain words = 7229 sentences = 399 flesch = 52 summary = Here, we will summarize the insights gathered so far on an important aspect of virulence and host adaptation, the interactions of SARS-CoV and MERS-CoV with antiviral interferon (IFN) responses of human cells. The broad antiviral activity of IFNs occurs on several levels, namely virus entry, viral polymerase function, host cell translation, RNA availability, RNA stability, particle budding, apoptosis, or general boosting of innate and adaptive immune responses. Crystal structure of the middle east respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in the innate antiviral response cache = ./cache/cord-290744-m0vpizuh.txt txt = ./txt/cord-290744-m0vpizuh.txt === reduce.pl bib === id = cord-291765-97lk5qfo author = Eckerle, Lance D. title = Effects of Mutagenesis of Murine Hepatitis Virus NSP1 and NSP14 on Replication in Culture date = 2006 pages = extension = .txt mime = text/plain words = 2187 sentences = 105 flesch = 50 summary = To test the requirements for nsp1 and nsp14 in replication and to probe their functions, deletions or mutations were engineered into the viral genome in nsp1 and nsp14 and mutant viruses were analyzed for virus viability, replication, protein expression, and RNA synthesis. When infectious genome RNA containing these changes was electroporated into permissive cells, only the carboxy-terminal nsp1 deletion allowed recovery of an infectious mutant virus (nsp1 124-242). Based on the above results, systematic mutagenesis of clustered-charged residues was performed, both within the putative essential amino-terminal two-thirds of nsp1 as well as the dispensable carboxy-terminal third of the nsp1 protein domain. Deletions of P1-Gln residues in the flanking cleavage sites between nsp13-14 (VUSS6) and nsp14-15 (VUSS17) were engineered in the infectious clone cDNA and used to generate full-length genome RNA for electroporation into permissive cells. cache = ./cache/cord-291765-97lk5qfo.txt txt = ./txt/cord-291765-97lk5qfo.txt === reduce.pl bib === id = cord-291029-oldket3n author = Sefers, Susan E. title = QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date = 2005-07-21 pages = extension = .txt mime = text/plain words = 3532 sentences = 182 flesch = 53 summary = The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. In this study, we have chosen both nasopharyngeal swab (NPS) and cerebrospinal fluid (CSF) specimens submitted for influenza A virus, enterovirus and herpesvirus testing to validate the MinElute nucleic acid extraction system. Nucleic acid recovery rates between the MinElute and RNAzol B were further determined by quantitating HIV-1 or CMV viral loads in extracted RNA or DNA specimens using a real-time TaqMan PCR. The MinElute kits possessed an equivalent sensitivity in nucleic acid recovery and detection, in comparison to the IsoQuick and RNAzol B, for both DNA and RNA extraction. cache = ./cache/cord-291029-oldket3n.txt txt = ./txt/cord-291029-oldket3n.txt === reduce.pl bib === id = cord-291063-de7v4e5s author = Moens, Ugo title = Silencing Viral MicroRNA as a Novel Antiviral Therapy? date = 2009-05-28 pages = extension = .txt mime = text/plain words = 9122 sentences = 526 flesch = 49 summary = The expressions of EBV-encoded miRNAs in clinical samples and computational analysis to predict putative targets were applied to unravel the biological functions of EBV miRNAs. These approaches showed that the miR-BARTs are abundantly expressed in latently infected epithelial cells, nasopharyngeal carcinomas, EBV-associated gastric carcinoma cell lines and tissues, Burkitt's lymphomas latency type I, EBV positive primary effusion lymphomas, and diffuse large B-cell lymphomas, but at a significantly lower level in B cells. However, computational alignment of the potential HIV-1 miRNAs with specific human T-cell mRNAs identified potential cellular targets including genes encoding CD4, CD28 and interleukin-2, IL-3, and IL-12 [119] . The idea of targeting viral transcripts is not new, and RNA interference has been demonstrated to efficiently mediate inhibition of replication of human pathogenic viruses such as HIV-1, HCV, dengue virus, severe acute respiratory syndrome (SARS) coronavirus, poliovirus, human rhinovirus, influenza A virus, hepatitis D virus, HBV, HSV-1, HPV, JCV, EBV, and CMV in cell culture (reviewed in [12] ). cache = ./cache/cord-291063-de7v4e5s.txt txt = ./txt/cord-291063-de7v4e5s.txt === reduce.pl bib === id = cord-291749-revhbd0q author = Mongan, Arthur Elia title = Portable sequencer in the fight against infectious disease date = 2019-10-03 pages = extension = .txt mime = text/plain words = 3735 sentences = 222 flesch = 40 summary = Diagnosis can be upheld by observing the cause of disease under the microscope or detecting the presence of nucleic acid and proteins of the pathogens. Sequencing of PCR amplicons or whole pathogen genomic DNA can be applied to comprehensively screen for infecting agents and their drug resistance phenotype, if exists, at the same time. Sequencing ensures detection of DNA composition unique to an organism, the presence of antimicrobials-destroying genes, or mutation that can change the function or conformation of proteins related to drug resistance. Targeted sequencing with MinION is powerful and fast to detect pathogens in clinical samples. A novel diagnostic method for malaria using loopmediated isothermal amplification (LAMP) and MinION TM nanopore sequencer Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis MinION nanopore sequencing of multiple displacement amplified Mycobacteria DNA direct from sputum. cache = ./cache/cord-291749-revhbd0q.txt txt = ./txt/cord-291749-revhbd0q.txt === reduce.pl bib === id = cord-290801-dv6aak01 author = Ivanyi-Nagy, Roland title = Reprint of: Core protein-mediated 5′–3′ annealing of the West Nile virus genomic RNA in vitro() date = 2012-09-27 pages = extension = .txt mime = text/plain words = 6522 sentences = 296 flesch = 49 summary = Since the core protein of flaviviruses is also endowed with potent RNA chaperone activities, we decided to examine the effect of West Nile virus (WNV) core on 5′–3′ genomic RNA annealing in vitro. These results indicate that core protein – besides its function in viral particle formation – might be involved in the regulation of flavivirus genomic RNA cyclization, and thus virus replication. In this study, we examined the effect of WNV core protein chaperoning on viral 5 -3 UTR annealing, using an in vitro model system with separate 5 and 3 RNAs. We found that core protein binding greatly increases the rate of 5 -3 complex formation, and is required for the interaction when full-length 3 UTR RNAs are used (Fig. 2) . cache = ./cache/cord-290801-dv6aak01.txt txt = ./txt/cord-290801-dv6aak01.txt === reduce.pl bib === id = cord-287658-c2lljdi7 author = Lopez-Rincon, Alejandro title = Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date = 2020-09-10 pages = extension = .txt mime = text/plain words = 4766 sentences = 253 flesch = 55 summary = The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. For example, we can use this sequencing data with cDNA, resulting from the PCR of the original viral RNA; e,g, Real-Time PCR amplicons to identify the SARS-CoV-2 16 . The global impact of SARS-CoV-2 prompted researchers to apply effective alignment-free methods to the classification of the virus: For example, in 26 the authors propose the use of Machine Learning Digital Signal Processing for separating the virus from similar strains, with remarkable accuracy. We calculated the frequency of appearance of different primer sets' sequences used in SARS-CoV-2 RT-PCR tests developed by WHO referral laboratories and compared it to our primer design in the dataset from the GISAID ( Table 2) repository. cache = ./cache/cord-287658-c2lljdi7.txt txt = ./txt/cord-287658-c2lljdi7.txt === reduce.pl bib === id = cord-291513-vpehn6nx author = Minich, Jeremiah title = Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date = 2020-08-18 pages = extension = .txt mime = text/plain words = 6429 sentences = 326 flesch = 55 summary = Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. Here we characterize the suitability of detecting SARS-CoV-2 RNA in experimental conditions as well as COVID-19 patient and built-environment samples using viral-inactivating storage solutions and alternative medical-grade and consumer-grade swabs. In a subset of seven COVID-19 patient nares samples stored in 95% EtOH, we also detected signi cantly higher SARS-CoV-2 viral load in RNA extracted from the swab head versus eluent ( Fig. 1b ; one-tailed paired Student's t-test p = 0.03). Based on the results from these initial experiments, we conducted a proof-of-concept study in the clinical setting by performing RT-qPCR for the SARS-CoV-2 N1 amplicon and human RNase P gene on RNA extracted from the swab head of nasal samples collected using TMI and/or CGp swabs alongside the recommended SYN swabs. cache = ./cache/cord-291513-vpehn6nx.txt txt = ./txt/cord-291513-vpehn6nx.txt === reduce.pl bib === id = cord-290254-m9l8ntur author = Rodriguez-Manzano, J. title = A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date = 2020-06-30 pages = extension = .txt mime = text/plain words = 5622 sentences = 340 flesch = 54 summary = In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 {+/-} 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Currently, reverse transcriptase polymerase chain reaction using real-time benchtop platform (RT-qPCR) is considered the gold standard for COVID-19 diagnosis due to its capability to detect the presence of SARS-CoV-2 RNA close to the onset of symptomatic illness which is critical for isolation. In this paper, we combined LAMP with an in-house LoC device to develop a rapid PoC diagnostic test (< 20 min) for the detection of SARS-CoV-2 RNA from extracted samples. cache = ./cache/cord-290254-m9l8ntur.txt txt = ./txt/cord-290254-m9l8ntur.txt === reduce.pl bib === id = cord-290813-6ylwj5je author = Ng, Enders K. O. title = Molecular Diagnosis of Severe Acute Respiratory Syndrome date = 2006 pages = extension = .txt mime = text/plain words = 3125 sentences = 179 flesch = 53 summary = To date, based on the publicly released full genomic sequences of SARS-CoV, various molecular detection methods based on reverse-transcription polymerase chain reaction (RT-PCR) have been developed. Subsequently, together with the improvement of viral RNA extraction in which plasma or serum requires no ultracentrifugation, two real-time quantitative RT-PCR assays, one aimed toward the polymerase region and the other toward the nucleocapsid region of the virus genome ( Fig. 1) , were developed for measuring the concentration of SARS-CoV RNA in serum/plasma samples from SARS patients (13, 14) . With the use of the real-time quantitative RT-PCR assay, SARS-CoV RNA has recently been shown to be detectable in the plasma samples of pediatric patients during different stages of SARS (Fig. 4) (14) . Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome cache = ./cache/cord-290813-6ylwj5je.txt txt = ./txt/cord-290813-6ylwj5je.txt === reduce.pl bib === id = cord-291677-zcbyhsf1 author = Wilamowski, M. title = Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date = 2020-08-16 pages = extension = .txt mime = text/plain words = 5348 sentences = 308 flesch = 56 summary = To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We conducted serial synchrotron crystallography (SSX) experiments at 297 K to test whether low radiation dose could help uncover the structure of Nsp10/16 in a complex with Cap-1. The SARS-CoV-2 Nsp10/16 2′-O MTase complex provides a molecular arrangement for binding of the mRNA Cap-0 and subsequent methylation of the first transcribed nucleotide. The further development of SSX and implementation of time-resolved SSX crystallography is an approach that could visualize chemical processes and protein molecular dynamics -such as of the transfer of the methyl group catalyzed by Nsp10/16 2′O-MTase from SARS-CoV-2. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-o-methyltransferase nsp10/nsp16 complex cache = ./cache/cord-291677-zcbyhsf1.txt txt = ./txt/cord-291677-zcbyhsf1.txt === reduce.pl bib === id = cord-286603-4p3t0vre author = Duan, Zhiqiang title = TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein date = 2020-06-27 pages = extension = .txt mime = text/plain words = 10674 sentences = 464 flesch = 40 summary = title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein Therefore, the reduced viral RNA synthesis and transcription caused by M/NLS mutation might be one of the reasons responsible for the attenuated replication of rSS1GFP-M/NLSm. Virus-host protein interactions based on quantitative proteomics analysis have become important methods in understanding cellular proteins involved in virus replication and pathogenesis [22, 23, 41, 42] . Therefore, together with the above results, we speculated that the relatively decreased expression of DEPs involved in ribosome structure, protein posttranslational modification and trafficking due to the disrupted nuclear accumulation of M protein affected viral protein synthesis and budding, which might be the third reason responsible for the attenuated replication of rSS1GFP-M/NLSm. Inflammatory responses are important aspects of the innate immune system during virus infection. cache = ./cache/cord-286603-4p3t0vre.txt txt = ./txt/cord-286603-4p3t0vre.txt === reduce.pl bib === id = cord-291860-dw1sfzqx author = van Boheemen, Sander title = Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date = 2019-12-16 pages = extension = .txt mime = text/plain words = 5398 sentences = 276 flesch = 40 summary = Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI's nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. cache = ./cache/cord-291860-dw1sfzqx.txt txt = ./txt/cord-291860-dw1sfzqx.txt === reduce.pl bib === id = cord-287018-g4y5kjju author = Konstantinova, P title = Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA date = 2006-05-18 pages = extension = .txt mime = text/plain words = 7164 sentences = 454 flesch = 56 summary = In order to solve this durability problem, we tested DNA constructs encoding virus-specific long-hairpin RNAs (lhRNAs) for their ability to inhibit HIV-1 production. The lhRNA constructs were compared with in vitro diced double-stranded RNA and a DNA construct encoding an effective nef-specific shRNA for their ability to inhibit HIV-1 production in cells. For this reason, the DNA constructs encoding lhRNAs (a single-hairpin molecule) and long dsRNAs (two complementary molecules that form a duplex) were designed to target tat, rev and nef sequences as indicated in Figure 1 . 21 nef2 dsRNA induced a decrease in luciferase expression, but an even more pronounced level of inhibition was Figure 1 Scheme of the human immunodeficiency virus type 1 (HIV-1) pLAI proviral genome and target sequences used for the design of long-hairpin RNAs (lhRNAs). cache = ./cache/cord-287018-g4y5kjju.txt txt = ./txt/cord-287018-g4y5kjju.txt === reduce.pl bib === id = cord-287931-cxqzac4a author = Huang, Weiwei title = An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date = 2013-09-20 pages = extension = .txt mime = text/plain words = 5161 sentences = 256 flesch = 45 summary = RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. To facilitate the application of EOPM in multiple surveillance sites for infectious diseases, we designed software with a user-friendly interface, which is supported by a statistical analysis method based on a comprehensive microbial sequence identification database. Analysis of the enrichment results at the genus level revealed Cardiovirus as the number one match, showing significant enrichment ( The microarray raw data of other symptom-causing pathogens, such as streptococcus and mycoplasma, identified by EOPM in peripheral blood in infectious patients, were also submitted to the GEO database. These microarray platforms use long oligonucleotide probes (60-70-mer) and random PCR amplification, and have successfully identified unexpected pathogens in infectious disease outbreaks, even discovering novel viruses with homology to known species [8, 11] . cache = ./cache/cord-287931-cxqzac4a.txt txt = ./txt/cord-287931-cxqzac4a.txt === reduce.pl bib === id = cord-291962-rp172ugk author = Jing, Huiyuan title = Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 date = 2019-07-15 pages = extension = .txt mime = text/plain words = 5726 sentences = 366 flesch = 51 summary = title: Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 To test this, increasing dose of NLRX1 was transfected into Marc-145 cells followed by PRRSV infection, qPCR was then performed to test the total viral RNA levels. On the other hand, recent literature indicated that the interaction of Nsp9 with SUMO E2 conjugating enzyme Ubc9 and cellular protein interleukin-2 enhancer binding factor 2 (ILF2) through its RdRp domain resulted in a significantly decrease of virus titers, indicating that cells utilize host antiviral factors as defense mechanisms to limit PRRSV infection Wen et al., 2017) . An intracellularly expressed Nsp9-specific nanobody in MARC-145 cells inhibits porcine reproductive and respiratory syndrome virus replication Porcine reproductive and respiratory syndrome virus nucleocapsid protein interacts with Nsp9 and cellular DHX9 to regulate viral RNA synthesis The DEADbox RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro cache = ./cache/cord-291962-rp172ugk.txt txt = ./txt/cord-291962-rp172ugk.txt === reduce.pl bib === id = cord-286842-04cuk2cn author = Plyusnina, Angelina title = Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture date = 2005-02-22 pages = extension = .txt mime = text/plain words = 2147 sentences = 115 flesch = 51 summary = title: Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture Tula hantavirus carrying recombinant S RNA segment (recTULV) grew in a cell culture to the same titers as the original cell adapted variant but presented no real match to the parental virus. Using the two specific RT-PCR conditions, the presence of V-type and REC-type S RNA was monitored on ten sequential passages of the mixture of TULV02 and RecTULV5 variants (Fig. 2 ). Although relatively short, the observed survival time of the recTULV in the presence of the original variant TUL02 seems to be sufficient for transmission of a recombinant virus, in a hypothetical in vivo situation, from one rodent to another. The data presented in this paper show that the recTULV presents no real match to the original cell adapted variant and that the lower fitness of the recombinant virus can not be increased by pre-passaging in cell culture. cache = ./cache/cord-286842-04cuk2cn.txt txt = ./txt/cord-286842-04cuk2cn.txt === reduce.pl bib === id = cord-289965-qcezqpze author = Lehmann, Kathleen C. title = Arterivirus nsp12 versus the coronavirus nsp16 2′-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins date = 2015-09-01 pages = extension = .txt mime = text/plain words = 6580 sentences = 356 flesch = 50 summary = The 39-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 29-O-methyltransferase (29-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 59 cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 59 cap although no candidate MTases have been identified thus far. The 39-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 29-O-methyltransferase (29-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 59 cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 59 cap although no candidate MTases have been identified thus far. cache = ./cache/cord-289965-qcezqpze.txt txt = ./txt/cord-289965-qcezqpze.txt === reduce.pl bib === id = cord-293215-6flf5ig0 author = Eriksson, Klara Kristin title = Generation of Recombinant Coronaviruses Using Vaccinia Virus as the Cloning Vector and Stable Cell Lines Containing Coronaviral Replicon RNAs date = 2007-11-28 pages = extension = .txt mime = text/plain words = 4682 sentences = 325 flesch = 58 summary = title: Generation of Recombinant Coronaviruses Using Vaccinia Virus as the Cloning Vector and Stable Cell Lines Containing Coronaviral Replicon RNAs Based on cloned coronaviral cDNA, we describe the generation of recombinant coronaviruses and stable cell lines containing coronaviral replicon RNAs. Initially, the vaccinia virus-based reverse genetic system was established for the generation of recombinant human coronavirus 229E. This section describes the preparation of purified vaccinia virus DNA that can be used: (i) for the in vitro ligation with the assembled coronavirus full-length cDNA (see Section 3.1.4), and (ii) as template for in vitro transcription reactions (see Section 3.3.1). First, a fulllength coronavirus RNA is produced using the genomic DNA of a vaccinia virus containing the full-length coronavirus cDNA insert as a template for in vitro transcription. 1. Based on a full-length coronavirus cDNA cloned in vaccinia virus, a replicon RNA-encoding cDNA can be generated using vaccinia virus-mediated homologous recombination as described in Section 3.2. cache = ./cache/cord-293215-6flf5ig0.txt txt = ./txt/cord-293215-6flf5ig0.txt === reduce.pl bib === id = cord-294138-h7sfd1wa author = McIver, David J. title = Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date = 2020-06-01 pages = extension = .txt mime = text/plain words = 2780 sentences = 130 flesch = 56 summary = Both countries were involved in the United States Agency for International Development's (USAID) Emerging Pandemic Threats PREDICT program, and surveillance of bats in wildlife markets in rural areas in Laos using family-level PCR assays revealed the presence of CoV RNA in 41 animals [5] . Considering the significant interactions of wildlife and especially rodents with humans in Laos, we were interested in investigating the presence of CoVs in these animals, which can be primary or intermediate hosts for CoVs with zoonotic potential. Since there are abundant contact opportunities for wildlife pathogens and humans in Laos, and considering that coronavirus-zoonotic events can involve intermediate hosts, as in the cases of SARS and MERS, we focused our screening on non-bat species potentially capable of playing that role. It is worth noting that we targeted rodents most likely to be in contact with humans and transmit virus and found fewer CoV-RNA-positive animals than in other studies of rodents in the region or elsewhere. cache = ./cache/cord-294138-h7sfd1wa.txt txt = ./txt/cord-294138-h7sfd1wa.txt === reduce.pl bib === id = cord-291727-4wfhuvww author = Ketteler, Robin title = On programmed ribosomal frameshifting: the alternative proteomes date = 2012-11-19 pages = extension = .txt mime = text/plain words = 6681 sentences = 353 flesch = 51 summary = There are two main mechanisms that produce out of frame peptides: changes in the genome sequence that result in insertions or deletions (indels) and programmed ribosomal frameshifting as a consequence of the ribosome either slipping back one nucleotide (−1 frameshifting) or skipping one nucleotide (+1 frameshifting) (Figure 1) . By contrast, programmed ribosomal frameshifting can result in dual-coding genes that produce alternative functional proteins, which form an integral part of the organism's physiology. Although the slippery sequence and pseudoknot are the most common motifs for frameshifting identified thus far, there are alternative mechanisms that may result in the production of out-of-frame proteins. First, one has to identify in mRNAs the requirements for a productive frameshift peptide: One might argue that a slippery sequence and a pseudoknot are a good predictor of frameshifting events, but-as pointed out above-there are alternative mechanisms that result in frameshifting (see also Figure 2 ). searched the genome for slippery sequences and pseudoknot FIGURE 3 | Methods to detect frameshifting events and out-of-frame peptides. cache = ./cache/cord-291727-4wfhuvww.txt txt = ./txt/cord-291727-4wfhuvww.txt === reduce.pl bib === id = cord-291754-1zxztadu author = Zhao, Ye title = Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date = 2019-10-15 pages = extension = .txt mime = text/plain words = 6848 sentences = 344 flesch = 54 summary = In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above. Collectively, these results demonstrate the successful rescue of the pathogenic IBV strain YN from cloned cDNA by using electroporation of full-length IBV in vitro transcripts into N-protein expressing cells and subsequent virus amplification in the allantoic cavities of ECE. cache = ./cache/cord-291754-1zxztadu.txt txt = ./txt/cord-291754-1zxztadu.txt === reduce.pl bib === id = cord-290948-cuu78cvl author = Imbert, Isabelle title = The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date = 2008-02-05 pages = extension = .txt mime = text/plain words = 7091 sentences = 356 flesch = 53 summary = Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. SARS-CoV nsp3 is a large multidomain protein of 1922 amino acids Thiel et al., 2003) that is thought to contain at least seven domains: (1) an N-terminal Glu-rich acidic domain (AD); (2) an X domain (XD) with poly(ADP-ribose) binding properties Saikatendu et al., 2005) ; (3) the SUD domain (for SARS-CoV Unique Domain, an insertion not found in any other coronavirus thus far) with a specific affinity for oligo(G)-strings (Tan et al., in press); (4) a papain-like protease (PLP2), recently shown to exhibit deubiquitinating activity (Barretto et al., 2005; Harcourt et al., 2004; Lindner et al., 2005; Ratia et al., 2006) ; (5) an unknown domain possibly extending the papain-like protease domain, termed PLnc for Papain-Like noncanonical (see below); (6) a transmembrane domain (Kanjanahaluethai et al., 2007) corresponding to the N-terminal of the Y domain; and (7) the remainder of the Y domain, the abbreviation "Y domain" will be used for this part in this study. cache = ./cache/cord-290948-cuu78cvl.txt txt = ./txt/cord-290948-cuu78cvl.txt === reduce.pl bib === id = cord-287748-co9j3uig author = Kobayashi, Tomoya title = Detection of bat hepatitis E virus RNA in microbats in Japan date = 2018-05-29 pages = extension = .txt mime = text/plain words = 1388 sentences = 70 flesch = 55 summary = Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV). Here, we collected and screened 81 bat fecal samples from nine bat species in Japan to detect BatHEV RNA by RT-PCR using HEV-specific primers, and detected three positive samples. These data support the first detection of BatHEVs in Japanese microbats, indicating their wide geographical distribution among multiple bat species. BLAST analysis indicated that BtHEV-Ej1/-Ej2 showed the highest sequence identities to BatHEV/BS7, a German strain detected from the Serotine bat (Eptesicus serotinus), among strains previously reported in other countries. The closely related BatHEVs (BtHEV-Ej1/-Ej2 and Bat HEV/BS7) have been detected in different species of Eptesicus bats (E. PCR amplifications were performed using the KOD FX Neo (Toyobo) with consensus HEV primer sets (PanHEV F and R), which were designed in this study to amplify a 191-bp fragment of the RNA-dependent into Orthohepevirus D, in Japanese bats, suggesting wide geographical distribution of BatHEV among multiple bat species. cache = ./cache/cord-287748-co9j3uig.txt txt = ./txt/cord-287748-co9j3uig.txt === reduce.pl bib === id = cord-291965-9r9ll83m author = Pfefferle, Susanne title = Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date = 2009-09-17 pages = extension = .txt mime = text/plain words = 4306 sentences = 245 flesch = 56 summary = Studies conducted in China in the aftermath of the SARS epidemic have identified CoVs in bats (Chiroptera) and implicated this speciose mammalian order as the most likely reservoir of all known coronaviruses (3) (4) (5) (6) (7) . Bayesian phylogenetic inference with different substitution models and parallel analysis using Metropolis coupling now placed the virus reliably next to a common ancestor with the 2b group of CoV (SARS-like viruses, Figure 3 ). These fragments could be combined into contig*MRCA, most recent common ancestor; CI, confidence interval; HPD, high population density; SARS, severe acute respiratory syndrome; hCoV, human coronavirus; GTR + + I, general time reversible gamma-shaped rate distribution across sites and an invariant site assumption. One of our Hipposideros CoVs was in a basal phylogenetic relationship with the SARS-like clade (group 2b); their most recent common ancestors date back to ≈400 bc. cache = ./cache/cord-291965-9r9ll83m.txt txt = ./txt/cord-291965-9r9ll83m.txt === reduce.pl bib === id = cord-292353-z86rjwle author = Hussein, Islam T.M. title = Recent Advances in Hantavirus Molecular Biology and Disease date = 2011-04-01 pages = extension = .txt mime = text/plain words = 13579 sentences = 708 flesch = 47 summary = Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). The sequences at both the 3 0 and 5 0 termini of each RNA segment are complementary forming ''panhandle'' structures that are specifically recognized by the N protein and were shown to be important for viral transcription and replication. Further studies revealed that cellular 5 0capped mRNA oligoribonucleotides are rescued by N in virus-infected cells and stored in P-bodies for the later use as primers by the viral RdRp during transcription initiation . The UTRs are encapsidated by nucleocapsid protein and associate with RdRp both in the host cells and in the virion, and only these nucleocapsids are believed to be functional templates for mRNA synthesis and RNA replication by the viral RdRp. c. cache = ./cache/cord-292353-z86rjwle.txt txt = ./txt/cord-292353-z86rjwle.txt === reduce.pl bib === id = cord-294056-7e477y1x author = La Monica, Nicola title = Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences date = 1992-05-31 pages = extension = .txt mime = text/plain words = 3341 sentences = 173 flesch = 58 summary = Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. To understand the mechanism of MHV mRNA transcription, we have attempted to determine whether the differential regulation of transcription initiation by leader RNA containing different UCUAA copy numbers is unique to mRNA 2-l. The analysis of several other recombinant viruses with different genome structures suggested that mRNA 3-l was synthesized only by viruses with a leader RNA containing three copies of UCUAA and gene 3 sequence derived from A59 but not JHM (10, 13). Using various primers representing sequences of different regions of gene 1 of the JHM strain of MHV (2) and a second primer representing the 5'-end of the leader RNA, we detected several PCR products which represented mRNAs initiated from various sites. cache = ./cache/cord-294056-7e477y1x.txt txt = ./txt/cord-294056-7e477y1x.txt === reduce.pl bib === id = cord-287758-da11ypiy author = Mônica Vitalino de Almeida, Sinara title = COVID-19 therapy: what weapons do we bring into battle? date = 2020-09-10 pages = extension = .txt mime = text/plain words = 17412 sentences = 1034 flesch = 45 summary = The increase in studies related to SARS-CoV-2 during the first semester in 2020 has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. 5, 64 So far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-CoVs therapies (FIG. Based on results from previous studies as well, nelfinavir was considered a likely therapy for COVID-19 after its indication for clinical trials as a promising anti-SARS drug. 218 In addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during CoV infection), by interfering with virus-cell fusion, 219 and other RNA viruses including coxsackie virus, 220 hepatitis C virus, 221 Ebola, 222 among others, mainly by blocking viral entry or egress from the host cell. cache = ./cache/cord-287758-da11ypiy.txt txt = ./txt/cord-287758-da11ypiy.txt === reduce.pl bib === id = cord-293038-pjjvfdnq author = Fontana, Juan title = The unique architecture of Bunyamwera virus factories around the Golgi complex date = 2008-06-10 pages = extension = .txt mime = text/plain words = 7389 sentences = 386 flesch = 50 summary = We propose that this new structure, unique among enveloped viruses, assembles in association with the most stable component of Golgi stacks, the actin‐containing matrix scaffold, connecting viral replication and morphogenesis inside viral factories. Modified membranes harbouring viral replication complexes (RCs) frequently integrate into a complex structure known as the 'viral factory' where the cytoskeleton participates, cell organelles are recruited and the different steps of the virus life cycle are sequentially connected. We propose that this new multifunctional structure associates with the actin-containing matrix of the Golgi stacks providing a stable scaffold for viral replication and early morphogenesis. LtA and CyD had very little or no effect, respectively, on viral replication and assembly as determined by measurement of infectious viral particles released to the culture supernatants at 6 and 10 h p.i. Complete tubes, virus budding profiles and viral particles assembled in Golgi stacks of cells treated with LtA, as observed in thin sections of treated cells studied by EM (not shown). cache = ./cache/cord-293038-pjjvfdnq.txt txt = ./txt/cord-293038-pjjvfdnq.txt === reduce.pl bib === id = cord-295733-f3rt1fyk author = Ge, Tianxiang title = Evaluation of disinfection procedures in a designated hospital for COVID-19 date = 2020-08-22 pages = extension = .txt mime = text/plain words = 2492 sentences = 142 flesch = 49 summary = When compared with previous study, more places that could be potentially contaminated by COVID-19 patients were sampled for viral RNA detection, such as the flush button of the toilet bowl, medical refuse transfer trolley, elevators, and the examination rooms for these patients. These areas could not be used for non-COVID-19 patients until all the environmental samples collected were negative for SARS-CoV-2 RNA detection. In this study, surface samples collected from the examination rooms were all negative for SARS-CoV-2 RNA detection, and the samples collected from isolation wards and other places were also negative for viral RNA detection, which indicated that the terminal disinfection was effective. Other researches had revealed the presence of SARS-CoV-2 RNA in aerosol, which indicated the air could be contaminated by the virus, and patients could be infected in the isolation wards [12, 28] . Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients cache = ./cache/cord-295733-f3rt1fyk.txt txt = ./txt/cord-295733-f3rt1fyk.txt === reduce.pl bib === id = cord-293747-ds8rhbkv author = Lani, Rafidah title = Antiviral activity of silymarin against chikungunya virus date = 2015-06-16 pages = extension = .txt mime = text/plain words = 5074 sentences = 254 flesch = 51 summary = Three compounds: silymarin, quercetin and kaempferol were evaluated for their in vitro antiviral activities against CHIKV using a CHIKV replicon cell line and clinical isolate of CHIKV of Central/East African genotype. A cytopathic effect inhibition assay was used to determine their activities on CHIKV viral replication and quantitative reverse transcription PCR was used to calculate virus yield. Different non-cytotoxic concentrations of silymarin, kaempferol and quercetin were tested on CHIKV-infected Vero cells to find the effective compound. To confirm the post-entry antiviral activity of silymarin against CHIKV a virus yield assay using qRT-PCR was used. In contrast, dose-dependent reduction of amounts of nsP1, nsP3 and E2 proteins was observed (Fig. 6) indicating that silymarin limited CHIKV replication and virus-encoded protein synthesis within the treated cells. However, as in virus expression and replicon cell lines the synthesis of viral RNAs and proteins are coupled further study is necessary to evaluate the direct effect of silymarin on inhibition of newly synthesized CHIKV proteins. cache = ./cache/cord-293747-ds8rhbkv.txt txt = ./txt/cord-293747-ds8rhbkv.txt === reduce.pl bib === id = cord-292045-pnid9dmq author = Kumar, Manish title = First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date = 2020-07-28 pages = extension = .txt mime = text/plain words = 3037 sentences = 183 flesch = 58 summary = While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic. Consistency between abundance of SARS-CoV-2 genetic materials and number of confirmed cases was observed in the previous reports in Australia, France, Italy, Spain and Japan Further, referring to the limitations of the present study owing to lockdown scenario, we recommend that although based MPC analysis, the efficiency of RNA extraction and RT-PCR is considered high for all the wastewater samples collected for this study, the efficiency of PEG method could have been better established. The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2 cache = ./cache/cord-292045-pnid9dmq.txt txt = ./txt/cord-292045-pnid9dmq.txt === reduce.pl bib === id = cord-293988-f5gvwjyh author = Musso, Nicolò title = New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date = 2020-09-11 pages = extension = .txt mime = text/plain words = 3223 sentences = 186 flesch = 54 summary = The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. The World Health Organization (WHO) declared COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a worldwide pandemic [1] . As the cat's pathology evolved rapidly and harmfully (the animal died in as little as three days), with clinical signs and rate of disease progression similar to human COVID-19 patients, and because previously published papers reported different cases of feline infection [10, [13] [14] [15] [16] , a nasal swab was collected in order to verify a possible infection with SARS-CoV-2. cache = ./cache/cord-293988-f5gvwjyh.txt txt = ./txt/cord-293988-f5gvwjyh.txt === reduce.pl bib === id = cord-296309-i1mpov7k author = Houldcroft, Charlotte J. title = Clinical and biological insights from viral genome sequencing date = 2017-01-16 pages = extension = .txt mime = text/plain words = 9050 sentences = 389 flesch = 35 summary = We will also explore two areas in which viral WGS has recently proven its clinical utility: metagenomic sequencing to identify viruses that cause encephalitis (BOX 1) ; and the role of WGS in molecular epidemiology and public health management of the Pan-American Zika virus outbreak (BOX 2) . However, the increasing number of resistance genes that are located across viral genomes, together with decreasing costs of sequencing and the use of sequence data for transmission studies, are driving a reappraisal of the need for WGS. The numerous phylogenetically informative variant sites that can be obtained from full-length or near full-length genomes removes the need for high-quality sequences, which enabled the robust linking of cases of Ebola virus infection and public health interventions in real time during the 2015 epidemic 39 . There are several methods that are available to achieve WGS of viruses from clinical samples; amplicon sequencing, target enrichment or metagenomics. cache = ./cache/cord-296309-i1mpov7k.txt txt = ./txt/cord-296309-i1mpov7k.txt === reduce.pl bib === id = cord-289612-4x5t4c5u author = Alsuliman, Tamim title = COVID-19 paraclinical diagnostic tools: Updates and future trends date = 2020-06-20 pages = extension = .txt mime = text/plain words = 7353 sentences = 387 flesch = 48 summary = Laboratory-confirmed SARS-CoV-2 infection requires the detection of viral nucleic acid in respiratory tract samples by the use of real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay. In the course of this phase, upper respiratory specimens were tested by RT-PCR for viral RNA and the majority of the patients showed positive results for SARS-CoV-2. These results contrast with another German smaller study by Wolfel et al., conducted on 9 COVID-19 patients, with no discernible difference in viral loads or detection rates when comparing nasal and throat swabs [38] . found that 66.67% of laboratory-confirmed COVID-19 patients were tested positive for SARS-CoV-2 RNA in stool specimens. enrolled a total of 173 confirmed cases of COVID-19 by the use of rRT-PCR on samples from the respiratory track reported that the seroconversion sequentially appeared for the total antibody (Ab), IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases cache = ./cache/cord-289612-4x5t4c5u.txt txt = ./txt/cord-289612-4x5t4c5u.txt === reduce.pl bib === id = cord-288669-46tkedw7 author = Lee, Changhee title = The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties date = 2006-11-10 pages = extension = .txt mime = text/plain words = 9258 sentences = 455 flesch = 51 summary = P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Our study suggests that the PRRSV E protein may function as a viroporin in the virion envelope that facilitates uncoating of the virus in order to release the genomic RNA into the cytoplasm for subsequent replication. At 24 h postinoculation, Marc-145 cells were fixed, and virus infection was examined by immunofluorescent staining with N-specific MAb. Marc-145 cells inoculated with a culture fluid from cells cotransfected with P129-ΔE and E gene showed bright N-specific fluorescent signal, indicating that the P129-ΔE replication may be rescued by trans-complementation of the E protein (Fig. 2C ). Strand-specific RT-PCR experiments were carried out and demonstrated that PRRSV-infected Marc-145 cells produced reduced levels of positive-sense genomic RNA at 2 days post-infection in the presence of the drugs chloroquine, amantadine and verapamil (Fig. 5A, upper panel) . cache = ./cache/cord-288669-46tkedw7.txt txt = ./txt/cord-288669-46tkedw7.txt === reduce.pl bib === id = cord-290218-dvyeg5fk author = Jiang, Yi title = RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date = 2020-09-04 pages = extension = .txt mime = text/plain words = 2249 sentences = 143 flesch = 53 summary = Interestingly, the structure of complexed nsp12 is almost identical to nsp12 in apo RdRp, with an RMSD of 0.5 Å [17] , coinciding with the high processivity of the viral RNA polymerase, which does not need to consume extra energy for conformation changes in the active site during the replication cycle (Fig. 3B ). These "sliding poles" are stabilized by interactions formed between the positively charged residues at the extended N-terminal of nsp8 and bases in RNA backbones ( Fig. 3E ) and reported to account for the known processivity of the RdRp, which is required for replicating the long coronavirus genomes [39] . Although the sequence identity of nsp12 across the RNA viruses is low, the polymerase active site is structurally highly conserved, suggesting that RdRp inhibitors may serve as a potential J o u r n a l P r e -p r o o f broad-spectrum antiviral drug against RNA viruses. cache = ./cache/cord-290218-dvyeg5fk.txt txt = ./txt/cord-290218-dvyeg5fk.txt === reduce.pl bib === id = cord-293375-qcy56ui7 author = Strauss, Ellen G. title = Identification of the active site residues in the nsP2 proteinase of sindbis virus date = 1992-12-31 pages = extension = .txt mime = text/plain words = 5192 sentences = 265 flesch = 56 summary = coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine. cache = ./cache/cord-293375-qcy56ui7.txt txt = ./txt/cord-293375-qcy56ui7.txt === reduce.pl bib === id = cord-296847-r752bcsu author = Campanini, Giulia title = Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants date = 2007-04-23 pages = extension = .txt mime = text/plain words = 3045 sentences = 163 flesch = 55 summary = In the present study, we quantified the hRSV RNA load (both subgroups A and B) in NPAs from hRSV-infected infants by quantitative RT-PCR to investigate the possibility of defining the etiologic role of hRSV in the current ARTI episode from a series of infants admitted to the hospital either with a single hRSV infection or with two or three simultaneous or sequential viral infections including hRSV. NPAs from a series of 253 infants aged less than 1 year and admitted to the hospital in the period November 2005-May 2006 with a diagnosis of ARTI were examined for hRSV as well as other respiratory viruses by DFA, CC, and qualitative RT-PCR, as reported (Rovida et al., 2005) . In addition, 14 infants with multiple simultaneous (coinfections) or sequential (within 30 days) infections in the respiratory tract (including hRSV) were examined prospectively in order to identify the virus responsible for the current ARTI episode. cache = ./cache/cord-296847-r752bcsu.txt txt = ./txt/cord-296847-r752bcsu.txt === reduce.pl bib === id = cord-294800-akr4f5p8 author = Kabir, Md. Tanvir title = nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date = 2020-07-10 pages = extension = .txt mime = text/plain words = 14084 sentences = 700 flesch = 44 summary = They also summarized that as viral load is quite high during the time of hospital admissions, use of potent antiviral agents at an early stage might prove Abbreviations: ACE2, angiotensin converting enzyme 2; AP, antigen presentation; APCs, antigen presentation cells; APN, aminopeptidase N, ARBs, angiotensin II receptor blockers; ARDS, acute respiratory distress syndrome; CDC, Centers for Disease Control; nCOVID-19, novel coronavirus disease 2019; CoVs, coronaviruses; DPP4, dipeptidyl peptidase 4; dsRNA, double-strand RNA; EC 50 , half maximal effective concentration; ED, emergency department; ELISA, enzymelinked immunosorbent assay; EUA, emergency use authorization; FDA, Food and Drug Administration; GGO, ground-glass opacity; HCV, hepatitis C virus; HIV, human immunodeficiency virus;, MHC, major histocompatibility complex; or HLA, human leukocyte antigen; ICU, intensive care unit; IL-6, interleukin 6; LPV/r, lopinavir/ritonavir; mAbs, monoclonal antibodies; MERS, Middle East respiratory syndrome; N7-MTase, N7-methyltransferase; NSAIDs, nonsteroidal anti-inflammatory drugs; PRRs, pattern recognition receptors; PUI, patient under investigation; RdRp, RNA-dependent RNA polymerase; RSV, respiratory syncytial virus; S protein, spike protein; SAM, S-adenosyl-methionine; SARS, severe acute respiratory syndrome; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; WHO, World Health Organization. cache = ./cache/cord-294800-akr4f5p8.txt txt = ./txt/cord-294800-akr4f5p8.txt === reduce.pl bib === id = cord-293646-d4qcckh1 author = Meanwell, Nicholas A. title = Chapter 22. Non-HIV antiviral agents date = 2003-12-31 pages = extension = .txt mime = text/plain words = 4178 sentences = 198 flesch = 46 summary = The first small molecule inhibitor of Hepatitis C Virus (HCV), the NS3 protease inhibitor BILN-2061, entered phase 2 clinical trials, producing a striking reduction in viral load in treated individuals. Inhibitors of Hepatitis B Virus (HBV) -Adefovir dipivoxil iHepsera'") (1) was approved in the US for the treatment of HBV on September 20', 2002 and in the European Union on March 1 lth, 2003, providing a second small molecule antiviral to add to lamivudine (3TC) and the injectable protein IFNa as the only approved agents for treating HBV infection. Pyridinedicarboxamide S represents the first report of a non-nucleoside inhibitor of HBV reverse transcriptase enantiomer of q is active in cell culture and appears to prevent proper formation of the viral nucleocapsrd. A significant advance towards establishing a correlation between replicon inhibition and clinical efficacy was recently accomplished with the disclosure of preliminary clinical data for BILN-2061, a selective inhibitor of the NS3 serine protease of HCV that is structurally related to 13. cache = ./cache/cord-293646-d4qcckh1.txt txt = ./txt/cord-293646-d4qcckh1.txt === reduce.pl bib === id = cord-293766-vpfda3pd author = Ji, Jingjing title = Glucocorticoid therapy does not delay viral clearance in COVID-19 patients date = 2020-09-21 pages = extension = .txt mime = text/plain words = 740 sentences = 54 flesch = 63 summary = authors: Ji, Jingjing; Zhang, Jinxia; Shao, Ziyun; Xie, Qifeng; Zhong, Li; Liu, Zhifeng Patients were diagnosed as mild type, general type, severe type, and critical type according to the Chinese Recommendations for Diagnosis and Treatment of Novel Coronavirus (SARS-CoV-2) Infection (Trial 7th version) [4] . The current multicenter cohort study demonstrates that GC therapy does not change viral clearance and peripheral lymphocyte counts in COVID-19 patients. Low-dose corticosteroid therapy does not delay viral clearance in patients with COVID-19 Persistence and clearance of viral RNA in 2019 novel coronavirus disease rehabilitation patients Jinxia Zhang, Ziyun Shao, Qifeng Xie, and Li Zhong were responsible for collecting the data. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication. The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.Ethics approval and consent to participate cache = ./cache/cord-293766-vpfda3pd.txt txt = ./txt/cord-293766-vpfda3pd.txt === reduce.pl bib === id = cord-293481-bmfj50fb author = Malin, Jakob J. title = Remdesivir against COVID-19 and Other Viral Diseases date = 2020-10-14 pages = extension = .txt mime = text/plain words = 9097 sentences = 428 flesch = 42 summary = Remdesivir or GS-5734 is a prodrug of a nucleoside analog with direct antiviral activity against several single-stranded RNA viruses, including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, preliminary data from a randomized placebo-controlled clinical trial showed that remdesivir reduces the time to recovery in patients with COVID-19 (5) , leading to an emergency-use authorization (EUA) by the U.S. Food and Drug Administration (FDA) only 2 days after the first press release from the National Institute of Allergy and Infectious Diseases (NIAID) (6) . There were strong arguments for the antiviral effect of remdesivir against coronaviruses emerging from multiple cell-based in vitro models, including primary human airway epithelial (HAE) cell cultures (25) , and, for MERS-CoV, from a mouse model of pulmonary infection (28) . After the outbreak of SARS-CoV-2 in January 2020, remdesivir was rapidly tested in a Vero E6 cell-based model that made use of direct viral quantification by rtPCR along with the antimalaria and immune-modulating drug chloroquine and known antivirals such as ribavirin and penciclovir. cache = ./cache/cord-293481-bmfj50fb.txt txt = ./txt/cord-293481-bmfj50fb.txt === reduce.pl bib === id = cord-294890-93ldjyi5 author = Chen, Yan title = Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour date = 2018-11-06 pages = extension = .txt mime = text/plain words = 8668 sentences = 451 flesch = 54 summary = KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. CONCLUSION: Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE. Additionally, 11 potential target genes (mRNAs) and five lncRNAs related to auxin response factors were verified by qPCR in the three stages of early longan SE. Based on the functions of miRNAs and mRNAs in longan and other plants, we speculate that some lncRNAs are involved in regulation of gene expression by acting as miRNA precursors during early longan SE. cache = ./cache/cord-294890-93ldjyi5.txt txt = ./txt/cord-294890-93ldjyi5.txt === reduce.pl bib === id = cord-292673-00s3wgem author = Buonaguro, Luigi title = SARS-CoV-2 RNA polymerase as target for antiviral therapy date = 2020-05-05 pages = extension = .txt mime = text/plain words = 2062 sentences = 120 flesch = 50 summary = In the quest of an effective antiviral drug, the most specific target for an RNA virus is the RNA-dependent RNA-polymerase (RdRp) which shows significant differences between positive-sense and negative-sense RNA viruses. Journal of Translational Medicine *Correspondence: l.buonaguro@istitutotumori.na.it 1 Innovative Immunological Models, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale"-IRCCS, Via Mariano Semmola, 52, 80131 Naples, Italy Full list of author information is available at the end of the article SARS-CoV-2 is a positive-sense RNA virus belonging to the Orthocoronavirinae (coronavirus, CoV) family and, in particular, to the genus beta (group 2) together with the other two new human coronaviruses SARS-CoV and MERS-CoV. However, all three of them have been developed for negative-sense RNA viruses which show a significant difference in the RdRp sequence and structure compared to the positive-sense SARS-CoV-2 RNA virus. In conclusion, as for all RNA viruses, the RdRp of the newly identified positive-sense human SARS-CoV-2 RNA virus represents the most optimal target for an antiviral drug. cache = ./cache/cord-292673-00s3wgem.txt txt = ./txt/cord-292673-00s3wgem.txt === reduce.pl bib === id = cord-293852-r72c6584 author = Greco, S. title = Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date = 2020-10-31 pages = extension = .txt mime = text/plain words = 8163 sentences = 468 flesch = 40 summary = Different studies found that the values of cardiac Troponins were increased in COVID-19 patients with more severe disease [4, 5, [68] [69] [70] , indicating an association of SARS-CoV-2 with myocardial damage. Moreover, the single-cell RNA-sequencing (scRNAseq) approach has been used to profile the SARS-CoV-2 host-response in the PBMCs of COVID-19 patients, and to comprehensively characterize the immunological changes [124] [125] [126] [127] [128] [129] [130] . However, SARS-CoV-2 infection of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) induced cytotoxic effects and RNA-seq findings highlighted significant transcriptional changes in gene pathways related to cellular metabolism and immune response [131] [132] [133] . This analysis also revealed several host-derived lncRNAs differentially expressed in COVID-19 patient-derived lung tissue, and in SARS-CoV-2 infected epithelial cells, including MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) and NEAT1 (nuclear-enriched autosomal transcript 1) [151] (Fig. 5) . cache = ./cache/cord-293852-r72c6584.txt txt = ./txt/cord-293852-r72c6584.txt === reduce.pl bib === id = cord-294483-mozabpcs author = Choudhary, Manohar Lal title = Development of in vitro transcribed RNA as positive control for laboratory diagnosis of SARS-CoV-2 in India date = 2020-04-28 pages = extension = .txt mime = text/plain words = 637 sentences = 50 flesch = 66 summary = Ten-fold serial dilutions of each transcribed RNA products were tested with respective gene primer probe sets for specific detection and limit of detection. Further, the IVT RNA of each gene was serially diluted 10-fold (10 1 to 10 10 ), and the performance was tested with genespecific primer probe by real-time RT-PCR. When the assay was first set up at the National Influenza Centre of ICMR-NIV, Pune, the IVT RNA for E and SARS coronavirus Frankfurt 1 strain were received from EVAg. The real-time PCR screening assay (E gene) was also established at the 13 VRDLs as part of ICMR's efforts to expand testing to VRDLs closer to major airports 3 . This necessitated the development of an indigenous IVT RNA for E and RdRp. In addition, majority of the WHO screening protocols (5 of 6) are based on N gene targeting different nucleotide positions and require multiple specific positive controls 4 . cache = ./cache/cord-294483-mozabpcs.txt txt = ./txt/cord-294483-mozabpcs.txt === reduce.pl bib === id = cord-289926-y1rjgbui author = Veretnik, S. title = RNA binding domain of HDV antigen is homologous to the HMG box of SRY date = 2014-05-18 pages = extension = .txt mime = text/plain words = 6679 sentences = 309 flesch = 53 summary = Using sequence analysis methods we have discovered significant sequence similarity between this central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene [40] , whose product binds to DNA and is essential for sex determination. The sequence similarity between the central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene suggests that SRY may be a cellular cognate of HDAg. Another candidate for the 'captured' cellular RNA was recently proposed: a 202 residue cellular protein referred to as DIPA (delta interacting protein A) was identified by co-immunoprecipitation with HDAg and by its in vivo ability to inhibit viral replication [5] . Statistically significant sequence similarities are limited to the functionally essential regions of both genes: in the SRY gene the similarity is confined to the HMG (High Mobility Group) box, a DNA binding motif found in the HMG protein superfamily [24, 31] , in HDAg the similarity is limited to RNA-binding domain. cache = ./cache/cord-289926-y1rjgbui.txt txt = ./txt/cord-289926-y1rjgbui.txt === reduce.pl bib === id = cord-292643-n6xp5mlz author = Hall, Richard J. title = Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date = 2013-09-13 pages = extension = .txt mime = text/plain words = 4803 sentences = 219 flesch = 44 summary = The relative abundance of a virus (or viral nucleic acid) in a sample, compared to that of other organisms such as bacteria or host cells (or their genomes), is a critical factor for the discovery of viruses when using metagenomics. A study on human liver tissue compared enrichment techniques of freeze-thaw, centrifugation and nuclease-treatment for the detection of Hepatitis C Virus using both Roche 454 and Illumina high-throughput sequencing platforms (Daly et al., 2011) . After an initial 10 min reverse transcription step at 45 • C and 10 min denaturation Table 1 Virus enrichment process prior to sequencing in metagenomic studies on human and animal samples. This artificial sample represents a starting point to evaluate simple and rapid viral enrichment methods for use in virus metagenomics studies that seek to detect a virus that is causing disease in humans or animals. cache = ./cache/cord-292643-n6xp5mlz.txt txt = ./txt/cord-292643-n6xp5mlz.txt === reduce.pl bib === id = cord-291916-5yqc3zcx author = Hozhabri, Hossein title = The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date = 2020-08-05 pages = extension = .txt mime = text/plain words = 16737 sentences = 847 flesch = 45 summary = cache = ./cache/cord-291916-5yqc3zcx.txt txt = ./txt/cord-291916-5yqc3zcx.txt === reduce.pl bib === id = cord-289248-6mx4o0eb author = Wang, Yilong title = Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date = 2018-05-01 pages = extension = .txt mime = text/plain words = 7018 sentences = 388 flesch = 59 summary = These two mutants grew to high titer in Vero cells, were genetically stable, and were significantly more attenuated in vitro and in vivo compared to the parental rMV-Hu191 vaccine strain. We next compared the replication kinetics of the rMV-Hu191 mutants and the parental virus in Vero cells in the time course of 120 h after infection (Fig. 5 ). These data suggest that rMVs carrying mutations in the SAM binding site were more attenuated in Vero cells than the parental MV vaccine strain. In this study, we successfully generated two recombinant measles viruses with amino acid substitutions in the SAM binding site of L protein and examined the effects of these mutations on viral replication, safety, and immunogenicity. We generated two recombinant MV-Hu191 carrying mutations in the SAM binding site, which not only grew to high titer in Vero cells and were genetically stable but also were significantly more attenuated and immunogenic compared to the currently used Chinese MV vaccine strain. cache = ./cache/cord-289248-6mx4o0eb.txt txt = ./txt/cord-289248-6mx4o0eb.txt === reduce.pl bib === id = cord-297078-pxggjaby author = Poole, Anthony M. title = Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome? date = 2005-03-16 pages = extension = .txt mime = text/plain words = 8279 sentences = 391 flesch = 50 summary = Leipe, Aravind, and Koonin (1999) suggest that LUCA possessed a hybrid DNA/RNA genome, thereby providing an explanation for the universal distribution of certain components of the DNA replication/repair apparatus. We argue from structural and functional data that the second of these, RNA polymerase-dependent proofreading and repair, is likely to have been a feature of LUCA rather than a recent innovation as part of selection for improved messenger RNA (mRNA) quality control, though this is no doubt the current function of this phenomenon. In this scenario, cleavage-stimulatory factors evolved twice independently (GreA/GreB in bacteria and transcription factor S/TFIIS in archaea/eukaryotes) with an initial function in RNA genome repair. This implies that the LUCA possessed an RNA genome, and in this scenario, bacterial RNA polymerase-associated cleavage-stimulatory factors (GreA/GreB) and their archaeal/eukaryotic equivalents (TFS/TFIIS) were originally involved in proofreading and repair of the genome, as indicated by [Gen] . cache = ./cache/cord-297078-pxggjaby.txt txt = ./txt/cord-297078-pxggjaby.txt === reduce.pl bib === id = cord-291590-24psoaer author = Ogando, Natacha S. title = The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date = 2020-06-20 pages = extension = .txt mime = text/plain words = 4299 sentences = 228 flesch = 52 summary = In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. cache = ./cache/cord-291590-24psoaer.txt txt = ./txt/cord-291590-24psoaer.txt === reduce.pl bib === id = cord-293355-0v71xwqy author = Aguiar, Eric Roberto Guimarães Rocha title = Virus‐derived small RNAs: molecular footprints of host–pathogen interactions date = 2016-05-12 pages = extension = .txt mime = text/plain words = 6830 sentences = 446 flesch = 50 summary = Thus, the pattern of small RNAs generated in infected cells can be used as a molecular footprint to identify and characterize viruses independent on sequence homology searches against known references. Different RNAi mechanisms can generate vsRNAs during viral infection including the mammalian miRNA pathway, Drosophila small interfering RNA (siRNA) pathway, and mosquito piRNA pathway. 22, 23 In animals, there are at least three separate RNAi mechanisms that can generate vsRNAs during viral infection: the microRNA (miRNA), piwi-interacting RNA (piRNA), and small interfering RNA (siRNA) pathways ( Figure 1 ). Interestingly, EVEs seemed to favor the generation of small RNAs with molecular characteristics of piRNAs rather than siRNAs. Second, some viruses have developed viral suppressors of the siRNA pathway (VSRs) that can significantly affect the pattern of vsRNAs. VSRs allow for accumulation of viral RNA that can be degraded by other host mechanisms. cache = ./cache/cord-293355-0v71xwqy.txt txt = ./txt/cord-293355-0v71xwqy.txt === reduce.pl bib === id = cord-297323-l3f12hg4 author = Amor, Sandra title = Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date = 2020-09-26 pages = extension = .txt mime = text/plain words = 4982 sentences = 304 flesch = 43 summary = Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. These subsequently induce expression of type I IFNs (IFNα/β) and interferon stimulated genes (ISGs) [figure 2] many of which have potent antiviral activities, as well as other proinflammatory mediators e.g. cytokines, chemokines and antimicrobial peptides that are essential to initiate the host innate and adaptive immune response. Likewise, viral load, obesity, gender, race, blood groups and comorbidities have all been reported to influence the response to SARS-CoV-2 infection, [ Table 4 ; (101) (102) (103) (104) (105) (106) (107) (108) (109) (110) (111) (112) ] although few studies have fully examined the extent to which subversion and activation of innate immune components contribute to susceptibility in these cases. Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune Response to Severe Acute Respiratory Syndrome Coronavirus Infection cache = ./cache/cord-297323-l3f12hg4.txt txt = ./txt/cord-297323-l3f12hg4.txt === reduce.pl bib === id = cord-298847-szezd2vb author = Jacomy, Hélène title = Vacuolating encephalitis in mice infected by human coronavirus OC43 date = 2003-10-10 pages = extension = .txt mime = text/plain words = 6882 sentences = 338 flesch = 47 summary = Virus inoculation of 21-day postnatal C57BL/6 and BALB/c mice led to a generalized infection of the whole CNS, demonstrating HCoV-OC43 neuroinvasiveness and neurovirulence. Moreover, mice inoculated with supernatants from cell cultures infected with brain tissue from affected mice developed the same disease, demonstrating that the virus was responsible for pathology. Cells positive for viral antigens were first observed at HCoV-OC43-infected mice gained weight normally during the first 5 days after infection, after which they all lost weight during the acute phase of the disease. (A) 100% of brains from C57BL/6 mice inoculated ic with 10 TCID 50 of HCoV-OC43 were positive for viral RNA between 3 and 11 days postinfection. However, RT-PCR analysis revealed that viral RNA could not be detected after the second week postinfection, suggesting a nonpersistent infection of HCoV-OC43 virus in 21 DPN mice. Every 2 days postinfection, five animals from two groups of infected mice of each strain were sacrificed and processed for detection of viral RNA, viral proteins, and infectious virus. cache = ./cache/cord-298847-szezd2vb.txt txt = ./txt/cord-298847-szezd2vb.txt === reduce.pl bib === id = cord-290802-761wqgbe author = Zhao, Zheng title = Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date = 2020-09-18 pages = extension = .txt mime = text/plain words = 3890 sentences = 237 flesch = 51 summary = title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus. In sum, structurally, SARS-CoV-2 has high global/ core structural similarity to the RDRP catalytic domains of all other RNA viruses, which provides an opportunity for structure-based COVID-19 drug design and repurposing, noting that keys differences lie in the subtle details. According to the similarity of functionsite interaction fingerprints over all complexes, it was possible to divide the binding modes into four classes, where each class contains multiple PDB structures from different kinds of viruses (Table 1) . cache = ./cache/cord-290802-761wqgbe.txt txt = ./txt/cord-290802-761wqgbe.txt === reduce.pl bib === id = cord-294363-bv6xa8v8 author = Zhou, Hong title = Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date = 2020-05-05 pages = extension = .txt mime = text/plain words = 8902 sentences = 456 flesch = 46 summary = Several studies demonstrated angiotensin converting enzyme 2 (ACE2) as an important therapeutic target of SARS-CoV-2 entry and infection, and many potential targets were subsequently proposed, such as the spike (S) protein and transmembrane serine protease 2 (TMPRSS2). Therefore, accelerating research for potential therapeutic target confirmation, promising drug discovery, and clinical verification development will speed up efforts to combat SARS-CoV-2. In addition to inhibiting the virus directly, ASOs are also expected to target the disease-related proteins involved in the inflammatory cytokine storm process, which could be considered a promising therapeutic strategy for combating SARS-CoV-2 . Although many strategies have been used to block the attachment, entry, replication and release processes to inhibit SARS-CoV-2 infection, how to prevent viral evasion from host immune responses and virus-induced cytopathic effects is considered one of the most urgent problems that need to be solved in SARS-CoV-2-induced pneumonia-associated respiratory syndrome (PARS) patients. cache = ./cache/cord-294363-bv6xa8v8.txt txt = ./txt/cord-294363-bv6xa8v8.txt === reduce.pl bib === id = cord-289535-srrfr1es author = Tregoning, J. S. title = Vaccines for COVID‐19 date = 2020-10-18 pages = extension = .txt mime = text/plain words = 14329 sentences = 793 flesch = 44 summary = One concern with vaccine development for SARS-CoV-2 is that the immune response can cause disease, often in the act of clearing the infection. Preclinical animal studies have demonstrated that DNA vaccines encoding the M, N, 3a or S proteins of the SARS-CoV-1 virus could elicit immune responses [180] [181] [182] . The S protein is the target of the only SARS-CoV-1 DNA vaccine to progress to Phase I clinical trial, delivered by bio-injector, and it was safe and induced neutralizing antibody responses [183] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial cache = ./cache/cord-289535-srrfr1es.txt txt = ./txt/cord-289535-srrfr1es.txt === reduce.pl bib === id = cord-292831-oihcay6w author = Choudhary, Manohar L. title = Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR date = 2013-01-08 pages = extension = .txt mime = text/plain words = 3725 sentences = 210 flesch = 53 summary = The purpose of this study was to develop a one step mRT-PCR that could detect respiratory viruses including influenza A viruses, H1N1pdm09, seasonal H1N1, H3N2, influenza B viruses, respiratory syncytial virus (RSV) A and B, human metapneumovirus (HMPV), parainfluenza viruses (PIV) 1, 2, 3, 4, rhinovirus, enterovirus, corona viruses OC43, 229E, NL63 and HKU1 in three sets in human clinical samples and to compare it with rRT-PCR. The specificity of the multiplex PCR assay was evaluated by cross reaction tests with known viral isolates and different panels of sequence confirmed known clinical respiratory samples as reference material. Specificity of the mRT-PCR assay was evaluated by cross reaction tests against known respiratory virus isolates/positive samples and a WHO QA/QC panel for influenza viruses showed no cross reactivity amongst different viruses. For validation of set 1 of the multiplex assay, 114 respiratory clinical specimens previously positive for influenza viruses by rRT-PCR were used and results were 100% concordant. cache = ./cache/cord-292831-oihcay6w.txt txt = ./txt/cord-292831-oihcay6w.txt === reduce.pl bib === id = cord-293913-frkb8iso author = Gao, Hong-Qiang title = Identification of the polymerase polyprotein products p72 and p65 of the murine coronavirus MHV-JHM date = 1996-12-31 pages = extension = .txt mime = text/plain words = 3624 sentences = 176 flesch = 53 summary = Abstract The RNA polymerase gene of murine coronavirus MHV-JHM encodes a polyprotein of greater than 750 kDa. This polyprotein is proposed to be processed by two papain-like cysteine proteinases, PCP-1 and PCP-2, and a poliovirus 3C-like proteinase domain, 3C-pro, to generate protein products. To investigate which viral proteinase may be responsible for generating p72 and p65, we expressed the 5′-region of the MHV-JHM RNA polymerase gene including the two papain-like cysteine proteinase domains in an in vitro transcription/translation system and analyzed the translation products for proteolytic processing. To determine how p72 and p65 are generated from the polymerase polyprotein, we expressed cDNA clones encoding the 5'-end of ORF l a, including the 2 papain-like cysteine proteinase domains, and analyzed the translation reactions for the presence of proteolytic products. cache = ./cache/cord-293913-frkb8iso.txt txt = ./txt/cord-293913-frkb8iso.txt === reduce.pl bib === id = cord-294764-v28wbrqp author = Deval, Jerome title = Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses date = 2017-04-15 pages = extension = .txt mime = text/plain words = 8316 sentences = 433 flesch = 46 summary = The in vitro assays and in vivo animal models that have been developed to identify and characterize inhibitors of norovirus RdRp are also summarized, followed by an update on the current antiviral research targeting different regions of norovirus RdRp. In the future, structure-based drug design and rational optimization of known nucleoside and non-nucleoside inhibitors of norovirus RdRp may pave the way towards the next generation of direct-acting antivirals. Despite this limitation, the in vitro effect of small molecules on HuNoV replication has been studied using a stable human hepatoma cell line expressing the part of the Norwalk virus RNA genome encoding the non-structural proteins and carrying the neomycin resistance gene (Chang et al., 2006) . Finally, since norovirus RdRp shares functional and structural features with proteins from other RNA viruses such as HCV, it may be possible to identify nucleo(s/t)ide analogs, like 2CM-C, which inhibits a range of viral polymerases. cache = ./cache/cord-294764-v28wbrqp.txt txt = ./txt/cord-294764-v28wbrqp.txt === reduce.pl bib === id = cord-298032-3zlu8g8y author = Nan, Yuchen title = Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date = 2018-04-20 pages = extension = .txt mime = text/plain words = 10577 sentences = 524 flesch = 46 summary = An earlier study showed that a 22mer PPMO targeting the translation start site region of EBOV VP35 positive-sense RNA exhibited sequence-specific, time-and dose-dependent inhibition of EBOV replication in cultured cells (Enterlein et al., 2006) . However, PPMO targeting conserved internal ribosome entry site (IRES) sequences have been shown to be highly effective in protecting cultured cells against infection by human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1) (Stone et al., 2008) , with reduction of PV1 titers by up to 6 log10. In this study, virus replication in MDCK cells was significantly inhibited by three PPMO targeting either the translation start site region of PB1 or NP mRNA or the 3 -terminal region of NP viral RNA (vRNA). Inhibition of influenza virus infection in human airway cell cultures by an antisense peptide-conjugated morpholino oligomer targeting the hemagglutinin-activating protease TMPRSS2 cache = ./cache/cord-298032-3zlu8g8y.txt txt = ./txt/cord-298032-3zlu8g8y.txt === reduce.pl bib === id = cord-298036-2zurc60t author = Imre, Gergely title = Cell death signalling in virus infection date = 2020-09-12 pages = extension = .txt mime = text/plain words = 8002 sentences = 414 flesch = 37 summary = Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . cache = ./cache/cord-298036-2zurc60t.txt txt = ./txt/cord-298036-2zurc60t.txt === reduce.pl bib === id = cord-293163-udcw1mx5 author = Lu, Patrick Y. title = Modulation of angiogenesis with siRNA inhibitors for novel therapeutics date = 2005-02-04 pages = extension = .txt mime = text/plain words = 6378 sentences = 329 flesch = 34 summary = The functional validation of angiogenic factors for their specific role has been greatly facilitated by the use of RNAi inhibitors, revealing a network involving the early activation of the VEGF pathway and interactions among MMPs and adhesion molecules, leading to the regulation of signal transduction pathways. MMP9 and MMP2 are important for the mobilization of sequestered VEGF and initiation of tumor angiogenesis [17] , whereas specific integrins mediate interactions between endothelial cells and the BM by activating the integrin receptor signaling that controls many key functions, such as proliferation [18] . The involvement, revealed by siRNA, of diacylglycerol kinase a (Dgka) in hepatocyte growth factor (HGF)-stimulated cell migration, which impaired angiogenesis in vitro, indicated its essential role in both proliferative and migratory response to VEGF, and suggested that it is a novel therapeutic target for controlling angiogenesis [43] . cache = ./cache/cord-293163-udcw1mx5.txt txt = ./txt/cord-293163-udcw1mx5.txt === reduce.pl bib === id = cord-293417-oqusfhei author = Ma, Yanlin title = Structures of the N- and C-terminal domains of MHV-A59 nucleocapsid protein corroborate a conserved RNA-protein binding mechanism in coronavirus date = 2010-07-01 pages = extension = .txt mime = text/plain words = 5142 sentences = 292 flesch = 55 summary = The higher resolution provides more detailed structural information than previous reports, showing that the NTD structure from MHV shares a similar overall and topology structure with that of SARS-CoV and IBV, but varies in its potential surface, which indicates a possible difference in RNA-binding module. To gain insight into the precise mechanism of N protein, several crystallographic or NMR structural results were reported, including MHV N-terminal RNA binding domain (residues 60-195) (Grossoehme et al., 2009) , two proteaseresistant domains of the N protein from SARS-CoV (Huang et al., 2004; Luo et al., 2006; Yu et al., 2006; Chen et al., 2007; Saikatendu et al., 2007; Takeda et al., 2008) , and IBV (Beaudette strain and Gray strain) (Fan et al., 2005; Jayaram et al., 2006) . In overall ribbon posture, the high resolution structure of MHV-NTD determined using two forms of crystals with different packing modes is similar to previously reported SARS-CoV and IBV structures, with a remarkable difference in surface electrostatic distribution. cache = ./cache/cord-293417-oqusfhei.txt txt = ./txt/cord-293417-oqusfhei.txt === reduce.pl bib === id = cord-295351-0zr2e8lh author = Mohd Ropidi, Muhammad Izzuddin title = Endoplasmic reticulum: a focal point of Zika virus infection date = 2020-01-20 pages = extension = .txt mime = text/plain words = 7845 sentences = 389 flesch = 35 summary = Following ZIKV infection, the accumulation of misfolded virus polyproteins in the ER lumen overwhelms the ER protein-folding capacity leading to ER stress and triggers the activation of the UPR (Fig. 2) [47] . Following the dissociation of GRP78 that unmasks the GLS, ATF6 translocate to the Golgi apparatus and undergoes sequential proteolytic processing by Fig. 2 ZIKV-induced ER stress initiates host cell unfolded protein response (UPR). ZIKV infection induces ER stress due to the increased amount of unfolded/misfolded viral (red strand) and host cell (grey strand) protein aggregates in the ER lumen. To summarize, ZIKV virus bypasses the UPR by inhibiting stress granules assembly and reticulophagy to ensure continuous viral protein translation and virion production while simultaneously protecting the virus from host cell defense mechanisms. cache = ./cache/cord-295351-0zr2e8lh.txt txt = ./txt/cord-295351-0zr2e8lh.txt === reduce.pl bib === id = cord-299509-7xjdryoq author = Scholte, Florine E. M. title = Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates date = 2013-08-01 pages = extension = .txt mime = text/plain words = 9607 sentences = 442 flesch = 48 summary = Infectious cDNA clones of viruses have become invaluable tools that allow reverse genetics studies to elucidate the contribution of specific amino acids or RNA structures to viraemia, virulence, antigenicity, replication kinetics, interactions with host factors, adaptation to new vectors, and many other aspects of the viral life cycle. To obtain a virus that -in terms of virulence, sensitivity to antiviral compounds, and CHIKV-host interactions -is expected to have the general characteristics of the E1-226V CHIKV strains that were circulating during the 2005-2009 outbreaks, we have constructed a completely synthetic CHIKV cDNA clone based on the consensus sequence of the aligned genomes of these recent isolates. Indirect immunofluorescence analysis of Vero E6 cells infected with CHIKV LS3, LS3-GFP, or ITA07-RA1 at various time points showed that the localization and expression kinetics of E2 and dsRNA were similar for the natural isolate and the synthetic viruses (Fig. 6) . cache = ./cache/cord-299509-7xjdryoq.txt txt = ./txt/cord-299509-7xjdryoq.txt === reduce.pl bib === id = cord-297974-sduz0j35 author = Bokelmann, L. title = Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date = 2020-08-06 pages = extension = .txt mime = text/plain words = 4761 sentences = 307 flesch = 55 summary = Here we describe a method to detect SARS-CoV-2 RNA of a single infected individual within a bulk sample comprised of up to 26 individual patient samples by combining a hybridizationcapture-based RNA extraction approach with smartphone app-assisted colorimetric detection of RT-LAMP products, a procedure that can be performed in less than one hour ( Figure 1A) . To investigate whether it is possible to detect single infected individuals in pools of gargle lavage samples, we created eleven pools of 25 patient samples each, all of which had been tested negative in RT-qPCR assay and in the Cap-iLAMP assays for the Orf1a and the N gene ( Figure 2D ). All tested gargle lavages from single healthy individuals (n=6) and 11 pools of 25 healthy individuals (n=275) correctly tested negative for both the Orf1a gene and N gene in the Cap-iLAMP assay ( Figure 2C and E), indicating that false positive results which were sometimes observed when samples are added directly into the iLAMP reaction (Supp. cache = ./cache/cord-297974-sduz0j35.txt txt = ./txt/cord-297974-sduz0j35.txt === reduce.pl bib === id = cord-293790-7hyelm88 author = Guévin, Carl title = Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection date = 2010-09-01 pages = extension = .txt mime = text/plain words = 5267 sentences = 290 flesch = 54 summary = title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection To identify novel cellular factors that may play an essential role in HCV RNA replication, we have previously screened a human liver cDNA library for proteins interacting with the HCV NS5B RNAdependent RNA polymerase (RdRp). Here we report that ATG5, a protein required for the formation of DMV in embryonic stem cell (Mizushima et al., 2001) , specifically interacts with HCV NS5B. As a control, a panel of proteins (RAR-β, RAR-α, HCV core, and nonstructural protein: NS3 prot , NS3 hel , NS4A, and NS4B) cloned in the GAL4 DNA binding domain was tested for interaction with ATG5. A. Soluble yeast extracts containing NS5BΔ21 (N-terminal c-myc tag) and ATG5 (N-terminal HA tag) were incubated with different monoclonal antibodies and the immunoprecipitates were pulled down using protein A/G beads. cache = ./cache/cord-293790-7hyelm88.txt txt = ./txt/cord-293790-7hyelm88.txt === reduce.pl bib === id = cord-297834-me1ajoyb author = Schountz, Tony title = Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date = 2014-03-14 pages = extension = .txt mime = text/plain words = 6425 sentences = 334 flesch = 38 summary = The immune response is energetically expensive for wild animals, thus the findings of experimental studies will be critical for understanding the ecoimmunology of reservoir hosts of hantaviruses [6, 7] , and experiments using wild rodents in natural or semi-natural environments [8, 9] will be required to validate laboratory findings. Currently, three laboratory infection systems have been developed to study hantavirus infections of reservoir hosts: Seoul virus (SEOV) infection of the Norway rat (Rattus norvegicus), Puumala virus (PUUV) infection of the bank vole (Myodes glareolus), and Sin Nombre virus (SNV) infection of the deer mouse (Peromyscus maniculatus) [12, 14, 16] . Experimental data have also shown that patterns of the expression of genes related to the immune response are different in infected males and females [32] , and it is likely these differences have important roles in hantavirus ecology. cache = ./cache/cord-297834-me1ajoyb.txt txt = ./txt/cord-297834-me1ajoyb.txt === reduce.pl bib === id = cord-294108-uvnh0s9r author = Dube, Taru title = Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date = 2020-10-25 pages = extension = .txt mime = text/plain words = 13885 sentences = 845 flesch = 44 summary = [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. cache = ./cache/cord-294108-uvnh0s9r.txt txt = ./txt/cord-294108-uvnh0s9r.txt === reduce.pl bib === id = cord-294842-aesiff1f author = Romero-Brey, Inés title = Membranous Replication Factories Induced by Plus-Strand RNA Viruses date = 2014-07-22 pages = extension = .txt mime = text/plain words = 11038 sentences = 520 flesch = 40 summary = Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein cache = ./cache/cord-294842-aesiff1f.txt txt = ./txt/cord-294842-aesiff1f.txt === reduce.pl bib === id = cord-291225-75ys908n author = Martins, Nelson title = A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells date = 2018-12-12 pages = extension = .txt mime = text/plain words = 5964 sentences = 366 flesch = 51 summary = title: A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells Here we describe transgenic Drosophila melanogaster lines encoding a Flock House Virus-derived replicon (FHV∆B2eGFP), expressing GFP as a reporter of viral replication. This replicon is efficiently controlled by the siRNA pathway in most somatic tissues, with GFP fluorescence providing a reliable marker for the activity of antiviral RNAi. Interestingly, in follicular somatic cells (FSC) of ovaries, this replicon is still partially repressed in an siRNA independent manner. We did not detect replicon derived Piwi-interacting RNAs in FSCs and identified 31 differentially expressed genes between restrictive and permissive FSCs. Altogether, our results uncovered a yet unidentified RNAi-independent mechanism controlling FHV replication in FSCs of ovaries and validate the FHV∆B2eGFP replicon as a tool to screen for novel tissue specific antiviral mechanisms. cache = ./cache/cord-291225-75ys908n.txt txt = ./txt/cord-291225-75ys908n.txt === reduce.pl bib === id = cord-293651-96cmduez author = Callison, Scott A. title = Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens date = 2006-08-28 pages = extension = .txt mime = text/plain words = 4742 sentences = 216 flesch = 56 summary = We also collected a total of 120 tracheal swabs at six different time points from birds experimentally infected with different dosages of IBV and found that, independent of the dose given, the viral load in the trachea plateau at 5 days post-inoculation. Molecular assays use the reverse transcriptase-polymerase chain reaction (RT-PCR) to detect viral RNA directly from a clinical sample or from virus isolated in a laboratory host system. Clinical samples consisting of 229 tracheal swabs from commercial chickens experiencing upper-respiratory disease, submitted as routine diagnostic cases to the Delaware (Georgetown, DE) and Maryland (Salisbury, MD) State Diagnostic Laboratories were tested by the real-time RT-PCR assay, as well as, by virus isolation at those laboratories (Gelb and Jackwood, 1998) . In this report we present the development and evaluation of a real-time Taqman ® -based RT-PCR assay for the detection and quantification of IBV genomic RNA directly from tracheal swabs. cache = ./cache/cord-293651-96cmduez.txt txt = ./txt/cord-293651-96cmduez.txt === reduce.pl bib === id = cord-299943-wzkh04dv author = Santhanam, Manikandan title = DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment date = 2020-08-18 pages = extension = .txt mime = text/plain words = 7350 sentences = 438 flesch = 41 summary = In a sensor detection scheme, ssDNA(s) specifically hybridizes with a target DNA sequence that is being employed as a probe(s): a capture probe used to attach the target DNA to the surface of materials and/or a reporter probe labeled with signaling molecules, e.g., redox-active molecules. To make a quantitative measurement, the DNA hybridization event is coupled with electrochemical reactions, in a way that a probe-target complex increases/decreases a coupled redox reaction at the electrode surface. DPV-Differential pulse voltammetry, CV-Cyclic Voltammetry, EIS-Electrochemical Impedance spectroscopy, CSD-Circular strand displacement, RCA-Rolling circle amplification, EXPAR-Isothermal exponential amplification, HCR-Hybridization chain reaction, HDA-Helicase dependent amplification, TMB-3,3 ,5,5 -tetramethylbenzidine, N,S-GQDs@AuNP-Nitrogen, sulfur codoped graphene quantum, CNT-PANI-Carbon nanotube-polyanilline, NA-Not applicable, * If limit of detection is not reported, lowest detected value is provided. Different methods have been employed in signal amplification approaches to detect a low copy number of target DNA on the electrode surface. cache = ./cache/cord-299943-wzkh04dv.txt txt = ./txt/cord-299943-wzkh04dv.txt === reduce.pl bib === id = cord-300884-rqfxe0x1 author = Zhang, Jianqiang title = Genomic characterization of equine coronavirus date = 2007-12-05 pages = extension = .txt mime = text/plain words = 6804 sentences = 378 flesch = 56 summary = Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). In contrast to the replicase proteins which are directly translated from the genomic RNA, coronavirus structural and accessory proteins are expressed from a nested set of 3′ coterminal subgenomic (sg) mRNAs that also possess a common 5′ leader sequence derived from the 5′ end of the genome (Pasternak et al., 2006; Sawicki et al., 2007) . Following multiple alignments with the S proteins of other group 2a coronaviruses, a potential cleavage recognition sequence (RRQRR) was identified at residues 764-768 which would predict a cleavage between amino acids 768 and 769, separating the ECoV S protein into S1 and S2 subunits (Fig. 1) . cache = ./cache/cord-300884-rqfxe0x1.txt txt = ./txt/cord-300884-rqfxe0x1.txt === reduce.pl bib === id = cord-294718-n3gx862b author = Tam, Patrick C K title = Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date = 2020-05-30 pages = extension = .txt mime = text/plain words = 1606 sentences = 135 flesch = 61 summary = title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. cache = ./cache/cord-294718-n3gx862b.txt txt = ./txt/cord-294718-n3gx862b.txt === reduce.pl bib === id = cord-299754-tgexahwd author = van Tol, Sarah title = The TRIMendous Role of TRIMs in Virus–Host Interactions date = 2017-08-22 pages = extension = .txt mime = text/plain words = 18211 sentences = 1015 flesch = 41 summary = Downstream of the initial pattern recognition, TRIMs also influence the recruitment and interaction of adaptor molecules (stimulator of IFN genes (STING), mitochondrial antiviral signaling protein (MAVS), TGF-β-activated kinase 1(TAK1)/MAP3K7-binding protein (TAB) 2, Myeloid differentiation primary response gene 88 (MyD88), TIR-domain-containing adapterinducing interferon-β (TRIF), NF-κB essential modulator (NEMO), nucleosome assembly protein (NAP-1), and tumor necrosis factor (TNF) receptor-associated factors (TRAF) family memberassociated NF-κB activator (TANK)) and enzymes (TRAF3, TRAF6, TAK1, inhibitor of NF-κB (IκB) kinase (IKK) α,β,ε, TANK binding kinase 1 (TBK1)) to signaling complexes in order to activate transcription factors. Downstream of the initial pattern recognition, TRIMs also influence the recruitment and interaction of adaptor molecules (stimulator of IFN genes (STING), mitochondrial antiviral signaling protein (MAVS), TGF-β-activated kinase 1(TAK1)/MAP3K7-binding protein (TAB) 2, Myeloid differentiation primary response gene 88 (MyD88), TIR-domain-containing adapter-inducing interferon-β (TRIF), NF-κB essential modulator (NEMO), nucleosome assembly protein (NAP-1), and tumor necrosis factor (TNF) receptor-associated factors (TRAF) family member-associated NF-κB activator (TANK)) and enzymes (TRAF3, TRAF6, TAK1, inhibitor of NF-κB (IκB) kinase (IKK) α,β,ε, TANK binding kinase 1 (TBK1)) to signaling complexes in order to activate transcription factors. cache = ./cache/cord-299754-tgexahwd.txt txt = ./txt/cord-299754-tgexahwd.txt === reduce.pl bib === id = cord-295217-z2erqkr9 author = Seow, Justine Jia Wen title = Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art date = 2020-06-02 pages = extension = .txt mime = text/plain words = 4353 sentences = 249 flesch = 48 summary = Majority of scRNA-seq approaches provide the steady state kinetics of mRNA (messenger RNA) expression without deeper insights into transcriptional dynamics of cells. However, a recent method called scSLAMseq (single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing) profiles the transcriptional activity at the singlecell resolution which can help in differentiating old and new RNA for thousands of genes 14 A very recent method SMART-Seq3 provides the allele and isoform resolution in scRNA-seq approach 17 . This results in a data set that is roughly symmetric and often roughly normal Mutual Nearest Neighbours: a pair of cells from each batch is contained in each other's set of nearest neighbours Batch correction: scRNA-seq datasets generated across different conditions or from technologies that contain batch specific systematic bias leading to batch-effect. From single-cell transcriptomic data, Cell-PhoneDB calculates significant receptor-ligand pairs from cluster information and differentially expressed genes. A benchmark of batch-effect correction methods for single-cell RNA sequencing data cache = ./cache/cord-295217-z2erqkr9.txt txt = ./txt/cord-295217-z2erqkr9.txt === reduce.pl bib === id = cord-297790-tpjxt0w5 author = Mandl, Judith N. title = Going to Bat(s) for Studies of Disease Tolerance date = 2018-09-20 pages = extension = .txt mime = text/plain words = 9486 sentences = 393 flesch = 40 summary = Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. It is likely that differences in evolutionary history of pathogen exposure between bats and humans have led to distinct adaptations in anti-viral immune responses and the ability to tolerate certain infections without disease while being susceptible to others. We summarize this work below, but comparisons of observations made across species suggest that although a number of species appear to be capable of avoiding the pathological effects of RNA virus infection, each bat species may have achieved this through distinct pathways, possibly involving changes to both increase pathogen replication control and to mitigate any immunopathology through decreased inflammatory responses and hence increased disease tolerance. cache = ./cache/cord-297790-tpjxt0w5.txt txt = ./txt/cord-297790-tpjxt0w5.txt === reduce.pl bib === id = cord-295019-8tf8ah6g author = Weber, Wilfried title = Emerging biomedical applications of synthetic biology date = 2011-11-29 pages = extension = .txt mime = text/plain words = 9511 sentences = 475 flesch = 36 summary = Synthetic mammalian transcription circuits consisting of a chimeric small-molecule-responsive transcription factor and a cognate synthetic promoter were originally designed for future gene-based therapies, and the aim was to adjust therapeutic transgene expression in mammalian cells in response to a pharmacologically active substance 34, 47, 49, 91 . When mammalian cells that are transgenic for the screening circuit are exposed to a compound library, they detect and modulate reporter gene expression in the presence of a non-toxic, cellpermeable and bioavailable molecule that has a classspecific core structure and corresponding drug activity (for example, antibiotic activity) (FIG. The availability of compact RNA sensor-actuators that are easy to design and to alter and that control transgene expression in response to intracellular levels of key proteins may also improve the ability to link metabolic disease states with gene-based therapeutic interventions. cache = ./cache/cord-295019-8tf8ah6g.txt txt = ./txt/cord-295019-8tf8ah6g.txt === reduce.pl bib === id = cord-292751-tk1oggi9 author = Hosseini, Elahe Seyed title = The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date = 2020-09-24 pages = extension = .txt mime = text/plain words = 3784 sentences = 222 flesch = 46 summary = Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan cache = ./cache/cord-292751-tk1oggi9.txt txt = ./txt/cord-292751-tk1oggi9.txt === reduce.pl bib === id = cord-292112-dejrksum author = Wang, Jinglu title = Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells date = 2020-08-03 pages = extension = .txt mime = text/plain words = 4709 sentences = 267 flesch = 52 summary = This study provides a lncRNA catalog for future research concerning the mechanism of the transdifferentiation of cBMSCs into IPCs. Long noncoding RNAs (LncRNAs) are the rest of the protein-coding transcripts >200 nt in length that lack coding potential [1] . The expression levels were verified by qRT-PCR, and the trends were consistent with the RNA-Seq data; however, the expression level of the lncRNAs was much lower than that of the protein-coding transcripts (Figure 8 ). The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. cache = ./cache/cord-292112-dejrksum.txt txt = ./txt/cord-292112-dejrksum.txt === reduce.pl bib === id = cord-292983-msuluuuu author = Ballesteros-Briones, María Cristina title = A new generation of vaccines based on alphavirus self-amplifying RNA date = 2020-09-06 pages = extension = .txt mime = text/plain words = 4942 sentences = 277 flesch = 47 summary = In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. This type of LNP-delivered saRNA vaccines, named SAM (for self-amplifying mRNA) platform, have shown great potential to generate immune responses against influenza virus [20] [21] [22] and Toxoplasma gondii [23] . Despite the fact that the ta-RNA system was able to induce good immune responses in vivo against influenza virus HA, it did not outperform vaccination with a single saRNA molecule expressing the same antigen. cache = ./cache/cord-292983-msuluuuu.txt txt = ./txt/cord-292983-msuluuuu.txt === reduce.pl bib === id = cord-294592-zwvr57a0 author = Mukherjee, Moumita title = Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date = 2020-08-11 pages = extension = .txt mime = text/plain words = 6099 sentences = 371 flesch = 57 summary = title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. We have also looked at the possible regulation of viral genomic RNA through binding of host RNA binding proteins (RBPs) and miR-NAs in specific sequences of the viral UTRs. There are experimentally validated evidences of human RBPs binding to the regulated signals within the untranslated region of SARS-CoV RNA in order to control the viral RNA synthesis and turnover. cache = ./cache/cord-294592-zwvr57a0.txt txt = ./txt/cord-294592-zwvr57a0.txt === reduce.pl bib === id = cord-299848-fft1brwz author = Claridge, Jolyon K. title = A picornaviral loop-to-loop replication complex date = 2009-03-04 pages = extension = .txt mime = text/plain words = 8818 sentences = 459 flesch = 60 summary = Using human rhinovirus as a model system, we have combined NMR contact information, small-angle X-ray scattering (SAXS) data, and previous mutagenesis results to determine the shape, position and relative orientation of the 3C(pro) and SLD components. Binding between SLD and 3C(pro) induces structural changes in the proteolytic active site that is positioned on the opposite side of the protease relative to the RNA/protein interface, suggesting that subtle conformational changes affecting catalytic activity are relayed through the protein. NMR and small-angle X-ray scattering data were combined with results from previous mutational analysis (Andino et al., 1993; Leong et al., 1993) (Fig. 1) to construct a structural model of the HRV-14 3C pro -SLD complex. The largest SLD-induced chemical shift perturbations on the 3C pro surface cluster primarily to a patch (dark red in Fig. 5A ) that includes D32 from the loop connecting b-strands 2-3, N80, F83 and F89 from the inter-domain linker and V179 from the C-terminal region. cache = ./cache/cord-299848-fft1brwz.txt txt = ./txt/cord-299848-fft1brwz.txt === reduce.pl bib === id = cord-292416-3hhi4wps author = Sarid, Ronit title = Investigating an Emerging Virus During a Sudden Pandemic Outbreak date = 2020-07-31 pages = extension = .txt mime = text/plain words = 4869 sentences = 230 flesch = 41 summary = Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. cache = ./cache/cord-292416-3hhi4wps.txt txt = ./txt/cord-292416-3hhi4wps.txt === reduce.pl bib === id = cord-295130-e7j7kac0 author = Moreno-Contreras, Joaquín title = Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2906 sentences = 122 flesch = 58 summary = In this study, we compared the RT-qPCR results from 253 paired samples obtained from saliva and swabs of ambulatory patients; the RNA in the swab samples was extracted using a commercial RNA purification kit, and the saliva samples were directly mixed with a lysis buffer, boiled, and used for the RT-qPCR protocol. To evaluate if saliva is a good source of viral RNA for the RT-qPCR, we determined the presence of the SARS-CoV-2 genome in paired saliva and swab samples from 253 ambulatory patients. Direct lysis of nasopharyngeal or oropharyngeal swab samples in viral transport medium using the QE buffer has been reported as a suitable method for direct RT-qPCR for SARS-CoV-2 detection, with rates similar to those of methods based on column purification (11, 15) . cache = ./cache/cord-295130-e7j7kac0.txt txt = ./txt/cord-295130-e7j7kac0.txt === reduce.pl bib === id = cord-300685-bcjnujlj author = Poon, Leo L M title = Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date = 2003-06-01 pages = extension = .txt mime = text/plain words = 2425 sentences = 115 flesch = 54 summary = The detection of live virus (4 ) and the detection of high copy numbers of viral sequence from NPA samples in the current study clearly support that the concept that cough and sneeze droplets from SARS patients are a major route of spread of this infectious agent. Interestingly, two of four available stool samples from the SARS patients in this study were positive in the assay (data not shown). RNA samples from this study were subjected to nested reverse transcription-PCR (4 ), and no evidence of metapneumovirus infection was detected in any of the patients in this study (data not shown), suggesting that the novel coronavirus is the key player in the pathogenesis of SARS. The PCR products from all 23 positive cases in this study had the same melting point, strongly suggesting that there was no viral sequence variation in the target region of samples collected at the two Hong Kong hospitals during the 1-month period of patient accrual. cache = ./cache/cord-300685-bcjnujlj.txt txt = ./txt/cord-300685-bcjnujlj.txt === reduce.pl bib === id = cord-297092-oq14cwka author = Tan, Shaoyuan title = Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model date = 2020-10-07 pages = extension = .txt mime = text/plain words = 6982 sentences = 332 flesch = 53 summary = This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases. For the sequencing of cell culture samples, raw pass reads were mapped to the SVA reference genome (GenBank: MN164664) using Minimap2 [34] , then analyzed using Qualimap [35] , generating raw error rates and coverage information which was then visualized using GraphPad prism software (GraphPad Software, San Diego, CA, USA). After determining the consensus generation strategies for both sequencing methods, optimization was performed in terms of total input sequencing yield and the pre-treatment of raw reads using the cell culture virus in which the whole genome sequence was already known. In order to evaluate and compare the general performance of DRS and PCS for viral whole genome recovery, two whole genome sequencing runs using a cell culture-grown virus with a known reference sequence were carried out for each method (Table 1 ). cache = ./cache/cord-297092-oq14cwka.txt txt = ./txt/cord-297092-oq14cwka.txt === reduce.pl bib === id = cord-293525-c7nwygl1 author = Saldanha, I. F. title = Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date = 2019-04-03 pages = extension = .txt mime = text/plain words = 5041 sentences = 235 flesch = 46 summary = An EriCoV-specific BRYT-Green(®) real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Characterisation of these Erinaceus coronavirus (EriCoV) nucleotide sequences revealed high nucleotide identity to MERS-CoV [3] , the cause of an acute respiratory syndrome in humans with high case fatality rates [5, 6] . Many animal species seem to have the capacity for coronavirus infection in the absence of apparent disease, including bats [15] , aquatic birds [16] and rabbits when inoculated with MERS-CoV [17] . Whole genome sequencing was performed on RNA extracted from one faecal sample collected in 2014 (R618/14) which was identified as EriCoV-positive by real-time RT-PCR. The highest proportion of EriCoV-positive hedgehog samples were submitted from the South of England (34/217, 16%); however, BLR showed no significant association (P = 0.678) between EriCoV infection status and wider region when other factors including age and year were included. cache = ./cache/cord-293525-c7nwygl1.txt txt = ./txt/cord-293525-c7nwygl1.txt === reduce.pl bib === === reduce.pl bib === id = cord-301226-hmc2wmst author = Randazzo, Walter title = Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date = 2020-04-27 pages = extension = .txt mime = text/plain words = 2158 sentences = 127 flesch = 52 summary = Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Here, we show that SARS-CoV-2 can be reproducibly detected by RT-qPCR in longitudinal samples from sewage treatment plants that receive wastewaters from over one million inhabitants in the metropolitan area of Valencia, Spain. Following concentration of viral content by flocculation, a standard RT-qPCR procedure allowed us to detect SARS-CoV-2 RNA in 12/12 samples collected from March 9 to April 14, 2020, with Ct values ranging between 34•00 and 37•84, correspondingly revealing between 5•22 and 5•99 log 10 genomic copies (gc)/L (Table 1) . Interestingly, we consistently detected SARS-CoV-2 RNA in samples collected on March 9 and March 11, when only 50 and 76 cumulative cases were declared in the entire Region of Valencia. cache = ./cache/cord-301226-hmc2wmst.txt txt = ./txt/cord-301226-hmc2wmst.txt === reduce.pl bib === === reduce.pl bib === id = cord-299747-qovrstak author = Deval, Jerome title = Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus date = 2014-09-17 pages = extension = .txt mime = text/plain words = 4336 sentences = 247 flesch = 45 summary = title: Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus Jerome Deval, Julian A Symons and Leo Beigelman A number of important human infections are caused by positive-strand RNA viruses, yet almost none can be treated with small molecule antiviral therapeutics. The initial major class of nucleoside analogs of therapeutic potential to demonstrate potent inhibition of HCV RNA polymerase activity were 2 0 C-methyl-ribonucleosides, The first 2 0 C-methyl ribonucleosides were originally synthesized in the 1960s [18] . 0 -azidocytidine) is a potent inhibitor of NS5B-dependent RNA synthesis and hepatitis C virus replication in cell culture cache = ./cache/cord-299747-qovrstak.txt txt = ./txt/cord-299747-qovrstak.txt === reduce.pl bib === === reduce.pl bib === id = cord-292347-d7xq7x5g author = Carter, Linda J. title = Assay Techniques and Test Development for COVID-19 Diagnosis date = 2020-04-30 pages = extension = .txt mime = text/plain words = 3426 sentences = 227 flesch = 51 summary = 375 While RT-PCR-based viral RNA detection has been widely 376 used in diagnosis of COVID-19, it cannot be used to monitor 377 the progress of the disease stages and cannot be applied to 378 broad identification of past infection and immunity. 46,47 410 The determination of SARS-CoV-2 exposure relies largely 411 on the detection of either IgM or IgG antibodies that are 412 specific for various viral antigens including, but not exclusively, 413 the spike glycoprotein (S1 and S2 subunits, receptor-binding 414 domain) and nucleocapsid protein. While RT-PCR has been 571 the dominant technique for detection of viral RNA, other 572 nucleic acid assays including isothermal amplification assays, 573 hybridization microarray assays, amplicon-based metagenomics 574 sequencing, and the cutting-edge CRISPR-related technologies 575 are also under development or have resulted in approved 576 tests. cache = ./cache/cord-292347-d7xq7x5g.txt txt = ./txt/cord-292347-d7xq7x5g.txt === reduce.pl bib === id = cord-297880-jlnv90vn author = Stewart, Hazel title = Transcriptional and Translational Landscape of Equine Torovirus date = 2018-08-16 pages = extension = .txt mime = text/plain words = 10291 sentences = 491 flesch = 49 summary = Using the prototype species equine torovirus (EToV), we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyze the relative expression levels of the known torovirus proteins and transcripts, chimeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle), and changes in host transcription and translation as a result of EToV infection. The genomes of members of the order Nidovirales are positive-sense, polycistronic RNAs. One of the hallmarks of this virus order is the utilization of an unusual transcription mechanism to express the genes encoding structural and accessory proteins, which reside downstream of the large replicase open reading frames (ORFs) 1a and 1b (Fig. 1) . RNA sequencing (RNA-seq) confirmed previous reports that EToV utilizes a unique combination of both discontinuous and nondiscontinuous RNA synthesis to generate its repertoire of sgRNAs. Strikingly, we also identified a small proportion of chimeric transcripts spanning from the leader to the body TRS of the N protein gene, indicating that discontinuous and nondiscontinuous mechanisms compete in this location. cache = ./cache/cord-297880-jlnv90vn.txt txt = ./txt/cord-297880-jlnv90vn.txt === reduce.pl bib === id = cord-297579-ohpm5ys0 author = Netzler, Natalie E. title = Norovirus antivirals: Where are we now? date = 2018-12-25 pages = extension = .txt mime = text/plain words = 6471 sentences = 375 flesch = 37 summary = Despite the clinical significance of norovirus infection, antiviral studies have been hindered, because until recently, human norovirus could not be successfully propagated in cell culture. The cross-genotypic activity displayed by Nbs illustrates that these molecules have the potential to overcome the narrow antigenic spectrum typically displayed by conventional mAbs. However, despite these findings, mAb and Nb studies have been based mostly on VLP-binding and structural analysis of that binding (Table 1 ) and thus the effects of such compounds against norovirus in cell culture or in vivo need to be explored further before continued development toward clinical application. Most recently NTZ was shown to potently inhibit FCV replication in cell culture with an EC 50 of 0.6 µM, 189 and the GI norovirus replicon at a clinically relevant concentration (5 μg/mL), 190 which was later shown to result in a broad antiviral response. The viral polymerase inhibitor 2′-C-methylcytidine inhibits Norwalk virus replication and protects against norovirus-induced diarrhea and mortality in a mouse model cache = ./cache/cord-297579-ohpm5ys0.txt txt = ./txt/cord-297579-ohpm5ys0.txt === reduce.pl bib === id = cord-300963-1n1f8mf2 author = Gajendran, Mahesh title = Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date = 2020-10-12 pages = extension = .txt mime = text/plain words = 6681 sentences = 350 flesch = 46 summary = Previous studies based on SARS-CoV-1 showed that the "cytokine storm" was strongly associated with viral sepsis, inflammation-induced lung injury, and acute respiratory distress syndrome (ARDS) [32, 34] . With regard to IBD-specific risk factors, it is speculated that patients on immunosuppressive agents, those with active IBD symptoms, malnutrition, and frequent visits to clinics or hospitals are at greater risk of acquiring SARS-CoV-2 infection [50] . The International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) maintains a registry for reporting COVID-19 in IBD patients called SECURE-IBD registry. Hence, all the societies have recommended that patients continue their IBD medications to sustain remission, because the risk of disease flare-up outweighs the chance of contracting SARS-CoV-2 infection. The management strategy will depend on multiple factors, such as the patient's age, the severity of the COVID-19 infection, the clinical status of the IBD, and the presence of other comorbid conditions. cache = ./cache/cord-300963-1n1f8mf2.txt txt = ./txt/cord-300963-1n1f8mf2.txt === reduce.pl bib === id = cord-298078-uqrwq5qk author = Kwak, Hoyun title = Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date = 2011-08-30 pages = extension = .txt mime = text/plain words = 5346 sentences = 318 flesch = 56 summary = The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs. Ribosomal frameshifing is a recoding process of translation where a specific messenger RNA (mRNA)-mediated signal directs a ribosome to shift its reading frame and to continue in the new frame. To search for cellular proteins that directly interacted with IBV pseudoknot RNA, a RNA pull down assay was performed in the presence of cell extracts (Figure 2A ). Through the RNA-immunoprecipitation assay, we showed that ANXA2 specifically interacted with wild-type IBV pseudoknot RNA but not with mutant IBV RNA in LNCaP and HEK293T cells ( Figure 3C and 3D). To test how ANXA2 regulates the frameshifting efficiency of IBV pseudoknot RNA, we first overexpressed ANXA2 protein in the presence of the reporters and measured the luciferase activities. cache = ./cache/cord-298078-uqrwq5qk.txt txt = ./txt/cord-298078-uqrwq5qk.txt === reduce.pl bib === id = cord-298938-xemarhlv author = Goswami, Biswendu B. title = Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase date = 2004-04-07 pages = extension = .txt mime = text/plain words = 7455 sentences = 369 flesch = 51 summary = title: Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase We have presented previously evidence that the cytopathogenic 18f strain of hepatitis A virus (HAV) induced degradation of ribosomal RNA (rRNA) in infected cells [Arch. Based on the pattern of rRNA degradation in intact ribosomes, we suggested that the 18f virus activates the interferon (IFN) controlled 2 -5 oligoadenylic acid-dependent RNase L pathway (for recent reviews, see Stark et al., 1998; Barber, 2001; Sen, 2001) . First, the level of IFN, 2 -5 OAS and RNase L mRNAs were investigated by RT-PCR to determine if any of these RNAs were induced following virus infection (Fig. 8) . RT-PCR amplification of selected cellular and viral mRNAs. Two microgram of RNA isolated from virus infected, IFN-␤, or dsRNA treated cells were reverse transcribed in a volume of 20 l using oligo(dT) 15 as primer as described in Section 2. cache = ./cache/cord-298938-xemarhlv.txt txt = ./txt/cord-298938-xemarhlv.txt === reduce.pl bib === === reduce.pl bib === id = cord-301233-nenw0f81 author = Naydenova, Katerina title = Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date = 2020-10-21 pages = extension = .txt mime = text/plain words = 4059 sentences = 217 flesch = 51 summary = Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Here we report the structure of the SARS-CoV-2 RdRp, comprising subunits nsp7, nsp8 and nsp12, in complex with template:primer double-stranded RNA and favipiravir ribonucleoside triphosphate (favipiravir-RTP), determined by cryoEM at 2.5Å resolution. In this study, we determined the cryoEM structure of favipiravir-RTP at the catalytic site of the SARS-CoV-2 RdRp, in complex with template:primer dsRNA, and investigated the influence of this nucleotide analogue inhibitor on RNA synthesis in vitro. cache = ./cache/cord-301233-nenw0f81.txt txt = ./txt/cord-301233-nenw0f81.txt === reduce.pl bib === id = cord-298905-c2uuvfm5 author = Horzinek, M. C. title = Molecular pathogenesis of virus infections date = 1987 pages = extension = .txt mime = text/plain words = 3888 sentences = 193 flesch = 40 summary = Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organor animal species-spectrum) can dramatically change. Parainfluenzaviruses, for example, attach to neuraminic acid-containing receptors; since glycolipids and glycoproteins containing neuraminic acid abound in vertebrate cell membranes the adsorption/penetration process lacks the specificity required to explain the restrictions in host range and tissue tropism of paramyxoviruses 29. Also in influenza virus infection cap structures are essential: these are cannibalized from host cell nuclear RNA precursor molecules and used as primers for viral RNA replication and synthesis 28. Autoimmune phenomena involving both the humoral and cellular limbs of the immune response have been identified in neurological conditions following infections with e.g. canine distemper virus3; invasion of brain tissue is supposed to cause changes in the molecular constitution of myelin and membrane components, making them recognizable as 'nonself'. cache = ./cache/cord-298905-c2uuvfm5.txt txt = ./txt/cord-298905-c2uuvfm5.txt === reduce.pl bib === id = cord-297039-vfuem6bk author = Beltrán-García, Jesús title = Circular RNAs in Sepsis: Biogenesis, Function, and Clinical Significance date = 2020-06-25 pages = extension = .txt mime = text/plain words = 7502 sentences = 468 flesch = 46 summary = Recent findings propose that circular RNAs (circRNAs) may play a prominent role in regulating the patients' immune system against different pathogens, including bacteria and viruses. Due to the role that circRNAs play in the modulation of different cytokines and immune proteins [62, 63] , altered states of alternative splicing in sepsis may alter the expression of circRNAs, which could partially explain the changes in the immune response of septic patients. However, circRNAs may play a key role in sepsis because of their ability to modulate different molecular mechanisms [10] , including inflammation [83] and immune response [62] , and to control multiple biological processes in metabolic organs (i.e., liver, pancreas [84] ) ( Figure 3 and Table 1 ). Interestingly, circRNAs may function as "molecular sponges", by controlling the expression of different types of non-coding RNAs, such as miRNAS, involved in regulating different processes in sepsis [105] [106] [107] [108] . cache = ./cache/cord-297039-vfuem6bk.txt txt = ./txt/cord-297039-vfuem6bk.txt === reduce.pl bib === id = cord-297760-uzzuoy9v author = Naito, Yuki title = siVirus: web-based antiviral siRNA design software for highly divergent viral sequences date = 2006-07-01 pages = extension = .txt mime = text/plain words = 1142 sentences = 80 flesch = 59 summary = title: siVirus: web-based antiviral siRNA design software for highly divergent viral sequences siVirus () is a web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi). siVirus searches for functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. siVirus will be a useful tool for designing optimal siRNAs targeting highly divergent pathogens, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), influenza virus and SARS coronavirus, all of which pose enormous threats to global human health. Consequently, only a limited fraction of 21mers is suitable for use as antiviral siRNAs. In this study, we developed a novel web-based online software system, siVirus, which provides functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference cache = ./cache/cord-297760-uzzuoy9v.txt txt = ./txt/cord-297760-uzzuoy9v.txt === reduce.pl bib === id = cord-296977-yzhsdz9c author = Soares, R. R. G. title = Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date = 2020-11-06 pages = extension = .txt mime = text/plain words = 6533 sentences = 391 flesch = 55 summary = ; https://doi.org/10.1101/2020.11.04.20225888 doi: medRxiv preprint imaging camera and SYBR Green I derived fluorescence transduction by naked eye or smartphone camera 27 ; (3) Microfluidic cartridge combining immune-capture, lysis and LAMP to detect viable bacteria using a reader platform comprising two light sources for fluorometric and/or turbidimetric analysis resorting to a smartphone camera 30 ; (4) a hermetic container providing power-free chemical-based heating for LAMP amplification followed by detection using a smartphone flashlight and camera for fluorometric detection 32 ; (5) Centrifugal platform combining silica-based DNA extraction and integrated LFA strips to multiplex the detection of multiple LAMP products using anti-DIG antibodies and colorimetric detection 32 ; (6) Centrifugal platform with automated bead-beating lysis followed by direct RT-LAMP by continuous measurement of fluorescence with UVC illumination and a standard camera 22 ; and (7) Centrifugal platform incorporating non-contact heating of the disc and colorimetric detection of LAMP products using a white LED for illumination and filtered photodiodes for signal acquisition 24 . cache = ./cache/cord-296977-yzhsdz9c.txt txt = ./txt/cord-296977-yzhsdz9c.txt === reduce.pl bib === id = cord-297776-k38jssr0 author = Volk, Aaron title = Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages date = 2020-05-18 pages = extension = .txt mime = text/plain words = 5843 sentences = 293 flesch = 42 summary = gene expression, we report significant transcriptional upregulation of multiple genes associated with activation of ER sensors IRE1, ATF6, and PERK, such as Edem1, Hspa5 (encoding BiP protein), and Ddit3 (encoding CHOP), in response to virus replication, with the most robust response detected in cells infected with the wild-type or DUBmut virus infection (Fig. 5B, C, and D) . Overall, these differential gene expression analyses in macrophages reveal similar host responses to the wild-type and DUBmut viruses that include activation of UPR pathways and proinflammatory genes, whereas a distinct transcriptional profile during infection with the EndoUmut virus is predominately defined by a focused, robust antiviral response. The results presented here, and from studies of the MERS-CoV dORF3-5 mutant virus (26) Upon infection of a BMDM with EndoUmut, host double-stranded RNA (dsRNA) sensors (including MDA5, PKR, and OAS) are activated, resulting in robust transcription of type I IFN genes and rapid induction of apoptosis, the latter of which precludes the development of a potent inflammatory response. cache = ./cache/cord-297776-k38jssr0.txt txt = ./txt/cord-297776-k38jssr0.txt === reduce.pl bib === id = cord-298820-nogoqyxl author = Zhang, Qi title = Transcriptome altered by latent human cytomegalovirus infection on THP-1 cells using RNA-seq date = 2016-12-05 pages = extension = .txt mime = text/plain words = 4670 sentences = 261 flesch = 45 summary = Here, we profiled the expression of mRNAs and long noncoding RNAs (lncRNAs) in THP-1 cells using the emerging RNA-seq to investigate the transcriptional changes during HCMV latent infection. These studies identified a subset of differently expressed genes, which are involved in a variety of biological functions including innate immunity response, inflammation pathway, cell cycle regulation, cellular metabolism and cell adhesion, during lytic HCMV infection. The present study adopted RNA-seq to identify global changes of mRNAs and lncRNAs in host cell during HCMV experimental latent infection of THP-1 cells, in an attempt to derive insights into the mechanism underlying alterations in response to infection. In this study, we profiled the expression of mRNAs and lncRNAs in host cell using the emerging RNA-seq to investigate the transcriptional changes in HCMV latent infection. cache = ./cache/cord-298820-nogoqyxl.txt txt = ./txt/cord-298820-nogoqyxl.txt === reduce.pl bib === id = cord-298779-0mjizsoo author = Narendrula, Rashmi title = RNA disruption is associated with response to multiple classes of chemotherapy drugs in tumor cell lines date = 2016-02-24 pages = extension = .txt mime = text/plain words = 7172 sentences = 364 flesch = 49 summary = The abnormal RNA disruption bands that occur upon chemotherapy drug exposure are smaller in molecular weight than the 28S and/or 18S rRNAs. To determine whether the abnormal bands originate from the 28S and/or 18S rRNAs, Northern blotting experiments were performed on total RNA prepared from A2780 cells after incubation in the absence or presence of docetaxel for up to 48 h (Fig. 4) . Previous studies have shown that a variety of apoptosisinducing agents with distinct mechanisms of action (glucocorticoids, okadaic acid, tumor necrosis factor (TNF), dexamethasone, a calcium ionophore and a tricothecene mycotoxin) were able to induce an ordered, apoptosis-associated rRNA degradation in several different cell types, including plant cells and the unicellular organism yeast [11-13, 15-17, 24] . However, this study is the first to report the ability of structurally distinct cytotoxic chemotherapy agents with different mechanisms of action to induce the formation of high molecular weight rRNA degradation fragments (Figs. cache = ./cache/cord-298779-0mjizsoo.txt txt = ./txt/cord-298779-0mjizsoo.txt === reduce.pl bib === id = cord-298281-wkje5jyt author = Chan, Vinson Wai-Shun title = A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date = 2020-05-27 pages = extension = .txt mime = text/plain words = 3492 sentences = 271 flesch = 54 summary = Primary outcomes were the urological manifestations of COVID-19, and SARS-CoV-2 viral RNA detection in urine and stool samples. Primary outcomes of our study included urological manifestations of COVID-19, detection rates of SARS-CoV-2 viral RNA in urine and stool samples, and special considerations in urological conditions. For the urological manifestations and viral RNA detection rates, data were pool analysed using MetaXL and Microsoft Excel when there are two or more studies with at least four patients reporting the same outcome under the same definition. There were a total of 11 studies that reported the number of patients who had their urine tested for SARS-CoV-2 viral RNA. Our meta-analysis included 12 studies that reported the number of patients with stools tested for SARS-CoV-2 viral RNA. Our study showed that 5.74% of the COVID-19 patients had positive viral RNA in urine samples. cache = ./cache/cord-298281-wkje5jyt.txt txt = ./txt/cord-298281-wkje5jyt.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-301904-mjfbvl5n author = Schultz-Cherry, S. title = Astroviruses date = 2014-11-28 pages = extension = .txt mime = text/plain words = 5493 sentences = 270 flesch = 39 summary = Astrovirus as a cause of hospital-acquired viral diarrhea in young children is second only to rotavirus and norovirus, occurring at rates of 4.5-6%, and, in some studies, surpasses rotavirus in rates of nosocomial infections. Recent studies reported that an HAstV-VA1-like strain was detected in a patient with new-onset celiac disease and associated with extra-intestinal dissemination (including neural tissue) in immunocompromised children. Given the susceptibility of different cell lines for HAstV infection (depending on the serotype and genotype) it is possible that astroviruses use a variety of attachment proteins or receptors including carbohydrate moieties. The immunological response to astrovirus infection is poorly defined; however, observations in humans and animal models suggest that both the adaptive and innate responses play important roles in controlling and eliminating the virus. While astrovirus antibodies protected individuals from symptoms associated with infection, virus was identified in the feces, suggesting that such antibodies do not necessarily prevent viral replication. cache = ./cache/cord-301904-mjfbvl5n.txt txt = ./txt/cord-301904-mjfbvl5n.txt === reduce.pl bib === id = cord-301115-sedfbjlw author = Han, Mingfeng title = Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date = 2020-08-28 pages = extension = .txt mime = text/plain words = 4577 sentences = 255 flesch = 53 summary = title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity The results of our analysis demonstrated that the initial SARS-CoV-2 RNA loads varied in patients, but were comparable in different patient groups stratified by age, gender, comorbidities and disease severity. We compared the measured SARS-CoV-2 RNA levels in sputum specimens from COVID-19 patients at admission among groups divided according to age, sex, underlying diseases and disease severity (Fig. 2a) . a, b The measured SARS-CoV-2 RNAs levels in sputum (a) and throat swab (b) specimens from COVID-19 patients at admission were compared according to the age, sex, comorbidity, and the disease severity. In this study, we analyzed the clinical features including SARS-CoV-2 RNA load and immunological characteristics of peripheral blood in a patient cohort with COVID-19 from Anhui Province, China. cache = ./cache/cord-301115-sedfbjlw.txt txt = ./txt/cord-301115-sedfbjlw.txt === reduce.pl bib === id = cord-294260-g410mavp author = Sztuba-Solińska, Joanna title = Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle date = 2011-04-10 pages = extension = .txt mime = text/plain words = 9531 sentences = 506 flesch = 54 summary = Arrow, RNA3 start site at nt 2721 (Lindenbach et al., 2002) ; (D) Schematic of the RCNMV genome showing the relative positions of the in trans interacting RNA elements: the loop portion of a stem-loop in RNA2 (termed trans-activator or TA) and a complementary sequence in RNA1 (termed TA binding site or TABS) located just upstream from the initiation site for SG mRNA transcription (Guenther et al., 2004) ; (E) Representation of CLSV genome and the proposed AS2 and RS2 interaction during regulation of SG RNA2 synthesis (Xu and White, 2008) ; (F) Overview of the BYDV genome and the in cisinteraction between genomic 5′-UTR stem-loop (BCL) and the genomic 3′-BTE, and the in trans interaction between the genomic 3′ BTE and the 5′ UTR of SG RNA1 . cache = ./cache/cord-294260-g410mavp.txt txt = ./txt/cord-294260-g410mavp.txt === reduce.pl bib === id = cord-301285-p83ondy8 author = Kautz, Tiffany F title = Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date = 2018-03-06 pages = extension = .txt mime = text/plain words = 8836 sentences = 472 flesch = 53 summary = To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Due to the error-prone nature of the RNA-dependent RNApolymerase (RdRp), RNA virus replication is characterized by a high mutation rate that results in increased genetic diversity of progeny viruses (Domingo et al. When compared with unpassaged, wild-type (wt) viruses, fidelity mutants have similar growth kinetics in vitro, but are attenuated in vivo due to the alteration of diversity produced during replication, which hampers the ability of the virus to overcome bottlenecks in the host (Pfeiffer and Kirkegaard 2005; Vignuzzi et al. The 4x mutant, while exhibiting phenotypic similarities with other altered fidelity mutants, had no significant difference in virus diversity compared with the TC-83 parent after one cell culture passage. cache = ./cache/cord-301285-p83ondy8.txt txt = ./txt/cord-301285-p83ondy8.txt === reduce.pl bib === id = cord-302425-aaxvlktp author = Cortey, Martí title = High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date = 2019-12-05 pages = extension = .txt mime = text/plain words = 4998 sentences = 248 flesch = 52 summary = In contrast, other RNA viruses including Kobuvirus, Astrovirus, Sapovirus, Sapelovirus, Teschovirus, and Torovirus, have been detected in pig faeces but its role as causative agents of neonatal diarrhoea has not so far been fully elucidated [10] [11] [12] [13] [14] . The results reported among the 47 diarrhoeic samples analysed include representatives of 12 virus species corresponding to 8 genera of RNA viruses (Additional file 1): Kobuvirus, Rotavirus (RVA, RVB and RVC), Sapovirus (SAV), Mamastrovirus (Porcine Astrovirus types 3 -AstV3 -, 4 -AstV4 -and 5 -AstV5 -), Alphacoronavirus (PEDV), Enterovirus (Enterovirus G, EntVG), Pasivirus (PasiV) and Posavirus (PosaV). Regarding KobuV, our results also agree with an increased prevalence of this agent observed in cases of diarrhoea in suckling piglets worldwide: Brazil [22] , Korea [29] and Vietnam [30] ; despite several (See figure on previous page.) Fig. 5 Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus B. cache = ./cache/cord-302425-aaxvlktp.txt txt = ./txt/cord-302425-aaxvlktp.txt === reduce.pl bib === id = cord-295467-9fnis6ci author = Botella, Leticia title = The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history date = 2014-12-12 pages = extension = .txt mime = text/plain words = 5926 sentences = 330 flesch = 52 summary = title: The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history Phylogenetic analysis based on 46 partial coat protein (CP) cDNA sequences divided the GaRV-MS1 population into two closely related clades, while RNA-dependent RNA polymerase (RdRp) sequences revealed only one clade. (2) to analyse their genetic diversity and population structure; and (3) to assess evolutionary processes, such as recombination and selection, to better understand possible host-virus coevolution. The Spanish isolate of Gremmeniella abietina H1-4 was chosen for determination of the full-length sequence of a putative new strain of GaRV-MS1 (GenBank accession numbers for the CP, RdRp, and the unknown protein III: KJ786411eKJ786413). abietina appears to be composed of a single species (GaRV-MS1) with low genetic variability, which is seemingly stable within the different populations of the fungal host. cache = ./cache/cord-295467-9fnis6ci.txt txt = ./txt/cord-295467-9fnis6ci.txt === reduce.pl bib === id = cord-302355-3se1wp8o author = Chen, Yi-Shiuan title = The conserved stem-loop II structure at the 3' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date = 2018-07-26 pages = extension = .txt mime = text/plain words = 6004 sentences = 292 flesch = 53 summary = Although XRN1 digestion of a 3'-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Furthermore, the minus-strand templates covering the putative promoter region used for an in vitro RdRp assay gave rise to synthetic products, suggesting that the JEV sfRNA could be initially transcribed from the antigenome and may be further trimmed by XRN1 or other unidentified exoribonucleases. Although efficient RNA replication is required for the detection of any flaviviral RNAs despite which mechanism used for the sfRNA formation, our results were clearly different from the observations from WNV that BHK-21 cells transfected with replicon constructs containing various deletions had no effect on the accumulation of sfRNA when compared to the WT [8] . cache = ./cache/cord-302355-3se1wp8o.txt txt = ./txt/cord-302355-3se1wp8o.txt === reduce.pl bib === id = cord-302195-25gjbyi1 author = Al Huraimel, Khalid title = SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date = 2020-07-15 pages = extension = .txt mime = text/plain words = 7089 sentences = 386 flesch = 50 summary = This article aims to examine the latest investigations on SARS-CoV-2 plausible environmental transmission modes, employment of wastewater surveillance for early detection of COVID-19, and elucidating the role of solid waste, water, and atmospheric quality on viral infectivity. There is no conclusive evidence for aerosol or faecal-oral transmission of SARS-CoV-2 despite several researchers considering them as plausible routes that may explain the high infectivity and global spread of COVID-19 (Chen et al., 2020; van Doremalen et al., 2020; Wang et al., 2020a) . From the literature studied, concerns of COVID-19 infection through environmental contact pertain mainly to areas that lack proper sanitation and wastewater treatment, lack adequate solid waste management infrastructure, in areas where raw sewage is discharged directly into natural water bodies, and in cities where air pollution is problematic.  Robust evidence is needed to assess impact of air pollution, solid waste management, and sewage contamination of water bodies on COVID-19 spread and infectivity. cache = ./cache/cord-302195-25gjbyi1.txt txt = ./txt/cord-302195-25gjbyi1.txt === reduce.pl bib === id = cord-302020-ypsh3rjv author = Kim, Dongwan title = The Architecture of SARS-CoV-2 Transcriptome date = 2020-04-23 pages = extension = .txt mime = text/plain words = 6092 sentences = 403 flesch = 57 summary = In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2. (A) Read counts from nanopore direct RNA sequencing of total RNA from Vero cells infected with SARS-CoV-2. We further discovered RNA modification sites and measured the poly(A) tail length of gRNAs and sgRNAs. To delineate the SARS-CoV-2 transcriptome, we first performed DRS runs on a MinION nanopore sequencer with total RNA extracted from Vero cells infected with SARS-CoV-2 (Be-taCoV/Korea/KCDC03/2020). To unambiguously investigate the modifications, we generated negative control RNAs by in vitro transcription of the viral sequences and performed a DRS run on these unmodified controls ( Figure S4A ). cache = ./cache/cord-302020-ypsh3rjv.txt txt = ./txt/cord-302020-ypsh3rjv.txt === reduce.pl bib === id = cord-301997-63160t7f author = Schwer, Beate title = Discontinuous transcription or RNA processing of vaccinia virus late messengers results in a 5′ poly(A) leader date = 1987-07-17 pages = extension = .txt mime = text/plain words = 4743 sentences = 236 flesch = 55 summary = We have shown that RNA transcripts from a translocated 11K and from the authentic 11K and 4b late promoters are extended by approximately 35 nucleotides beyond the "start site" determined by Sl mapping using vaccinia genomic DNA as a probe. We have shown that RNA transcripts from a translocated 11K and from the authentic 11K and 4b late promoters are extended by approximately 35 nucleotides beyond the "start site" determined by Sl mapping using vaccinia genomic DNA as a probe. As a negative control, we have performed primer extension with a dhfr primer and wild-type mRNA that does not contain dhfr sequences ( Figure 1, cDNA-RNA hybrids were incubated in the presence or absence of RNAase A at a final concentration of 10 Kg/ml and the hybrids were cap-selected by immunoprecipitation using a rabbit anti-m7G antiserum as described. After RNAase treatment-cap selection of the cDNA-RNA hybrids, we obtained the same results as for the wild-type translocated promoter-dhfr messengers (data not shown). cache = ./cache/cord-301997-63160t7f.txt txt = ./txt/cord-301997-63160t7f.txt === reduce.pl bib === id = cord-303111-iv4lzpev author = Almazán, Fernando title = Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date = 2014-12-19 pages = extension = .txt mime = text/plain words = 7071 sentences = 314 flesch = 42 summary = Until recently, the study of CoV genetics was broadly restricted to the analysis of temperature-sensitive (ts) mutants Baric, 1992, 1994; Lai and Cavanagh, 1997; Schaad and Baric, 1994; Stalcup et al., 1998) , defective RNA templates which depend on replicase proteins provided in trans by a helper virus (Izeta et al., 1999; Narayanan and Makino, 2001; Repass and Makino, 1998; Williams et al., 1999) , and recombinant viruses generated by targeted recombination (Masters, 1999; Masters and Rottier, 2005 reverse genetic system devised for CoVs at a time when it was not clear whether the construction of full-length infectious cDNA clones would ever be technically feasible. These reverse genetic systems have been established using non-traditional approaches, which are based on the use of targeted recombination, BACs, in vitro ligation of CoV cDNA fragments, and vaccinia virus as a vector for the propagation of CoV genomic cDNAs. The availability of CoV full-length infectious clones and recombinant viruses expressing reporter genes constitute important tools for the study of CoV replication and transcription mechanisms, virus-host interaction and pathogenesis, and also for the rapid and rational development and testing of genetically defined vaccines. cache = ./cache/cord-303111-iv4lzpev.txt txt = ./txt/cord-303111-iv4lzpev.txt === reduce.pl bib === id = cord-301535-eui41zyg author = Chandler-Brown, Devon title = A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date = 2020-04-10 pages = extension = .txt mime = text/plain words = 4143 sentences = 228 flesch = 52 summary = This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Quantitative analysis of the Sanger sequence chromatogram gives qSanger an extremely high sensitivity and specificity for all positive results with a limit of detection of 10-20 genome copy equivalents (GCE), equivalent to gold-standard qPCR methods. To further evaluate the feasibility of a direct VTM, extraction-free method for Sars-CoV-2 detection, we also examined the ability of qSanger to quantify the amount of viral particles in the Seracare positive control specimens (Fig. 3B ). cache = ./cache/cord-301535-eui41zyg.txt txt = ./txt/cord-301535-eui41zyg.txt === reduce.pl bib === id = cord-302316-raf5rlkq author = Brüssow, Harald title = COVID‐19: From pathogenesis models to the first drug trials date = 2020-06-23 pages = extension = .txt mime = text/plain words = 6944 sentences = 350 flesch = 44 summary = US researchers studied the viral and cellular transcriptional response upon infection of cell cultures and in animal models with different respiratory viruses including influenza A virus and SARS-CoV-2. A French study randomizing 181 COVID-19 patients with pneumonia on hydroxychloroquine or placebo, observed, however, no significant effect of treatment on transfer to ICU, mortality, or in the prevention of development of acute respiratory distress syndrome (Mah evas et al., 2020). A total of 86 COVID-19 cases of patients from China with mild/moderate disease were randomized on the antiviral lopinavir (an inhibitor of HIV protease combined with ritonavir, which prolongs the presence of drugs in the body) or the antiviral arbidol (an influenza virus fusion inhibitor only registered in Russia) or in a control group in a 2:2:1 ratio. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial cache = ./cache/cord-302316-raf5rlkq.txt txt = ./txt/cord-302316-raf5rlkq.txt === reduce.pl bib === id = cord-302085-xyru2q9o author = Shepard, Samuel S. title = Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler date = 2016-09-05 pages = extension = .txt mime = text/plain words = 10341 sentences = 540 flesch = 50 summary = IRMA provides segment level read sorting based on LABEL, a sequence classification tool ideal for segmented genomes [11] ; iteratively gathers reads and iteratively edits the reference templates to account for high population diversity and mutational rates; and provides redesigned variant calling (heuristics as well as statistical tests) and phasing to allow for the analysis of diverse viral sub-populations. We solve these referenced-based assembly complications by using iterative refinement-moving the reference template closer to the reads-to obtain quality assemblies with increased sensitivity to distant and novel reads BLAT* or LABEL match sort into segments rough align chimeric low quality high quality templates removed module consensuses [1] de-multiplexed sample [1] [2] [3] [4] [5] READ GATHERING: do steps [3] to [5] optimize assembly [6] insertion, deletion, substitution merge reads+ [7] call variants [8] phase variants [9] Perl scripts, samtools, R Steps in (b) are also labeled under the steps of (a) where they correspond genetic variants. cache = ./cache/cord-302085-xyru2q9o.txt txt = ./txt/cord-302085-xyru2q9o.txt === reduce.pl bib === id = cord-303265-v6ci69n0 author = Domingo, Esteban title = Introduction to virus origins and their role in biological evolution date = 2019-11-08 pages = extension = .txt mime = text/plain words = 15685 sentences = 764 flesch = 42 summary = Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution). cache = ./cache/cord-303265-v6ci69n0.txt txt = ./txt/cord-303265-v6ci69n0.txt === reduce.pl bib === id = cord-302368-uhhtvdif author = Longhini, Andrew P. title = Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations date = 2016-04-07 pages = extension = .txt mime = text/plain words = 6542 sentences = 323 flesch = 49 summary = Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Additionally, we show that the measurements of relaxation parameters using CPMG, R 1 , and CEST are possible for both small and large RNAs. Furthermore, we demonstrate substantial improvements in signalto-noise and line width for relaxation optimized spectroscopy (TROSY) experiments compared to the traditional heteronuclear single quantum coherence (HSQC) exNucleic Acids Research, 2016, Vol. 44, No. 6 e52 periments for isolated two-spin systems approximated by our purine and pyrimidine labeling schemes (30) (31) (66) (67) . Thus, RNAs synthesized with our selective site-specifically labeled NTPs should benefit from TROSY based NMR experiments that reduce the problems of crowding, fast signal decay, low resolution, and decreased S/N ratios (12, 34, 31, (66) (67) (80) (81) . cache = ./cache/cord-302368-uhhtvdif.txt txt = ./txt/cord-302368-uhhtvdif.txt === reduce.pl bib === id = cord-302980-2jlz4c58 author = Crucière, C. title = Sequence and analysis of bovine enteritic coronavirus (F15) genome I.—Sequence of the gene coding for the nucleocapsid protein; analysis of the predicted protein date = 1988-03-31 pages = extension = .txt mime = text/plain words = 3914 sentences = 386 flesch = 70 summary = Summary Sequences encoding the N protein of the bovine enteritic coronavirus-F15 strain (BECV-F15) have been cloned in PBR322 plasmid using cDNA produced by priming with oligo-dT on purified viral genomic RNA. The 3′-non-coding end of the gene has an 8-nucleotide sequence in common with the homologous genome areas of MHV, TGE and IBV viruses. The location of the insert along the viral genome was determined by Northern blot analysis: full length or purified products of insert restriction cleavage were hybridized with poly(A) § RNA extracted from infected or non-infected cells. We have determined, by cDNA cloning of BECV-F15 genomic RNA using an oligo-dT primer, a sequence of 1,710 nucleotides. For every coronavirus so far studied, the gene coding for the N protein is located at the 3'-end of the viral genome. Recently [11] it was described for the US Mebus strain of the related bovine corona virus (BCV), that the N protein gene was at the 3'-end of the viral genome. cache = ./cache/cord-302980-2jlz4c58.txt txt = ./txt/cord-302980-2jlz4c58.txt === reduce.pl bib === id = cord-303153-z7bdiuvx author = Ulasli, Mustafa title = Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus date = 2010-01-20 pages = extension = .txt mime = text/plain words = 8709 sentences = 521 flesch = 59 summary = This approach has allowed us to establish that MHV induces the formation of six membranous rearrangements in the following order: DMVs, CMs, virions, LVCVs, TBs and CMSs. Importantly, we were able to show that most membrane rearrangements (LVCVs, TBs, CMSs and possibly CMs) observed in addition to the key structures in the infection (DMVs and virions) actually appear to be the consequence of a massive synthesis of viral proteins. In order to be able to correlate our EM and IEM analyses with the progression of a CoV infection inside the host cells, we first measured important known parameters that reflect the CoV life cycle: viral RNA replication/transcription, viral protein synthesis and secretion of progeny virus. In the centre of the DMV clusters, we frequently observed a small network of membranes with a diameter varying from 200 to 600 nm, which have recently been described in SARS-CoV-infected cells and called CMs [ Fig. 2A and B, arrowheads; (Knoops et al., 2008) . cache = ./cache/cord-303153-z7bdiuvx.txt txt = ./txt/cord-303153-z7bdiuvx.txt === reduce.pl bib === id = cord-304306-rxjahqwh author = Vlachakis, Dimitrios title = Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date = 2020-10-08 pages = extension = .txt mime = text/plain words = 8517 sentences = 459 flesch = 48 summary = The currently available antiviral option for hospitalized patients is remdesivir, which may inhibit the replication process by targeting the RdRp. Previously proposed treatments for hospitalized patients included hydroxychloroquine, which thought to disrupt virus endocytosis, and lopinavir/ritonavir, which thought to inhibit SARs-CoV-2 main protease (Astuti and Ysrafil, 2020; Magro, 2020) . Silibilin is predicted to have a dual activity against SARS-CoV-2 infection; silibilin can potentially reduce viral replication activity by targeting NSP12 as a remdesivir-like inhibitor, and modulate inflammatory responses by direct inhibition of STAT3 (BoschBarrera et al., 2020) . A recombinant form of the human ACE2 protein was synthesized as a therapeutic treatment for COVID-19, functioning as a decoy for SARS-CoV-2 and essentially preventing the virus from binding to the cell surface ACE2 (Schuster et al., 2010) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response cache = ./cache/cord-304306-rxjahqwh.txt txt = ./txt/cord-304306-rxjahqwh.txt === reduce.pl bib === id = cord-302409-40ktyt5q author = Wang, Jie title = SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date = 2020-04-18 pages = extension = .txt mime = text/plain words = 2771 sentences = 166 flesch = 51 summary = OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. cache = ./cache/cord-302409-40ktyt5q.txt txt = ./txt/cord-302409-40ktyt5q.txt === reduce.pl bib === id = cord-301362-f3lp10lm author = Delgui, Laura R. title = A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses' Replicases date = 2017-01-20 pages = extension = .txt mime = text/plain words = 7007 sentences = 343 flesch = 42 summary = Recognition of viral double-strand RNA (dsRNA) molecules by intracellular Toll-like receptors (TLRs) or retinoic acid inducible gene I-like receptors (RLRs) is a central event which entails the early steps of the immune response elicited during viral infections. Despite several differences among host range, viral structure, genome organization or membrane-donor organelles from the cell, these analyses revealed that +sRNA viruses are able to induce two types of membranous modifications as replicative niches: invaginated vesicles or spherules or a double membrane vesicle type. Endogenous RNAs forming secondary double-stranded structures that are released after necrosis and tissue damage after viral infection represent another source of dsRNA molecules reaching the endosomes, inducing host-derived dsRNA-mediated inflammatory responses through TLR-3 recognition (Kawai and Akira, 2010) . Other +sRNA viruses such as the enterovirus Coxsackievirus (Kemball et al., 2010) , Hepatitis C virus (Flaviviridae family) (Sir et al., 2012) , or Coronavirus such as MVH (Reggiori et al., 2010) also usurp the autophagy pathway and induce remarkably alterations in intracellular membranous components to harbor the sites for viral RNA replication. cache = ./cache/cord-301362-f3lp10lm.txt txt = ./txt/cord-301362-f3lp10lm.txt === reduce.pl bib === id = cord-302047-vv5gpldi author = Willemsen, Anouk title = On the stability of sequences inserted into viral genomes date = 2019-11-14 pages = extension = .txt mime = text/plain words = 12557 sentences = 598 flesch = 43 summary = Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Viruses genera covered in relevant studies Conclusions of this review All viruses • Inserted sequences are often unstable and rapidly lost upon passaging of an engineered virus • The position at which a sequence is integrated in the genome can be important for stability • Sequence stability is not an intrinsic property of genomes because demographic parameters, such as population size and bottleneck size, can have important effects on sequence stability • The multiplicity of cellular infection affects sequence stability, and can in some cases directly affect whether there is selection for deletion variants • Deletions are not the only class of mutations that can reduce the cost of inserted sequences, although they are the most common I: dsDNA cache = ./cache/cord-302047-vv5gpldi.txt txt = ./txt/cord-302047-vv5gpldi.txt === reduce.pl bib === id = cord-303408-coesfldm author = Konstantinova, Pavlina title = Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome date = 2007-03-01 pages = extension = .txt mime = text/plain words = 4886 sentences = 277 flesch = 53 summary = BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) can be inhibited by means of RNA silencing or interference (RNAi) using synthetic short interfering RNAs (siRNAs) or gene constructs encoding short hairpin RNAs (shRNAs) or long hairpin RNAs (lhRNAs). Although these escape variants lost the ability to trans-inhibit HIV-1, they effectively outgrew the wild-type virus in competition experiments in SupT1 cells. In the current study, we constructed the HIV-lhNef variant, which contains a 300 bp extended hairpin structure at the 3' genome position of the Nef gene of the otherwise wild-type HIV-1. HEK293T cells were transfected with the wild type HIV-1 construct or HIV-lhNef. We measured CA-p24 in the culture supernatant as a measure of virus production 2 days post-transfection. Compared to the effective HIV-lhNef inhibitor, all AS escape variants had lost the ability to actively inhibit wild-type virus production (Fig. 4B ). cache = ./cache/cord-303408-coesfldm.txt txt = ./txt/cord-303408-coesfldm.txt === reduce.pl bib === id = cord-304356-jyp9gjh9 author = Grant, Rogan A. title = Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date = 2020-08-05 pages = extension = .txt mime = text/plain words = 7453 sentences = 427 flesch = 44 summary = We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. b. Sankey diagram illustrating relationship between number of BAL samples from participants with COVID-19, other viral pneumonia, non-viral pneumonia (other pneumonia) and non-pneumonia controls 1) enrolled in the SCRIPT study (534 samples), 2) analyzed via flow cytometry (344 samples), 3) bulk RNA-seq on flow-sorted alveolar macrophages (243 samples) and 4) single-cell RNA-seq (6 samples). To define the immune cell profile over the course of severe SARS-CoV-2-induced pneumonia, we analyzed 116 samples from 61 patients with confirmed COVID-19 in our cohort. As our analysis of transcriptomic data from alveolar macrophages suggested that SARS-CoV-2 pneumonia is uniquely associated with the activation of pathways induced by interferons, we looked for the expression of type I interferons in our single cell dataset. cache = ./cache/cord-304356-jyp9gjh9.txt txt = ./txt/cord-304356-jyp9gjh9.txt === reduce.pl bib === id = cord-304044-i1ikf96b author = Wu, Yue title = Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date = 2007-10-03 pages = extension = .txt mime = text/plain words = 4733 sentences = 304 flesch = 58 summary = Here, we described specific silencing of five white spot syndrome virus (WSSV) genes in Litopenaeus vannamei in vivo with sequence-specific siRNAs. These genes included DNA polymerase (dnapol), ribonucleotide reductase small subunit (rr2), thymidine kinase and thymidylate kinase (tk-tmk), vp24 and vp28. control for interference action of siRNAs. Delivery of the selected sequence-specific siRNAs resulted in increase of survival rate of shrimp infected by WSSV, as compared to the virus injected controls (Fig. 1) . To examine if treatment of specific and mutant siRNAs resulted in a reduced expression level of the selected WSSV genes in shrimp in vivo, semiquantitative and highly sensitive RT-PCR analyses were used to compare the relative silencing effects. The results showed that sequence-specific siRNAs significantly inhibited replication of WSSV relative to that of positive controls and the mutant siRNA injected group at 24 h during experiment (Fig. 3) . Our data strongly indicated that sequence-specific siRNAs significantly inhibited expression of target genes and viral replication to protect shrimp from WSSV. cache = ./cache/cord-304044-i1ikf96b.txt txt = ./txt/cord-304044-i1ikf96b.txt === reduce.pl bib === id = cord-303319-v3iyur78 author = Abe, Takayuki title = Cytosolic DNA‐sensing immune response and viral infection date = 2019-02-26 pages = extension = .txt mime = text/plain words = 7788 sentences = 355 flesch = 38 summary = The findings of these studies have suggested that antiviral responses are mediated by cytosolic or intracellular compartment sensors and their adaptor molecules (e.g., TLR, myeloid differentiation primary response 88, retinoic acid inducible gene‐I, IFN‐β promoter stimulator‐1, cyclic GMP‐AMP synthase and stimulator of IFN genes axis) for the primary sensing of virus‐derived nucleic acids, leading to production of type I IFNs, pro‐inflammatory cytokines and chemokines by the host cells. Thus far, many different immune evasion strategies employed by various viruses have been identified, including: (i) interference with the functions of the host innate immune response via physical interactions with viral antagonistic proteins targeted to sensors, adaptors, related intracellular kinases and transcription factors; (ii) inducing degradation or specific cleavage at the protein level; and (iii) sequestration of signal transduction molecules targeting the PTM systems. cache = ./cache/cord-303319-v3iyur78.txt txt = ./txt/cord-303319-v3iyur78.txt === reduce.pl bib === id = cord-302895-471zei5o author = Deng, Zengqin title = Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase date = 2013-12-24 pages = extension = .txt mime = text/plain words = 8471 sentences = 369 flesch = 50 summary = Biochemical studies using recombinant arterivirus and coronavirus helicases revealed similar enzymatic properties, including nucleic acid-stimulated ATPase and 5 0 -3 0 duplex unwinding activities on both RNA and DNA substrates containing 5 0 single-stranded regions (34, 35) . Amino acid substitutions in ZBD or the adjacent 'spacer' that connects it to the downstream domain can profoundly affect EAV helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replicationnegative virus phenotypes (36, 37) . Thus, our study not only highlights how nidovirus helicase activity depends on the extensive relay of interactions between the ZBD, accessory and HEL1 domains but also provides a framework to propose and explore a role for the enzyme in the posttranscriptional quality control of nidovirus RNAs. Nsp10 of the EAV-Bucyrus isolate (NCBI Reference Sequence NC_002532) is composed of amino acids 2371-2837 of replicase pp1ab, which will throughout this study be referred to as nsp10 residues 1-467. cache = ./cache/cord-302895-471zei5o.txt txt = ./txt/cord-302895-471zei5o.txt === reduce.pl bib === id = cord-304058-i8cywew0 author = Pfefferle, Susanne title = Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date = 2009-08-24 pages = extension = .txt mime = text/plain words = 9548 sentences = 514 flesch = 53 summary = title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. In the context of viral host switching, it is interesting that several SARS-CoV proteins encoded on subgenomic (sg) RNAs seem to be dispensable for virus replication in cultured cells of primate or rodent origin, as well as in rodent models [17] [18] [19] . Both BACs were sequenced, confirming presence of all marker mutations and absence of any further mutations (refer to Influence on apoptosis and type I interferon induction by overexpression of ORF 7a, ORF 7b, and ORF 7b with the Frankfurt-1-specific deletion Interferon beta promoter-specific reporter gene expression (y-axis), shown as the factor of induction as compared to the mock-transfected, non-superinfected control (see below). cache = ./cache/cord-304058-i8cywew0.txt txt = ./txt/cord-304058-i8cywew0.txt === reduce.pl bib === id = cord-303377-lkewcf8a author = Dimke, H. title = Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date = 2020-05-27 pages = extension = .txt mime = text/plain words = 4112 sentences = 205 flesch = 52 summary = Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. A total of 87 clinical sample specimens were chosen based on SARS-CoV-2 status from the Cobas ® 6800 system and used to evaluate the analytical sensitivity, specificity and accuracy of our in-house SARS-CoV-2 RT-qPCR assay after RNA purification using the Maxwell ® RSC 48 and AGPC methods. The AGPC method delivers high analytical sensitivity, specificity and accuracy for SARS-CoV-2 testing To evaluate whether conventional AGPC based extraction of RNA could serve as a viable alternative to automated systems with respect to reliability and accuracy, we isolated RNA using the AGPC method from 87 clinical specimens (oropharyngeal or nasopharyngeal swabs) with known SARS-CoV-2 status (57 positive and 30 negative), and performed a side-by-side comparison with the identical samples extracted on a Maxwell ® RSC 48 instrument. cache = ./cache/cord-303377-lkewcf8a.txt txt = ./txt/cord-303377-lkewcf8a.txt === reduce.pl bib === id = cord-306948-wkisfz1m author = Han, Mingyuan title = Engineering the PRRS virus genome: Updates and perspectives date = 2014-12-05 pages = extension = .txt mime = text/plain words = 9514 sentences = 480 flesch = 45 summary = Serologic marker candidates identified among B-cell linear epitopes of Nsp2 and structural proteins of a North American strain of porcine reproductive and respiratory syndrome virus A full-length cDNA infectious clone of North American type 1 porcine reproductive and respiratory syndrome virus: expression of green fluorescent protein in the Nsp2 region Identification of nonessential regions of the nsp2 replicase protein of porcine reproductive and respiratory syndrome virus strain VR-2332 for replication in cell culture Establishment of a DNA-launched infectious clone for a highly pneumovirulent strain of type 2 porcine reproductive and respiratory syndrome virus: identification and in vitro and in vivo characterization of a large spontaneous deletion in the nsp2 region Recovery of viable porcine reproductive and respiratory syndrome virus from an infectious clone containing a partial deletion within the Nsp2-encoding region Determination of the complete nucleotide sequence of a vaccine strain of porcine reproductive and respiratory syndrome virus and identification of the Nsp2 gene with a unique insertion cache = ./cache/cord-306948-wkisfz1m.txt txt = ./txt/cord-306948-wkisfz1m.txt === reduce.pl bib === id = cord-304553-gbwb7fqi author = Christopher, Mary E. title = Broad-Spectrum Drugs Against Viral Agents date = 2008-09-01 pages = extension = .txt mime = text/plain words = 11323 sentences = 550 flesch = 40 summary = Nonspecific, broad-spectrum immune responses can be induced by double-stranded (ds)RNAs such as poly (ICLC), or oligonucleotides (ODNs) containing unmethylated deocycytidyl-deoxyguanosinyl (CpG) motifs. Poly (ICLC), a dsRNA, and CpG ODNs, molecular mimics for TLR3 and TLR9, respectively, have been reported to non-specifically stimulate the innate immune system and to provide protection against various bacterial and viral pathogens, including influenza. Mice treated with two doses of poly (ICLC), 48 h apart, up to 12 d prior to viral challenge were completely protected from infection, whereas survival rates decreased to 80, 40 and 0%, when pre-treatment was given 14, 16 or 20 d prior to virus challenge, respectively [32] . CpG ODN treatment of splenocytes from senescence-accelerated SAM-P1 strain of mice increased IFN-γ and administration in vivo generated virus-specific cytotoxic T lymphocyte responses, NK cell activation, virus-specific Ig isotype switch from IgG1 to IgG2a, increased viral clearance and survival following influenza viral challenge. Viral infection and Toll-like receptor agonists induce a differential expression of type I and lambda interferons in human plasmacytoid and monocyte-derived dendritic cells cache = ./cache/cord-304553-gbwb7fqi.txt txt = ./txt/cord-304553-gbwb7fqi.txt === reduce.pl bib === id = cord-303189-ktl4jw8v author = Coccia, Eliana M. title = Early IFN type I response: Learning from microbial evasion strategies date = 2015-03-31 pages = extension = .txt mime = text/plain words = 15202 sentences = 738 flesch = 40 summary = Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. In these cells, the HCV-induced miR-21 has been recently reported to be involved in evasion of IFN-I production and stimulation of HCV replication, upon suppression of MyD88 and IRAK1 expression, that is required for the TLR7-mediated sensing of the virus [100] . Amongst RNA viruses that, as HCV, can establish a persistent infection, HIV-1, a lentivirus from the Retroviridae family, represents a paradigm for its ability to prevent or circumvent the innate immune response mediated by IFN-I. Overall, viruses as HCV and HIV-1 have evolved nifty strategies to dampen the host innate response in cells where a productive infection may take place, while they induce infection-independent mechanisms in non-permissive cells to facilitate the viral life cycle and promote a chronic inflammation. cache = ./cache/cord-303189-ktl4jw8v.txt txt = ./txt/cord-303189-ktl4jw8v.txt === reduce.pl bib === id = cord-302830-5psqxxc8 author = Ávila‐Pérez, Ginés title = Ultrastructural characterization of membranous torovirus replication factories date = 2016-07-05 pages = extension = .txt mime = text/plain words = 9037 sentences = 426 flesch = 51 summary = To characterize the torovirus RTCs, we generated specific sera for BEV M pro , Hel and RdRp, three key proteins in the formation and functioning of nidovirus RTCs, that were used in confocal and transmission electron microscopy (TEM) assays to analyse the location of viral components involved in BEV replication. It has been shown that in cells infected with different nidoviruses, virus-induced membrane reorganization produces characteristic DMVs, as well as other membranous structures, which have been related with the viral RNA replication and transcription processes. To investigate whether torovirus DMVs are the sites where replication and transcription occur, we obtained specific sera for the BEV M pro , Hel and RdRp, three key proteins in the formation and functioning of RTCs. All showed a high colocalization with each other and with newly synthesized RNAs. However, the dsRNA, widely used as a marker of RTC in several positive-strand RNA viruses, only showed a partial colocalization with the nsps. cache = ./cache/cord-302830-5psqxxc8.txt txt = ./txt/cord-302830-5psqxxc8.txt === reduce.pl bib === id = cord-305811-987dhnf7 author = Cho, Che-Pei title = Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date = 2013-04-29 pages = extension = .txt mime = text/plain words = 5837 sentences = 301 flesch = 49 summary = Because both 59CC-WT and 13363-13520 constructs share 27 identical nucleotides upstream of their slippery sites, the attenuation activity difference is not likely to be caused by an E-site flanking sequences effect [12, 13] but rather by the disruption of the two potential AU base pairs. We noticed a potential to form four extra base pairs between 59and 39-flanking sequences (GACG and CGUU, respectively) of the 6BPGC hairpin stem (and other deletion mutants) due to the existence of a 59 SalI cloning site (Fig. S1A ). The results (Fig. S1C ) indicate that the two potential base pairs involving E-site sequences are not the main cause of observed attenuation activity in 293T cell cultures. Furthermore, mutating two nucleotides (27 nucleotides upstream of the E site) to disrupt Watson-Crick base pairs in the lower hairpin stem dramatically impairs attenuation activity (Fig. 2) , indicating that attenuation is not caused by primary sequencemediated flanking-sequences effects [12, 13] . cache = ./cache/cord-305811-987dhnf7.txt txt = ./txt/cord-305811-987dhnf7.txt === reduce.pl bib === id = cord-304876-txaoz7oh author = Jordan, Paul C title = Nucleosides for the treatment of respiratory RNA virus infections date = 2018-03-21 pages = extension = .txt mime = text/plain words = 10962 sentences = 654 flesch = 46 summary = 42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein cache = ./cache/cord-304876-txaoz7oh.txt txt = ./txt/cord-304876-txaoz7oh.txt === reduce.pl bib === id = cord-308216-s6rd8p41 author = Duan, Fang title = Small interfering RNA targeting for infected‐cell polypeptide 4 inhibits herpes simplex virus type 1 replication in retinal pigment epithelial cells date = 2011-10-20 pages = extension = .txt mime = text/plain words = 5037 sentences = 317 flesch = 54 summary = title: Small interfering RNA targeting for infected‐cell polypeptide 4 inhibits herpes simplex virus type 1 replication in retinal pigment epithelial cells Background: This study sought to inhibit herpes simplex virus type 1 replication using small interfering RNA which targeting infected‐cell polypeptide 4 genes to mediate transcription of early and late viral genes in herpes simplex virus type 1 lytic (productive) infection in retina epithelial cells. Compared with herpes simplex virus type 1 infection alone or transfection with negative control small interfering RNA, the viral titre and the retina epithelial cell cytopathic effect were significantly decreased in retina epithelial cells transfected with infected‐cell polypeptide 4‐targeting small interfering RNA (50 and 100 nM) (P < 0.05). The inhibition of infected‐cell polypeptide 4‐targeting small interfering RNA on infected‐cell polypeptide 4 protein expression was also verified by Western blot in herpes simplex virus type 1 infected human cornea epithelial cell, human trabecular meshwork cells and Vero cells. cache = ./cache/cord-308216-s6rd8p41.txt txt = ./txt/cord-308216-s6rd8p41.txt === reduce.pl bib === id = cord-308835-999kewdw author = Leibowitz, Julian L. title = The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM date = 1981-10-15 pages = extension = .txt mime = text/plain words = 6447 sentences = 404 flesch = 56 summary = Abstract Seven virus-specific, polyadenylated RNA species have been identified in mouse cells infected with the murine coronaviruses MHV-A59 (A59V) or MHV-JHM (JHMV). MHV-infected 17CL·1 cells were labeled with [32P]orthophosphate in the presence of actinomycin D and the cytoplasmic RNA was extracted and analyzed by agarose gel electrophoresis. The largest intracellular RNA species is identical to RNA isolated from purified virions, as determined by agarose gel electrophoresis and oligonucleotide fingerprint studies of ribonuclease T1 digests. Oligonucleotide fingerprints of the six subgenomic RNAS show that the sequences they contain are present in virion RNA, confirming their virus-specific nature. Identification of MHV-Specific RNA Species A59V, JHMV, and mock-infected cells were labeled with [32P]orthophosphate from 4 to 8 hpi in the presence of actinomycin D. To determine if there is temporal regulation of MHV-specific RNA synthesis, replicate cultures of A59V, JHMV, or mock-infected cells were pulse labeled for 1 hr at hourly intervals and the intracellular RNA was extracted and analyzed by gel electrophoresis. cache = ./cache/cord-308835-999kewdw.txt txt = ./txt/cord-308835-999kewdw.txt === reduce.pl bib === id = cord-305591-ir3wz6nr author = Ji, Danyang title = Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date = 2020-06-01 pages = extension = .txt mime = text/plain words = 5138 sentences = 315 flesch = 55 summary = We have analyzed and identified 25 four contiguous GG runs (G(2)N(x)G(2)N(y)G(2)N(z)G(2)) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). We confirm Gquadruplex structure forming in the top-ranked PQSs by multiple spectroscopic assays in vitro and characterize the crosstalk between G-quadruplexes and viral helicase by microscale thermophoresis (MST) and molecular docking. Our analysis of Gquadruplex-forming sequences in SARS-CoV-2 provides insights into the design of anti-viral treatment by targeting the viral helicase and G-quadruplex structures. Interestingly, PQSs at positions 13385 and 24268 with the highest G-scores indicating high probability to adopt G-quadruplex structures only share high sequence similarity to the bat CoVs (see Supplementary Information S1 available online at https://academic.oup.com/bib and Table 2 ). In comparison, our G-quadruplex search across the genome of SARS-CoV-2 also identified a number of GG PQSs. PQS at position 13385 was confirmed to adopt G-quadruplex structures, which also contains a [GAAAG] sequence in the middle ( Table 1 ). cache = ./cache/cord-305591-ir3wz6nr.txt txt = ./txt/cord-305591-ir3wz6nr.txt === reduce.pl bib === id = cord-305859-vt8vwo3y author = Jung, Kwonil title = Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus date = 2017-04-03 pages = extension = .txt mime = text/plain words = 3232 sentences = 167 flesch = 56 summary = Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. Our study demonstrated that Gn calves orally inoculated with the PDCoV strain OH-FD22 (ICs of cell-culture grown PDCoV from infected Gn pigs) develop an acute infection with persistent fecal PDCoV RNA shedding and PDCoVspecific serum IgG antibody responses, but show no signs of significant intestinal lesions or clinical disease [8] . In our study, there were no detectable fecal viral RNA shedding, virus-specific serum IgG antibody responses, histological lesions, and clinical disease in Gn calves orally inoculated with the PEDV strain PC21A (ICs of wild-type PEDV-infected Gn pigs) [6] . cache = ./cache/cord-305859-vt8vwo3y.txt txt = ./txt/cord-305859-vt8vwo3y.txt === reduce.pl bib === id = cord-304014-k62mtr9j author = Ma, Xuelian title = Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection date = 2019-11-04 pages = extension = .txt mime = text/plain words = 4474 sentences = 325 flesch = 54 summary = Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML). CONCLUSIONS: The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins. The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins. cache = ./cache/cord-304014-k62mtr9j.txt txt = ./txt/cord-304014-k62mtr9j.txt === reduce.pl bib === id = cord-303403-9th2jiq6 author = Qing, Jie title = Cyclophilin A Associates with Enterovirus-71 Virus Capsid and Plays an Essential Role in Viral Infection as an Uncoating Regulator date = 2014-10-02 pages = extension = .txt mime = text/plain words = 10095 sentences = 479 flesch = 56 summary = CypA is also known to play critical roles in the proliferation of a number of viruses, including human immunodeficiency virus type 1 (HIV-1), influenza virus, hepatitis C virus (HCV), vesicular stomatitis virus (VSV), vaccinia virus, severe acute respiratory syndrome coronavirus (SARS-CoV), rotavirus (RV) and human papillomavirus (HPV), by interacting with viral proteins or facilitating IFN-b production [2, 3] . CypA was further revealed to interact with extracellular CD147, which is the main receptor for CypA on the cell membrane of human leukocytes, and this interaction can induce the phosphorylation of HIV-1 matrix protein to regulate the liberation of the reverse transcriptase complex into cytoplasm during an early stage of HIV-1 infection or can function in HIV-1 attachment to host cells [8] . The results we report here demonstrate that the CypA host factor played a crucial role in the uncoating process during the entry step of EV71 infection, and the action site of CypA was mapped to the H-I loop of capsid protein VP1. cache = ./cache/cord-303403-9th2jiq6.txt txt = ./txt/cord-303403-9th2jiq6.txt === reduce.pl bib === id = cord-307860-iqk1yiw4 author = Ionescu, Mihaela Ileana title = An Overview of the Crystallized Structures of the SARS-CoV-2 date = 2020-10-24 pages = extension = .txt mime = text/plain words = 9856 sentences = 668 flesch = 57 summary = Structures retrieved from PDB (August 12, 2020) were analyzed for relevant information on COVID-19 infection, synthesis of new inhibitors, SARS-CoV-2 interaction with host receptors, and the neutralizing antibodies interactions with spike glycoprotein. The first X-ray structure found (PDB ID 6LU7) belongs to the nonstructural protein 5 (3C-like protease) of the SARS-CoV-2 in complex with the Michael acceptor-based inhibitor N3 (PRD_002214). There is a cryo-EM crystal structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex (nsp12/nsp8/nsp7) with the antiviral drug remdesivir (PDB ID 7BV2) [37] . Previous studies on the crystal structures of SARS-CoV S glycoprotein mutants neutralized by 80R-specific antibodies have been considered a hope for the immunotherapeutic Fig. 8 The phylogenetic tree (cladogram) of the CoVs Spike (S) sequences of CoVs with different origin. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites cache = ./cache/cord-307860-iqk1yiw4.txt txt = ./txt/cord-307860-iqk1yiw4.txt === reduce.pl bib === id = cord-303915-14yfs4pa author = Almazán, Fernando title = Engineering a Replication-Competent, Propagation-Defective Middle East Respiratory Syndrome Coronavirus as a Vaccine Candidate date = 2013-09-10 pages = extension = .txt mime = text/plain words = 7132 sentences = 336 flesch = 50 summary = The construction of a full-length infectious cDNA clone of the MERS-CoV genome in a bacterial artificial chromosome is reported here, providing a reverse genetics system to study the molecular biology of the virus and to develop attenuated viruses as vaccine candidates. The mutant viruses presented growth kinetics similar to those of the wild-type virus, indicating that accessory genes were not essential for MERS-CoV replication in cell cultures. Using this clone, recombinant MERS-CoV (rMERS-CoV) deletion mutants were constructed lacking genes nonessential for virus replication. An infectious cDNA clone was assembled as a BAC under the control of the cytomegalovirus (CMV) immediate-early pro-moter, based on the genome sequence of the MERS-CoV-EMC12 strain (GenBank accession number JX869059) (15) . Based on published data showing that the deletion of CoV E protein resulted in either replication-competent, propagation-defective viruses (24) or attenuated viruses (25, 26, 31) , a cDNA clone with the E gene deleted (pBAC-MERS-⌬E) was constructed from pBAC-MERS FL . cache = ./cache/cord-303915-14yfs4pa.txt txt = ./txt/cord-303915-14yfs4pa.txt === reduce.pl bib === id = cord-305290-xnjwv0d7 author = Atkins, John F. title = Ribosome gymnastics—Degree of difficulty 9.5, style 10.0 date = 1990-08-10 pages = extension = .txt mime = text/plain words = 7996 sentences = 417 flesch = 62 summary = A single base change in the mouse mammary tumor virus (MMTV) gag-pro shift site, from the normal A AAA AAC to A AAA AAG, surprisingly leads from ~2% to 50% -1 frameshifting at this sequence (a 25-fold increase); and the lo-fold decrease between A AAA AAG and A AAA AAA affords an interesting glimpse at how the nuances of codon-anticodon interaction can govern the efficiency of this type of shifting. These results should be interpreted with caution, as all the higher eukaryotic frameshifting studies with altered sequences have been done with a reticulocyte lysate cell-free translation system; there are likely to be differences in the number of ribosomes loaded per message, and perhaps in the tRNA balance, from less specialized cells in vivo. cache = ./cache/cord-305290-xnjwv0d7.txt txt = ./txt/cord-305290-xnjwv0d7.txt === reduce.pl bib === id = cord-304873-ppb9k3zu author = Kang, Hunseung title = Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1 date = 1998-04-01 pages = extension = .txt mime = text/plain words = 2497 sentences = 177 flesch = 66 summary = Our S1, V1, and T1 endonuclease mappings, together with UV melting analysis, clearly indicate that this sequence element of the HIV-1 mRNA frameshift site forms a stem-loop structure, not a pseudoknot structure. The enhancer secondary RNA structure, either a stem-loop or a pseudoknot, downstream of the shift site induces pausing of the ribosome and stimulates w x slippage at the shift sequence 4-7 . Here, we determine the secondary structure of the HIV-1 mRNA frameshifting sequence elements including the shift site, the spacer, and the downstream enhancer sequence by using ultraviolet melting and enzymatic mapping analysis. Our results agree well with the mutational studies showing a simple stem-loop structure for the downstream enhancer sequence of the frameshifting region of the HIV-1 mRNA. Nucleotides A24-A27 were cleaved This cleavage pattern, as summarized in Fig. 4 , indicates that in the context of the frameshifting sequence elements of the HIV-1 RNA consisting of the spacer and the enhancer, the enhancer sequence adopts a stem-loop structure separated from the shift site by a spacer sequence. cache = ./cache/cord-304873-ppb9k3zu.txt txt = ./txt/cord-304873-ppb9k3zu.txt === reduce.pl bib === id = cord-310141-2jofy8fo author = Qureshi, Abid title = A review on current status of antiviral siRNA date = 2018-04-15 pages = extension = .txt mime = text/plain words = 3380 sentences = 254 flesch = 42 summary = Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. For example, siRNAs directed against different genes of deadly viruses like human immunodeficiency virus (HIV), 9, 10 influenza virus (INFV), 11, 12 hepatitis B virus (HBV), 13 SARS coronavirus (SARS-CoV), 14, 15 human papillomavirus (HPV), 16 and West Nile virus (WNV) 17 in infected cells displayed encouraging results in inhibiting viral replication. 18, 19 Short interfering RNAs for various human viruses like respiratory syncytial virus (RSV), hepatitis C virus (HCV), HBV, and HIV are also appearing in clinical trials, which further elucidate their importance in inhibiting viral infections. Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice cache = ./cache/cord-310141-2jofy8fo.txt txt = ./txt/cord-310141-2jofy8fo.txt === reduce.pl bib === id = cord-310748-ao29zx1u author = Banner, Lisa R. title = Random nature of coronavirus RNA recombination in the absence of selection pressure date = 1991-11-30 pages = extension = .txt mime = text/plain words = 2839 sentences = 155 flesch = 52 summary = Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. To study RNA recombination in the absence of selection pressure, we developed a polymer-ase chain reaction (PCR) assay using two primers specific for the potential recombinant viruses which have a crossover site between the two primers. Only recombinant RNAs which had a crossover between the two primers and contained A59-specific sequences on the 5'-side and JHM-DL-specific sequences on the 3'-side could be detected by this PCR approach. DNA sequence analysis of 35 cloned PCR products showed that the crossover sites were almost randomly distributed throughout the nearly 1-kb region of the peplomer gene studied ( Fig. 2A) . Analysis of 53 recombinant clones revealed that, similar to the intracellular recombinants, the crossover sites in the viral recombinant RNAs were almost randomly distributed over the 1 -kb region of the peplomer gene (Fig. 2B) . cache = ./cache/cord-310748-ao29zx1u.txt txt = ./txt/cord-310748-ao29zx1u.txt === reduce.pl bib === id = cord-305393-96mrxt8a author = Lai, Yvonne title = Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3 date = 2011-10-10 pages = extension = .txt mime = text/plain words = 9604 sentences = 587 flesch = 60 summary = Recombinant 1b hepatitis C virus polymerase was found to enhance TLR3 signaling in the lung epithelial BEAS-2B cells when added to the media along with either poly(I:C) or viral dsRNAs. The polymerase from the genotype 2a JFH-1 HCV was a poor enhancer of TLR3 signaling until it was mutated to favor a conformation that could bind better to a partially duplexed RNA. These results demonstrate that several viral RNA-binding proteins can enhance the dsRNA-dependent innate immune response initiated by TLR3. Transfection of two plasmids, one containing an interferon stimulated response element (ISRE) promoter-driven firefly luciferase and a second encoding a constitutively expressed Renilla luciferase allow the analysis of TLR3 activation by different RNAs. HEK 293T cells expressing WT TLR3 responded to poly(I:C) (1-2 mg/ml), better than viral dsRNAs (1-2 mg/ml) purified from Reovirus and BPEV (Fig. 1B) . cache = ./cache/cord-305393-96mrxt8a.txt txt = ./txt/cord-305393-96mrxt8a.txt === reduce.pl bib === id = cord-306076-ygfnkgqp author = Fujita, Yu title = RNAi Therapeutic Platforms for Lung Diseases date = 2013-02-06 pages = extension = .txt mime = text/plain words = 8419 sentences = 495 flesch = 43 summary = Although the success in delivering siRNAs intranasally in rodents cannot be completely extrapolated to human use because of the significant differences in lung anatomy [37] , this approach has potential for the clinical application of siRNAs. Phase II clinical trials have been initiated for the treatment of respiratory syncytial virus (RSV) infection, making use of intranasal application of naked chemically modified siRNA molecules that target viral gene products [17, 38] (see Section 3.1.1. The simultaneously inhibition of several genes would also minimize the risk of drug resistance normally encountered with small molecule-based therapies, involving siRNAs and miRNAs. There have already been significant improvements in siRNAs for primary or metastatic lung cancer treatment by targeting oncogenes such as Akt1 [9] , Wilms tumor 1 (WT1) [12] , overexpressed genes such as the insulin-like growth factor receptor 1 (IGF-1R) [77] , NUPR1 [53] and EZH2 [78] . cache = ./cache/cord-306076-ygfnkgqp.txt txt = ./txt/cord-306076-ygfnkgqp.txt === reduce.pl bib === id = cord-307893-mvl0wrsj author = Goulter-Thorsen, R.M. title = Disciplines Associated with Food Safety: Food Virology date = 2014-01-13 pages = extension = .txt mime = text/plain words = 4993 sentences = 249 flesch = 46 summary = Poliovirus was the first enteric virus to be widely recognized, causing foodborne disease outbreaks in the early 1900s associated with the consumption of contaminated raw milk. This method, as well as cultivation methods for the vaccine strain of poliovirus, eventually allowed for the quantification of infective virus plaque forming units and facilitated studies on detection and control of enteric viruses in water and foods, with a particular focus on molluscan shellfish. Although promising, the utility of these molecular amplification methods for virus detection in food and environmental samples was limited by low levels of contamination; high levels of matrix-associated inhibitory substances that interfered with nucleic acid amplification; and the lack of broadly reactive primers and probes for HuNoV. Recent epidemiological data continue to support the fact that viruses, particularly HuNoV, are the most common cause of foodborne disease of known etiology in USA. HEV is a positive-sense single-stranded RNA virus that is transmitted via the fecal-oral route, generally through the consumption of water and sometimes food that has become contaminated with human feces. cache = ./cache/cord-307893-mvl0wrsj.txt txt = ./txt/cord-307893-mvl0wrsj.txt === reduce.pl bib === id = cord-308034-9b219k0v author = Murray, James L. title = A Role for H/ACA and C/D Small Nucleolar RNAs in Viral Replication date = 2014-01-30 pages = extension = .txt mime = text/plain words = 3654 sentences = 218 flesch = 12 summary = We have employed gene-trap insertional mutagenesis to identify candidate genes whose disruption confer phenotypic resistance to lytic infection, in independent studies using 12 distinct viruses and several different cell lines. Expression of nine SNORA/Ds encoded within RCC1 (which also encodes the shorter non-coding SNHG3 gene), or SNHG1 were silenced with siRNAs for 2 days prior to infection with either cowpox virus (CPV), Dengue Fever virus (DFV), influenza A (FLU), human rhinovirus 16 (HRV16), herpes simplex virus 2 (HSV2), or respiratory syncytial virus (RSV). While a previous study showed that RCC1 supports HSV1 replication [21] , we did not observe that silencing RCC1 or the non-coding Small Nucleolar RNA Host Gene 3 (SNHG3) inhibits HSV2 (data not shown), whereas inhibiting expression of the RCC1encoded SNORA73A did. The discovery of these classes of non-coding genes prominently represented in the mutant clones selected in our virus surviving cell lines suggests an importance of SNORAs and SNORDs in facilitating viral replication. cache = ./cache/cord-308034-9b219k0v.txt txt = ./txt/cord-308034-9b219k0v.txt === reduce.pl bib === id = cord-310192-8x37nx4s author = Zhang, Huaqun title = Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date = 2019-04-25 pages = extension = .txt mime = text/plain words = 7235 sentences = 355 flesch = 43 summary = In this review, we will give a broad overview of different methods for structure determination and discuss some recent advancements in both sample preparation and data acquisition that have advanced the study of large RNAs by nuclear magnetic resonance (NMR) spectroscopy. Base-pairing, hydrogen bonding, nucleotide accessibility and other secondary structure-related characteristics, can be obtained by treating RNAs with specific chemical reagents (typically dimethyl sulfate [DMS] and/or one or more SHAPE reagents) and probing for the sites of modification by sequencing (Cordero, Kladwang, VanLang, & Das, 2012; Merino, Wilkinson, Coughlan, & Weeks, 2005; Tian & Das, 2016; Weeks, 2010) . Traditionally, these studies have been applied to relatively small RNAs. The ability to site-specifically incorporate 13 C labels within an RNA ribose and/or base makes NMR spectroscopy a powerful tool for dynamics studies of large RNAs, expanding the types of experiments that can be conducted and simplifying analysis (see data acquisition and analysis advancements below). cache = ./cache/cord-310192-8x37nx4s.txt txt = ./txt/cord-310192-8x37nx4s.txt === reduce.pl bib === id = cord-307934-84zfabti author = Lai, Chao-Kuen title = Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport date = 2014-06-06 pages = extension = .txt mime = text/plain words = 8211 sentences = 465 flesch = 55 summary = Further studies by cofractionation analysis and immunoelectron microscopy of the released particles showed that NS5A-Core complexes, but not NS4B, were present in the low-density fractions, but not in the high-density fractions, of the HCV RNA-containing virions and associated with the internal virion core. Overall, our results suggest that HCV NS5A is associated with the core of the low-density virus particles which exit the cell through a preexisting endosome/exosome pathway and may contribute to HCV natural infection. Both NS5A and Core proteins are found to be closely associated with and co-transported along the microtubules from the perinuclear region of cells via the LDs and endosomes to the plasma membrane. (A) The HCV-infected cells (at day 10 p.i.) were labeled with antibodies specific for Core protein (red) and NS5A (green) (upper row) or NS4B (green) (lower row). cache = ./cache/cord-307934-84zfabti.txt txt = ./txt/cord-307934-84zfabti.txt === reduce.pl bib === id = cord-306535-j26eqmxt author = Robertson, Matthew J. title = Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets date = 2020-08-19 pages = extension = .txt mime = text/plain words = 16758 sentences = 846 flesch = 49 summary = The majority of candidate genes identified in our screen that were testis-specific were already identified by the Human Protein Atlas [9] and/or our reanalysis of (See figure on previous page.) Fig. 1 Summary of the human and mouse RNA-seq samples used in the identification of novel male reproductive tract-specific drug targets. Additional file 14: Fig. S6 shows the complete list of male reproductive tract-specific human genes for which a previously generated mouse model shows male infertility phenotype, as identified in each of the respective cell and/or tissue datasets. Through the integration of hundreds of published and newly acquired human and mouse reproductive and non-reproductive tissue and cell RNA-seq datasets, we have generated a list of novel genes expressed predominantly or exclusively in the male reproductive tract that are worthy of consideration for functional validation in an animal model and potential targeting for a male contraceptive. cache = ./cache/cord-306535-j26eqmxt.txt txt = ./txt/cord-306535-j26eqmxt.txt === reduce.pl bib === id = cord-307354-dkwcheu0 author = Abernathy, Emma title = Emerging roles for RNA degradation in viral replication and antiviral defense date = 2015-05-31 pages = extension = .txt mime = text/plain words = 7160 sentences = 359 flesch = 45 summary = Alpha-herpesviruses such as herpes simplex-1 (HSV-1) express a FEN1-like nuclease termed virion host shutoff protein (vhs) that is directed to mRNAs through interactions with the translation Fig. 1 . Quality control decay pathways such as NMD recognize aberrant mRNAs during translation, including the presence of premature termination codons (PTC), and induce endonucleolytic cleavage, whereupon the fragments are degraded by exonucleases. The RNAi pathway restricts gene expression by processing the long double stranded RNAs frequently generated during viral replication into short interfering RNAs (siR-NAs), which guide endonucleolytic cleavage of complementary target mRNAs. Although mammalian cells possess the RNAi machinery, in most cases RNAi does not appear to play a significant antiviral role, and has instead been supplanted by the protein-based interferon response (Cullen, 2014) . Small interfering RNAs that deplete the cellular translation factor eIF4H impede mRNA degradation by the virion host shutoff protein of herpes simplex virus cache = ./cache/cord-307354-dkwcheu0.txt txt = ./txt/cord-307354-dkwcheu0.txt === reduce.pl bib === id = cord-304283-nv4ret1f author = Hung, Chuan-Fu title = A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells date = 2006-08-04 pages = extension = .txt mime = text/plain words = 7080 sentences = 367 flesch = 45 summary = Since only a readily available short synthetic DNA fragment is needed for constructing this novel reporter-based siRNA validation system, this system not only provides a powerful strategy for screening highly effective siRNAs but also implicates in the use of RNAi for studying novel gene function in mammals. Since only a readily available short synthetic DNA fragment is needed for constructing both the targeting reporter and triggering siRNA expression vectors, this novel system should not only greatly facilitate large-scale lossof-function genetic screens in mammalian cells but also provide the basis for an improved approach to screen and identify the most potent siRNA for the purpose of the therapeutics. As the results shown in Fig. 5A , the siLMP1-2 exhibited no inhibition effects on pEGFP-3UTR-siLMP1-2-induced EGFP and pLuc+-3UTR-siLMP1-2-induced firefly luciferase expression as compared with the two standard positive controls, siEGFP and siLuc, indicating that the selected RNAi targeting sequence siLMP1-2 was inactive and non-functional. cache = ./cache/cord-304283-nv4ret1f.txt txt = ./txt/cord-304283-nv4ret1f.txt === reduce.pl bib === id = cord-304498-ty41xob0 author = Denison, Mark R title = Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date = 2011-03-01 pages = extension = .txt mime = text/plain words = 7332 sentences = 345 flesch = 38 summary = Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. cache = ./cache/cord-304498-ty41xob0.txt txt = ./txt/cord-304498-ty41xob0.txt === reduce.pl bib === id = cord-310086-9e4txeck author = Fu, Wei title = Letter to the Editor: Three cases of re‐detectable positive SARS‐CoV‐2 RNA in recovered COVID‐19 patients with antibodies date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1149 sentences = 86 flesch = 55 summary = Here, we report three confirmed cases of COVID‐19 whose IgM was negative and IgG was positive before the first discharge, while nasopharyngeal swab test of SARS‐CoV‐2 RNA turned positive again during hotel isolation. The SARS-CoV-2 RNA test of all three patients was positive before being admitted to hospital. The results of SARS-CoV-2 RNA test during the two periods of hospitalization were shown in Table 1 . Although no special discomfort was found, all patient's nasopharyngeal swab test of SARS-CoV-2 RNA were positive during the isolation. The detoxification procedure does occur which will cause re-detectable positive SARS-CoV-2 RNA in recovered COVID-19 Accepted Article patients [6] . However, these patients re-detectable positive for SARS-CoV-2 RNA displayed high levels of IgG and negative IgM in the plasma during two hospitalization periods. Results of SARS-CoV-2 RNA and Antibody tests of re-admission patients Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report cache = ./cache/cord-310086-9e4txeck.txt txt = ./txt/cord-310086-9e4txeck.txt === reduce.pl bib === id = cord-312544-vip4jtlv author = Ng, Lisa FP title = Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay date = 2006-03-02 pages = extension = .txt mime = text/plain words = 2142 sentences = 108 flesch = 57 summary = METHODS: A one-step reverse-transcription PCR assay was developed to detect the H5N1 avian influenza A virus. RESULTS: Validation on 145 field specimens from Vietnam and Malaysia showed that the assay was specific without cross reactivity to a number of other infuenza strains as well as human respiratory related pathogens. In this study, we describe the development of a nucleic acid detection test that is rapid, specific and sensitive, thus allowing greatly improved detection of the H5N1 avian influenza A virus. To establish the specificity of the assays for H5N1 subtype detection, we then tested the primers on several known strains of influenza A viruses derived from avian sources (H3N8, H5N3, H7N3 and H9N2). A total of 145 field samples comprising of known and suspect cases from chickens, ducks and muscovies isolated from Vietnam and Malaysia during the 2004 to 2005 outbreak were tested for H5N1 RNA (Table Detection of H5N1 avian influenza A virus by one-step RT-PCR 2). cache = ./cache/cord-312544-vip4jtlv.txt txt = ./txt/cord-312544-vip4jtlv.txt === reduce.pl bib === id = cord-306921-3afgpunj author = Owino, Collins Oduor title = Recent advances on the role of host factors during non-poliovirus enteroviral infections date = 2019-06-19 pages = extension = .txt mime = text/plain words = 11725 sentences = 568 flesch = 39 summary = A small siRNA screen targeting human membrane trafficking genes identified vasolin-containing protein (VCP-p97) as an important protein essential after PV viral replication and it interacts and colocalizes with 2 BC/2C as well as 3AB/3B in poliovirus infected cells [83] . Human host factors-viral protein studies identified nuclear factor; adenosine-uridine (AU)-rich element RNA binding factor 1 (AUF1) is targeted for cleavage by CV-B3 viral 3C protease upon translocation to the cytoplasm for enhanced stability of the IRES dependent viral RNA production [112] , similar antiviral observations were made for poliovirus, coxsackievirus and human rhinovirus [113] . A subsequent study by Mohamud and colleagues demonstrated that SQSTM1 and another host factor calcium binding and coiled-coil domain-containing protein 2/nuclear dot 10 protein 52 (CALCOCO2) regulate CV-B3 virus infection by targeting autophagy receptors; via their interaction with viral protein 1 [177] . cache = ./cache/cord-306921-3afgpunj.txt txt = ./txt/cord-306921-3afgpunj.txt === reduce.pl bib === id = cord-304794-z2kx314h author = Métifiot, Mathieu title = G-quadruplexes in viruses: function and potential therapeutic applications date = 2014-11-10 pages = extension = .txt mime = text/plain words = 9102 sentences = 490 flesch = 47 summary = Conversely, a G-quadruplex or G4 is formed by nucleic acid sequences (DNA or RNA) containing G-tracts or Gblocks (adjacent runs of guanines) and composed of various numbers of guanines. Short RNA templates from the central region of the HIV-1 genome contain G-rich sequences near the central polypurine tract (cPPT) at the 3 end of the pol gene (IN coding sequence); this is a region where one of the two primers used for synthesizing the (−) strand DNA is produced during reverse transcription. In addition, one could imagine alternative therapeutic strategies focused on targeting RNA structures within viral ORFs to interfere with the virus cycle as well as to promote antigen presentation and to stimulate the host immune response. Topology of a DNA G-quadruplex structure formed in the HIV-1 promoter: a potential target for anti-HIV drug development U3 Region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence cache = ./cache/cord-304794-z2kx314h.txt txt = ./txt/cord-304794-z2kx314h.txt === reduce.pl bib === id = cord-310771-tnwfp1je author = Revilla-Fernández, Sandra title = The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date = 2005-02-23 pages = extension = .txt mime = text/plain words = 5933 sentences = 297 flesch = 51 summary = A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. As endogenous control for one-step real-time reverse transcription (RT)-PCR UBE2D2 mRNA was selected. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36). For the development of one-step real-time RT-PCR for four endogenous reference RNAs (HPRT, UBE2D2, PPIA, and HMBS) appropriate target regions were selected and the assay conditions were optimised for amplification efficiency. One-step real-time RT-PCR assays for PRRSV-1 and -2 RNA allowed quantitation with optimal efficiency (Fig. 1a ; standard curves for two additional viremic pigs infected with PRRSV-1 (data not shown)) as achieved for endogenous and Fig. 1 . cache = ./cache/cord-310771-tnwfp1je.txt txt = ./txt/cord-310771-tnwfp1je.txt === reduce.pl bib === id = cord-311982-wkg56xeq author = Dye, Charlotte title = Genomic RNA sequence of feline coronavirus strain FCoV C1Je date = 2007-06-17 pages = extension = .txt mime = text/plain words = 5240 sentences = 250 flesch = 55 summary = Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted 'internal mutation theory' of FIPV pathogenicity. Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted 'internal mutation theory' of FIPV pathogenicity. Furthermore, the structural and accessory gene regions of viral RNA isolated from the liver of the same cat (FCoV C1Li) were sequenced and the data derived from the enteric (jejunum) and non-enteric (liver) sources were compared. Sequence data previously generated for the laboratory strain FCoV, FIPV 79-1146, were used to design primers for conventional reverse transcriptase polymerase chain reaction (RT-PCR) amplification of short lengths (100e500 bases) of the field strain RNA. Analysis of the accessory gene 7 region of the FCoV C1Je genome identifies two ORFs, which have translation products sharing high amino acid identity with proteins 7a and 7b of FIPV 79-1146. cache = ./cache/cord-311982-wkg56xeq.txt txt = ./txt/cord-311982-wkg56xeq.txt === reduce.pl bib === id = cord-304424-048xo7jn author = Greninger, Alexander L. title = A decade of RNA virus metagenomics is (not) enough date = 2018-01-15 pages = extension = .txt mime = text/plain words = 9606 sentences = 495 flesch = 43 summary = That same year 36,789 colony sequences from DNase-treated RNA extracted from viral concentrates of human feces revealed a preponderance of pepper mild mottle virus and other plant viruses, but no new human viruses (Zhang et al., 2005) . While finding a new virus in the environment is not necessarily a problem in either DNA or RNA, the low fidelity of RNA polymerases and the sequence space they are capable of sampling, along with the possibility of recombination, lend themselves to new species and genera that are the trophies of metagenomic viral discovery. While metagenomics delivered on the promise of finding novel human viruses, viral discovery in humans has increasingly become a tragic story of patients interacting with the wrong squirrel or tick on the wrong day and most samples sequenced are frankly negative (Hoffmann et al., 2015; McMullan et al., 2012) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates. cache = ./cache/cord-304424-048xo7jn.txt txt = ./txt/cord-304424-048xo7jn.txt === reduce.pl bib === id = cord-306288-w43wec48 author = Jang, Sungho title = RNA-based dynamic genetic controllers: development strategies and applications date = 2017-11-10 pages = extension = .txt mime = text/plain words = 4613 sentences = 285 flesch = 36 summary = The aptamers and expression platforms were reassembled in a mix-and-match fashion to create chimeric riboswitches that retained their regulatory activities to turn off transcription upon ligand binding, and even combinations using artificial RNA aptamers were successful in regulating gene expression. Engineering of natural RNA-based regulation for dynamic control of gene expression requires detailed knowledge of each mechanism. Aptamers were placed upstream of IRES and several base-pairing sequences were designed to control the formation of critical structures (PK-III) depending on ligand binding (Figure 2b ). RNA molecules that regulate translation (IS10) or transcription (pT181) were combined with aptamers to control the formation of intramolecular structures depending on ligand binding [24] (Figure 2c ). Moreover, simultaneous utilization of high-throughput measurement of activity and next-generation sequencing analysis can not only screen and optimize dynamic RNA controllers, but also provide new design principles from sequence-structure-function relationships [14 ,15] . cache = ./cache/cord-306288-w43wec48.txt txt = ./txt/cord-306288-w43wec48.txt === reduce.pl bib === id = cord-306688-po4p1466 author = Wang, X. title = Brome Mosaic Virus date = 2008-07-30 pages = extension = .txt mime = text/plain words = 4563 sentences = 177 flesch = 41 summary = Among other advances, BMV was used to define the first ribosome binding sites in eukaryotic mRNAs, and to produce the first template-selective eukaryotic viral RNA-dependent RNA polymerase extract, the first infectious transcripts from cloned RNA virus cDNA, the first engineered RNA virus expression vectors expressing foreign genes, the first definition of subgenomic mRNA synthesis pathways and determinants, and the first demonstration of higher eukaryotic viral replication in yeast. In parallel to in vitro systems, cultured plant protoplasts provided a valuable substrate for in vivo replication studies due to their ability to be infected or transfected with nearly 100% efficiency with virions, virion RNAs, or in vitro transcripts from cloned viral cDNAs. For BMV, barley protoplast systems developed and refined by the groups of Okuno and Furusawa, Hall and others in the late 1970s have allowed studies of all aspects of BMV RNA replication, subgenomic RNA synthesis, progeny RNA encapsidation, and the like. cache = ./cache/cord-306688-po4p1466.txt txt = ./txt/cord-306688-po4p1466.txt === reduce.pl bib === id = cord-305336-wxiazglk author = Li, Ji Lian title = Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date = 2014-01-21 pages = extension = .txt mime = text/plain words = 6907 sentences = 319 flesch = 50 summary = In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV. cache = ./cache/cord-305336-wxiazglk.txt txt = ./txt/cord-305336-wxiazglk.txt === reduce.pl bib === id = cord-305737-bnzd7b25 author = Rehwinkel, Jan title = Targeting the viral Achilles’ heel: recognition of 5′-triphosphate RNA in innate anti-viral defence date = 2013-05-23 pages = extension = .txt mime = text/plain words = 4133 sentences = 246 flesch = 55 summary = Targeting the viral Achilles' heel: recognition of 5 0 -triphosphate RNA in innate anti-viral defence Jan Rehwinkel 1 and Caetano Reis e Sousa 2 Some RNA virus genomes bear 5 0 -triphosphates, which can be recognized in the cytoplasm of infected cells by host proteins that mediate anti-viral immunity. Both the innate sensor RIG-I and the interferon-induced IFIT proteins bind to 5 0 -triphosphate viral RNAs. RIG-I signals for induction of interferons during RNA virus infection while IFITs sequester viral RNAs to exert an antiviral effect. Recent work shows that the IFN system targets 5PPP RNAs during both phases: both RIG-I, a virus sensor that induces IFN expression, and IFITs, effector molecules that execute anti-viral activities, can specifically recognize 5PPP RNAs. As such, 5PPP RNAs appear to be Achilles' heel of many RNA viruses in their interaction with the innate immune system (Figure 3a ). cache = ./cache/cord-305737-bnzd7b25.txt txt = ./txt/cord-305737-bnzd7b25.txt === reduce.pl bib === id = cord-305871-w1quh4fx author = Hindawi, Salwa I. title = Inactivation of Middle East respiratory syndrome‐coronavirus in human plasma using amotosalen and ultraviolet A light date = 2017-12-14 pages = extension = .txt mime = text/plain words = 4522 sentences = 212 flesch = 49 summary = Furthermore, inoculation of inactivated plasma on Vero E6 cells did not result in any cytopathic effect (CPE) even after 7 days of incubation and three consecutive passages, nor the detection of MERS RNA compared to pretreatment samples which showed complete CPE within 2 to 3 days postinoculation and log viral RNA titer ranging from 9.48 to 10.22 copies/ mL in all three passages. Furthermore, inoculation of inactivated plasma on Vero E6 cells did not result in any cytopathic effect (CPE) even after 7 days of incubation and three consecutive passages, nor the detection of MERS RNA compared to pretreatment samples which showed complete CPE within 2 to 3 days postinoculation and log viral RNA titer ranging from 9.48 to 10.22 copies/ mL in all three passages. Similar to SARS-CoV, there is no proven evidence so far of transfusion-transmitted MERS-CoV infections, 25 but the presence of viral RNA in plasma and serum of acute patients raises this concern especially in endemic areas like Saudi Arabia. cache = ./cache/cord-305871-w1quh4fx.txt txt = ./txt/cord-305871-w1quh4fx.txt === reduce.pl bib === id = cord-310371-pylrg91h author = Bishop, R.F. title = Enteric Viruses date = 2008-07-30 pages = extension = .txt mime = text/plain words = 4467 sentences = 253 flesch = 41 summary = The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. . viruses causing localized inflammation at any level of the intestinal tract, predominantly in small intestinal mucosa, resulting in acute gastroenteritis, for example, rotaviruses, caliciviruses, adenoviruses, astroviruses; . The family Caliciviridae contain small RNA viruses that cause enteric disease in a wide variety of hosts including cattle, pigs, rabbits, and humans. Caliciviruses causing enteric infections (in humans and other animals) are classified as belonging to the family Caliciviridae, which is divided into four genera. The recent demonstration that human noroviruses can infect and replicate in a three-dimensional cell culture model of human intestinal epithelium, should improve our understanding of the pathogenesis, and antigenic diversity of this important group of enteric viruses. cache = ./cache/cord-310371-pylrg91h.txt txt = ./txt/cord-310371-pylrg91h.txt === reduce.pl bib === id = cord-306934-29ljbl7g author = Tonelli, Michele title = Antiviral and cytotoxic activities of aminoarylazo compounds and aryltriazene derivatives date = 2009-07-01 pages = extension = .txt mime = text/plain words = 8526 sentences = 442 flesch = 58 summary = Finally, molecular modeling investigations indicated that compounds of structure A–C, active against BVDV, could work targeting the viral RNA-dependent RNA-polymerase (RdRp), having been observed a good agreement between the trends of the estimated IC50 and the experimental EC50 values. First of all, the binding site identified by our procedure is very close to the putative binding site proposed for two allosteric inhibitors of BVDV RdRp, VP32947 and BPIP, 23 Table 5 Cytotoxicity against MT-4, MDBK, BHK and Vero-76 cell lines and YFV, Reo-1, CVB-2, RSV, HSV-1 and Sb-1 inhibitory activity of triazene derivatives of structure F and G Tables 3 and 4. In view of these considerations, molecular modeling investigations were performed to study wether the active compounds of structures A-C could target the BVDV RNA-dependent RNA-polymerase (RdRp), which shares some structural similarity with HCV RdRp. Indeed a good agreement was observed between the trend exhibited by the IC 50 (calculated from the estimated free energies of binding) and the corresponding biological activities determined for these compounds in BVDV infected MDBK cell line. cache = ./cache/cord-306934-29ljbl7g.txt txt = ./txt/cord-306934-29ljbl7g.txt === reduce.pl bib === id = cord-312431-de7zhswl author = Ganesh, Atheesha title = Detecting Virus‐Like Particles from the Umgeni River, South Africa date = 2013-08-30 pages = extension = .txt mime = text/plain words = 7112 sentences = 376 flesch = 48 summary = These results indicate the potential of viruses in the water samples especially from the lower catchment areas of the Umgeni River to infect human hosts throughout the year. It is well recognised that monitoring the presence of enteric viruses could be challenging due to the relatively low level of infectious viral particles towards the respective host species and small viral particle size existing in environmental waters, thus making it essential to start with a large water sample volume and concentrate it to several orders of magnitude [27] [28] [29] [30] [31] . The present study was conducted to optimise procedures to extract and enumerate indigenous virus-like particles (VLPs) and to determine the community structures and infectivity of these viruses from river water. Canonical correspondence analysis (CCA) was used to reveal the association amongst the bacteriophages, VLPs and the physical and chemical water quality variables, which were measured from the same sites and seasons in concurrent studies performed in this laboratory [46] , with a view to defining the significant variables accountable for the observed spatial and temporal distribution of the communities. cache = ./cache/cord-312431-de7zhswl.txt txt = ./txt/cord-312431-de7zhswl.txt === reduce.pl bib === id = cord-307603-uqr6r14u author = Kauppinen, S. title = Locked Nucleic Acid: High-Affinity Targeting of Complementary RNA for RNomics date = 2006 pages = extension = .txt mime = text/plain words = 5782 sentences = 298 flesch = 47 summary = Several studies have demonstrated that LNA-modified oligonucleotides exhibit unprecedented thermal stability when hybridized with their DNA and RNA target molecules (Koshkin et al. 2005 ); (2) easy access-LNAs (fully modified or mixmers) are commercially available; (3) high-affinity and sequence-selective targeting of RNA molecules in vitro or in vivo Koshkin et al. Recently, it has been demonstrated that LNAzymes containing 3-4 LNA monomers at the ends of the binding arms cleave viral RNA structures that are resistant to hydrolysis by the corresponding unmodified DNAzyme, i.e., that efficient cleavage is correlated with improved binding affinity towards the target (Schubert et al. Efficient selection of polyadenylated mRNA from eukaryotic cells and tissues is an essential step for a wide selection of functional genomics applications, including full-length complementary (c)DNA library construction and sequencing, Northern and dot blot analyses, gene expression profiling by microarrays, and quantitative RT-PCR. LNA (locked nucleic acid): high affinity targeting of complementary RNA and DNA cache = ./cache/cord-307603-uqr6r14u.txt txt = ./txt/cord-307603-uqr6r14u.txt === reduce.pl bib === id = cord-310605-r63sg73c author = Dorward, D. A. title = Tissue-specific tolerance in fatal Covid-19 date = 2020-07-04 pages = extension = .txt mime = text/plain words = 4482 sentences = 256 flesch = 39 summary = Here we report an aberrant immune response in fatal Covid-19, principally involving the lung and reticuloendothelial system, that is not clearly topologically associated with the virus, indicating tissue-specific tolerance of SARS-CoV-2. This supports prioritising pathogen tolerance as a therapeutic strategy in Covid-19, by better understanding non-injurious organ-specific viral tolerance mechanisms and targeting aberrant macrophage and plasma cell responses. As analysis of SARS-CoV-2 RNA confirmed presence in numerous organs, detailed histological analysis of multiple tissues was undertaken on every patient to determine the associated pathological consequences and inflammatory responses. The present study shows that fatal Covid-19 is associated with variable but widespread distribution of viral RNA and protein but with a discordant inflammatory response to local viral presence, both between and within tissues, demonstrating tissue-specific tolerance of SARS-CoV-2. cache = ./cache/cord-310605-r63sg73c.txt txt = ./txt/cord-310605-r63sg73c.txt === reduce.pl bib === id = cord-307904-lnagg1uw author = Johnson, Jennifer A title = Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo date = 2003-08-15 pages = extension = .txt mime = text/plain words = 10666 sentences = 536 flesch = 58 summary = One RNA, ␥KpnI/HpaI, provided a source of the ␥a replicase protein and also contained a 350-nt deletion (from positions 2112 to 2461 on RNA␥) to remove the majority of the ␥b ORF, and a second derivative designed to assess promoter activity contained deletions engineered within the putative sgRNA␥ promoter ( Fig. 2A) . This result implies that competition between the two promoters has a major role in regulating the differential rates of synthesis of the two sgRNAs. To initially define sequences flanking the sgRNA␤2 promoter, two large deletions were generated in the ␤1Ϫ34/ ϩ14 clone that eliminated RNA␤ positions 1705 to 2109 and 2287 to 2434. Analysis of four deletions extending from position Ϫ179 to positions Ϫ110, Ϫ76, Ϫ52, and Ϫ28 relative to the transcription start site revealed that the mutant RNAs were able to replicate in protoplasts, but only mutants containing the deletions Ϫ179/Ϫ110 or Ϫ179/Ϫ76 were able to direct synthesis of sgRNA␤2 (Fig. 4A ). cache = ./cache/cord-307904-lnagg1uw.txt txt = ./txt/cord-307904-lnagg1uw.txt === reduce.pl bib === id = cord-309048-emmtplv3 author = Lomonossoff, George P. title = TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date = 2018-07-26 pages = extension = .txt mime = text/plain words = 9017 sentences = 407 flesch = 46 summary = (1999) displayed peptides of either 10 or 15 amino acids from the spike protein of the coronavirus murine hepatitis virus on the surface of assembled particles. coli-produced protein with a minimum of 20% of plant-made TMV CP, an approach that enabled efficient RNA-guided assembly of TMV-CP His6 into particles of the expected length (Eiben et al., 2014) . Assembly of the particle of tobacco mosaic virus from RNA and disks of protein β-Structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli In vitro assembly of tobacco mosaic virus coat protein variants derived from fission yeast expression clones or plants Modified tobacco mosaic virus particles as scaffolds for display of protein antigens for vaccine applications Display of peptides on the surface of tobacco mosaic virus particles Assembly of hybrid RNAs with tobacco mosaic virus coat protein. cache = ./cache/cord-309048-emmtplv3.txt txt = ./txt/cord-309048-emmtplv3.txt === reduce.pl bib === id = cord-311625-d7iycdyh author = Choong, Oi Kuan title = In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication date = 2014-02-20 pages = extension = .txt mime = text/plain words = 4014 sentences = 231 flesch = 52 summary = The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log(10) from 10(14) in the virus-inoculated cells to 10(9) in the circular TFO RNAs-transfected cells. The data analyzed by one-way ANOVA, Tukey post hoc test showed significant high viral RNA genome copy number of 4.03 × 10 14 for virus inoculated cells as compared to circular TFO1, TFO3, TFO4, and TFO5 treatments ( ≤ 0.05). In this study, circular Triple Helix Forming Oligonucleotide (TFO) RNAs, specifically targeting the short regions of viral genome for triplex formation, were designed and evaluated. cache = ./cache/cord-311625-d7iycdyh.txt txt = ./txt/cord-311625-d7iycdyh.txt === reduce.pl bib === id = cord-311628-ep795pil author = Fu, Yu title = A novel delivery platform based on Bacteriophage MS2 virus-like particles date = 2016-01-04 pages = extension = .txt mime = text/plain words = 6014 sentences = 309 flesch = 51 summary = Our objective here is to review the novel delivery platform based on Bacteriophage MS2 virus-like particles (VLPs), including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. A series of research findings showed that an MS2 VLP-based vaccine can effectively induce innate and cognate immune responses and can be used as a specific preventive intervention in some diseases, such as foot-and-mouth disease (Bittle et al., 1982; Dong et al., 2015; Van Lierop et al., 1992; Wong et al., 2000) , prostate cancer (Li et al., 2014) , and illnesses caused by human papilloma virus (HPV) (Tumban et al., 2012) . These particles offer an effective and convenient way to package RNAs, DNAs, epitope peptides, and drugs into bacteriophage capsids, forming different kinds of VLPs. MS2 VLPs can not only deliver various kinds of agents with a good safety profile and strong immunogenicity but also ensure tissue-specific targeting, which is determined by the species of the virus. cache = ./cache/cord-311628-ep795pil.txt txt = ./txt/cord-311628-ep795pil.txt === reduce.pl bib === id = cord-308331-55ge7kmr author = Routh, Andrew title = Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data date = 2013-10-09 pages = extension = .txt mime = text/plain words = 6014 sentences = 285 flesch = 52 summary = Using ViReMa, we demonstrate that by mapping the distribution and frequency of recombination events in the genome of flock house virus (FHV), we can discover de novo functional genomic motifs required for viral replication and encapsidation. Here, segments at the 5 0 and the 3 0 end of a complex recombination event have been mapped to nt 500-550 and nt 1040-1080 of FHV RNA 1, but there remain a small number of trimmed nucleotides in the middle. We generated 5 043 791 synthetic reads containing 99 033 unique recombination events and aligned these reads to the FHV genome with ViReMa using a seed length of 20 nt. Our analysis of FHV demonstrates that by isolating a small number of virus particles, deep sequencing the encapsidated RNA and mapping the positions of recombination events, functional RNA motifs can be discovered. cache = ./cache/cord-308331-55ge7kmr.txt txt = ./txt/cord-308331-55ge7kmr.txt === reduce.pl bib === id = cord-311007-0i1abjfa author = Schwarz, Megan C. title = Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone date = 2016-09-28 pages = extension = .txt mime = text/plain words = 4857 sentences = 241 flesch = 50 summary = High levels of infectious virus were produced following transfection of the plasmid bearing the wild-type MR766 ZIKV genome, but not one with a disruption to the viral nonstructural protein 5 (NS5) polymerase active site. Multicycle growth curve and plaque assay experiments indicated that the MR766 virus resulting from plasmid transfection exhibited growth characteristics that were more similar to its parental isolate than previously published 2010 Cambodia and 2015 Brazil cDNA-rescued ZIKV. Indeed, sequence analysis of bacterial plasmid clones of these RT-PCRs demonstrated that all products from wild-type plasmid-transfected cell RNA lacked the inserted intron (Fig. 3B) . In contrast to parental virus RT-PCR products (Fig. 3B) , these sequences carried a single silent G3127A mutation that was inserted during intron cloning, which indicated that these RNAs were generated from the MR766 plasmid. The addition of supernatants from wild-type plasmid-transfected or parental virus-infected 293T cells resulted in readily detectable levels of viral proteins. cache = ./cache/cord-311007-0i1abjfa.txt txt = ./txt/cord-311007-0i1abjfa.txt === reduce.pl bib === id = cord-308884-erofmh39 author = Yang, Seung Won title = Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date = 2018-01-08 pages = extension = .txt mime = text/plain words = 11025 sentences = 560 flesch = 53 summary = authors: Yang, Seung Won; Jang, Yo Han; Kwon, Soon Bin; Lee, Yoon Jae; Chae, Wonil; Byun, Young Ho; Kim, Paul; Park, Chan; Lee, Young Jae; Kim, Choon Kang; Kim, Young Seok; Choi, Seong Il; Seong, Baik Lin It should be noted that specificity of the antibody response to a reporter protein relative to the RID docking protein was not appreciably different regardless of the origin of an RID and the animal species to be immunized (compare Fig. 5A with 5D for eGFP and Fig. 5B with 5F for the HAgD), probably as a result of high homology (;80%) in an amino acid sequence between the murine and rabbit counterparts. D) ELISA data showing that according to the number of boosts, high-titer antibodies in serum samples from mice (n = 5) immunized with mRID-HAgD (20 mg/mouse) bound to the PR8 (H1N1) virus (10 4 PFU/well). cache = ./cache/cord-308884-erofmh39.txt txt = ./txt/cord-308884-erofmh39.txt === reduce.pl bib === id = cord-310268-8q4tk6fd author = Zhu, Qinchang title = DNA Aptamers in the Diagnosis and Treatment of Human Diseases date = 2015-11-25 pages = extension = .txt mime = text/plain words = 8649 sentences = 411 flesch = 47 summary = Nucleic acid aptamers are RNA and single-stranded (ss) DNA oligonucleotides with lengths typically ranging from 15 to 70 mers, which have the same level of target-binding affinity as monoclonal antibodies (the dissociation constant (K d ) usually ranges from 0.1 to 50 nM) [5, 6] . This SELEX is able to generate DNA aptamers that recognize the cell-surface or intracellular target protein in their native conformation, which shows great potential in cell-specific therapeutics and diagnostic applications [26] [27] [28] . Recently, modified cell-SELEX methods have been developed to select aptamers targeting specific cells like disease state cells and metastatic cells. In the era of personalized medicine, DNA aptamer-based therapeutics and diagnostics are believed to have great potential for extensive application because of their flexibility to specifically bind to any molecule targets. cache = ./cache/cord-310268-8q4tk6fd.txt txt = ./txt/cord-310268-8q4tk6fd.txt === reduce.pl bib === id = cord-312332-rwmuucsp author = Dicker, Kate title = The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date = 2020-09-10 pages = extension = .txt mime = text/plain words = 9235 sentences = 480 flesch = 45 summary = title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the 'knowns' and 'unknowns' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . cache = ./cache/cord-312332-rwmuucsp.txt txt = ./txt/cord-312332-rwmuucsp.txt === reduce.pl bib === id = cord-306424-gf0bglm0 author = Scutigliani, Enzo Maxim title = Interaction of the innate immune system with positive-strand RNA virus replication organelles date = 2017-06-27 pages = extension = .txt mime = text/plain words = 8320 sentences = 382 flesch = 36 summary = Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus cache = ./cache/cord-306424-gf0bglm0.txt txt = ./txt/cord-306424-gf0bglm0.txt === reduce.pl bib === id = cord-307817-2vy28i4m author = Lou, Zhiyong title = Current progress in antiviral strategies date = 2014-01-14 pages = extension = .txt mime = text/plain words = 7555 sentences = 343 flesch = 36 summary = The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Based on the complex structure of the PA C-terminal domain (PA C ) and the first 25 amino acids of PB1 [99] , a subset of modifications on N-terminal peptide of PB1 was shown to diminish the binding affinity of PA and PB1, inhibit polymerase activity, and attenuate the replication of influenza virus [100] [101] [102] . Because both the polymerase complex and NP show significant conservation between different influenza viruses, these results demonstrated that targeting the formation of viral RNP is a valid approach to the development of small molecule therapies against serious antiviral resistance to currently available drugs, such as adamantanes or neuraminidase inhibitors. cache = ./cache/cord-307817-2vy28i4m.txt txt = ./txt/cord-307817-2vy28i4m.txt === reduce.pl bib === id = cord-309043-dlmx12vt author = von Brunn, Albrecht title = Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date = 2007-05-23 pages = extension = .txt mime = text/plain words = 6706 sentences = 341 flesch = 52 summary = The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. There are reports that a number of MHV and SARS-CoV replicase proteins colocalize and eventually interact in cytoplasmic membrane bound complexes, in which viral RNA synthesis occurs [18, 19] . We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. To systematically study the subcellular localization of viral proteins within eukaryotic HeLa cells the SARS-CoV ORFs were transfected in eukaryotic vectors with either N-or C-terminal Flag tags and detected with an anti-Flag antibody. In this study we report the cloning of the complete ORFeome of SARS-CoV and the results of a matrix-based yeast two-hybrid screen of pairwise viral protein-protein interactions. cache = ./cache/cord-309043-dlmx12vt.txt txt = ./txt/cord-309043-dlmx12vt.txt === reduce.pl bib === id = cord-306754-qohrnpgq author = Lee, Justin S. title = Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species date = 2017-05-23 pages = extension = .txt mime = text/plain words = 7158 sentences = 335 flesch = 48 summary = Our report provides advances in investigating several important aspects of TGC assay design, including (i) the range of fold enrichment possible for targeted nucleic acids, (ii) comparison of TGC pathogen detection with traditional methods currently used by diagnostic laboratories, (iii) documentation that a single assay design can be applied to more than one host species, (iv) the applicability of TGC to characterize pathogens in the context of veterinary medicine, and (v) the ability of TGC-NGS to characterize intrahost genetic diversity of viral pathogens (4) (5) (6) . Mean enrichment values of 250,000-fold and 9,100,000-fold with the DNA and RNA probes, respectively, and 147,000-fold for FIV contained in tissues clearly demonstrate the ability of the targeted capture probes to dramatically alter the relative abundance of specific nucleic acids across a range of sample types and diverse pathogen taxa. cache = ./cache/cord-306754-qohrnpgq.txt txt = ./txt/cord-306754-qohrnpgq.txt === reduce.pl bib === id = cord-309722-04pp3lv0 author = Qiu, Yingshan title = Delivery of RNAi Therapeutics to the Airways—From Bench to Bedside date = 2016-09-20 pages = extension = .txt mime = text/plain words = 13203 sentences = 800 flesch = 42 summary = Notes: AHR, airway hyperresponsiveness; ALI, Acute lung injury; BALF, bronchoalveolar lavage fluid; CD86, cluster of differentiation 86; C-kit, a stem cell factor receptor; DCs, dendritic cells; HMGB1A, high mobility group box-1 A peptide; IFU, infectious unit; LPS, lipopolysaccharide; Mpl, myeloproliferative leukemia virus oncogene; OVA, ovalbumin; R3V6, an arginine-rich peptide; Rip2, receptor-interacting protein 2; RSV, respiratory syncytial virus; S1Plyase, sphingosine-1-phosphate lyase, SOCS, Suppressors of cytokine signaling protein 3; STAT6, signal transducer and activator of transcription factor 6; Syk, spleen tyrosine kinase; Tf-PEI, transferrin polyethylenimine; T h 2, T helper 2 cells; TNF-α, tumor necrosis factor-α; VEGFR, Vascular endothelial growth factor. After siRNA targeting, SOCS3 was intranasally administered to the lungs of chronic asthmatic mouse model [12] , the silencing of SOCS3 down-regulated the expression of T h 2 cell associated cytokines, IL-4, IL-5 and IL-13, leading to substantial reduction of airway inflammation, AHR as well as IgE production. cache = ./cache/cord-309722-04pp3lv0.txt txt = ./txt/cord-309722-04pp3lv0.txt === reduce.pl bib === id = cord-312240-0k8y86pf author = Schlaberg, Robert title = Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date = 2017-05-01 pages = extension = .txt mime = text/plain words = 4837 sentences = 239 flesch = 46 summary = Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. We first assessed the ability of RNA-seq and PVG PCR to detect known respiratory pathogens using specimens from children with CAP (n = 63) and asymptomatic control (n = 52) subjects in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. We validated RNA-seq and PVG PCR methods to detect known respiratory pathogens by testing specimens using both methods from children with CAP (n = 63) and asymptomatic control subjects (n = 52) in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. Using RNA-seq and PVG PCR, we identified additional viruses from upper respiratory tract specimens in >30% children hospitalized with clinical and radiographic pneumonia but in whom no pathogen was identified despite extensive testing by culture, molecular, and serologic methods. cache = ./cache/cord-312240-0k8y86pf.txt txt = ./txt/cord-312240-0k8y86pf.txt === reduce.pl bib === id = cord-310920-itqwhi6a author = Haddad, Christina title = Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3698 sentences = 205 flesch = 44 summary = Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. cache = ./cache/cord-310920-itqwhi6a.txt txt = ./txt/cord-310920-itqwhi6a.txt === reduce.pl bib === id = cord-309469-2naxn580 author = An, Hongliu title = Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date = 2019-01-05 pages = extension = .txt mime = text/plain words = 3600 sentences = 234 flesch = 54 summary = For example, polyadenylated nuclear (PAN) RNA encoded by Kaposi's sarcoma-associated herpesvirus (Sun et al., 1996; Zhong and Ganem, 1997) , the~2-kb latency-associated transcript (LAT) expressed by Herpes simplex virus (Bloom, 2004 ), a con-served~5-kb intron expressed by Human cytomegalovirus (hCMV) (Kulesza and Shenk, 2004) , and a 7.2-kb RNA expressed by mouse CMV (Kulesza and Shenk, 2006) , U-rich RNAs (HSURs) produced by Herpesvirus saimiri (HVS), (Albrecht and Fleckenstein, 1992; Ensser and Fleckenstein, 2005) ; (3) Subgenomic ncRNAs from single-stranded RNA viruses by incomplete degradation of genomic RNA by the cellular 5-3′ exonuclease XRN1. The results confirmed previous report that IBV can synthesize sgRNA via template switch mediated by a noncanonical core sequence (Bentley et al., 2013) Notably, the mutant virus carrying four mutations (A27100U/A27111U/G27113C/G27114C) was also unable to produce ncRNA (Fig. 4) , suggesting these nucleotides are required for ncRNA production. cache = ./cache/cord-309469-2naxn580.txt txt = ./txt/cord-309469-2naxn580.txt === reduce.pl bib === id = cord-314254-9ye8tfvz author = Pfaender, Stephanie title = Natural reservoirs for homologs of hepatitis C virus date = 2014-03-26 pages = extension = .txt mime = text/plain words = 6841 sentences = 322 flesch = 47 summary = To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaciand pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Non-primate hepaciviruses (NPHV) were initially discovered in domestic dogs and subsequently in horses 12, 13 and other diverse and widespread HCV-like viruses have been reported in wild populations of rodents and bats. Furthermore, liver function analyses revealed no indication for hepatic inflammation as c-glutamyl transferase and glutamate dehydrogenase values were within reference range, with the exception of a mildly elevated c-glutamyl transferase New HCV-like viruses in different mammalian hosts Pfaender et al 4 level in one horse. cache = ./cache/cord-314254-9ye8tfvz.txt txt = ./txt/cord-314254-9ye8tfvz.txt === reduce.pl bib === id = cord-313138-y485ev30 author = Magor, Katharine E. title = Defense genes missing from the flight division date = 2013-04-24 pages = extension = .txt mime = text/plain words = 10638 sentences = 610 flesch = 51 summary = Whether cause or effect, the lack of TLR8 in avian monocytes/ macrophages likely does contribute to the susceptibility of birds to RNA viruses (West Nile virus, Newcastle disease virus, influenza virus and others) and intracellular bacterial infections, including mycobacteria. The gene encoding RIG-I, DDX58, is not annotated in the chicken genome sequence, and is missing in some fish species, but MDA5 homologues are present in all vertebrate families (Zou et 2009). Riplet/RNF135 is a cytoplasmic E3-ligase identified by yeast two-hybrid as one of the proteins binding RIG-I, and is essential for RIG-I activation in human cell lines upon infection with an RNA virus (Oshiumi et al., 2009; Oshiumi et al., 2010) . The upregulation of IFIT5 following viral infection of chicken cells expressing duck RIG-I ( Barber et al., 2013) or infection of ducks (Vanderven et al., 2012) suggests IFIT5 is an important antiviral effector in avian species. cache = ./cache/cord-313138-y485ev30.txt txt = ./txt/cord-313138-y485ev30.txt === reduce.pl bib === id = cord-307914-lgprrwee author = Bartok, Eva title = Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids date = 2020-07-14 pages = extension = .txt mime = text/plain words = 17726 sentences = 1100 flesch = 51 summary = Indeed, the functionalization of CRISPR/Cas systems as a tool for genomic editing have revealed important differences in human and murine NA sensing, including distinct cell subset expression patterns of NA-sensing Toll-Like Receptors (TLRs) or species differences in the structural requirements for the detection of cyclic dinucleotide cGAMP by STING. As a long dsRNA with a 5 0 diphosphate terminus, polyI:C is known to activate the sensing receptors TLR3, MDA5, and RIG-I (Alexopoulou et al., 2001; Gitlin et al., 2006; Kato et al., 2008; Yoneyama et al., 2005) , accessory proteins such including LGP2 and members of the DDX and DHX families (reviewed in Oshiumi et al., 2016) as well as the restriction factors PKR and the OAS family (Farrell et al., 1978; Hovanessian et al., 1977; Zilberstein et al., 1978) . cache = ./cache/cord-307914-lgprrwee.txt txt = ./txt/cord-307914-lgprrwee.txt === reduce.pl bib === id = cord-313161-07iwwsfz author = Lundstrom, Kenneth title = Alphavirus-Based Vaccines date = 2014-06-16 pages = extension = .txt mime = text/plain words = 6844 sentences = 322 flesch = 30 summary = Furthermore, sequential immunization with SIN and VEE replicon particles expressing the type 1 HIV gp140 envelope (Env) and trimeric Env protein in MF59 adjuvant provided partial protection in macaques against intravenous challenges with high doses of simian-human immunodeficiency virus (SHIV) [61] . In another study, chimeric VEE/SIN replicon particles were applied for the expression of measles virus hemagglutinin (H) and fusion (F) proteins, which elicited high-titer neutralizing antibody and IFNɤ-producing T-cells in macaques after intradermal vaccination [48] . Furthermore, vaccination with recombinant particles expressing the P1A gene [105] and the human papilloma virus (HPV) E7 gene [89] from SFV and VEE vectors, respectively, provided protection against further tumor development in mice. When TRAMP mice were prophylactically immunized with a prostate stem cell antigen (PSCA) DNA plasmid followed by VEE-PSCA particle administration, a specific immune response and anti-tumor protection were observed in 90% of vaccinated animals [102] . cache = ./cache/cord-313161-07iwwsfz.txt txt = ./txt/cord-313161-07iwwsfz.txt === reduce.pl bib === id = cord-310947-aqau2n7q author = Pan, Ji'An title = Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date = 2008-10-01 pages = extension = .txt mime = text/plain words = 6821 sentences = 302 flesch = 43 summary = In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. However, the viral protein interaction maps have been generated until now only for a limited number of viruses, including T7 bacteriophage [1] , vaccinia virus [2] , potato virus A [3] , pea seed-borne mosaic virus [3] , wheat steak mosaic virus [4] , hepatitis C virus [5, 6] , porcine teschovirus [7] , Kaposi sarcoma-associated herpesvirus [8] , and very recently severe acute respiratory syndrome coronavirus (SARS-CoV) [9, 10] . cache = ./cache/cord-310947-aqau2n7q.txt txt = ./txt/cord-310947-aqau2n7q.txt === reduce.pl bib === id = cord-314369-o4nis91y author = Lopez-Lopes, G. I. S. title = Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date = 2020-08-01 pages = extension = .txt mime = text/plain words = 3684 sentences = 211 flesch = 55 summary = Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. During the initial months of the COVID-19 swabs and other collection methods were used by LHW in the institute to identify SARS-Cov-2 RNA in upper respiratory tract, but occasionally throat wash (TW) was alternatively used. We compared the CT obtained at this survey to results generated from contemporary swab collections, sent as routine testing at the institute, that provide SARS-CoV-2 rtPCR testing to clinical services. The study did not compare the rate of positivity in paired samples, and only one individual was documented that performed both a swab test (negative) and a positive throat wash collection at a same day. The study suggests that throat wash may be a valid alternative to the detection of SARS-CoV-2 RNA. cache = ./cache/cord-314369-o4nis91y.txt txt = ./txt/cord-314369-o4nis91y.txt === reduce.pl bib === id = cord-313439-cadyykks author = Felten, Sandra title = Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date = 2019-11-15 pages = extension = .txt mime = text/plain words = 12466 sentences = 522 flesch = 44 summary = Studies evaluating sensitivity and specificity of the detection of serum antibodies in comparison to either histopathology, a combination of diagnostic tests or clinical suspicion of feline infectious peritonitis (FIP). Recent studies evaluated the use of a quantitative RT-PCR (RT-qPCR) to detect FCoV RNA in FNA samples of the mesenteric lymph nodes and other abnormal tissues of clinical cases [119, 140] and hypothesized that this technique would be a useful tool to diagnose FIP for veterinary practitioners, especially in cats without effusion. Sensitivity and specificity from different studies evaluating the detection of feline coronavirus (FCoV) spike (S) gene mutations in tissue samples. RT-nPCR and subsequent S gene sequencing of serum and plasma samples from cats with FIP (diagnosed by histopathology ± IHC or by positive immunofluorescence in effusion) and control cats (diagnosed with another disease either ante or post mortem) revealed a sensitivity of only 7%, which confirms the very low virus load in blood. cache = ./cache/cord-313439-cadyykks.txt txt = ./txt/cord-313439-cadyykks.txt === reduce.pl bib === id = cord-314753-xflhxb13 author = Manso, Carmen F. title = Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date = 2017-06-23 pages = extension = .txt mime = text/plain words = 6333 sentences = 296 flesch = 48 summary = The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls. The depth plots in Fig. 3 again show unbiased and even coverages across both genomes, and the percentages of reads mapping to viral targets was again much higher in the rRNA-depleted sample than in the untreated comparator (61-fold and 85-fold for HCV and HPgV respectively). By depleting host-derived nucleic acids and making modifications to an existing library preparation protocol to account for ultra-low RNA input quantities, we have been able to reconstruct effectively full-length genomes of HCV, HEV and HIV from plasma samples with viral loads of 10 4 IU/ml (copies/ml for HIV) and substantial fractions of complete genomes at 10 3 IU/ml. Additionally, our system was able to recover viral sequences from a panel of diverse RNA viruses diluted in human plasma, with a broad correlation between the genomic coverage and depth metrics and approximate concentration. cache = ./cache/cord-314753-xflhxb13.txt txt = ./txt/cord-314753-xflhxb13.txt === reduce.pl bib === id = cord-314560-rswa5zdn author = Manjunath, N. title = Interfering antiviral immunity: application, subversion, hope? date = 2006-06-06 pages = extension = .txt mime = text/plain words = 5875 sentences = 352 flesch = 48 summary = RNA interference (RNAi), initially recognized as a natural antiviral mechanism in plants, has rapidly emerged as an invaluable tool to suppress gene expression in a sequence-specific manner in all organisms, including mammals. However, in recent years, a new type of genomic immunity mediated by RNA interference (RNAi) has emerged and has sparked intense interest as a potential treatment strategy for a variety of diseases, including viral infections, cancer and degenerative diseases [1] [2] [3] [4] . In RNAi, long double-stranded (ds) RNA generated during viral infection is cleaved by an enzyme termed Dicer into short, 21-23 nucleotide (nt) dsRNA molecules termed small interfering (si)RNAs that mediate sequence-specific gene silencing [5, 6] . A landmark development in the field occurred with the discovery that the introduction of 21-nt-long synthetic RNA resembling the Dicer-processed siRNA into mammalian cells induces sequence-specific gene silencing without evoking the interferon response [10] . cache = ./cache/cord-314560-rswa5zdn.txt txt = ./txt/cord-314560-rswa5zdn.txt === reduce.pl bib === id = cord-310967-15mv5yx7 author = Morris, Vincent L. title = Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease date = 1989-03-31 pages = extension = .txt mime = text/plain words = 5838 sentences = 301 flesch = 56 summary = One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In this report, we investigated viral variants that arose in the CNS of rats with a JHM-induced demyelinating disease and studied the effect of alterations in their mRNAs. When lo-day-old rats were inoculated with ATllf brain virus or ATlIe brain virus, the rats developed a rapid encephalitis instead of the more chronic demyelinating disease that has previously been seen with wild-type parental JHM virus (Sorensen et al., 1980; Jackson et al., 1984) and was observed with ATIIf cord virus-injected rats. In contrast, when 2-day-old rats were inoculated with ATllf cord virus, the more chronic CNS disease resulted instead of the rapid encephalitis that has been reported for wild-type JHM (Sorensen et a/., 1980; Parham et a/., 1986) and was observed with the ATIIf brain virus variant. cache = ./cache/cord-310967-15mv5yx7.txt txt = ./txt/cord-310967-15mv5yx7.txt === reduce.pl bib === id = cord-307598-p54p7enk author = Schlee, Martin title = Master sensors of pathogenic RNA – RIG-I like receptors date = 2013-07-01 pages = extension = .txt mime = text/plain words = 12853 sentences = 779 flesch = 56 summary = Similar to TLRs, RIG-I and MDA5 induce type I IFN and chemokines (but no IL12) upon activation by viral but also bacterial RNA. Since type I IFN induction by this RNA required RNase L, the authors concluded that RNase L recognizes and processes viral mRNA into a MDA5 activating structure. Before 5 triphosphate was identified as the crucial RNA modification to induce RIG-I activation, Marques and colleagues observed that synthetic blunt ended dsRNA oligonucleotides can stimulate RIG-I ( Fig. 3 ) (Marques et al. (2010b) confirmed the requirement of a base paired 5 -ppp end of dsRNA for RIG-I activation and suggested that some arenaviruses and bunyaviruses use a prime and realign mechanism for genome synthesis, leading to 5 overhangs in order to evade RIG-I recognition (Marq et al. pneumophilae did not induce type I IFN in HEK293 cells, thus excluding RIG-I-mediated recognition of RNA polymerase-III transcripts in the host cell, as previously suggested (Chiu et al. cache = ./cache/cord-307598-p54p7enk.txt txt = ./txt/cord-307598-p54p7enk.txt === reduce.pl bib === id = cord-312741-0au4nctt author = Lin, Panpan title = Coronavirus in human diseases: Mechanisms and advances in clinical treatment date = 2020-10-01 pages = extension = .txt mime = text/plain words = 14665 sentences = 840 flesch = 42 summary = 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein cache = ./cache/cord-312741-0au4nctt.txt txt = ./txt/cord-312741-0au4nctt.txt === reduce.pl bib === id = cord-310861-9kb0b6rq author = Koo, Bonhan title = An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections date = 2017-04-15 pages = extension = .txt mime = text/plain words = 5584 sentences = 295 flesch = 58 summary = In this study, we report an isothermal and rapid one-step RNA amplification/detection (iROAD) assay to simultaneously amplify and detect the viral RNA in a label-free and real-time manner. Furthermore, we demonstrated the clinical utility of the iROAD assay by detecting respiratory viral RNAs extracted from the 63 nasopharyngeal samples with either IFN-A/B or HCoV-OC43/229E or RSV-A/B. Subsequently, the iROAD assay detected the respiratory viral targets from the clinical sample by measuring the resonance wavelength shift within 15-20 min (Fig. 1) . In case of the iROAD assay with label-free and real-time capabilities, the wavelength shift was sequentially increased based on the concentrations (2.5×10 1 to 10 5 copies/reaction) of IFN-B within 20 min, as compared to the negative control. In the case of the real-time RT-PCR assay, the fluorescent SYBR Green signal was observed in RNA samples diluted up to 2.5×10 2 copies/reaction and showed good linearity (R 2 =0.9795) for different concentrations of the target (Fig. 3C ). cache = ./cache/cord-310861-9kb0b6rq.txt txt = ./txt/cord-310861-9kb0b6rq.txt === reduce.pl bib === id = cord-312392-8zxl48af author = Buonavoglia, Canio title = Canine Coronavirus Highly Pathogenic for Dogs date = 2006-03-17 pages = extension = .txt mime = text/plain words = 1169 sentences = 67 flesch = 53 summary = We report an outbreak of fatal disease in puppies caused by a pathogenic variant of CCoV that was isolated from organs with severe lesions. NSP 3b (22 aa) was 49 aa shorter than expected because of a 38-nucleotide deletion and a frame shift mutation in the downstream sequence that introduced To confirm the pathogenic potential of strain CB/05, we experimentally infected two 6-month-old dogs (authorization no. Experimental infection of dogs with the virus isolate resulted in a severe systemic disease that mimicked the clinical symptoms observed in the outbreak. Epidemiologic studies are required to determine whether the pantropic CCoV strain is a new coronavirus variant emerging in canine populations or a widespread infectious agent of dogs that usually goes undetected. Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease Genotype-specific fluorogenic RT-PCR assays for the detection and quantitation of canine coronavirus type I and type II RNA in faecal samples of dogs cache = ./cache/cord-312392-8zxl48af.txt txt = ./txt/cord-312392-8zxl48af.txt === reduce.pl bib === id = cord-315069-xo4mbxei author = Knorr, D. A. title = De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage date = 1991-03-31 pages = extension = .txt mime = text/plain words = 5134 sentences = 250 flesch = 52 summary = Abstract Defective interfering (DI) RNAs were generated de novo in each of 12 independent isolates of tomato bushy stunt virus (TBSV) upon serial passage at high multiplicities of infection (m.o.i.) in plants, but not in any of 4 additional isolates after 11 serial passages at low m.o.i. The DI RNAs were detected in RNA isolated from virus particles and in 2.3 M LiCl-soluble RNA fractions isolated from inoculated leaves. On each host species, six isolates were passed at high m.o.i. and two control isolates were passed at low m.o.i. In these hosts, DI-free TBSV induces lethal necrosis within 7-l 0 days postinoculation (d.p.i.), except in the presence of DI RNAs which are associated with attenuation and the establishment of persistent infections (Hillman et a/., 1987) . The small RNAs which developed in each of the high m.o.i. isolates hybridized to both 5'-and 3'-proximal TBSV genomic sequences, but generally were larger (-600 bases) than the previously characterized DI 1 RNA species (-400 bases). cache = ./cache/cord-315069-xo4mbxei.txt txt = ./txt/cord-315069-xo4mbxei.txt === reduce.pl bib === id = cord-312223-qgwzgazd author = Shafagati, Nazly title = The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date = 2013-07-04 pages = extension = .txt mime = text/plain words = 8834 sentences = 495 flesch = 57 summary = RESULTS: Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Our study demonstrates that NanoTrap particles are capable of capturing whole virus, and can be assayed with both qRT-PCR and plaque assays. A) Seven different types of NanoTrap particles were incubated with viral supernatants containing RVFV (1E+7 pfu/ml) for 30 minutes at room temperature and washed 4 times with water. In order to determine if the amplification observed in the qRT-PCR assay was due to the NanoTrap particle capturing intact viral particles or association of viral RNA (presumably due to lysed virus) with the particles, plaque assays were performed. cache = ./cache/cord-312223-qgwzgazd.txt txt = ./txt/cord-312223-qgwzgazd.txt === reduce.pl bib === id = cord-314572-1pou702r author = Lin, Ya-Hui title = Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date = 2016-10-14 pages = extension = .txt mime = text/plain words = 7182 sentences = 337 flesch = 47 summary = Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. In a first step to constructing a ligand-responsive −1 PRF stimulator, we designed Switch-0 RNA with a theophylline aptamer replacing the stem 3 of SARS-PK ( Figure 1A and C). We rationalized that such an engineered switch hairpin of reasonable stability (predicted free energy of −12.7 kcal/mole (37)) would be the dominant conformation that could interfere with the formation of pseudoknot stem 2 in the absence of theophylline (Supplementary Figure S2A) . To improve the dynamic range of ligand response and to see if theophylline aptamers can be functional while existing in both positive and negative regulators of −1 PRF, we fused previously designed theophylline-dependent upstream attenuator, theoOFF2 (24) with Switch-1 ( Figure 5A ) and examined theophylline-dependent −1 PRF activity in vitro. cache = ./cache/cord-314572-1pou702r.txt txt = ./txt/cord-314572-1pou702r.txt === reduce.pl bib === id = cord-315909-vwugf0wp author = Letko, Michael title = Studying Evolutionary Adaptation of MERS-CoV date = 2019-09-14 pages = extension = .txt mime = text/plain words = 1236 sentences = 100 flesch = 52 summary = Here, we describe methods for in vitro serial passaging of Middle East respiratory syndrome coronavirus (MERS-CoV) to select for mutations which increase replication on semi-permissive cell lines as described in Letko et al., Cell Rep 24, 1730–1737, 2018. Forced adaptation experiments have been used to determine viral mutations that facilitate escape from drugs [4] [5] [6] , monoclonal antibodies [7, 8] , host restriction factors [9] [10] [11] , and species variation in host receptors [12] [13] [14] and to elucidate various viral mechanisms of infection and replication [15] [16] [17] . Below is the method employed to adapt MERS-CoV to a semi-permissive host receptor, Desmodus rotundus DPP4. To increase selective pressures on a viral population which is beginning to show signs of adaptation, one can apply a population bottleneck in the subsequent passage by reducing the amount of viral Evolution of MERS-CoV supernatant passaged to the next cell culture. cache = ./cache/cord-315909-vwugf0wp.txt txt = ./txt/cord-315909-vwugf0wp.txt === reduce.pl bib === id = cord-314891-brgtwxhe author = Fumian, Tulio M. title = Potential Therapeutic Agents for Feline Calicivirus Infection date = 2018-08-16 pages = extension = .txt mime = text/plain words = 5483 sentences = 278 flesch = 47 summary = Using cell culture assays, PPNDS, quercetagetin and GC376 did not display antivirals effects, however, we identified nitazoxanide and 2′-C-methylcytidine (2CMC) as potent inhibitors of FCV replication, with EC(50) values in the low micromolar range (0.6 μM and 2.5 μM, respectively). The combined inhibitory effects of nitazoxanide (0 to 0.6 µM) and 2CMC (0 to 4 µM) were tested over a range of combinations against FCV in the cell culture using the plaque reduction assay. Of the six NNI compounds tested in the current study, PPNDS and quercetagetin showed an inhibition of FCV RdRp activity with IC 50 values in the low micromolar range (Figure 2 and Table 1 ). Finally, we reported the identification of two compounds (nitazoxanide and 2CMC) with antiviral activity against FCV in cell culture at low micromolar concentrations with a potential combinational therapeutic utility to treat FCV-infected cats. cache = ./cache/cord-314891-brgtwxhe.txt txt = ./txt/cord-314891-brgtwxhe.txt === reduce.pl bib === id = cord-313684-61hkogdh author = Samaddar, Arghadip title = Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date = 2020-09-17 pages = extension = .txt mime = text/plain words = 11700 sentences = 585 flesch = 42 summary = Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. cache = ./cache/cord-313684-61hkogdh.txt txt = ./txt/cord-313684-61hkogdh.txt === reduce.pl bib === id = cord-317244-4su5on6s author = Maganga, Gael D. title = Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date = 2014-12-31 pages = extension = .txt mime = text/plain words = 3476 sentences = 191 flesch = 50 summary = In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. To further investigate the presence of the virus in bat populations, a strain-specific real-time RT-PCR assay (primers: GB09-478-F, 59-GGCGGCTCTTAAAAGT-GAATG-39; GB09-478-R, 59-GCGGGGTCAAATTGGTCAT-39; probe: GB09-478-P, 59-TCCAGCACAAACATATCCGAGAAGGCTAG-39) was designed within the initial PCR fragment and was used to test total RNA extracted from mixed liver and spleen samples from each of all the other bat species. In order to determine the organ distribution of this virus in infected bats, total RNA was extracted from heart, liver, spleen, kidney, lung, intestine and brain samples from all 14 real-time RT-PCR-positive bats, as described previously, and screened, using the same strain-specific real-time RT-PCR assay shown above. cache = ./cache/cord-317244-4su5on6s.txt txt = ./txt/cord-317244-4su5on6s.txt === reduce.pl bib === id = cord-316134-lkd2mj27 author = Sungsuwan, Suttipun title = Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication date = 2020-01-15 pages = extension = .txt mime = text/plain words = 9236 sentences = 495 flesch = 52 summary = Investigation of possible molecular interactions between components of PEDV, PDCoV and TGEV and their influence on replication of each virus would provide a crucial insight into comprehensive understanding of these CoVs. Of all viral proteins, we have chosen to start with the N protein, as it is among the most abundant and ubiquitous structural proteins in infected cells. For viral infection in the transient CoV N expression experiment, VeroE6 cells were transfected with 1 or 2 μg of pCAGGS-PEDV N-Myc, pCAGGS-PDCoV N-HA, pCAGGS-TGEV N-FLAG, or the empty pCAGGS vector and were incubated for 24 h to allow for protein expression. To investigate how this protein-protein interaction might affect PEDV replication, we transiently transfected VeroE6 cells with varying amounts of the pCAGGS plasmid expressing N proteins from either PDCoV or TGEV for 24 h before infection with PEDV-mCherry (MOI = 0.0001) and followed the course of viral replication for each condition. cache = ./cache/cord-316134-lkd2mj27.txt txt = ./txt/cord-316134-lkd2mj27.txt === reduce.pl bib === id = cord-315072-b28yikvj author = Giotis, Efstathios S. title = Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) date = 2016-08-05 pages = extension = .txt mime = text/plain words = 5878 sentences = 285 flesch = 48 summary = title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) To generate a chicken ISG database we have compared data from three transcriptomic technology platforms: (i) the classical 3′-biased GeneChip Chicken Genome Array (32K; Affymetrix, High Wycombe, UK), (ii) the Chicken Gene 1.0 Sense Target (ST) whole transcriptome Array (Affymetrix) and (iii) Illumina (Little Chesterford, UK) RNA-seq. One of the most highly-expressed contigs was one which, when analysed by BLAST, proved to represent a homologue of STAT2, which is missing from the current ENSEMBL annotated reference chicken genome In (B) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5. Technologies identifying significant IRGs are listed as "1" RNA-seq (using Kal's Z test); "2" Affymetrix 32K GeneChip Chicken Genome Array and "3" Chicken Gene 1.0 ST Array' . cache = ./cache/cord-315072-b28yikvj.txt txt = ./txt/cord-315072-b28yikvj.txt === reduce.pl bib === id = cord-315483-l6dm82pp author = Santhakumar, Diwakar title = Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses date = 2018-05-01 pages = extension = .txt mime = text/plain words = 10776 sentences = 579 flesch = 47 summary = To confirm the sequence of the cDNA and to identify the genomic structure of the identified IFIT gene, the transcript was amplified from RNA extracted from NDV-infected CEFs. Complete sequence analysis of the gene revealed an open reading frame (ORF) of 1440 bps (479 amino acids excluding stop codon) with high sequence identity (48% and 67%) with the human and duck IFIT5 proteins, respectively ( Supplementary Fig. 1B) . The levels of chIFN-β gene induction was proportional to the NDV replication (Fig. 2D) , therefore, it can be inferred that the virus-induced expression of chicken IFIT5 is IFN-dependent and that chIFIT5 is an early-ISG with capacity to modulate initial steps of virus life cycle. To compare anti-viral effects of chIFIT5 (only IFIT gene identified in chickens so far) with its orthologous and homologous human proteins, huIFIT1, huIFIT2, huIFIT3 and huIFIT5 were expressed in chicken cells and antiviral affect was monitored (Fig. 5A ). cache = ./cache/cord-315483-l6dm82pp.txt txt = ./txt/cord-315483-l6dm82pp.txt === reduce.pl bib === id = cord-314877-db7tze8j author = Chkuaseli, Tamari title = Activation of viral transcription by stepwise largescale folding of an RNA virus genome date = 2020-08-12 pages = extension = .txt mime = text/plain words = 8535 sentences = 421 flesch = 48 summary = When viewed in the context of the RNA secondary structure model for the TBSV genome (48) , the DE/CE interaction corresponds to the closing stem of a sizable RNA domain, termed large domain 3 (LD3), which, along with formation of the adjacent LD2, acts to unite the AS2 and RS2 sequences ( Figure 1B) . Translational readthrough for the CIRV genome requires a long-distance RNA-RNA interaction (LDRI) between RTSL and the 3 UTR, involving the PRTE and DRTE partner sequences, respectively ( Figure 1A , B) (39) . The binding of RTSL-TL to SL59-5 was investigated functionally by introducing compensatory nucleotide substitutions into the candidate partner sequences and assessing the effects on sg mRNA1 accumulation following transfection of mutant viral RNA genomes into protoplasts pairing potential in mutants TC-6 and TC-7 diminished sg mRNA1 plus-and minus-strand levels below ∼10% of wt, while regenerating pairing capacity with alternate nucleotides in mutant TC-8 restored levels up to ∼50-62% of wt ( Figure 3B, C) . cache = ./cache/cord-314877-db7tze8j.txt txt = ./txt/cord-314877-db7tze8j.txt === reduce.pl bib === id = cord-312517-b24zlaqt author = Kim, Denny title = The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines date = 2020-06-19 pages = extension = .txt mime = text/plain words = 1948 sentences = 98 flesch = 44 summary = title: The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) has prepared a standardized template to describe the key considerations for the benefit-risk assessment of nucleic acid vaccines. The Brighton Collaboration formed the Viral Vector Vaccines Safety Working Group (V3SWG) in October 2008 to improve the ability of key stakeholders to anticipate potential safety issues and meaningfully assess or interpret safety data, thereby facilitating greater public acceptance when viral vector vaccines are licensed [2] . When completing information on adverse effects in Section 8, please provide as many details as possible based on the Brighton Collaboration Guidelines for collection, analysis and presentation of vaccine safety data in pre-and post-licensure clinical studies [13] . cache = ./cache/cord-312517-b24zlaqt.txt txt = ./txt/cord-312517-b24zlaqt.txt === reduce.pl bib === id = cord-303533-6s01qplg author = Neuman, Benjamin W. title = Does form meet function in the coronavirus replicative organelle? date = 2014-07-15 pages = extension = .txt mime = text/plain words = 3642 sentences = 177 flesch = 39 summary = This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. Whatever their purpose, it is clear that the coronavirus organelle is dynamic [9] , closely tied to vesicular transport in the host cell [5, 10] , and consists mainly of paired membranes that form a variety of complex shapes including convoluted membranes and double-membrane vesicles (DMVs) [2, 11] . Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulum-targeted viral protein cache = ./cache/cord-303533-6s01qplg.txt txt = ./txt/cord-303533-6s01qplg.txt === reduce.pl bib === id = cord-313301-7mkadtp9 author = Duffy, Siobain title = EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date = 2007-08-23 pages = extension = .txt mime = text/plain words = 6091 sentences = 273 flesch = 45 summary = In particular, the high pernucleotide mutation rates of RNA viruses (Drake 1993) provide extensive genetic variation that fuels evolution by natural selection, making the study of reproductive isolation and speciation especially feasible (Holmes 2004) . We tested the plausibility of the no-gene mechanism of speciation by examining the consequences of adaptation to a novel host in laboratory populations of the RNA phage 6, which infects a number of Pseudomonas species. The same microevolutionary processes of mutation and natural selection, which led to the adaptation of 6 populations to a novel host also resulted in a macroevolutionary event: the evolution of a new virus species that is reproductively isolated from the ancestral phage 6 wt . Beyond uniquely demonstrating the evolution of reproductive isolation in the laboratory, our study extends the literature describing the evolutionary genetics of narrowed host range when viruses adapt to a single host. cache = ./cache/cord-313301-7mkadtp9.txt txt = ./txt/cord-313301-7mkadtp9.txt === reduce.pl bib === id = cord-316179-kmdxltie author = Fozouni, P. title = Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date = 2020-09-30 pages = extension = .txt mime = text/plain words = 8244 sentences = 507 flesch = 58 summary = Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. When the SARS-CoV-2 sequence became public in January 2020, we set out to develop a Cas13-based direct-detection assay for viral RNA that would avoid the need for amplification and enable point-of-care testing. We tested the performance of the device for detecting SARS-CoV-2 RNA using the triple-crRNA Cas13a assay and a dilution series with full viral RNA isolated from supernatants of infected Vero CCL-81 cells . (B) RNPs made with crRNA 2 and crRNA 4 individually and in combination (50 nM total RNP concentration for each reaction) were tested against 2.9 x 10 5 copies/µL (480 fM) of SARS-CoV-2 IVT N gene RNA, and compared to fluorescence from no target RNA RNP alone controls ("RNP 2," "RNP 4," and "RNP 2+4"). cache = ./cache/cord-316179-kmdxltie.txt txt = ./txt/cord-316179-kmdxltie.txt === reduce.pl bib === id = cord-316503-wtmmewiz author = Warren, Travis K. title = Advanced morpholino oligomers: A novel approach to antiviral therapy date = 2012-02-14 pages = extension = .txt mime = text/plain words = 6825 sentences = 315 flesch = 40 summary = Phosphorodiamidate morpholino oligomers (PMOs) are synthetic antisense oligonucleotide analogs that are designed to interfere with translational processes by forming base-pair duplexes with specific RNA sequences. Peptide conjugated PMOs (PPMOs; Fig. 2 ), which include positively charged amino acid residues such as arginine, have been viewed as particularly promising transporters and have shown efficacy in multiple in vivo models of viral infection (Enterlein et al., 2006; Paessler et al., 2008; Stein, 2008; Swenson et al., 2009) . While PPMOs are efficacious in multiple in vivo models of viral infections, PPMOs are more poorly tolerated in vivo compared to neutral-charge PMOs. In mice, dose-dependent reductions in weight, behavioral alterations, and mild liver histopathology were observed following repeat administration of 200-300 lg doses of a PMO conjugated to an arginine-rich peptide (Deas et al., 2007) . cache = ./cache/cord-316503-wtmmewiz.txt txt = ./txt/cord-316503-wtmmewiz.txt === reduce.pl bib === id = cord-315611-xbj41ekc author = Ahmad, Mohammed title = Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date = 2020-07-14 pages = extension = .txt mime = text/plain words = 5038 sentences = 301 flesch = 49 summary = Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. 20−22 In this report, using computer-aided homology modeling, docking, and molecular simulations, we have predicted the protein structure and probable small-molecule inhibitors against SARS-CoV2 RdRp (CoV2-RdRp). Taking together the aforementioned interaction and comparison of the model and experimentally determined structures, we propose the probable initiation complex of CoV2-RdRp bound to RNA and GTP molecules in Figure 2D . Molecular Dynamics simulation studies of the native and ligand-bound complexes of CoV2-RdRp. MD (Molecular dynamics) simulations were performed for the modelled structure of the RdRp protein and docked complexes for the GTP, lead optimized, and FIH compounds for a 50 ns time period. cache = ./cache/cord-315611-xbj41ekc.txt txt = ./txt/cord-315611-xbj41ekc.txt === reduce.pl bib === id = cord-312688-12san3m7 author = Martin, Baptiste title = Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date = 2016-09-14 pages = extension = .txt mime = text/plain words = 10226 sentences = 530 flesch = 50 summary = title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry After replication of the viral genome and RNA transcription, nascent viral particles are assembled in a process mediated by the matrix protein VP40, and virus budding occurs at the cell surface membrane in a process that involves hijacking the host ESCRT machinery (Hartlieb and Weissenhorn, 2006; Noda et al., 2006) . However, no direct interaction between both molecules has been demonstrated yet, and recent studies suggest that a 5 b 1 -integrin is not required for GP-mediated binding of internalization, but rather is a positive regulator of cathepsins, which play an important role in processing GP 1 into its fusion-competent form within the endosomes of infected cells (Schornberg et al., 2009) . After attachment mediated by interaction between the filovirus surface protein GP 1,2 (PDB: 3CSY) and various attachment factors, the complex is internalized and routed to the endosome, where GP 1,2 is processed to trigger fusion of viral and host membranes. cache = ./cache/cord-312688-12san3m7.txt txt = ./txt/cord-312688-12san3m7.txt === reduce.pl bib === id = cord-317591-qa6oxy4j author = Fukushima, Akiko title = Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date = 2009-05-07 pages = extension = .txt mime = text/plain words = 3605 sentences = 196 flesch = 53 summary = To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. A chimeric DNA-RNA hammerhead ribozyme was designed and synthesized to target a common nucleotide sequence between SARS-CoV and mouse hepatitis virus (MHV), and its effectiveness on suppression of MHV and SARS-CoV RNA expression evaluated in vitro. Figure 4 shows effect of the chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV RNA on the multiplication of MHV in DBT cells. Therefore, the chimeric DNA-RNA hammerhead ribozyme was designed with complementarity to common regions of SARS-CoV and MHV that included the target GUC sequence. In the present study, inhibition on the multiplication of MVH was approximately 60%, with 60% transfection efficiency of the chimeric DNA-RNA ribozyme targeting SARS-CoV into DBT cells. cache = ./cache/cord-317591-qa6oxy4j.txt txt = ./txt/cord-317591-qa6oxy4j.txt === reduce.pl bib === id = cord-312461-5qzpo6l1 author = Adalja, Amesh A. title = Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date = 2019-08-30 pages = extension = .txt mime = text/plain words = 6830 sentences = 290 flesch = 40 summary = A substantial proportion of pandemic and biological threat preparedness activities have focused on list-based approaches that were in part based on pandemic influenzas of the past, historical biological weapon development programs, or recent outbreaks of emerging infectious diseases (e.g., SARS, MERS, Ebola) (Centers for Disease Control and Prevention 2017; Casadevall and Relman 2010) . Cultivating and maintaining expertise in the epidemiology, surveillance, and pathogenicity of all classes of microbes, with explicit incorporation of a One Health approach-which incorporates and integrates information from infectious diseases of plants, amphibians, and reptiles-will help foster the broad capacities needed for emerging pandemic and global catastrophic biological risks. Pathogen-based lists, both USA and global, based on influenza precedents, historical biological weapon programs, and emerging infectious diseases were responsible for galvanizing early activities in the field of pandemic preparedness and have helped drive many important contributions. cache = ./cache/cord-312461-5qzpo6l1.txt txt = ./txt/cord-312461-5qzpo6l1.txt === reduce.pl bib === id = cord-315384-eqiokrub author = van der Hoek, Lia title = Croup Is Associated with the Novel Coronavirus NL63 date = 2005-08-23 pages = extension = .txt mime = text/plain words = 4403 sentences = 209 flesch = 57 summary = The viral RNA was more prevalent in samples from outpatients (7.9%) than from hospitalised patients (3.2%, p = 0.003), and co-infection with either respiratory syncytial virus or parainfluenza virus 3 was observed frequently. The samples had been collected from hospitalised patients and outpatients from December 1999 to October 2001 in four different regions in Germany as part of the prospective population-based PRI.DE study and analysed for RNA from respiratory viruses. The samples had been collected from hospitalised patients and outpatients from December 1999 to October 2001 in four different regions in Germany as part of the prospective population-based PRI.DE study and analysed for RNA from respiratory viruses. To investigate the prevalence of HCoV-NL63 and its involvement in respiratory diseases, we now analysed 949 samples from the Paediatric Respiratory Infection in Germany (PRI.DE) study, a prospective population-based study on lower respiratory tract infections (LRTIs) in children under 3 y of age in Germany [8, 9] . cache = ./cache/cord-315384-eqiokrub.txt txt = ./txt/cord-315384-eqiokrub.txt === reduce.pl bib === id = cord-317037-1qydcc5e author = Kumar, Asit title = Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date = 2020-08-13 pages = extension = .txt mime = text/plain words = 9406 sentences = 511 flesch = 37 summary = Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. HIV-infected U1 macrophages upon Cigarette smoke condensate (CSC) treatment enhanced the packaging of IL-6 in EVs; IL-8 served as a biomarker for HIV patients with altered immune function due to alcohol and tobacco abuse [20, 116, 117] Host protein APOBEC3G Inhibit replication of viral infectivity factor (vif) -deficient and wild-type HIV-1 in recipient cells [118] miRNA vmiR-88 and vmiR-99 Hepatocytes secreted exosomes participate in virus replication [142] Viral miRNAs HBV-miR-3 Represses viral protein production and HBV replication [143] HTLV-1 Viral proteins gp61, Tax, and HBZ Increase cell-to-cell contact and promote a potential increase in viral spread [144] Zika Viral genetic material and protein RNA and ZIKV-E EVs derived from Infected C6/36 cells promote infection and activation of monocytes with enhanced TNF-α mRNA expression. cache = ./cache/cord-317037-1qydcc5e.txt txt = ./txt/cord-317037-1qydcc5e.txt === reduce.pl bib === id = cord-312001-8p7scli8 author = Majzoub, Karim title = The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans date = 2019-08-16 pages = extension = .txt mime = text/plain words = 10056 sentences = 548 flesch = 46 summary = Consequently, animal cells have evolved devoted pathways which (1) sense and recognize pathogen-associated molecular patterns (PAMPs) and, more particularly, virus-associated molecular signatures; (2) initiate signaling cascades stemming from the site of detection, translocating the information to the nucleus; and (3) induce a transcriptional program that confers an antiviral state to the host ( Figure 1 ). While the cytosolic recognition of viral RNA is almost exclusively mediated by RLRs, several proteins have been proposed to play a role in DNA sensing and triggering innate immune responses, such as the DNA-dependent activator of IFN-regulatory factors (DAI), DDX41, RNA polymerase III, IFI16 and DNA-PK [62] [63] [64] [65] [66] [67] . Although the pathway leading to the transcriptional activation of Vago is still poorly understood in insects, these studies established that DExD/H-box helicase containing proteins, like Dicer and RLRs, may represent an evolutionarily conserved set of viral nucleic acid sensors that direct antiviral responses in animals [159] . cache = ./cache/cord-312001-8p7scli8.txt txt = ./txt/cord-312001-8p7scli8.txt === reduce.pl bib === id = cord-317851-lj07947c author = Elena, S F title = Experimental evolution of plant RNA viruses date = 2008-02-06 pages = extension = .txt mime = text/plain words = 4184 sentences = 191 flesch = 42 summary = In this review, we will focus on recent studies that used plant viruses to address evolutionary questions of general interest, such as the rate and fitness effects of deleterious mutations and the role of neutrality as a source of mutational robustness, the evolution of generalist viruses, or the effect of vertical versus horizontal transmission on virulence. Despite mutation rate is still high compared to that of DNA-based microorganisms, a classic field observation is that natural plant virus populations generally exhibit limited genetic variation (García-Arenal et al., 2001) , which may imply either that purifying selection may be strong or that genome replication occurs mainly by Luria's stamping machine model (Luria, 1951) rather than exponentially (French and Stenger, 2003) , the two hypotheses being nonexclusive. cache = ./cache/cord-317851-lj07947c.txt txt = ./txt/cord-317851-lj07947c.txt === reduce.pl bib === id = cord-318359-41h90h05 author = Irigoyen, Nerea title = Ribosome profiling of the retrovirus murine leukemia virus date = 2018-01-22 pages = extension = .txt mime = text/plain words = 4488 sentences = 238 flesch = 54 summary = Here, we report the first high resolution analysis of retrovirus gene expression through tandem ribosome profiling (RiboSeq) and RNA sequencing (RNASeq) of MuLV-infected cells. Translation may proceed contiguously from this codon through the gag ORF; thus, presumably, giving rise to an alternative Glyco-Gag isoform which is N-terminally extended by a further 12 amino acids (MELTSSEHPAAT, assuming GUG is decoded by Met-tRNA i ) relative to the canonical Glyco-Gag. The GUG codon is present in some but not all MuLV strains, and is not well conserved among other gammaretroviral lineages for which sequence data are currently available (Additional file 1: Fig. S3-highlighted in green) , although some sequences have alternative nearby potential non-AUG initiation sites. Our data indicate the existence of new translation initiation sites, new translated short ORFs and the first measurement of the gag-pol stop codon readthrough efficiency in the context of the full-length virus genome during infection. cache = ./cache/cord-318359-41h90h05.txt txt = ./txt/cord-318359-41h90h05.txt === reduce.pl bib === id = cord-313541-fpqwzf9k author = Ulloa, S. title = A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date = 2020-08-22 pages = extension = .txt mime = text/plain words = 1776 sentences = 104 flesch = 55 summary = The growing demand for commercial kits used for automated extraction of SARS-CoV-2 RNA, a key step before rRT-PCR diagnosis, could cause a shortage of stocks that hinders the rapid processing of samples. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction and inactivating samples at 95 °C for 5 minutes, was showed from specimens placed in UTM and molecular water, but not from samples in Hanks medium and saline buffer (Merindol et al., 2020) . Thus, the four different media used in this study (UTM, PBS 1x solution, Hanks medium and DNA/RNA Shield TM ) did not affect analytical results, because all precipitated samples were able to be detected by rRT-PCR using the whole viral panel (Orf1ab, N and S genes) and the internal control gene. Here, a simple protocol to detect SARS-CoV-2 from NPSs using rRT-PCR after a heat inactivation and a precipitation/concentration step is proposed. cache = ./cache/cord-313541-fpqwzf9k.txt txt = ./txt/cord-313541-fpqwzf9k.txt === reduce.pl bib === id = cord-312886-o3ipzn05 author = Onomoto, Koji title = Antiviral innate immunity and stress granule responses date = 2014-08-19 pages = extension = .txt mime = text/plain words = 5136 sentences = 281 flesch = 39 summary = Viral infection and stress granules Viral invasion and replication are detected by innate immune sensors in cells, triggering downstream signaling pathways that can ultimately result in the activation of systemic immune responses. In some cases these bodies have been given different names in an attempt to distinguish them from SGs; in this review, however, we refer to virusinduced SG-like granules collectively as SGs. Many viruses induce SGs through the activation of the eukaryotic translation initiation factor (eIF)2a kinases PKR and, in some cases, general control non-depressible 2 (GCN2), which are both triggered by detection of RNA in the cytoplasm [28] ( Figure 2 ). In the stress-recovered condition, GADD34 protein is rapidly downregulated by an unknown mechanism and the phosphorylated form of eIF2a reaccumulates in the cells, resulting in an oscillating pattern of SGs. In cases where viral infection appears to not induce SGs, accumulating evidence suggest that these viruses inhibit SG formation. cache = ./cache/cord-312886-o3ipzn05.txt txt = ./txt/cord-312886-o3ipzn05.txt === reduce.pl bib === id = cord-314019-8n0jafsk author = Feng, Qian title = Induction and suppression of innate antiviral responses by picornaviruses date = 2014-07-18 pages = extension = .txt mime = text/plain words = 7215 sentences = 358 flesch = 43 summary = We focus on two important and well-studied genera of picornaviruses, namely Enterovirus and Cardiovirus, and discuss how their RNAs are recognized by RLRs, and how they antagonize the IFN-a/b induction pathway and SG formation in infected cells. Picornavirus infections activate a cytosolic RNA sensor, MDA5, which in turn, induces a type I interferon response, a crucial component of antiviral immunity. Picornavirus infections activate a cytosolic RNA sensor, MDA5, which in turn, induces a type I interferon response, a crucial component of antiviral immunity. However, it is important to point out that the caspase-and proteasome-mediated MDA5 cleavage events were observed under conditions where MDA5 expression level was artificially upregulated prior to infection (either by poly(I:C) or viral RNA transfections) [39, 42] , which may sensitize cells for virus-induced apoptosis, thereby promote caspase-and proteasome-mediated protein degradations. cache = ./cache/cord-314019-8n0jafsk.txt txt = ./txt/cord-314019-8n0jafsk.txt === reduce.pl bib === id = cord-314567-purplsjn author = Fernández-Ponce, Cecilia title = Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date = 2018-01-04 pages = extension = .txt mime = text/plain words = 7978 sentences = 382 flesch = 41 summary = HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. As studies using the whole virus do not allow for the elucidation of the specific molecular mechanisms in which each protein is implicated, in this work, we focused on a single viral protein, showing that in CD4 + T cells, HCV core protein mostly localizes in the nucleus and specifically in the nucleolus where it is greatly enriched. cache = ./cache/cord-314567-purplsjn.txt txt = ./txt/cord-314567-purplsjn.txt === reduce.pl bib === id = cord-315616-pvt0amth author = Poole, Anthony title = Methyl-RNA: an evolutionary bridge between RNA and DNA? date = 2004-06-17 pages = extension = .txt mime = text/plain words = 5623 sentences = 281 flesch = 54 summary = Ribonucleotide reductase itself, which synthesises deoxyribonucleotides from ribonucleotides, requires complex protein radical chemistry, and RNA world genomes may have reached their limits of coding capacity well before such complex enzymes had evolved. Even with this gap in the RNA world model, current knowledge suggests the RNA organism that evolved protein synthesis was likely to have been dangerously close to the Eigen limit for RNA, and probably emIn the ¢rst step, a radical is generated at some distance from the active site. By virtue of its non-speci¢c dsRNA methylating activity, this enzyme is hypothesised to have been recruited into methylation of genomic RNA, improving the stability of the genetic material prior to the origin of DNA. The predicted stabilising effect of 2P-O-methylation on genomic RNA argues that the coding capacity of the genome would have increased suf¢ciently for genuinely catalytic proteins such as RNA polymerase, and later ribonucleotide reductase, to arise, paving the way to the DNA world (Figure 4) . cache = ./cache/cord-315616-pvt0amth.txt txt = ./txt/cord-315616-pvt0amth.txt === reduce.pl bib === id = cord-314833-6fue84x6 author = Chang, Chung-ke title = The SARS coronavirus nucleocapsid protein – Forms and functions date = 2014-01-11 pages = extension = .txt mime = text/plain words = 9459 sentences = 464 flesch = 51 summary = The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. proposed a structure-based domain arrangement for SARS-CoV N protein where the NTD and CTD are sandwiched between three IDRs. Sequence alignments suggested that other coronavirus N proteins might share the same structural organization based on intrinsic disorder predictor profiles and secondary structure predictions (Fig. 2) . noticed that effective binding to RNA by MHV N protein in host cells required the presence of both the NTD and CTD (Hurst et al., 2009) , suggesting that the NTD and CTD formed a single bipartite RNA interaction site, a feature to be reiterated in the final SARS-CoV RNP model. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA cache = ./cache/cord-314833-6fue84x6.txt txt = ./txt/cord-314833-6fue84x6.txt === reduce.pl bib === id = cord-319664-gyktrd36 author = Mancini, Fabiola title = Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date = 2020-06-18 pages = extension = .txt mime = text/plain words = 2082 sentences = 112 flesch = 54 summary = Finally, to evaluate the performance of molecular assays a standard curve was generated by 10-fold dilutions of SARS-CoV-2 RNA, isolated and extracted at Istituto Superiore di Sanità in Rome, Italy, and quantified by a well-established copy number of RNA synthetic E gene (Wuhan coronavirus, EVAg, www. All specimens were also manually extracted and tested for the presence of SARS-CoV-2 by in-house rt-Realtime PCR and the 2019-nCoV TaqMan RT-PCR Kit. In particular, we investigated the RNA availability and virus detection using both the purified and thermal/non-extractive procedures also with this commercial kit because it is based on the same primers, probes and assays developed by the CDC and used in the inhouse molecular method. This study corroborates our results for in-house rt-Real Time PCR, showing a lower sensitivity of the heat treatment (range ΔCT value of 0.5-1.0) when compared with purified samples, but, dissimilar to our findings, a total inhibition was found by the commercial kit RealStar SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), where all positive samples failed in the detection of Sars-CoV-2 [14] . cache = ./cache/cord-319664-gyktrd36.txt txt = ./txt/cord-319664-gyktrd36.txt === reduce.pl bib === id = cord-318853-mxyxwkhx author = Sallie, Richard title = Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date = 2005-08-22 pages = extension = .txt mime = text/plain words = 10541 sentences = 396 flesch = 25 summary = Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. Hence, as relative concentrations of wild-type and variant viral proteins vary, alteration of both processivity and fidelity of RNA pol results, permitting viruses to adaptively respond to environmental changes, including immune recognition and reaction to evolving cell receptors. As clear evidence exists for viral disruption of leptin function [106] and virus-associated weight gain in humans [107] and monkeys [108] , is it possible the global epidemics of type II diabetes mellitus, insulin resistance, hyperlipidaemia and obesity now prevalent [109] [110] [111] [112] [113] [114] [115] [116] , are just that; epidemics fundamentally caused by viruses that co-opt insulin or leptin or other associated receptors for cell access and generate protein quasispecies that disrupt receptor function? cache = ./cache/cord-318853-mxyxwkhx.txt txt = ./txt/cord-318853-mxyxwkhx.txt === reduce.pl bib === id = cord-319100-3gdawhfn author = Kirkland, P.D. title = The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date = 2020-06-10 pages = extension = .txt mime = text/plain words = 4624 sentences = 204 flesch = 49 summary = authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses Also of concern are recommendations (3, 4) to include foetal bovine serum (fbs) as a source of protein to enhance the stabilising properties of VTMs. This report documents observations of the adverse impact of certain VTMs on real time reverse transcription PCR (qRT-PCR) assays for the detection of SARS-CoV-2 virus as well as on a Type A influenza virus and a herpesvirus and discuss the broader implications of the inclusion of foetal bovine serum as a protein supplement to VTMs. During the initial investigation, purified RNA from an Australian isolate (WMD DC1) of SARS-CoV-2 was supplied to the Elizabeth Macarthur Agriculture Institute (EMAI) by the Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales (NSW). cache = ./cache/cord-319100-3gdawhfn.txt txt = ./txt/cord-319100-3gdawhfn.txt === reduce.pl bib === id = cord-318576-dc5n6ni4 author = Jitobaom, Kunlakanya title = Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation date = 2020-05-08 pages = extension = .txt mime = text/plain words = 6821 sentences = 345 flesch = 53 summary = From the previous section, we demonstrated that human genes in the GO terms of the cell cycle and the regulation of the cell cycle process adopt codon usage patterns similar to those of þssRNA (subgroups 6, 7), -ssRNA (subgroup 4), retrovirus (HIV-1), and ambisense (subgroup 4) viruses. The lists of upregulated proteins upon viral infection were submitted to GO-TermFinder (Supplementary File 3) , and the enriched GO terms were compared to the enriched GO terms of human genes with codon usage patterns similar to RNA viruses from every subgroup. Several enriched GO terms of upregulated protein profiles during viral infections were found to be identical to the GO terms of human genes with codon usage patterns similar to RNA viruses ( Figure 4 ). Several GO terms of human genes with codon usage patterns similar to RNA viruses have been found by previous studies to be identical to the GO terms of upregulated protein profiles in viral infections. cache = ./cache/cord-318576-dc5n6ni4.txt txt = ./txt/cord-318576-dc5n6ni4.txt === reduce.pl bib === id = cord-318551-c1qr27lg author = Boguszewska‐Chachulska, Anna M. title = Rna Viruses Redirect Host Factors to Better Amplify Their Genome date = 2005-12-29 pages = extension = .txt mime = text/plain words = 10673 sentences = 511 flesch = 44 summary = (Adapted with permission from Pasternak et al., 2001.) Transcription of segmented (À) strand RNA viruses such as the Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Tenuiviruses requires a primer to initiate synthesis of the mRNAs. This is achieved by cap-snatching in which the replicase complex, or a protein thereof, binds to the 5 0 region of cell mRNAs, cleaves off the cap together with generally 7-15 nucleotides from the 5 0 end of the cell mRNA, and uses this fragment as a primer to initiate synthesis of the viral mRNAs (Bouloy et al., 1978; Nguyen and Haenni, 2003) . (1996) PV, poliovirus; MHV, mouse hepatitis virus; WNV, West Nile virus; BVDV, bovine viral diarrhea virus; HPIV-3, human parainfluenza virus-3; IG (À), intergenic region in (À) RNA; UTR, untranslated region; Leader RNA (À), 3' end of (À) RNA; Leader RNA (þ), 5' end of (þ) RNA; HF, host factor; PCBP, poly(C)-binding protein; PABP, poly(A)-binding protein; hnRNP A1, heterogeneous nuclear ribonucleoprotein A1; PTB, polypyrimidine tract-binding protein; TIA-1, T-cell-activated intracellular antigen; TIAR, TIA-1-related; RHA, RNA helicase A; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. cache = ./cache/cord-318551-c1qr27lg.txt txt = ./txt/cord-318551-c1qr27lg.txt === reduce.pl bib === id = cord-319842-4mnaicki author = Jackson, William T title = Subversion of Cellular Autophagosomal Machinery by RNA Viruses date = 2005-04-26 pages = extension = .txt mime = text/plain words = 6936 sentences = 320 flesch = 39 summary = Infection of human cells with poliovirus induces the proliferation of double-membraned cytoplasmic vesicles whose surfaces are used as the sites of viral RNA replication and whose origin is unknown. Here, we explore the role of several constituents of autophagosome machinery in poliovirus-and rhinovirusinfected cells by monitoring: the presence of autophagosomal protein LC3 in virally induced vesicles, the acquisition of colocalization of LC3 and LAMP1 in virally infected cells, the viral induction of punctate structures that stain with monodansylcadaverine (MDC), and the effects of perturbing the autophagosomal pathway pharmacologically and via RNA interference on intracellular and extracellular virus yield. To determine whether the autophagosome-like membranes induced during poliovirus infection perform an antiviral function or facilitate viral replication, we tested the effect on poliovirus yield of pretreating H1-HeLa cells with either tamoxifen or rapamycin, known inducers of autophagy. cache = ./cache/cord-319842-4mnaicki.txt txt = ./txt/cord-319842-4mnaicki.txt === reduce.pl bib === id = cord-318164-6rqi17oz author = Paoli, D. title = Sperm cryopreservation during the SARS-CoV-2 pandemic date = 2020-10-10 pages = extension = .txt mime = text/plain words = 3258 sentences = 177 flesch = 48 summary = This study therefore aimed to analyze the safety of sperm cryopreservation for cancer patients after the onset of the pandemic in Italy, through assessment of the risk of SARS-CoV-2 exposure and viral RNA testing of semen samples. CONCLUSION: This preliminary assessment suggests that a thorough evaluation (especially in the setting of a multidisciplinary team) and molecular confirmation of the absence of SARS-CoV-2 in seminal fluid from asymptomatic cancer patients may assist in ensuring the safety of sperm cryopreservation. This study thus aimed to evaluate the safety of sperm cryopreservation of cancer patients referred to our sperm bank after the onset of the pandemic in Italy through the assessment of the risk of SARS-CoV-2 exposure and, in selected volunteers, viral RNA testing of semen samples. This was further confirmed by testing seminal fluid samples from 10 asymptomatic cancer patients for SARS-CoV-2 RNA. cache = ./cache/cord-318164-6rqi17oz.txt txt = ./txt/cord-318164-6rqi17oz.txt === reduce.pl bib === id = cord-315054-kji2kfek author = Chakraborty, Nabarun title = Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration date = 2020-07-22 pages = extension = .txt mime = text/plain words = 4462 sentences = 214 flesch = 45 summary = In an effort to be economical with available resources, snap-frozen euthanized mice are the straightforward solution; however, this method increases the risk of temperature abuse during the thawing process at the beginning of the tissue collection. We found that prolonged immersion of snap frozen mouse carcass in 10% neutral buffered formalin at 4°C yielded minimal microscopic signs of ice crystallization and delivered tissues with histomorphology that is optimal for hematoxylin and eosin (H&E) staining and fixation on glass slides. An omics-pathology integration approach could be the most effective for phenometo-genome interpretation if omics assays are conducted using the particular tissue specimen, where injury signatures are informed by histopathology image analysis (Pathak and Dave, 2014; Yu et al., 2017) . These snap-frozen carcasses had to undergo onground freeze-thaw cycles before tissue collection, which is typically expected to compromise overall sample quality and make the histopathologic analysis challenging (Lyons et al., 1979; Pikal-Cleland et al., 2000) . cache = ./cache/cord-315054-kji2kfek.txt txt = ./txt/cord-315054-kji2kfek.txt === reduce.pl bib === id = cord-317720-gbi11oxx author = Lefferts, Joel A. title = Implementation of an Emergency Use Authorization Test During an Impending National Crisis date = 2020-05-14 pages = extension = .txt mime = text/plain words = 2148 sentences = 80 flesch = 39 summary = Concerned that the efforts of state laboratories would be further impacted by lack of resources, we began to identify sources -including the WHO, the CDC, and commercial vendors -of the required primers and probes for the reverse transcriptase polymerase chain reaction (RT-PCR) detection of the virus and placed orders for test reagents from potential suppliers. The document provided guidance for high complexity testing laboratories developing SARS-CoV-2 tests for submission for Emergency Use Authorization (EUA) status with respect to required validation experiments and reporting to the FDA. Initially laboratories were required to spike RNA transcripts into previously extracted nucleic acid from negative samples for the CDC assay to determine the limit of detection but this had its own challenges of not representing extraction of true clinical samples and issues with degradation were identified. Our plan included the production of enough contrived clinical specimens and control material to proceed with validation or verification of the multiple (laboratory-developed and CDC EUA) tests that we were evaluating. cache = ./cache/cord-317720-gbi11oxx.txt txt = ./txt/cord-317720-gbi11oxx.txt === reduce.pl bib === id = cord-319501-a2x1hvkk author = Wong, Lok-Yin Roy title = A molecular arms race between host innate antiviral response and emerging human coronaviruses date = 2016-01-15 pages = extension = .txt mime = text/plain words = 7759 sentences = 460 flesch = 51 summary = Particularly, the host pathogen recognition receptors and the signal transduction pathways to mount an effective antiviral response against SARS and MERS coronavirus infection are discussed. This suggests SARS-CoV N may interfere with RNA recognition by host immune sensors such as RIG-I and MDA5 thus achieving suppressive role in IFN production. Our group demonstrated that MERS-CoV ORF4a interacts with PACT, a cellular dsRNA-binding protein that optimally activates RIG-Iand MDA5-induced type I IFN production, in an RNAdependent manner (Siu et al., 2014c) . Infection with SARS-CoV and MERS-CoV has been accompanied with suppression of innate immune response, most notably with the suppression of type I IFN production and signaling pathways. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses pact-induced activation of RIG-I and MDA5 in the innate antiviral response cache = ./cache/cord-319501-a2x1hvkk.txt txt = ./txt/cord-319501-a2x1hvkk.txt === reduce.pl bib === id = cord-318749-k91oku7h author = Dong, Hui-Jun title = Selective regulation in ribosome biogenesis and protein production for efficient viral translation date = 2020-10-29 pages = extension = .txt mime = text/plain words = 7265 sentences = 384 flesch = 38 summary = Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Similarly, ribosomes are required for the protein synthesis of host cells and viruses, but the biogenesis factor RBFs can also impact the proliferation of virus and cell-intrinsic immune responses. The multifunctional nucleolar phosphoprotein nucleophosmin (NPM) plays a lead role in ribosome biogenesis to stimulate RNA Pol I-dependent transcription (Li and Hann 2013) and regulates SARS-CoV, IBV, HIV-1, HCV Recruited by viral proteins to facilitate viral replication Chen et al. RPS25 deletion in yeast or mammalian cells has minimal effects on cellular protein synthesis, which implies that this ribosomal protein may be selectively required for viral IRES-mediated translation (Jack et al. Conservation of multifunctional ribosomal protein metallopanstimulin-1 (RPS27) through complex evolution demonstrates its key role in growth regulation in Archaea, eukaryotic cells, DNA repair, translation and viral replication cache = ./cache/cord-318749-k91oku7h.txt txt = ./txt/cord-318749-k91oku7h.txt === reduce.pl bib === id = cord-318495-1w74wf02 author = Vignuzzi, Marco title = Defective viral genomes are key drivers of the virus–host interaction date = 2019-06-03 pages = extension = .txt mime = text/plain words = 8876 sentences = 429 flesch = 33 summary = The demonstration of hotspots for the generation of copyback DVGs from respiratory syncytial virus (RSV) and the identification of specific nucleotides that determine where copy-back DVGs rejoin further demonstrate that the generation of copy-back DVGs is not completely random, but instead that specific sequences encoded in the viral genome direct or facilitate their formation 50 in some infections, DVG generation is not a completely stochastic process and, instead, virus-encoded sequences favour the production and/or amplification of predominant DVGs. It remains to be determined whether conservation is a property of certain DVG types and which specific sequences and/or RNA structures lead to DVG generation in these conditions. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus cache = ./cache/cord-318495-1w74wf02.txt txt = ./txt/cord-318495-1w74wf02.txt === reduce.pl bib === id = cord-314316-hsspggp8 author = Sirinarumitr, Theerapol title = Rapid in situ hybridization technique for the detection of ribonucleic acids in tissues using radiolabelled and fluorescein-labelled riboprobes date = 1997-08-31 pages = extension = .txt mime = text/plain words = 3838 sentences = 205 flesch = 53 summary = Small intestinal sections from pigs experimentally and naturally infected with TGEV were hybridized for various times at 52°C and 70°C with a radiolabelled or a fluorescein-labelled RNA probe in a standard hybridization or a REH buffer. Small intestinal sections from pigs experimentally and naturally infected with TGEV were hybridized for various times at 52°C and 70°C with a radiolabelled or a fluorescein-labelled RNA probe in a standard hybridization or a REH buffer. With the fluorescein-labelled probe, viral RNA was detected in virus-infected cells of the intestines after 30 min of hybridization by using the REH buffer. With the fluorescein-labelled probe, viral RNA was detected in virus-infected cells of the intestines after 30 min of hybridization by using the REH buffer. Signal intensity was greater with the REH buffer than with the standard hybridization buffer when compared at each hybridization time and hybridization temperature using both radiolabelled and fluorescein-labelled probes. cache = ./cache/cord-314316-hsspggp8.txt txt = ./txt/cord-314316-hsspggp8.txt === reduce.pl bib === id = cord-319179-gqaxf7mz author = Denison, M. title = Identification of putative polymerase gene product in cells infected with murine coronavirus A59 date = 1987-04-30 pages = extension = .txt mime = text/plain words = 1638 sentences = 88 flesch = 59 summary = When infected cells and isolated virions were assayed for this protein by two-dimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. When infected cells and isolated virions were assayed for this protein by twodimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. To determine if p28 was a minor protein actually present in virions, infected 17CL-1 cells were labeled with [35S] methionine and virus was purified as described in Fig. 4 . A portion of the labeled virus preparation was analyzed directly by two-dimensional gel electrophoresis whereas a second part was mixed with the [35S] methionine-labeled cell-free products prior to analysis (Fig. 4) . cache = ./cache/cord-319179-gqaxf7mz.txt txt = ./txt/cord-319179-gqaxf7mz.txt === reduce.pl bib === id = cord-312892-p72zwmtb author = Chen, Nanhua title = RNA sensors of the innate immune system and their detection of pathogens date = 2017-04-04 pages = extension = .txt mime = text/plain words = 4237 sentences = 237 flesch = 44 summary = It in turn causes the multimerization of cytoplasmic TIR domains, which will recruit downstream adaptors TRIF or MyD88 through homotypic interaction, further forming signaling complex called signalosome and activating downstream transcription factors: one is NF-jB that induces proinflammtory cytokines, another is interferon regulatory factor (IRF) that induces anti-viral type I Interferon (IFN) (6) . The summary of cellular localizations and distributions, ligand recognitions, activation mechanisms, cell signaling, recognition of pathogens, and cross-talks for RNA PRRs (2) TLR3 (2) RIG-I (2) The understanding of RNA PRR immune biology including the ligand recognitions, cellular localizations, cell signaling pathways, mechanisms of activation, recognized pathogens and the interactions between different RNA PRRs will definitely be helpful to improve the anti-viral immune response. Third, TLR3, 7, 8 are primarily expressed by macrophages and DCs and recognize viral RNA within the endosomal compartment, whereas RLRs (RIG-I, MDA5) and NLRs (NLRP3, NOD2) are ubiquitously expressed and sense viral RNA within the cytoplasm of infected cells (Table 1 ). cache = ./cache/cord-312892-p72zwmtb.txt txt = ./txt/cord-312892-p72zwmtb.txt === reduce.pl bib === id = cord-317455-6qx0v28w author = Brown, Paul A. title = Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date = 2018-09-10 pages = extension = .txt mime = text/plain words = 3562 sentences = 174 flesch = 52 summary = Turkey coronavirus, originally identified in the USA in the 1970s as one of the agents responsible for an acute enteritis named bluecomb (Panigrahy, Naqi, & Hall, 1973; Ritchie, Deshmukh, Larsen, & Pomeroy, 1973) and since with a multifactorial disease known as poult enteritis complex of turkeys (PEC) , has now been detected in most areas where turkeys are farmed Cavanagh et al., 2001; Dea & Tijssen, 1988; Domańska-Blicharz, Seroka, Lisowska, Tomczyk, & Minta, 2010; Martin, Vinco, Cordioli, & Lavazza, 2002; Maurel et al., 2009; Teixeira et al., 2007) , although TCoVs isolated in Europe have been shown to have a different genetic lineage to those isolated in the USA (Brown et al., 2016; Maurel et al., 2011) . At 1-day post-inoculation (dpi), two SPF turkey contacts were introduced into groups 1-4 as sentinels to demonstrate horizontal transmission of infectious virus. They were housed in a negative pressure room, under the same rearing conditions as in Exp 2, with three 11-day-old SPF turkeys introduced as contact-birds at 1 dpi to demonstrate horizontal transmission. cache = ./cache/cord-317455-6qx0v28w.txt txt = ./txt/cord-317455-6qx0v28w.txt === reduce.pl bib === id = cord-319729-6lzjhn8j author = Tian, Bin title = Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway date = 2018-01-19 pages = extension = .txt mime = text/plain words = 7804 sentences = 409 flesch = 50 summary = title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. To assess innate immune responses in astrocytes, cells were infected with DRV or B2c at an MOI of 0.1 and the expression of several proteins involved in the MAVS signaling pathway, namely, RIG-I, p-IRF7, STAT1 and IFIT1 (ISG56), was measured by Western blot. cache = ./cache/cord-319729-6lzjhn8j.txt txt = ./txt/cord-319729-6lzjhn8j.txt === reduce.pl bib === id = cord-319780-rfj9t99r author = Alexander, S.P.H. title = A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date = 2020-05-01 pages = extension = .txt mime = text/plain words = 15196 sentences = 814 flesch = 47 summary = Analysis of the co-crystal structure suggested that the SARS spike protein binds to the active site of angiotensin converting enzyme 2 (ACE2, Li et al., 2005) . A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . A recent cryo-EM structure suggested that ACE2 and B 0 AT1/SLC6A19 form a heterodimer which pairs up through interfaces between the two ACE2 partners (Figure 1) , with the RBD of SARS-CoV-2 spike protein binding to the peptidase active site of ACE2 suggesting that B 0 AT1/SLC6A19 may facilitate entry of the novel coronavirus. Tumor necrosis factor- convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) cache = ./cache/cord-319780-rfj9t99r.txt txt = ./txt/cord-319780-rfj9t99r.txt === reduce.pl bib === id = cord-317715-xtsi663k author = Ortiz-Riaño, Emilio title = D471G Mutation in LCMV-NP Affects its Ability to Self-associate and Results in a Dominant Negative Effect in Viral RNA Synthesis date = 2012-10-16 pages = extension = .txt mime = text/plain words = 9164 sentences = 483 flesch = 52 summary = Reporter gene activation (FFL) is shown as percentage (%) of LCMV NP-NP wt interaction (pC-NP-VP16 and pC-NP-GAL4) after normalization of transfection efficiencies with the Renilla luciferase expression plasmid pRL SV40 (ii). Unexpectedly, the D471A substitution impeded both NP-NP and NP-Z interactions, as well as NP functions in replication and transcription of the LCMV MG and the ability of NP to counteract SeV-mediated induction of the host IFN-I response, suggesting that change D to A at position 471 might have affected the overall structure of NP without affecting its stability as reflected by its unchanged expression levels determined by WB using anti-VP16 ( Figures 6A and 6B ) or anti-HA ( Figures 6C and 6D) antibodies. (C) Replication and transcription activity: BHK-21 cells were co-transfected with the LCMV MG as described in Figure 3 together with expression plasmids for the viral polymerase (L) and wt or indicated mutant NPs, and pSV40-Cluc expression vector to normalize transfection efficiencies. cache = ./cache/cord-317715-xtsi663k.txt txt = ./txt/cord-317715-xtsi663k.txt === reduce.pl bib === id = cord-319116-2ts6zpdb author = Ruggiero, Emanuela title = G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy date = 2018-04-20 pages = extension = .txt mime = text/plain words = 9124 sentences = 410 flesch = 42 summary = Since the number of reports describing the presence of G4s in virus genomes has boomed in the past 2 years and treatment with several G4 ligands has shown potentially interesting therapeutic activity, we here aim at presenting, organizing and discussing an up-to-date close-up of the literature on G4s in viruses and the classes of molecules that have shown antiviral activity by viral G4 targeting. The research of G4s in the HIV-1 genome has been quite productive, concerning not only the two RNA viral genome copies, but also the integrated proviral genome, specifically For each virus the following information is shown: virion structure and dimension, genome size and organization; schematic representation of the G4 (red dots) location in the viral genomes or in the mRNA and G4 binding proteins; number of G4s assessed through bioinformatics analysis, according to the corresponding references; G4 ligands reported to date to display antiviral effect and corresponding references. cache = ./cache/cord-319116-2ts6zpdb.txt txt = ./txt/cord-319116-2ts6zpdb.txt === reduce.pl bib === id = cord-315085-rucfowvv author = Sekulic, Miroslav title = Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date = 2020-05-26 pages = extension = .txt mime = text/plain words = 5025 sentences = 302 flesch = 47 summary = In this study we report postmortem findings and detection and sequencing of SARS-CoV-2 viral RNA from formalin-fixed paraffinembedded (FFPE) samples of multiple organs collected in 2 patients with antemortem detection of SARS-CoV-2. The patient's medical history was otherwise notable for dementia, radiologic evidence of a left lung mass (managed with hospice care), coronary artery disease (status post coronary artery bypass grafting), atrial fibrillation (biventricular pacemaker implanted), congestive heart failure, peripheral artery disease (status post iliac stenting), diabetes mellitus, hypertension, dyslipidemia, chronic kidney disease, gout, smoking, cerebrovascular accidents, and urinary tract infections. On day 1 after admission, ❚Image 2❚ (Case 1) Postmortem microscopic examination of the lungs showed diffuse alveolar damage characterized by hyaline membrane formation (A, ×100) and scattered squamous metaplasia of distal airways (B, ×100) on a background of emphysematous changes. cache = ./cache/cord-315085-rucfowvv.txt txt = ./txt/cord-315085-rucfowvv.txt === reduce.pl bib === id = cord-319681-kjet3e50 author = Lin, Zhaoru title = Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U(6)A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting date = 2012-06-28 pages = extension = .txt mime = text/plain words = 8862 sentences = 391 flesch = 57 summary = The mRNA signal for À1 FS is composed of two elements, a slippery sequence with consensus X_XXY_ YYZ (underlines denote zero frame; X can be any base, Y is A or U, Z is not G in eukaryotic systems) where the ribosome changes frame, and a downstream stimulatory RNA structure, a stem-loop or pseudoknot (reviewed in 3, 4) . A version of the À1 FS reporter plasmid with the IBV slippery sequence (p2lucIBV-AON) was also Spacer-length dependence of programmed À1 or À2 ribosomal frameshifting on a U 6 A heptamer supports a role for mRNA tension in frameshifting Based on the published literature, including our own studies of 80S ribosomes stalled at the IBV frameshift-stimulatory pseudoknot (22, 37) , we proposed a mechanical model of frameshifting in which a failure of intrinsic ribosomal helicase activity (15, 28) to unwind efficiently the stimulatory RNA during the translocation step leads to the build up of tension in the mRNA and subsequently, breakage of codon:anticodon contacts and realignment of the tRNAs in the À1 reading frame. cache = ./cache/cord-319681-kjet3e50.txt txt = ./txt/cord-319681-kjet3e50.txt === reduce.pl bib === id = cord-318478-fn0gcxbb author = Ziv, Omer title = The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date = 2020-10-07 pages = extension = .txt mime = text/plain words = 5760 sentences = 343 flesch = 56 summary = Available models for the RNA structure of SARS-CoV-2 and related viruses are largely confined to short-distance base-pairing which result in local folding of important cis-acting elements (Andrews et al., 2020; Huston et al., 2020; Kelly et al., 2020; Lan et al., 2020; Manfredonia et al., 2020; Ryder, 2020; Sanders et al., 2020; Sun et al., 2020) . In addition to the canonical UTR structures, we provide here a direct in vivo evidence for genome cyclization in SARS-CoV-2, mediated by long-range base-pairing between the 5′ and 3′ UTRs ( Figures 5B and S4B ). The long-distance RNA structure map for SARS-CoV-2 provides a practical starting point to dissect the regulation of discontinuous transcription, as it identifies cis-acting elements that interact with each other to create genome topologies that favour the synthesis of the ensemble of sgmRNAs. RNA viruses evolve sophisticated mechanisms to enhance the functional capacity of their size-restricted genomes and to regulate the expression levels of their replicase components. cache = ./cache/cord-318478-fn0gcxbb.txt txt = ./txt/cord-318478-fn0gcxbb.txt === reduce.pl bib === id = cord-317537-wgu5cd0y author = Lu, Hsiang-Chia title = Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant date = 2009-05-25 pages = extension = .txt mime = text/plain words = 8155 sentences = 474 flesch = 57 summary = All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 4I) , and statistics analysis (ANOVA) of real-time RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV clone-infected protoplasts at 24 h postinoculation revealed no significant difference in percentage between these clones (P = 0.91). All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 6J) , and statistics analysis (ANOVA) of realtime RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV cloneinfected protoplasts at 24 h post-inoculation revealed no significant difference in percentage between these clones (P = 0.83). Our results indicated that the important amino acids of the CP that allowed for the CymMV systemic infection are located within the previously predicted RNA binding domain ( Fig. 7A; 1) . cache = ./cache/cord-317537-wgu5cd0y.txt txt = ./txt/cord-317537-wgu5cd0y.txt === reduce.pl bib === id = cord-320169-dtv7to3l author = Liu, Yen-Chin title = COVID-19: the First Documented Coronavirus Pandemic in History date = 2020-05-05 pages = extension = .txt mime = text/plain words = 1935 sentences = 127 flesch = 51 summary = The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. The spike glycoprotein of SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) in human and Chinese horseshoe bats, civet for cell entry, that is also dependent on S protein priming by the serine protease TMPRSS2. Domestic animals can suffer from disease as intermediate hosts that cause virus transmission from natural hosts to humans; for example, SARS-CoV and MERS-CoV crossed the species barriers into masked palm civets and camels, respectively [30, 31] [ Table 1 ]. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. cache = ./cache/cord-320169-dtv7to3l.txt txt = ./txt/cord-320169-dtv7to3l.txt === reduce.pl bib === id = cord-321053-lgae22f8 author = Gerold, Gisa title = Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date = 2013-10-04 pages = extension = .txt mime = text/plain words = 9393 sentences = 470 flesch = 42 summary = Numerous in vitro studies in combination with a growing number of HCV sequencing data from patients undergoing DAA treatment underline that the virus can develop drug-resistance and fitness restoring compensatory mutations [11] . An emerging third group of antivirals, so called hosttargeting antivirals (HTA), may be part of such future combination therapies, in particular as HTAs hold the promise of overcoming some of the caveats of DAAs. HTAs are antibodies, RNAs or small molecules, which interfere with host factors needed for HCV propagation. On the one hand, this demonstrates that HCV can in theory evade HTA therapy by mutating the viral binding partner of the targeted host factor and in fact suggests a low genetic barrier to resistance. Targeting HCV RNA Replication: Phosphatidylinositol 4-kinase III alpha (PI4KIIIα) Genome wide RNA interference screens and in depth cell culture replication assays with HCV replicons and full length infectious virus have revealed numerous additional host dependency factors, that could in principle serve as antiviral targets [99] [100] [101] [102] [103] [104] [105] [106] [107] . cache = ./cache/cord-321053-lgae22f8.txt txt = ./txt/cord-321053-lgae22f8.txt === reduce.pl bib === id = cord-319906-s7kzp795 author = Zemla, Adam T title = StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase date = 2011-06-02 pages = extension = .txt mime = text/plain words = 7496 sentences = 303 flesch = 40 summary = When for a given reference structure a structure-based search is performed on a set of proteins from the Protein Data Bank (PDB), StralSV identifies all structurally similar fragments from that set, evaluates the calculated structure-based alignments between the query (reference) motif (designated "segment" in this work) and the detected structure fragments, and quantifies the observed sequence variability at each residue position on the query structure. (For an illustration of a "span", see additional file 1: StralSV-RdRp_Suppl_Figure 1.docx.) All residue-residue pairs that are contained within a span's alignment are used to calculate the sequence variability data at the corresponding position in the query structure. The qualified hits (structure fragments from PDB with detected local similarities to the query structure) for six selected sequence positions (positional hits) of polio RdRp (positions identified in Figure 3 ) were categorized and quantified based on SCOP (Structure Classification of Proteins database; version 1.75, June 2009 release) identifiers [32] . cache = ./cache/cord-319906-s7kzp795.txt txt = ./txt/cord-319906-s7kzp795.txt === reduce.pl bib === id = cord-318751-4v2tl0gi author = Arias, Armando title = Progress towards the prevention and treatment of norovirus infections date = 2013-11-17 pages = extension = .txt mime = text/plain words = 6833 sentences = 310 flesch = 37 summary = While the efficient culture of human noroviruses (HuNoVs) in immortalized cells has yet to be achieved [5] , the development of a norovirus replicon [6] , which allows the generation of cell lines stably replicating Norwalk virus RNA, has facilitated many small molecule inhibitors to be tested in vitro. The discovery of murine norovirus (MNV) [7] , which replicates efficiently in immortalized macrophage cells and has both reverse genetics systems and small animal models available [8] , has also enabled the examination of the immune responses to noroviruses as well as the efficacy of inhibitors in vitro and in vivo. However, the vast majority of such studies are conducted with norovirus surrogates such as feline calicivirus or MNV, as testing decontamination procedures for HuNoV is difficult owing to the lack of an available cell culture system to detect any remaining infectivity. cache = ./cache/cord-318751-4v2tl0gi.txt txt = ./txt/cord-318751-4v2tl0gi.txt === reduce.pl bib === id = cord-317773-jdq1d98i author = Meng, Qing-Wen title = Enhanced inhibition of Avian leukosis virus subgroup J replication by multi-target miRNAs date = 2011-12-22 pages = extension = .txt mime = text/plain words = 3614 sentences = 214 flesch = 53 summary = RESULTS: In this study, the avian leukosis virus subgroup J (ALV-J) proviral genome, including the gag genes, were treated as targets for RNAi. Four pairs of miRNA sequences were designed and synthesized that targeted different regions of the gag gene. To avoid the generation of escape variants during virus infection, expression vectors of multi-target miRNAs were constructed using the multi-target serial strategy (against different regions of the gag, pol, and env genes). CONCLUSION: The strategy of multi-target miRNAs might be an effective method for inhibiting ALV replication and the acquisition of resistant mutations. In some studies, transfection of siRNA designed to target C virus (HCV) remarkably inhibited the expression of virus-specific proteins and protected cells against HCV RNA, in vitro [4, 5] . In another study, Hepatitis B virus (HBV) replication was successfully inhibited after plasmid expression of HBV siRNA transfected into mouse liver [6] . cache = ./cache/cord-317773-jdq1d98i.txt txt = ./txt/cord-317773-jdq1d98i.txt === reduce.pl bib === id = cord-320501-xqgqq55q author = Theobald, Nigel title = Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine date = 2020-06-24 pages = extension = .txt mime = text/plain words = 1203 sentences = 58 flesch = 47 summary = title: Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine Liposomal encapsulation of drugs with bioavailability issues was a proven approach in small molecule pharma, and it was apparent to biopharma R&D scientists that LNPs could meet the basic requirements of an RNA/DNA delivery system too, namely to protect nucleic acid from in vivo digestion as it travels to the target. As scientists looked to alternative carriers that could be adapted to encapsulate and protect nucleic acids, mesoporous silica nanoparticles (MSNs)silica-based nanostructured materials with excellent biocompatibility and chemical stability This surface simply and effectively traps and protects nucleic acids (such as mRNA/pDNA) from nuclease enzymes as it travels to the cells. Once inside the cell, the DNA/RNA is released and will result in synthesis of the foreign/target protein which will activate the immune system, leading to both a cellular and humoral immune response. cache = ./cache/cord-320501-xqgqq55q.txt txt = ./txt/cord-320501-xqgqq55q.txt === reduce.pl bib === id = cord-319635-kh99n7q2 author = Chiang, Wei-Wei title = Cell Type-Dependent RNA Recombination Frequency in the Japanese Encephalitis Virus date = 2014-07-22 pages = extension = .txt mime = text/plain words = 5101 sentences = 281 flesch = 55 summary = Such cleaved small RNA fragments may be further degraded through an RNA interference pathway triggered by viral double-stranded RNA during replication in mosquito cells, resulting in a lower frequency of RNA recombination in mosquito cells compared to that which occurs in mammalian cells. Yates' chi-square test was used to assess the frequency of RNA recombination in cells coinfected by two virus strains or transfected by viral RNA fragments. Two and one recombinant form(s) were, respectively, identified in selected samples from BHK-21 and C6/36 cells, when they were coinfected with the T1P1-S1 and CJN-S1 strains of the Japanese encephalitis virus. As in our previous report, different strains of the JEV can coinfect host cells derived from mosquitoes or mammals [25] , which actually generates recombinant forms of the virus [30] . In this study, we infected host cells with Nakayama strains of the JEV, followed by transfection of the (+)5 3 -UTR-I RNA fragment. cache = ./cache/cord-319635-kh99n7q2.txt txt = ./txt/cord-319635-kh99n7q2.txt === reduce.pl bib === id = cord-321505-m40s6uw9 author = Sakamoto, Naoya title = Inhibition of hepatitis C virus infection and expression in vitro and in vivo by recombinant adenovirus expressing short hairpin RNA date = 2007-08-07 pages = extension = .txt mime = text/plain words = 4424 sentences = 253 flesch = 45 summary = Background and Aim: We have reported previously that synthetic small interfering RNA (siRNA) and DNA‐based siRNA expression vectors efficiently and specifically suppress hepatitis C virus (HCV) replication in vitro. Intravenous delivery of the adenovirus expressing shRNA into transgenic mice that can be induced to express HCV structural proteins by the Cre/loxP switching system resulted in specific suppression of virus protein synthesis in the liver. Here, we report that HCV replication was suppressed in vitro by recombinant retrovirus and adenovirus vectors expressing short hairpin RNA (shRNA) and that the delivery of the adenovirus vector to mice in vivo specifically inhibited viral protein synthesis in the liver. These results indicated that the decrease in luciferase activities was due to specific suppressive effects of shRNA on expression of HCV genomic RNA and the viral proteins, and not due to non-specific effects caused by the delivery of shRNA or to toxicity of the adenovirus vectors. cache = ./cache/cord-321505-m40s6uw9.txt txt = ./txt/cord-321505-m40s6uw9.txt === reduce.pl bib === id = cord-320921-eumuid3r author = Widagdo, W. title = Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits date = 2019-04-24 pages = extension = .txt mime = text/plain words = 4829 sentences = 239 flesch = 51 summary = Our data indicate that despite relatively high viral RNA levels produced, low levels of infectious virus are excreted in the upper respiratory tract of rabbits as compared to dromedary camels, thus resulting in a lack of viral transmission. Besides dromedary camels, other animal species, i.e. llamas, alpacas, and pigs have been shown to be susceptible and develop upper respiratory tract infection upon experimental intranasal MERS-CoV inoculation [9] [10] [11] . We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). cache = ./cache/cord-320921-eumuid3r.txt txt = ./txt/cord-320921-eumuid3r.txt === reduce.pl bib === id = cord-319781-6thdg2up author = Payne, Kelly title = Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date = 2020-07-24 pages = extension = .txt mime = text/plain words = 8233 sentences = 454 flesch = 51 summary = To understand factors that may contribute to viral spread and address long-term health sequelae for survivors, it is important to review evidence regarding viral presence in semen, sexual transmission potential, and possible effects on fertility. We review evidence for the following viruses: Ebola, Zika, West Nile, pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-corona virus-2 (SARS-CoV-2). Then, we present the state of current research regarding presence in semen, sexual transmission, and fertility effects for the Zika virus (ZIKV), Ebola virus (EBOV), West Nile virus (WNV), pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-coronavirus-2 (SARS-CoV-2) ( Table 1) . In this article, we have reviewed the presence in semen, possibility of sexual transmission, and fertility implications of each of the major recent viral pandemics: Zika, Ebola, West Nile, pandemic influenza, SARS, and SARS-CoV-2. cache = ./cache/cord-319781-6thdg2up.txt txt = ./txt/cord-319781-6thdg2up.txt === reduce.pl bib === id = cord-320935-3n157yl4 author = Kumar, Manish title = Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date = 2020-09-12 pages = extension = .txt mime = text/plain words = 6613 sentences = 346 flesch = 44 summary = This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. cache = ./cache/cord-320935-3n157yl4.txt txt = ./txt/cord-320935-3n157yl4.txt === reduce.pl bib === id = cord-319821-ij34t1ae author = Bauer, Lisa title = Direct-acting antivirals and host-targeting strategies to combat enterovirus infections date = 2017-04-12 pages = extension = .txt mime = text/plain words = 4041 sentences = 235 flesch = 40 summary = Here, we will review recent efforts to develop direct-acting antivirals as well as host factor-targeting inhibitors to treat enterovirus infections (Table 1) . 2C ATPase and 3D pol may be more promising targets for direct-acting antiviral drugs as they can be inhibited by small molecules, and several inhibitors of these factors were found to have broad-range anti-enteroviral activity. Since targeted drug discovery depends heavily on basic knowledge of virus replication, fundamental research on the role of viral enzymes as well as essential host factors for enterovirus replication remains needed for the development of broad-range antiviral drugs against these important pathogens. FDA-aroved drug to target fungal infections, is identified as a broad-spectrum enterovirus inhibitor and shown to target the lipid shuttling activity of oxysterol-binding protein that is essential for viral replication organell formation and/or function cache = ./cache/cord-319821-ij34t1ae.txt txt = ./txt/cord-319821-ij34t1ae.txt === reduce.pl bib === id = cord-320709-2pnqpljt author = Munster, Vincent J. title = Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis) date = 2016-02-22 pages = extension = .txt mime = text/plain words = 3951 sentences = 219 flesch = 53 summary = The Mx1, ISG56 and RANTES gene expression in the lungs of Jamaican fruit bats was analyzed as an indicator of the induction of an innate immune response to MERS-CoV infection. The tissue tropism of MERS-CoV in Jamaican fruit bats is comparable to the respiratory tract tropism observed in dromedary camels and humans 49, 50 . MERS-CoV and related batCoV-HKU4 can inhibit innate immune signaling in a variety of human cell lines in vitro via the ORF4b-encoded accessory proteins 52 Lungs of Jamaican fruit bat 5 were stained with α -cytokeratin as an epithelial marker (purple) and with a polyclonal α -coronavirus antibody (brown-red) to demonstrate that viral antigen was located along the basement membrane of alveolar pneumocytes of bat 1 at 2 dpi (indicated by black arrows). Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels cache = ./cache/cord-320709-2pnqpljt.txt txt = ./txt/cord-320709-2pnqpljt.txt === reduce.pl bib === id = cord-319649-d6dqr03e author = Yang, Jie title = A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing date = 2013-12-05 pages = extension = .txt mime = text/plain words = 7876 sentences = 375 flesch = 53 summary = Here, we expressed VP5 from type 5 Helicoverpa armigera cypovirus (HaCPV-5) in a eukaryotic system and determined that this VP5 possesses RNA chaperone-like activity, which destabilizes RNA helices and accelerates strand annealing independent of ATP. In this study, we expressed HaCPV-5 VP5 in a eukaryotic expression system and determined that this CPV VP5 possesses an RNA chaperone-like activity to ATP-independently destabilize RNA helices and accelerate strand annealing. Moreover, we found that HaCPV-5 VP5 could facilitate the transcription initiation of an alternative polymerase (i.e. reverse transcriptase) through a CPV panhandle-structured RNA template, thereby strongly suggesting a direct role of the RNA chaperone activity of VP5 in the initiation of cypoviral dsRNA replication. In the family Reoviridae, CPV VP5 may not be the only RNA chaperone, as rotavirus nonstructural protein 2 (NSP2), which is a multifunctional enzyme involved in rotaviral dsRNA replication, was previously shown to contain ATP-independent nucleic acid helix-destabilizing activity (45) . cache = ./cache/cord-319649-d6dqr03e.txt txt = ./txt/cord-319649-d6dqr03e.txt === reduce.pl bib === id = cord-320325-sjab8zsk author = Mendez, Aaron S title = Site specific target binding controls RNA cleavage efficiency by the Kaposi's sarcoma-associated herpesvirus endonuclease SOX date = 2018-12-14 pages = extension = .txt mime = text/plain words = 6508 sentences = 329 flesch = 53 summary = Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. Using an RNA substrate that is efficiently cleaved by SOX in cells, we revealed that specific RNA sequences within and outside of the cleavage site significantly contribute to SOX binding efficiency and target processing. Given that both substrates contain the requisite unpaired bulge at the predicted cleavage site (see Figure 2A and Supplementary Figure S2 ), these observations suggest that additional sequence or structural features impact SOX targeting efficiency on individual RNAs. Two SOX point mutants, P176S and F179A, located in an unstructured region of the protein that bridges domains I and II have been shown to be selectively required for its endonucleolytic processing of RNA substrates (Supplementary Figure S3A and S3B) (8, 21) . cache = ./cache/cord-320325-sjab8zsk.txt txt = ./txt/cord-320325-sjab8zsk.txt === reduce.pl bib === id = cord-318276-so5jooj0 author = Bertholet, Christine title = Vaccinia virus produces late mRNAs by discontinuous synthesis date = 1987-07-17 pages = extension = .txt mime = text/plain words = 6225 sentences = 329 flesch = 60 summary = RNA was isolated from noninfected or infected cells and then hybridized to 32P-labeled probes isolated from the 5' end region, upstream of the 11K coding sequences of cDNA clones 3, 8, and 9 (see Figure 2 ). To confirm this, and to identify the regions from which they are transcribed, the cDNA-derived probes used in the previous experiment were hybridized to cloned DNA restriction fragments representing the entire vaccinia virus genome ( Figure 4 ). %P-labeled DNA probes (~3, ~9, p9, pllK) derived from the 5' region of the corresponding cDNA clones or from genomic DNA (see Figure 2 ) were hybridized lo RNA isolated from uninfected (HeLa) or infected (Early, Late) cells, or to tRNA immobilized on a nitrocellulose membrane. Total late RNA from infected cells protected fragments of 127 and 128 nucleotides of the genomic probe, consistent with the previous experiments, which demonstrated that the sequence complementarity between the genomic DNA and 11K mRNA ends just upstream of the 11K ATG codon. cache = ./cache/cord-318276-so5jooj0.txt txt = ./txt/cord-318276-so5jooj0.txt === reduce.pl bib === id = cord-320713-b37c8aye author = Roberts, Lisa O. title = Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date = 2009-10-27 pages = extension = .txt mime = text/plain words = 20205 sentences = 1067 flesch = 48 summary = 6 The rate of translation initiation in mammalian cells is also controlled by sequence elements within the 5 0 -and 3 0 -UTRs of mRNAs which regulate this process by providing sites for interaction of regulatory proteins and RNAs. These include upstream open reading frames (uORFs), microRNA (miRNA) target sites, and polyadenylation elements. 5 It was suggested that alternative eIF4F complexes lacking PABP could selectively promote the synthesis of viral, but not host, proteins, so that KSHV-encoded mRNAs would compete more effectively for host translation machinery in infected cells. Picornavirus translation is directed by internal ribosome entry sites (IRESs) within the 5 0 -UTRs of the viral RNAs. The central one-third of eIF4G, containing the eIF3 and one eIF4A-binding domain, is sufficient to support translation initiation from these IRESs. 43 This allows picornavirus RNAs to compete effectively for the host translation machinery following infection, although the situation appears to be more complicated than this (see Section III). cache = ./cache/cord-320713-b37c8aye.txt txt = ./txt/cord-320713-b37c8aye.txt === reduce.pl bib === id = cord-319194-ukuia48s author = Liò, Pietro title = Phylogenomics and bioinformatics of SARS-CoV date = 2004-02-04 pages = extension = .txt mime = text/plain words = 4488 sentences = 201 flesch = 45 summary = Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Figure 1 shows the maximum likelihood tree produced using a set of homologous replicases from five SARS-CoV strains, 12 other coronaviruses representing both groups 1 and 2 of the genus [2, 3] , one torovirus (Breda virus) and one okavirus [yellow head (YH) virus], which were determined to most closely represent the consensus coronavirus sequence by a PSI-Blast search [12] . cache = ./cache/cord-319194-ukuia48s.txt txt = ./txt/cord-319194-ukuia48s.txt === reduce.pl bib === id = cord-320212-fw51w4nm author = Friedman, Stephanie D. title = Genomic Sequences of two Novel Levivirus Single-Stranded RNA Coliphages (Family Leviviridae): Evidence for Recombinationin Environmental Strains date = 2012-09-13 pages = extension = .txt mime = text/plain words = 5349 sentences = 296 flesch = 51 summary = When the novel strains were compared to nine Levivirus genogroup I strains, they shared 95–100% similarity among the maturation, capsid and lysis proteins, but only 84–85% in the RNA-dependent RNA polymerase gene. In all analysis programs, the nucleotide or amino acid sequences were aligned to other strains and were therefore approximate positions on the replicase gene. Breakpoint nucleotides for strains DL52 and DL54 (when aligned to genogroup I strains) occurred between nt 84-592 and 84-401, respectively ( Figure 5 a, b) , corresponding to the approximate amino acid breakpoint positions of 133-197 within the replicase gene. Human Noroviruses, a positive sense ssRNA virus with a genome length of 7400-8300 nt, are considered to belong to a prototype strain if they share approximately 85% overall nucleotide sequence identity and a high amino acid sequence identity (>95%) in the polymerase gene [20] . cache = ./cache/cord-320212-fw51w4nm.txt txt = ./txt/cord-320212-fw51w4nm.txt === reduce.pl bib === id = cord-321013-8pkrg0mx author = McBride, Ruth title = The Coronavirus Nucleocapsid Is a Multifunctional Protein date = 2014-08-07 pages = extension = .txt mime = text/plain words = 10761 sentences = 476 flesch = 44 summary = The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The M protein is the main core shell component and a 16 amino acid domain (aa 237-252) on the CTD of M protein binds directly to N protein via an ionic interaction, leading to specific genome encapsidation in the budding viral particle [81] [82] [83] .The N protein therefore plays an essential structural role in the CoV virion through a network of interactions with (i) the genomic RNA; (ii) M protein and (iii) other N proteins. Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA cache = ./cache/cord-321013-8pkrg0mx.txt txt = ./txt/cord-321013-8pkrg0mx.txt === reduce.pl bib === id = cord-321957-ybtk9cp1 author = Carey, Brian D. title = Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation date = 2020-03-09 pages = extension = .txt mime = text/plain words = 6713 sentences = 384 flesch = 52 summary = title: Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation A virus with capsid phosphorylation sites mutated to alanine (VEEV CPD) displayed a lower genomic copy to pfu ratio than the parental virus; suggesting more efficient viral assembly and more infectious particles being released. These data suggest that cells infected with VEEV CPD output more functional viral particles than VEEV TC-83, potentially due to more efficient viral packaging and this phenotype is due to loss of capsid phosphorylation. Loss of PKCδ through siRNA transfection also resulted in increased capsid viral RNA binding, further solidifying the link between VEEV CPD and PKCδ (Fig 7B) . To determine the impact of VEEV capsid phosphorylation on vRNA binding, we utilized quantitative RNA-IP experiments to probe the interaction between the capsid protein and the vRNA at sites identified as highly enriched, intermediately enriched, and non-enriched by our CLIP-seq studies. cache = ./cache/cord-321957-ybtk9cp1.txt txt = ./txt/cord-321957-ybtk9cp1.txt === reduce.pl bib === id = cord-322240-z8zkl2xh author = Maeda, Ken title = Isolation of Novel Adenovirus from Fruit Bat (Pteropus dasymallus yayeyamae) date = 2008-02-17 pages = extension = .txt mime = text/plain words = 1686 sentences = 95 flesch = 51 summary = To date, only 1 case of disseminated infection has been reported in a solid-organ (kidney) transplant recipient; the diagnosis was made by molecular identifi cation in isolates from blood and marrow cultures. As a fi rst step in investigating unidentifi ed pathogens in bats and to help forecast the potential threat of emerging infectious diseases, we tried to isolate and characterize viruses that persistently infect bats. However, no viral nucleic acid sequence was detected from an RNA sample in the RV1-infected BKT1 cells. In addition, our success in DNA virus isolation might have resulted from usage of the adult animal latently and persistently infected with DNA viruses such as adenovirus and herpesvirus. Although its pathogenicity for humans is still unknown, knowledge of RV1 will be useful in epidemiologic studies of infectious diseases emerging from bats because persistently infecting viruses might be isolated together with primary pathogens. cache = ./cache/cord-322240-z8zkl2xh.txt txt = ./txt/cord-322240-z8zkl2xh.txt === reduce.pl bib === id = cord-320351-47d0nby0 author = Li, Zhouxiao title = The emerging landscape of circular RNAs in immunity: breakthroughs and challenges date = 2020-07-10 pages = extension = .txt mime = text/plain words = 5971 sentences = 339 flesch = 39 summary = Recently conducted researches indicated that circRNAs can be used as a miRNA sponge to inhibit targeted mRNA functions, showing interaction to RNA-binding proteins (RBPs) and translating proteins [9] . In contrast to the sensitive strains, the expression of 2909 circRNAs in A549 / Taxol was noticeably enriched and 8372 circRNAs were noticeably declined, demonstrating that abnormal cir-cRNA is likely to alter the occurrence of paclitaxel resistance [33] .Circ-PVT1 was found to facilitate paclitaxel resistance of gastric cancer cells by controlling ZEB1 expressing via the sponging process for miR-124-3p [34] . Lymphoblastic lymphoma [52] -T cell structure and degradation of circRNAs regulating PKR Activation in innate immunity circ-CDR1as B cell serving as the miR-7 "sponge" to increase expression of PTEN and restrain SLE [66] Other immune-related diseases circ_ 0057980 Circular RNA circ-PVT1 contributes to paclitaxel resistance of gastric cancer cells through the regulation of ZEB1 expression by sponging miR-124-3p cache = ./cache/cord-320351-47d0nby0.txt txt = ./txt/cord-320351-47d0nby0.txt === reduce.pl bib === id = cord-322084-gkg1059v author = JEONG, YONG SEOK title = Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence date = 1996-03-01 pages = extension = .txt mime = text/plain words = 6250 sentences = 302 flesch = 52 summary = Abstract In our studies of murine coronavirus transcription, we continue to use defective interfering (DI) RNAs of mouse hepatitis virus (MHV) in which we insert a transcription consensus sequence in order to mimic subgenomic RNA synthesis from the nondefective genome. By using PCR-based sequences flanking the same intergenic region between site-directed mutagenesis, a 12-nucleotide-long segenes 6 and 7 do not affect the efficiency of subgenomic quence, TCTAATCTAAAC, was inserted into DI cDNA DI RNA transcription (Makino and Joo, 1993) . For all of the constructs used in Deletion analysis of those MHV DI RNAs that contain this study we sequenced the inserts that were derived the intergenic sequence from gene 6-7 with its naturally from PCR products to confirm the presence of specific occurring flanking sequences showed that reducing the mutations and the absence of extraneous mutations. cache = ./cache/cord-322084-gkg1059v.txt txt = ./txt/cord-322084-gkg1059v.txt === reduce.pl bib === id = cord-321938-pda4a5n7 author = Weisshoff, Hardy title = Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date = 2020-11-02 pages = extension = .txt mime = text/plain words = 5076 sentences = 266 flesch = 57 summary = We therefore checked whether a clinically developed aptamer, BC 007, which is currently in phase 2 of clinical testing for a different indication, would also be able to efficiently bind DNA-susceptible peptide structures from SARS-CoV-2-spreading crucial proteins, such as the receptor binding domain (RBD) of the spike protein and the RNA dependent RNA polymerase of SARS-CoV-2 (re-purposing). In the Spike protein of SARS-CoV-2, several sequences which are highly susceptible to interaction with DNA (multiple amino acids with positive charged side chains) were identified, in particular at the angiotensin I-converting enzyme 2 (ACE2)-receptor binding domain (RBD): YRLFRK (SARS-CoV-2 specific from protein data bank (PDB) data base entry PBD ID: 6VXX, source: [23] ), as well as NRKRISN (PBD ID: 6VXX) and KIKRMK (PDB ID: 5X5B source: [24] ). This enabled us to exploit NMR-spectroscopy to investigate whether the selected peptide-sequences from SARS-CoV-2 proteins bind to this clinically advanced aptamer (BC 007), forcing it into its well described quadruple structure just by molecular interaction. cache = ./cache/cord-321938-pda4a5n7.txt txt = ./txt/cord-321938-pda4a5n7.txt === reduce.pl bib === id = cord-321155-dty18esg author = Zhang, Rongxin title = Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date = 2020-06-05 pages = extension = .txt mime = text/plain words = 4927 sentences = 331 flesch = 57 summary = We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. To get the potential G-quadruplexes in the SARS-CoV-2 genome, we took the strategy described as follows ( Fig. 2A) : (i) Predicting the PG4s with three software independently. To further characterize the potential canonical secondary structures competitive with Gquadruplexes, the landscape of thermodynamic stability of the SARS-CoV-2 genome was depicted by using ΔG°z-score [55] . The distributions of loop length between the SARS-CoV-2 PG4s and the human two-quartet Gquadruplexes did not show discrepancies (Fig. S1 , Wilcoxon test, p-value = 0.4552). Recent research revealed that the G-quadruplexes in human UTRs (Untranslated Regions) are under selective pressures [58] , and some coronaviruses on bats and pangolins are closely related to SARS-CoV-2. Thus, we started to explore whether the SARS-CoV-2 genome contains the protein-coding sequence similar to SUD and whether SARS-CoV-2 retains the ability to bind RNA G-quadruplexes. cache = ./cache/cord-321155-dty18esg.txt txt = ./txt/cord-321155-dty18esg.txt === reduce.pl bib === id = cord-321607-3r736dnk author = Ezelle, Heather J. title = The Roles of RNase-L in Antimicrobial Immunity and the Cytoskeleton-Associated Innate Response date = 2016-01-08 pages = extension = .txt mime = text/plain words = 11694 sentences = 588 flesch = 42 summary = The active nuclease then cleaves ssRNAs, both cellular and viral, leading to downregulation of their expression and the generation of small RNAs capable of activating retinoic acid-inducible gene-I (RIG-I)-like receptors or the nucleotide-binding oligomerization domain-like receptor 3 (NLRP3) inflammasome. Although cleavage of RNA virus genomes appeared as the most direct mechanism of action, other important pathways have become evident, such as the regulation of host gene expression, stimulation of IFNβ production, activation of the NACHT, LRR, and PYD-containing protein-3 (NLRP3) inflammasome, and maintenance of the cell's structural barrier to infection [27, 55, 83, 84] . These small RNAs are capable of stimulating RIG-I and MDA5 (melanoma differentiation associated gene-5) to activate mitochondrial antiviral signaling protein (MAVS) and induce the subsequent translocation of interferon regulatory factor 3 (IRF3) to the nucleus to drive transcription of IFNβ. cache = ./cache/cord-321607-3r736dnk.txt txt = ./txt/cord-321607-3r736dnk.txt === reduce.pl bib === id = cord-322062-nnefbeo6 author = Tam, Albert W. title = Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome date = 1991-11-30 pages = extension = .txt mime = text/plain words = 5738 sentences = 296 flesch = 49 summary = We now report on the molecular cloning and sequencing of the complete HEV (Burma; B) viral genome together with the deduced amino acid sequences of viral-encoded proteins General perspectives on the genetic organization of the virus, as deduced from sequence and open reading frame analyses, indicate that HEV bears some similarity to the caliciviridae but may represent a new class of nonenveloped RNA virus. Bife was chosen as the RNA source for cDNA synthesis because it contained relatively large numbers of virus particles when HEV cDNA clones were identified from libraries made from randomly primed cyno bile (solid square), or from cyno liver after priming by oligo-dT (solid circle), random sequence hexamers (open circle) and HEV-sequence specific oligonucleotides (open square). The presence of HEV-specific subgenomic RNAs localized to the 3' one-third of the genome suggests that these may be the transcripts from which these 3' end ORFs are expressed and is indicative of a unique expression strategy among nonenveloped positive-sense RNA viruses infecting humans. cache = ./cache/cord-322062-nnefbeo6.txt txt = ./txt/cord-322062-nnefbeo6.txt === reduce.pl bib === id = cord-321773-5fw9abzl author = Cheng, Wenyu title = DDX5 RNA Helicases: Emerging Roles in Viral Infection date = 2018-04-09 pages = extension = .txt mime = text/plain words = 6739 sentences = 370 flesch = 48 summary = Given the crucial roles of DDX5 in RNA biology, several RNA viruses were found to interact with the protein to promote viral replication (Table 1) , including severe acute respiratory syndrome (SARS) coronavirus (CoV) [16] , human immunodeficiency virus 1 (HIV-1) [17] , hepatitis C virus (HCV) [18] , Japanese encephalitis virus (JEV) [19] , porcine reproductive and respiratory syndrome virus (PRRSV) [20] , and influenza virus [21] . There are several studies that focus on specific inhibitors or drugs of the host DEAD-box helicase to inhibit virus replication or treat cancers [65] [66] [67] , but it remains to be determined whether small molecular inhibitors of the interaction between DDX5 and Rev can be found. The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3 UTR The DEAD-box RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro cache = ./cache/cord-321773-5fw9abzl.txt txt = ./txt/cord-321773-5fw9abzl.txt === reduce.pl bib === id = cord-323585-iv2dcpqj author = Li, Su title = eEF1A Interacts with the NS5A Protein and Inhibits the Growth of Classical Swine Fever Virus date = 2015-08-10 pages = extension = .txt mime = text/plain words = 6142 sentences = 343 flesch = 59 summary = The NS5A protein of classical swine fever virus (CSFV) is involved in the RNA synthesis and viral replication. The GST or GST-NS5A fusion proteins expressed in Escherichia coli BL21(DE3) were purified with glutathione Sepharose 4B resin and incubated with the lysate of HEK293T cells overexpressing the Myc-tagged eEF1A. The immunoprecipitate was analyzed by Western blotting using the anti-Flag MAb (1:1000) and a rabbit anti-Myc PAb (1:500); (D) Co-IP analysis of eEF1A and NS5A by the anti-Myc MAb. HEK293T cells were cotransfected with the indicated plasmids (+) or empty vectors ('), the cell lysate was collected at 48 h post-transfection (hpt), incubated with the anti-Myc MAb and Protein G-Agarose. The bound proteins were analyzed by immunoblotting using the anti-Myc monoclonal antibody (MAb) (1:1000); (B) eEF1A interacts with the CSFV IRES in a dose-dependent manner. The bound proteins were analyzed by immunoblotting using the anti-Myc monoclonal antibody (MAb) (1:1000); (B) eEF1A interacts with the CSFV IRES in a dose-dependent manner. cache = ./cache/cord-323585-iv2dcpqj.txt txt = ./txt/cord-323585-iv2dcpqj.txt === reduce.pl bib === id = cord-322756-ouvn71r9 author = Chow, Michael Y.T. title = Inhaled RNA Therapy: From Promise to Reality date = 2020-09-04 pages = extension = .txt mime = text/plain words = 7283 sentences = 454 flesch = 44 summary = Studies investigating RNA therapeutics in pulmonary diseases have rapidly expanded and drug administration by inhalation allows the direct delivery of RNA therapeutics to the target site of action while minimizing systemic exposure. Interestingly, it has been known for over a decade that naked RNA, including both siRNA and mRNA, can be transfected in the lung following pulmonary delivery, as shown in many in vivo studies [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] . Both studies demonstrated a gene-silencing effect of the powder formulations in lung tissues following intratracheal administration in mouse models of lung cancer, taking these delivery systems one step closer to clinical application. To take advantage of this phenomenon, pulmonary surfactant and surfactant protein B-coated dextran-based nanoparticles were developed for siRNA delivery, with successful gene-silencing effects observed in healthy mice and in a model of acute lung injury (ALI), respectively, following pulmonary administration [29, 69] (Table 1) . cache = ./cache/cord-322756-ouvn71r9.txt txt = ./txt/cord-322756-ouvn71r9.txt === reduce.pl bib === id = cord-322234-1zyy536y author = Lorusso, Alessio title = One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date = 2009-12-17 pages = extension = .txt mime = text/plain words = 4162 sentences = 195 flesch = 51 summary = To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. Swine and equine influenza virus isolates and the clinical samples from pigs infected experimentally with 2009 (H1N1)v were subjected to the USDA-validated qRT-PCR procedure for the general detection of type A influenza virus RNA (matrix screening assay), following procedures described previously (Spackman and Suarez, 2008) . All endemic North American swine influenza virus isolates were negative for (H1N1) 2009 specific matrix gene RNA using the present qRT-PCR assay, whereas the (H1N1) 2009 strains used as positive control were positive. cache = ./cache/cord-322234-1zyy536y.txt txt = ./txt/cord-322234-1zyy536y.txt === reduce.pl bib === id = cord-322206-roxa3ix6 author = I. Sardi, Silvia title = High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date = 2020-07-21 pages = extension = .txt mime = text/plain words = 4199 sentences = 212 flesch = 46 summary = Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. Here, we applied RNA-based metatranscriptomics associated with Ion Torrent deep sequencing and a newly developed Bioinformatics approach to the high-quality reconstitution of viral genomes. cache = ./cache/cord-322206-roxa3ix6.txt txt = ./txt/cord-322206-roxa3ix6.txt === reduce.pl bib === id = cord-322410-k23engcx author = Naguib, Mahmoud M. title = New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses date = 2017-03-21 pages = extension = .txt mime = text/plain words = 5012 sentences = 259 flesch = 52 summary = title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples. The specificity of RT-qPCR primer set was evaluated by examining different avian respiratory viruses circulating in poultry in Egypt including AIV H5N1, H9N2 and NDV as well as different coronaviruses including a panel of IBV reference strains as listed in the materials section. Within HVR 1, 2 sequences, however, the existence of two distinct Table 3 RT-qPCRs reveal frequent co-infections in Egyptian poultry samples with avian influenza (AIV), Newcastle Disease (NDV) and infectious bronchitis viruses (IBV). cache = ./cache/cord-322410-k23engcx.txt txt = ./txt/cord-322410-k23engcx.txt === reduce.pl bib === id = cord-323737-6ajqy0ch author = Jiang, Yuanyuan title = Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus date = 2020-10-04 pages = extension = .txt mime = text/plain words = 6799 sentences = 399 flesch = 51 summary = title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify potential inhibitors targeting 2 0 -O-MTase of SARS-CoV-2. To identify inhibitors targeting nsp16, we first performed comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs. Supplementary Table 1 lists the detailed genome and protein information that were employed in this study. As seen from MM-PBSA results and docking studies, drugs including Hesperidin, Osi-027, Rimegepant, Sonedenoson, and Gs-9667 had higher binding affinities than SAM with the 2 0 -O-MTase of SARS-CoV-2. cache = ./cache/cord-323737-6ajqy0ch.txt txt = ./txt/cord-323737-6ajqy0ch.txt === reduce.pl bib === id = cord-323668-evzzfu04 author = Yin, Zhixin title = lncRNA expression signatures in response to enterovirus 71 infection date = 2013-01-11 pages = extension = .txt mime = text/plain words = 3493 sentences = 208 flesch = 50 summary = To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. These findings suggest the widespread differential expression of lncRNAs in response to 0006 virus infection and their involvement in regulating the host response, including innate immunity [19] . Further analysis resulted in 313 differentially expressed lncRNAs and nearby coding gene pairs (distance < 300 kb) for each comparison between mock-and EV71-infected cells (Table S7) . In the present study, using Arraystar microarray analysis, we identified the differentially expressed lncRNAs in RD cells after EV71 infection, together with nearby differentially expressed mRNA pairs. They also observed the down-regulation of several genes encoding proteins involved in host RNA synthesis in EV71-infected SF268 cells. [19] performed functional enrichment analysis on the nearby protein-coding genes of differentially expressed lncRNAs in SARS-CoV infected mouse. cache = ./cache/cord-323668-evzzfu04.txt txt = ./txt/cord-323668-evzzfu04.txt === reduce.pl bib === id = cord-323691-5s5almd2 author = Mishin, Vasiliy P title = A ‘minimal’ approach in design of flavivirus infectious DNA date = 2001-12-04 pages = extension = .txt mime = text/plain words = 5060 sentences = 255 flesch = 49 summary = Abstract The 'infectious DNA' approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Substantial difficulties, however, were encountered in design of flavivirus 'infectious DNA', requiring either modification of the viral genome cassette (Yamshchikov et al., 2001) to prevent unwanted expression of viral genome segments encoding toxic for Escherichia coli products, or deletion of the structural protein region (Varnavski et al., 2000) . For this reason we sought to investigate if the stability of constructs containing an unmodified virus genome cassette can be improved by preventing its deleterious expression at the transcriptional level, i.e. by minimizing spurious transcription from eukaryotic promoters in E. cache = ./cache/cord-323691-5s5almd2.txt txt = ./txt/cord-323691-5s5almd2.txt === reduce.pl bib === id = cord-323756-atnrw9ew author = Vabret, Nicolas title = Sensing Microbial RNA in the Cytosol date = 2013-12-25 pages = extension = .txt mime = text/plain words = 6409 sentences = 355 flesch = 45 summary = When Janeway formulated the theory of pattern recognition in 1989, he proposed that host cells could sense microbial infection owing to receptors able to recognize invariant molecular structures defined as pathogen-associated molecular patterns (PAMPs). They share a similar organization with three distinct domains: (i) a C-terminal repressor domain (RD) embedded within the C-terminal domain (CTD); (ii) a central ATPase containing DExD/H-box helicase domain able to bind RNA; and (iii) a N-terminal tandem CARD domain that mediates downstream signaling, and which is present in RIG-I and MDA5 but absent in LGP2. DDX60 has also been shown to enhance the IFN-I response to RNA and DNA stimulation through formation of complexes with Frontiers in Immunology | Molecular Innate Immunity RIG-I, MDA5, and LGP2 but not with MAVS. Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses cache = ./cache/cord-323756-atnrw9ew.txt txt = ./txt/cord-323756-atnrw9ew.txt === reduce.pl bib === id = cord-323029-7hqp8xuq author = Bognár, Zsófia title = Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date = 2020-08-11 pages = extension = .txt mime = text/plain words = 19331 sentences = 873 flesch = 45 summary = For aptamer selection against rIgG [6] and IgE [7] , homogenous processes were used and the separation of bound and unbound nucleic Several different SELEX methods have been used to generate immunoglobulin aptamers including homogeneous, heterogeneous, bead-based SELEX processes, CE-SELEX (capillary electrophoresis-SELEX), µFFE-SELEX (micro-free flow electrophoresis-SELEX) and fully integrated selection processes selection of aptamers with proper binding properties. Molecular Light Switch Complex 100-800 100 [128] Fluorescence enhancement using a DNA aptamer 92-37,000 57 [130] Amplification through allostery-triggered enzymatic recycling amplification NA 5 [131] Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay 4.72-7560 0.095 [132] Fluorescence anisotropy 1000-60,000 350 [133] Fluorescence anisotropy assay NA 20 [134] Fluorescence protection assay 100-50,000 100 [136] Aptamer-barcode-based assay based on instantaneous derivatization chemiluminescence coupled to magnetic beads 4.88-20,000 4.6 [137] Competitive fluorescence quenching assay 350-35,000 170 [138] Rapid fluorescence detection of immunoglobulin E using an aptamer switch based on a binding-induced pyrene excimer NA 1600 [139] 6.1. cache = ./cache/cord-323029-7hqp8xuq.txt txt = ./txt/cord-323029-7hqp8xuq.txt === reduce.pl bib === id = cord-323973-wszo9s3d author = Zhu, Hanliang title = The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date = 2020-07-20 pages = extension = .txt mime = text/plain words = 9784 sentences = 493 flesch = 50 summary = [9] The analysis of larger volumes of biological fluids with a low viral load is likely to reduce the risk of false-negative results, but microfluidic point-of-care (POC) devices are typically unable to handle mL-scale volumes in a short time due to the requirement of slow flow rates. [15] The PCR test on samples prepared from blood and urine specimens is capable of detecting the virus in the early stages of the disease, resulting in early diagnosis and subsequent isolation of infected patients to block transmission. The total reaction time depends on a series of parameters, such as the chip size, the PCR master mix volume determining the value of C, the thermal conductivity of the substrate (G), and the temperature cycling rate. A number of fully integrated systems have so far been developed, starting with the non-portable GenExpert from Cepheid, which was first utilized for anthrax detection by the United States Postal Service, [64] and then with different primers to perform HIV and tuberculosis diagnostics in South Africa. cache = ./cache/cord-323973-wszo9s3d.txt txt = ./txt/cord-323973-wszo9s3d.txt === reduce.pl bib === id = cord-323845-s78t5qxj author = Soliman, H. title = Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) date = 2006-05-31 pages = extension = .txt mime = text/plain words = 3908 sentences = 217 flesch = 54 summary = title: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) A one step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of viral hemorrhagic septicaemia virus (VHS). Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) The aim of the present study was to develop a onestep, single-tube, accelerated RT-LAMP reaction for rapid detection of different serotypes of VHS virus. The specificity of the VHS-LAMP primers and conditions to VHS virus was confirmed by its aptitude to amplify only RNA from VHS virus serotypes, with no amplification of IHNVor non-infected fish (Fig. 5) . Detection of viral hemorrhagic septicaemia virus (VHS) in rainbow trout (Oncorhynchus mykiss) by reverse transcription followed by polymerase chain reaction. A loop mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss) cache = ./cache/cord-323845-s78t5qxj.txt txt = ./txt/cord-323845-s78t5qxj.txt === reduce.pl bib === id = cord-323987-gh1m05gi author = Dziąbowska, Karolina title = Detection Methods of Human and Animal Influenza Virus—Current Trends date = 2018-10-18 pages = extension = .txt mime = text/plain words = 11112 sentences = 760 flesch = 46 summary = RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional 'gold star' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. cache = ./cache/cord-323987-gh1m05gi.txt txt = ./txt/cord-323987-gh1m05gi.txt === reduce.pl bib === id = cord-324137-nau83mjv author = Saranathan, Nandhini title = G-Quadruplexes: More Than Just a Kink in Microbial Genomes date = 2018-09-14 pages = extension = .txt mime = text/plain words = 6722 sentences = 379 flesch = 42 summary = Several reports convincingly demonstrate antimicrobial activity of quadruplex-binding ligands against clinically challenging pathogens, including HIV-1, HCV, Ebola virus, Plasmodium falciparum, and Mycobacterium tuberculosis. An earlier study reports that, following concatemeric replication of HHV-1, the cleavage of unit length genomes and their encapsidation is achieved by the binding of virus proteins to a DNA secondary structure formed by a DNA packaging sequence (pac-1) [50] . G4s have been shown to inhibit the transcription or translation of structural and nonstructural proteins in viruses, deleteriously affecting the virus loads and their pathogenicity; the stabilization of these quadruplexes with ligands has been investigated as a potential mechanism for targeting viruses. Negative regulation of virus transcription, translation or replication by quadruplex motifs in virus genomes forms the basis of using G4-binding ligands as antiviral agents. G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions cache = ./cache/cord-324137-nau83mjv.txt txt = ./txt/cord-324137-nau83mjv.txt === reduce.pl bib === id = cord-324324-8ybfiz8f author = Decaro, Nicola title = Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date = 2020-04-14 pages = extension = .txt mime = text/plain words = 14927 sentences = 720 flesch = 49 summary = In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. cache = ./cache/cord-324324-8ybfiz8f.txt txt = ./txt/cord-324324-8ybfiz8f.txt === reduce.pl bib === id = cord-324212-aqp73hi9 author = Wyszko, Eliza title = Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum date = 2006-10-09 pages = extension = .txt mime = text/plain words = 4458 sentences = 298 flesch = 60 summary = We identified a leadzyme substrate target sequence in genomic tobacco mosaic virus RNA and designed a 16‐mer oligoribonucleotide capable of forming a specific leadzyme motif with a five‐nucleotide catalytic loop. We identified a leadzyme substrate target sequence in genomic tobacco mosaic virus RNA and designed a 16-mer oligoribonucleotide capable of forming a specific leadzyme motif with a five-nucleotide catalytic loop. To achieve this goal, we analyzed the inhibition of tobacco mosaic virus (TMV) as a model system for inhibiting viral infections caused by positive single-stranded RNA (+)ssRNA viruses. In this article, we show that exogenous ssRNA with sequence complementarity binds the target site in TMV RNA to form a leadzyme motif, and in the presence of a catalytic amount of Pb 2+ , cleaves viral (+)ssRNA. Control assays, with 16-nucleotide catalytic RNA only or Pb 2+ applied in the presence of TMV, were performed to demonstrate the specificity of leadzyme cleavage. cache = ./cache/cord-324212-aqp73hi9.txt txt = ./txt/cord-324212-aqp73hi9.txt === reduce.pl bib === id = cord-324638-gwd8qin6 author = Chiu, Rossa WK title = Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date = 2006-02-09 pages = extension = .txt mime = text/plain words = 3360 sentences = 152 flesch = 49 summary = We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The main objective of this study was to compare the resultant analytical sensitivity and quantitative performance of the serum SARS-CoV RNA test when either the manual or automated extraction protocol was used. The modified large volume protocol with the external lysis step was further compared with the external lysis protocol of the total nucleic acid isolation kit using a transport medium mixture containing 10 6 copies/mL of inactivated SARS-CoV. Serially diluted inactivated SARS-CoV isolate in transport medium was extracted by both the column-based manual method and the MagNA Pure LC instrument using the modified large volume protocol with external lysis. cache = ./cache/cord-324638-gwd8qin6.txt txt = ./txt/cord-324638-gwd8qin6.txt === reduce.pl bib === id = cord-324495-0pee1i3o author = Kang, Hyeonjeong title = Sasa quelpaertensis Nakai extract suppresses porcine reproductive and respiratory syndrome virus replication and modulates virus-induced cytokine production date = 2015-06-06 pages = extension = .txt mime = text/plain words = 6119 sentences = 300 flesch = 49 summary = Therefore, the present study was conducted to determine whether Sasa quelpaertensis Nakai extract (SQE) inhibits PRRSV infection in cultured porcine alveolar macrophages (PAMs). Further experiments revealed that SQE suppresses post-entry steps in the replication cycle of PRRSV, including viral genomic and sg RNA synthesis, viral protein expression, and virus production. The presence of SQE notably altered expression of cytokine genes in PRRSV-infected PAM cells, suggesting that SQE activity is involved in the modulation of inflammatory responses during viral infection. As shown in Fig. 5 , SQE treatment resulted in a maximal reduction in the synthesis of PRRSV genomic RNA and sg mRNA of 90 % and 80 %, respectively, at a concentration of 5 mg/ ml, when compared with untreated infected cells. Treatment of cells with SQE resulted in significant inhibition of post-entry steps during the replication of PRRSV, as demonstrated by reduced progeny production, diminished viral protein expression, and reduced synthesis of genomic RNA and sg mRNA. cache = ./cache/cord-324495-0pee1i3o.txt txt = ./txt/cord-324495-0pee1i3o.txt === reduce.pl bib === id = cord-324928-cpryxa6p author = Lello, Laura Sandra title = Cross-utilisation of template RNAs by alphavirus replicases date = 2020-09-04 pages = extension = .txt mime = text/plain words = 13762 sentences = 646 flesch = 50 summary = The differences between outgroup viruses and those belonging to the SFV complex had an impact on the design of the template RNAs. The 5' region of the CHIKV genome contains seven SL structures that affect genome replication in mammalian and/or mosquito cells [33] . Cross-utilisation of template RNAs by alphavirus replicases structures can be predicted for RNAs of other members of the SFV complex (S1 Fig), the 5' ends of the template RNAs of SFV, MAYV, RRV and ONNV had an identical design to that of the previously constructed CHIKV template, i.e. the 5' UTR was followed by 231nt encoding the N-terminus of nsP1 [43] . The levels of Fluc and Gluc expression in human cells, transfected with plasmids expressing template RNA and corresponding polymerase negative control replicase (P1234 GAA ), were similar for trans-replicases derived from different viruses and the same was observed for Ae albopictus cells. cache = ./cache/cord-324928-cpryxa6p.txt txt = ./txt/cord-324928-cpryxa6p.txt === reduce.pl bib === id = cord-324640-2zhaknbi author = Munday, Diane C. title = Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus date = 2010-07-20 pages = extension = .txt mime = text/plain words = 12318 sentences = 588 flesch = 39 summary = Although RNA synthesis and virus assembly occur in the cytoplasm, HRSV is known to induce nuclear responses in the host cell as replication alters global gene expression. More recently, 2DE was used to compare the potential effect of several different negative strand RNA viruses, including HRSV, parainfluenza virus, human metap-neumovirus, measles virus, and influenza virus, on the host cell proteome with common changes in proteins involved with apoptosis and endoplasmic reticulum stress being highlighted (27) . Together, the indirect immunofluorescence confocal microscopy images supported the observations from the quantitative proteomic analysis that the abundance of mitochondrial proteins (particularly pore proteins) was altered in HRSV-infected cells. Potential Disruption of Proteins Involved in Nucleocytoplasmic Trafficking-Network pathway analysis indicated that the abundance of nuclear pore complex components and proteins involved in the nucleocytoplasmic trafficking of proteins and RNA differed between HRSV-infected and mock-infected cells (Fig. 4) . cache = ./cache/cord-324640-2zhaknbi.txt txt = ./txt/cord-324640-2zhaknbi.txt === reduce.pl bib === id = cord-325043-vqjhiv7p author = Gorbalenya, Alexander E. title = An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication date = 1989 pages = extension = .txt mime = text/plain words = 6805 sentences = 361 flesch = 52 summary = title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication These observations, taken together with the results of comparative analysis of the positions occupied by respective proteins (domains) in viral multidomain proteins, suggest that all the NTP-motif-containing proteins of positive-strand RNA viruses are homologous, constituting a highly diverged monophyletic group. Preliminary comparative analysis of the amino acid sequences of the NTP-motif-eontaining proteins of positive-strand RNA viruses by use of the programs DIAGON and OPTAL (see Methods) revealed three distinct families and some additional proteins in whose close relatives the motif was not conserved. In the present study we demonstrate that in a highly diverged group including similar proteins of positive-strand RNA viruses, the consensus sequences of the NTP-motif constitute the most strictly conserved stretches, encompassing four of the five invariant amino acid residues. cache = ./cache/cord-325043-vqjhiv7p.txt txt = ./txt/cord-325043-vqjhiv7p.txt === reduce.pl bib === id = cord-324697-c0dv1zmi author = Rodriguez, William title = Fated for decay: RNA elements targeted by viral endonucleases date = 2020-06-07 pages = extension = .txt mime = text/plain words = 6407 sentences = 336 flesch = 50 summary = Consequently, viruses have evolved an arsenal of strategies to target these RNA features and ultimately take control of the pathways they influence, and these strategies contribute to the global shutdown of the host gene expression machinery known as "Host Shutoff". Throughout this section we will discuss how each of these RNA features render mRNA susceptible toand in many cases directviral endonuclease cleavage or similar strategies aimed at degradation of the host transcriptome during viral infection. Nsp1 thus emerges as a thorough RNA decay trigger that uses diverse and non-overlapping strategies to widely target host mRNAs. How the viral transcripts escape nsp-1 mediated is still under investigation. Overall, SARS coronavirus nsp1 is an interesting regulator of RNA stability: currently, nsp1 does not appear to have any endonucleolytic activity of its own, and instead binds to the 40 s subunit exploiting the host's RNA quality control pathways to trigger mRNA degradation. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression cache = ./cache/cord-324697-c0dv1zmi.txt txt = ./txt/cord-324697-c0dv1zmi.txt === reduce.pl bib === id = cord-324984-ojrpsdt9 author = Ji, Xingyue title = Medicinal chemistry strategies toward host targeting antiviral agents date = 2020-02-14 pages = extension = .txt mime = text/plain words = 16814 sentences = 825 flesch = 43 summary = In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. 3 Altogether, targeting host factors is a very promising strategy with possibility to address the critical challenges faced with the DAAs. In this review, we summarize the recent advances made in HTAs from a medicinal chemistry standpoint, and the host targets are generally classified into three different categories based on the development stage of their corresponding inhibitors/modulators, namely the ones which reached Food and Drug Administration (FDA) approval, that have entered clinical trials and those in preclinical studies. cache = ./cache/cord-324984-ojrpsdt9.txt txt = ./txt/cord-324984-ojrpsdt9.txt === reduce.pl bib === id = cord-325113-sou8xyld author = Kuiper, Johannes W. P. title = Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date = 2020-11-02 pages = extension = .txt mime = text/plain words = 4973 sentences = 241 flesch = 51 summary = The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. cache = ./cache/cord-325113-sou8xyld.txt txt = ./txt/cord-325113-sou8xyld.txt === reduce.pl bib === id = cord-324944-ixh3ykrc author = Mitsakakis, Konstantinos title = Diagnostic tools for tackling febrile illness and enhancing patient management date = 2018-12-05 pages = extension = .txt mime = text/plain words = 20805 sentences = 961 flesch = 45 summary = This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases). cache = ./cache/cord-324944-ixh3ykrc.txt txt = ./txt/cord-324944-ixh3ykrc.txt === reduce.pl bib === id = cord-325137-6c6er06a author = Moser, Lindsey A. title = A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date = 2016-06-07 pages = extension = .txt mime = text/plain words = 9945 sentences = 514 flesch = 53 summary = Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Thus, in some instances, large cDNAs, double-stranded DNAs (dsDNAs), or clones containing at least two-thirds of the genome may also be regulated as SAs. Positive-sense RNA viruses span multiple virus families, and the infectious nature of these genomic RNAs coupled with SA/biosafety/biosecurity concerns inhibit rapid removal from BSL-3/4 containment (7) or transport and handling of RNA samples that are known to contain viral genomes from outbreak settings. cache = ./cache/cord-325137-6c6er06a.txt txt = ./txt/cord-325137-6c6er06a.txt === reduce.pl bib === id = cord-325197-j1uo8qmf author = Crimi, Ettore title = Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date = 2020-08-20 pages = extension = .txt mime = text/plain words = 6066 sentences = 342 flesch = 34 summary = Viruses causing severe pulmonary illness can use epigenetic-regulated mechanisms during host–pathogen interaction to interfere with innate and adaptive immunity, adequacy of inflammatory response, and overall outcome of viral infections. In this article, we provide an update on epigenetic-sensitive mechanisms and repurposed drugs interfering with epigenetic pathways which may be clinically suitable for risk stratification and beneficial for treatment of patients affected by severe viral respiratory infections. The goal of the review was to provide an appropriate pathogenic scenario in which epigenetic-sensitive mechanisms and epidrugs may be clinically useful to stratify risk and treatment of patients in ICU affected by severe viral respiratory infections. Here, we give an update on clinical evidence about the usefulness of novel and FDA-approved drugs interfering with epigenetic pathways, which were applied to ICU patients affected by highly pathogenic strains of influenza virus and CoV, with a particular interest about the novel SARS-CoV-2 (Table 4 ). cache = ./cache/cord-325197-j1uo8qmf.txt txt = ./txt/cord-325197-j1uo8qmf.txt === reduce.pl bib === id = cord-325326-2bbqz4o7 author = Beitzel, Brett F. title = High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date = 2010-10-14 pages = extension = .txt mime = text/plain words = 7781 sentences = 388 flesch = 51 summary = We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. Toward this goal, we used transposon mutagenesis, reverse genetics, and fragment analysis by capillary electrophoresis to identify regions of the nsP3 gene that are important for replication and that result in temperature sensitive (ts) mutations. We used transposon mutagenesis to construct a cDNA library with small DNA fragments randomly inserted throughout the VEEV genome and then produced replication-competent virus through reverse genetics. Comparing transposon insertion sites in the resultant viruses to those in the starting library, we were able to produce a functional map of the entire genome of VEEV, and to identify several hundred potential ts mutations, including those we originally identified with the capillary electrophoresis method. cache = ./cache/cord-325326-2bbqz4o7.txt txt = ./txt/cord-325326-2bbqz4o7.txt === reduce.pl bib === id = cord-325280-4whzcmqv author = Takizawa, Naoki title = Current landscape and future prospects of antiviral drugs derived from microbial products date = 2017-10-11 pages = extension = .txt mime = text/plain words = 6601 sentences = 365 flesch = 34 summary = In this review, we summarize antiviral microbial products discovered by Institute of Microbial Chemistry (IMC) and discuss antiviral compounds against influenza virus and HBV, because these two viruses threaten global human health now and antiviral drug against these two viruses have been developed. THE CONTRIBUTIONS OF IMC TO ANTIVIRAL RESEARCH Nucleos(t)ide analogs are a major class of approved antiviral drugs that exert therapeutic effects through incorporation into viral DNA and RNA to inhibit virus replication. Viral polymerase complex is a promising target for the development of anti-influenza drugs, because transcription and replication are critical steps for virus propagation. Potential applications of microbial products in anti-HBV drug development Approved nucleos(t)ide analogs competitively inhibit DNA elongation of viral polymerase after the conversion to triphosphate form by cellular enzymes. cache = ./cache/cord-325280-4whzcmqv.txt txt = ./txt/cord-325280-4whzcmqv.txt === reduce.pl bib === id = cord-325230-3kg4oe4g author = Agol, Vadim I. title = Viral security proteins: counteracting host defences date = 2010-11-09 pages = extension = .txt mime = text/plain words = 8716 sentences = 426 flesch = 41 summary = These proteins include: capsid proteins; an RNA-dependent RNA polymerase (3D pol ); a protein (VPg, or 3B) that serves as a primer for the initiation of RNA synthesis; an ATPase with a conserved superfamily 3 helicase motif (2C ATPase ) and an essential but poorly defined role in viral RNA replication; a chymotrypsin-like protease (3C pro ), which, as the mature protein or as a precursor, is a major factor in polyprotein processing; two hydrophobic membrane-binding proteins (2B and 3A) that participate in the generation of a virus-friendly environment; and, flanking the precursor of the capsid proteins, one or two highly variable proteins (L and 2A), the structure and functions of which are the subject of this Review. cache = ./cache/cord-325230-3kg4oe4g.txt txt = ./txt/cord-325230-3kg4oe4g.txt === reduce.pl bib === id = cord-325529-pid58g2r author = Ben-Ami, Roni title = Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date = 2020-06-23 pages = extension = .txt mime = text/plain words = 2822 sentences = 158 flesch = 50 summary = METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Some key constrains are (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; and (3) favorability of simple algorithms which may minimize human error in a laboratory setting. Specifically, we have demonstrated that pooling lysates from 5 or 8 nasopharyngeal swab samples retains sufficient sensitivity of viral RNA detection, allowing identification of SARS-CoV-2-positive individuals, while increasing throughput 5-fold to 7.5-fold. cache = ./cache/cord-325529-pid58g2r.txt txt = ./txt/cord-325529-pid58g2r.txt === reduce.pl bib === id = cord-325479-2r4oomdp author = Torii, Shotaro title = Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date = 2020-10-17 pages = extension = .txt mime = text/plain words = 5881 sentences = 363 flesch = 58 summary = This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate–phenol–chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. This study aims (1) to compare the combination of primary concentration (UF, EMV, and PEG) and RNA extraction (QIAamp Viral RNA Mini Kit and TRIzol) for the whole process recovery of nonenveloped and enveloped virus surrogates and (2) to test the applicability of the method providing the highest φ6 recovery to detect SARS-CoV-2 cache = ./cache/cord-325479-2r4oomdp.txt txt = ./txt/cord-325479-2r4oomdp.txt === reduce.pl bib === id = cord-325328-3l3jznkj author = Holbrook, Stephen R title = RNA structure: the long and the short of it date = 2005-05-16 pages = extension = .txt mime = text/plain words = 3711 sentences = 165 flesch = 44 summary = Structural studies and comparative sequence analyses have suggested that biological RNAs are largely modular in nature, composed primarily of conserved structural building blocks or motifs [4] of secondary (helices, and internal, external and junction loops) and tertiary (coaxial stacks, kissing hairpin loops, ribose zippers, etc.) structure. Other structures include the specificity domains of both A[17] and B-type ribonuclease P [18 ] ; RNAs corresponding to a guanine-responsive riboswitch (xpt) complexed with guanine [19 ] or hypoxanthine [20] , and an adenosine-responsive riboswitch (add) complexed with adenosine [19 ] ; a highly conserved stem-loop motif found at the 3 0 end of the genome of SARS (severe acute respiratory syndrome) virus and other coronaviruses [21 ] ; the core encapsidation signal of MMLV [2 ] ; and complexes between a high-affinity RNA aptamer and the NF-kB p50 homodimer [22] , and between the archaeal RNAbinding protein L7Ae and an RNA K-turn derived from a H/ACA small RNA [23] . cache = ./cache/cord-325328-3l3jznkj.txt txt = ./txt/cord-325328-3l3jznkj.txt === reduce.pl bib === id = cord-325736-gs9d8y55 author = Marin, J title = Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date = 2000-07-31 pages = extension = .txt mime = text/plain words = 1874 sentences = 135 flesch = 61 summary = title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma Conclusions: The persistent presence of viruses in the upper respiratory tract of asthmatic children shows a possible connection between viral infections and asthma. 4 In this study nasopharyngeal swabs were taken from asthmatic children whose asthma was well controlled, and when they were at least 3 weeks free of any respiratory infections. The samples were examined for the presence of adenovirus DNA and rhinovirus and coronavirus RNA. Five microlitres of c-DNA product were subsequently amplified in 50µl PCR reaction mixture consisting of 10 reaction buffer, 25 mM MgCl 2 , 20 mM dNTP, 5 U/l of DNA Taq polymerase (all reagents provided by Perkin Elmer, New Jersey, USA) and 50 µM of each specific primer for rhinoviruses and coronaviruses (TIB MOLBIOL, Berlin, Germany) (Table I) . found that upper respiratory tract viruses were associated with over 80% of asthma exacerbations in children. cache = ./cache/cord-325736-gs9d8y55.txt txt = ./txt/cord-325736-gs9d8y55.txt === reduce.pl bib === id = cord-325624-6anybxnk author = Ireland, Derek D. C. title = RNase L Mediated Protection from Virus Induced Demyelination date = 2009-10-02 pages = extension = .txt mime = text/plain words = 8082 sentences = 397 flesch = 43 summary = The unique phenotype of infected RL(−/−) mice was rather manifested in earlier onset and increased severity of demyelination and axonal damage in brain stem and spinal cord without evidence for enhanced neuronal infection. RNase L specifically protected the brain stem from sustained infection and prevented spread of virus to microglia/macrophages located in spinal cord grey matter. The increased pathological changes in both brain stem and spinal cord thus correlated with the high mortality rates of RL 2/2 mice starting at day 9 p.i. The inability to directly link increased axonal damage with enhanced neuronal infection remains puzzling and supports dysregulation of oligodendrocyte function and/or neuroprotective functions of microglia as contributing factors to the severe pathological phenotype and clinical outcome. Numerous functions of RNase L, not directly associated with anti-viral activity, may contribute to the increased susceptibility of RL 2/2 mice to MHV-JHM infection. cache = ./cache/cord-325624-6anybxnk.txt txt = ./txt/cord-325624-6anybxnk.txt === reduce.pl bib === id = cord-325820-tnyzmrm8 author = Kovacikova, Kristina title = 6′-β-Fluoro-Homoaristeromycin and 6′-Fluoro-Homoneplanocin A Are Potent Inhibitors of Chikungunya Virus Replication through Their Direct Effect on Viral Nonstructural Protein 1 date = 2020-03-24 pages = extension = .txt mime = text/plain words = 9807 sentences = 519 flesch = 55 summary = To discover new antiviral agents, we performed a compound screen in cell culture-based infection models and identified two carbocyclic adenosine analogues, 6′-β-fluoro-homoaristeromycin (FHA) and 6′-fluoro-homoneplanocin A (FHNA), that displayed potent activity against CHIKV and Semliki Forest virus (SFV) with 50% effective concentrations in the nanomolar range at nontoxic concentrations. Enzymatic assays with purified wild-type (wt) SFV nsP1 suggested that an oxidized (3′-keto) form, rather than FHNA itself, directly inhibited the MTase activity, while a mutant protein with the K231R and K299E substitutions was insensitive to the compound. Our combined data suggest that FHA and FHNA inhibit CHIKV and SFV replication by directly targeting the MTase activity of nsP1, rather than through an indirect effect on host SAH hydrolase. Since we also identified FHNA analogues that efficiently inhibit host SAH hydrolase in vitro without being active against CHIKV in cell-based assays (31), we reconsidered the possibility of a direct effect of the compound on nsP1 activity. cache = ./cache/cord-325820-tnyzmrm8.txt txt = ./txt/cord-325820-tnyzmrm8.txt === reduce.pl bib === id = cord-325925-010xj69x author = Mordecai, Gideon J title = Endangered wild salmon infected by newly discovered viruses date = 2019-09-03 pages = extension = .txt mime = text/plain words = 5549 sentences = 259 flesch = 48 summary = Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations. High-throughput RT-PCR screening of >6000 wild juvenile Chinook and sockeye salmon showed dissimilar geographical distributions of infected fish, reflecting differences in epidemiological patterns of transmission and infection dynamics for each of the viruses ( Figure 2) . cache = ./cache/cord-325925-010xj69x.txt txt = ./txt/cord-325925-010xj69x.txt === reduce.pl bib === id = cord-325954-rhrkr97h author = Han, Mi Seon title = Viral RNA Load in Mildly Symptomatic and Asymptomatic Children with COVID-19, Seoul, South Korea date = 2020-10-17 pages = extension = .txt mime = text/plain words = 1423 sentences = 86 flesch = 57 summary = Along with positive SARS-CoV-2 RNA in nasopharyngeal swabs, viral RNA was detectable at high concentration for >3 weeks in fecal samples from 12 mildly symptomatic and asymptomatic children with COVID-19 in Seoul, South Korea. For this study, we included all children <18 years of age who were confirmed to have COVID-19 by positive results for SARS-CoV-2 in combined nasopharyngeal and oropharyngeal swab specimens and who were hospitalized in Seoul Metropolitan Government-Seoul National University Boramae Medical Center during March 8-April 28, 2020. In comparison, the median initial fecal RNA load was 7.68 (range <4.10-10.27) log 10 copies/mL and Along with positive SARS-CoV-2 RNA in nasopharyngeal swabs, viral RNA was detectable at high concentration for >3 weeks in fecal samples from 12 mildly symptomatic and asymptomatic children with COVID-19 in Seoul, South Korea. In addition, the RNA load in feces remained steadily high, whereas that in nasopharyngeal swab specimens and saliva declined with time in both symptomatic and asymptomatic children. cache = ./cache/cord-325954-rhrkr97h.txt txt = ./txt/cord-325954-rhrkr97h.txt === reduce.pl bib === id = cord-325958-1v1pg2z0 author = Lange, Clemens title = Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date = 2020-05-06 pages = extension = .txt mime = text/plain words = 2672 sentences = 149 flesch = 45 summary = In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high‐throughput RNA sequencing to assess mRNA expression of the SARS‐CoV‐2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. Since the outbreak, many studies described ACE2 expression across human tissues, including lung, stomach, ileum, colon, liver and kidney 8, 9 , supporting the clinical observation that SARS-CoV-2 can infect multiple organs. To obtain information on transcription of ACE2 and associated molecules required for cell entry by SARS-CoV-2, existing datasets of 38 conjunctival samples from 38 patients were included in this study. This study shows that ACE2, which is the main receptor for SARS-CoV-2 6 , is not significantly expressed in healthy and diseased human conjunctival samples. cache = ./cache/cord-325958-1v1pg2z0.txt txt = ./txt/cord-325958-1v1pg2z0.txt === reduce.pl bib === id = cord-325966-0g7a9s5z author = Shih, Hsin-I. title = Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date = 2020-05-30 pages = extension = .txt mime = text/plain words = 7324 sentences = 365 flesch = 39 summary = Some candidate drugs targeting different levels and stages of human responses against COVID-19 such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, interleukin 6 blocker, and convalescent plasma may improve the clinical outcomes of critical COVID-19 patients. However, these clinical, laboratory, and imaging findings are nonspecific and cannot differentiate COVID-19 from other viral respiratory infections; viral diagnostic methods specific for SARS-CoV-2 should be applied for disease confirmation. An open-label study published in 2004 suggested, by comparison with a control group that received only ribavirin, that the addition of lopinavir-ritonavir (400 mg and 100 mg, respectively) to ribavirin reduced the risk of adverse clinical outcomes (acute respiratory distress syndrome or death) and viral load among patients with SARS [29] . Some available candidate drugs targeting different levels of human responses to COVID-19, such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, IL-6 blocker and convalescent plasma, may improve the clinical outcomes of critical COVID-19 patients. cache = ./cache/cord-325966-0g7a9s5z.txt txt = ./txt/cord-325966-0g7a9s5z.txt === reduce.pl bib === id = cord-326017-qw4qynqv author = Laskar, Partha title = “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date = 2020-08-06 pages = extension = .txt mime = text/plain words = 14797 sentences = 760 flesch = 42 summary = Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Overall, real-time RT-PCR based method enables developing a high-throughput testing for rapid, on-demand, low-cost, reliable, quantitative detection technique against COVID-19 in clinical settings [39] . Another newly developed method, SARS-CoV-2 DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), was found to perform simultaneous reverse transcription and isothermal amplification by (i) RT-LAMP for RNA extracted (for nasopharyngeal or oropharyngeal swabs), (ii) Cas12 detection of predefined coronavirus sequences, and (iii) cleavage of a reporter molecule confirms, which detects the virus [56] . cache = ./cache/cord-326017-qw4qynqv.txt txt = ./txt/cord-326017-qw4qynqv.txt === reduce.pl bib === id = cord-326225-crtpzad7 author = Neill, John D. title = Simultaneous rapid sequencing of multiple RNA virus genomes date = 2014-06-01 pages = extension = .txt mime = text/plain words = 3804 sentences = 204 flesch = 55 summary = This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3′-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. There is a wealth of information in these isolates, but up till now, it has been time consuming and expensive to sequence these viral genomes, often requiring sets of strain-specific primers for PCR amplification and sequencing. These primers were developed so that the 20 base known sequence was used for PCR amplification of the library as well as served as a barcode for identifying each viral library following pooling and sequencing. This virus, a BVDV 1b strain isolated from alpaca (GenBank accession JX297520.1; Table 2 , library 3, barcode 10), was assembled from Ion Torrent data and was found to have only 1 base difference from the sequence determined earlier (data not shown). One virus, library 1, barcode 9, had only 658 viral sequence reads but 94.4% of the genome was assembled. cache = ./cache/cord-326225-crtpzad7.txt txt = ./txt/cord-326225-crtpzad7.txt === reduce.pl bib === id = cord-326217-ji0njeha author = Saleh, Maged title = Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date = 2018-11-27 pages = extension = .txt mime = text/plain words = 4731 sentences = 262 flesch = 48 summary = We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. To assess whether both GSK3 isoforms are required for HCV replication, we silenced GSK3α and / or GSK3β gene expression by transfecting siRNAs and quantified HCV RNA in Huh-7.5 cells harboring HCV subgenomic replicon (Con1) or infectious HCV (Jc1). Given the well-known dependency of HCV on miR-122 (Jopling et al., 2005 (Jopling et al., , 2008 Machlin et al., 2011) and the regulatory circuit between insulin-like growth factor 1 receptor, GSK3β, and miR-122 identified previously (Zeng et al., 2010) , we assessed the effect of GSK3 inhibition on miR-122 expression in Huh-7.5 cells harboring a subgenomic HCV replicon. cache = ./cache/cord-326217-ji0njeha.txt txt = ./txt/cord-326217-ji0njeha.txt === reduce.pl bib === id = cord-326257-rcv8sh22 author = Simmonds, P. title = Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date = 2020-05-01 pages = extension = .txt mime = text/plain words = 3499 sentences = 172 flesch = 47 summary = C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5'U/A and 3'U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. The possibility that the initial diversity within a viral population was largely host-induced would have major implications for 70 evolutionary reconstruction of SARS-CoV-2 variants in the current pandemic, as well as in our understanding both of host antiviral pathways against coronaviruses and the longer term shaping effects on their genome composition. To formally analyse 105 the excess of C->U transitions we calculated an index of asymmetry (frequency[C->U] / f[U->C]) x (fU/fC) and compared this with degrees of sequence divergence and dN/dS ratio in SARS-CoV-2 and other coronavirus datasets (Fig. 2B, 2C ). cache = ./cache/cord-326257-rcv8sh22.txt txt = ./txt/cord-326257-rcv8sh22.txt === reduce.pl bib === id = cord-326719-p1ma4akz author = Enjuanes, Luis title = Virus-based vectors for gene expression in mammalian cells: Coronavirus date = 2003-12-31 pages = extension = .txt mime = text/plain words = 5923 sentences = 282 flesch = 52 summary = Coronaviruses have several advantages as vectors over other viral expression systems: (1) coronaviruses are single-stranded RNA viruses that replicate within the cytoplasm without a DNA intermediary, making integration of the virus genome into the host cell chromosome unlikely, (2) these viruses have the largest RNA virus genome and, in principle, have room for the insertion of large foreign genes, (3) a pleiotropic secretory immune response is best induced by the stimulation of gut-associated lymphoid tissues, (4) the tropism of coronaviruses may be modified by manipulation of the spike (S) protein allowing engineering of the tropism of the vector, (5) non-pathogenic coronavirus strains infecting most species of interest (human, porcine, bovine, canine, feline, and avian) are available to develop expression systems, and (6) infectious coronavirus cDNA clones are available to design expression systems. cache = ./cache/cord-326719-p1ma4akz.txt txt = ./txt/cord-326719-p1ma4akz.txt === reduce.pl bib === id = cord-326911-va3x6au2 author = Ramos-Mandujano, G. title = A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date = 2020-06-29 pages = extension = .txt mime = text/plain words = 4424 sentences = 288 flesch = 55 summary = We developed an open-source method called Magneticnanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. To date, molecular diagnosis of COVID-19 predominantly relies on detection of SARS-CoV-2 RNA using real-time reverse transcription polymerase chain reaction (rRT-PCR) assays, such as those approved by the US Centers for Disease Control and Prevention (US CDC) 1 . MAVRICS performed on par or better than commercial RNA extraction kits in rRT-PCR detection of SARS-CoV-2, influenza viruses and respiratory syncytial virus in various clinical and environmental samples. . https://doi.org/10.1101/2020.06.28.20141945 doi: medRxiv preprint Next, we aimed to develop an efficient SiMNP-based RNA extraction protocol using the contrived SARS-CoV-2 samples and US CDC 2019-nCoV_N1 and N3 rRT-PCR assays. cache = ./cache/cord-326911-va3x6au2.txt txt = ./txt/cord-326911-va3x6au2.txt === reduce.pl bib === id = cord-327259-7o7fs4yb author = Correa, I. A. title = Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date = 2020-08-19 pages = extension = .txt mime = text/plain words = 4584 sentences = 265 flesch = 56 summary = We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. To assess the advantages of the pooling approach, we used previous qRT-PCR results obtained in the diagnostic analyses performed with industrial workers of Rio de Janeiro state as a base to calculate the prevalence rates (%) of positive cases and to build the statistical modeling methodology. Our study adopted the statistical modeling approach and validated the data with pooling biological samples for COVID-19 diagnostic, confirming that the pool size must be selected according to the prevalence rate of positive cases in the population (Figure 2) . cache = ./cache/cord-327259-7o7fs4yb.txt txt = ./txt/cord-327259-7o7fs4yb.txt === reduce.pl bib === id = cord-327024-1k5jucae author = Zhang, Qingshui title = Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date = 2018-04-19 pages = extension = .txt mime = text/plain words = 4167 sentences = 213 flesch = 47 summary = 18 reported the detection of avian nephritis virus infection in Croatian goose flocks and provided evidence that this AstV was associated with stunting and prehatching mortality of goose embryos. To determine the potential genetic mutation(s) that might occur during the goose embryo passage, the initial virus genome was sequenced using the total RNA extracted from the clinical case tissue homogenate. When the samples were tested by RT-PCR for virus shedding evaluation, the AAstV specific RNA was sequentially detected from the cloacal swabs of infected goslings from 2 to 12 dpi (Fig. 6 ). To evaluate the potential adaptive mutation (s) of the virus that might occur during the process of goose embryo passage, we sequenced the complete genome of initial virus using the total RNA extracted from the clinical case tissue homogenate of kidney, spleen, and liver using the method described above. cache = ./cache/cord-327024-1k5jucae.txt txt = ./txt/cord-327024-1k5jucae.txt === reduce.pl bib === id = cord-327660-p1b07b4t author = Wolf, Yuri I. title = Origins and Evolution of the Global RNA Virome date = 2018-11-27 pages = extension = .txt mime = text/plain words = 13927 sentences = 658 flesch = 45 summary = The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) . cache = ./cache/cord-327660-p1b07b4t.txt txt = ./txt/cord-327660-p1b07b4t.txt === reduce.pl bib === id = cord-327272-fspxett8 author = Buonaguro, Luigi title = Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date = 2020-05-12 pages = extension = .txt mime = text/plain words = 1432 sentences = 83 flesch = 46 summary = The new human coronavirus named SARS-CoV-2 is a positive-sense RNA virus for which no specific drugs are currently available. A knowledge-based analysis strongly suggests a possible repositioning of the anti-HCV direct antiviral agent (DAA) Sofosbuvir as treatment for SARS-CoV-2. The only positive-sense RNA virus, for which a very effective drug targeting specifically the RdRp is available and approved world-wide for clinical use, is hepatitis C virus (HCV). All these sequence and structural modelling evidences strongly support the concept that the SARS-CoV-2 RdRp is much more similar to the one from HCV than the one from negative-sense Influenza and Ebola RNA viruses. Therefore, repositioning of Sofosbuvir (Sovaldi®; Epclusa® by Gilead), the inhibitor of the HCV NS5B RdRp protein, as antiviral in the treatment of the SARS-CoV-2 infection has an extremely high potentiality of success, as recently postulated by others [17] , and is suggested as a potential drug for the treatment of COVID-19 in the very recent EASL-ESCMID position paper [18] . cache = ./cache/cord-327272-fspxett8.txt txt = ./txt/cord-327272-fspxett8.txt === reduce.pl bib === id = cord-327000-oyg3oyx1 author = Li, Shasha title = Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date = 2020-05-11 pages = extension = .txt mime = text/plain words = 11098 sentences = 688 flesch = 48 summary = This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. cache = ./cache/cord-327000-oyg3oyx1.txt txt = ./txt/cord-327000-oyg3oyx1.txt === reduce.pl bib === id = cord-327855-txryqil7 author = Kulka, M. title = The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date = 2003 pages = extension = .txt mime = text/plain words = 8706 sentences = 394 flesch = 50 summary = Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. In this study, we report that infection of FrhK4 cells with the HAV cp strain HM175/18f results in the degradation of ribosomal RNA (rRNA) and the reduction of several cellular mRNAs including β-actin and GAPDH. Degradation of rRNA is a feature of virus infection in interferon (IFN) treated cells and is believed to be due to the availability of double stranded RNA (dsRNA) during replication or transcription of the viral genome, resulting in the activation of the RNase L pathway [58, 59] . While the role of a viral protein in the activation of 2-5A/RNase L pathway in 18f or CBV1 infected FrhK4 cells cannot be ruled out, previous reports with EMC virus and the studies involving dsRNA clearly suggests a similar mechanism of rRNA degradation reported here. cache = ./cache/cord-327855-txryqil7.txt txt = ./txt/cord-327855-txryqil7.txt === reduce.pl bib === id = cord-327518-yilv9z2m author = nan title = Coronaviridae date = 2011-11-23 pages = extension = .txt mime = text/plain words = 7123 sentences = 351 flesch = 49 summary = In coronaviruses, proteolytic processing results in the production of 15 (in viruses belonging to the species Avian coronavirus) or 16 mature products, commonly referred to as non-structural proteins (nsp's) and numbered according to their position -from N-to C-terminus -in the viral polyproteins ( Figure 1 ). Apart from their relatively close phylogenetic relationship, the only general characteristics that would set them apart from other coronaviruses are (i) a unique type of nsp1, distinct in size and sequence from betacoronavirus nsp1 and without apparent counterpart in the gammacoronaviruses, and (ii) the presence of a commonly-shared accessory gene (designated ORF3 in most alphacoronavirus species, ORF3b and 3c in TGEV and in FCoV/CCoV, respectively) for a dispensable multi-spanning alphacoronavirus membrane protein (αmp). The structural proteins are expressed from three sg mRNA species that are 3 co-terminal with the genome and believed to be produced via a process of discontinuous minus-strand RNA synthesis similar to that of coronaviruses ( Figure 12 ). cache = ./cache/cord-327518-yilv9z2m.txt txt = ./txt/cord-327518-yilv9z2m.txt === reduce.pl bib === id = cord-328300-zehltghv author = Lin, Shing-Yen title = Structural Basis for the Identification of the N-Terminal Domain of Coronavirus Nucleocapsid Protein as an Antiviral Target date = 2014-02-24 pages = extension = .txt mime = text/plain words = 6628 sentences = 345 flesch = 53 summary = CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein's N-terminal domain (N-NTD). We report the crystal structures of HCoV-OC43 N-NTD complexed with ribonucleoside 5′-monophosphates as a model for understanding the molecular interactions that govern CoV N-NTD binding to RNA. To begin to elucidate how RNA and the N protein interact, we determined the crystal structure of HCoV-OC43 N-NTD complexed with AMP. These amino acids are sequentially and structurally conserved in other HCoV N proteins ( Figure S2 , Supporting Information); therefore, they are likely essential for RNA recognition and interaction in all coronavirus N proteins. Previous studies indicated that the positively charged amino acid, Arg 106, located at the cleft in the HCoV-OC43 N-NTD structure, is conserved in all CoV N proteins and interacts nonspecifically with the RNA phosphate backbone. cache = ./cache/cord-328300-zehltghv.txt txt = ./txt/cord-328300-zehltghv.txt === reduce.pl bib === id = cord-327997-noqbcxua author = Wu, Kevin E. title = RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date = 2020-06-20 pages = extension = .txt mime = text/plain words = 7201 sentences = 377 flesch = 42 summary = We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus, and that the 5' and 3' viral untranslated regions contain the strongest, most distinct localization signals. As previously discussed, since much of the APEX-seq mitochondrial data used to train RNA-GPS actually consists of nuclear-encoded transcripts likely picked up as the APEX-COX4 fusion protein is transported to the mitochondria, we hypothesize that our predicted mitochondrial residency is alluding to similarity in localization pathways, rather than localization destination. To further validate the robustness of these results, we also trained a different predictive algorithm (a recurrent neural network, see STAR Methods for additional details) on the APEX-seq data and performed a similar set of experiments, comparing SARS-CoV-2 dominant subcellular residency predictions to human and coronavirus baselines ( Figure S3A /B). cache = ./cache/cord-327997-noqbcxua.txt txt = ./txt/cord-327997-noqbcxua.txt === reduce.pl bib === id = cord-328042-e1is656g author = Klein, Steffen title = SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date = 2020-08-07 pages = extension = .txt mime = text/plain words = 6328 sentences = 329 flesch = 56 summary = The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Here, we show that the magnetic bead-based protocol yields RNA extracts comparable to the commercially available QIAcube viral RNA extraction kit, as determined by the commonly applied detection methods RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [16] . cache = ./cache/cord-328042-e1is656g.txt txt = ./txt/cord-328042-e1is656g.txt === reduce.pl bib === id = cord-328259-3g4klpyg author = Guajardo-Leiva, Sergio title = Metagenomic Insights into the Sewage RNA Virosphere of a Large City date = 2020-09-21 pages = extension = .txt mime = text/plain words = 7626 sentences = 370 flesch = 47 summary = Despite the overrepresentation of dsRNA viruses, our results show that Santiago's sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Viral sequences identified as Partitiviridae-like viruses included in the "unclassified RNA viruses ShiM-2016" category in the NCBI taxonomy (~25% abundance; Figure 2B ) and Totiviriade family were also highly abundant in treated and untreated sewage samples from the EU [5, 7] . Therefore, the abundance of these viruses in the Trebal metagenome can expand the known sequence space associated with this family (only 10 genomes are currently available in the NCBI database) and contribute to a better understanding of the bacteriophage biology related to RNA genomes. Taken together, our results show that metagenomic surveys of RNA viruses in sewage samples and the use of HMMs could uncover extraordinary viral diversity through the detection of remote homologs in these human-impacted environments. cache = ./cache/cord-328259-3g4klpyg.txt txt = ./txt/cord-328259-3g4klpyg.txt === reduce.pl bib === id = cord-328085-7wp18qb6 author = Barage, Sagar title = Identification and characterization of novel RdRp and Nsp15 inhibitors for SARS-COV2 using computational approach date = 2020-11-06 pages = extension = .txt mime = text/plain words = 6052 sentences = 362 flesch = 51 summary = This indicates that these compounds have a good binding affinity with RdRp. The resulting top 10 ligand conformations were evaluated for its binding mode and molecular interaction with active site residues of RdRP (Table 1 ). The first compound, namely, Chlorohexidine with binding free energy -10.11 Kcal/mol efficiently accommodated in the active site of RdRp and do molecular mimicry of nucleotides in terms of substructure interactions with RdRp residues (Figure 2(A) ). The second lead molecule, Ergotamine bound conformation, showed slight variation in the side-chain orientation with respect to Naldemedine binding in the active site of Nsp15 (Figure 4) . Thus, based on stability and molecular interaction and binding mode, Alectinib acts as lead molecule to design novel RdRp inhibitor to block the viral replication. The differences in NSP15 residues interaction with Naldemedine in simulated structure and predicted docked pose is due to flipped orientation of Naldemedine (Supporting Information Fig. S4B and Figure 4(B) ). cache = ./cache/cord-328085-7wp18qb6.txt txt = ./txt/cord-328085-7wp18qb6.txt === reduce.pl bib === id = cord-328471-oz99upzz author = Ahmad, Jamshaid title = SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date = 2020-07-23 pages = extension = .txt mime = text/plain words = 5089 sentences = 282 flesch = 55 summary = In this global health emergency, drug repurposing (or repositioning) is one of the fast track option that involves screening of existing FDA approved drugs for the identification of potential molecules that can disrupt the function of key proteins of the SARS-CoV-2 and can be used for treatment against COVID-19. Whereas, Demoxytocin showed ten H-bonds with both active site Asp760 and Asp761 and other key residues e.g. Trp617, Tyr619, Lys621, Ser682, Glu811, Lys621, Tyr619, Trp617, Ser682 and Glu811 with dock score -9.68kcal/mol and ligand efficiency of -0.142 (Supplementary Figure S3) . Colistin (polymyxin E, polypeptide antibiotics) showed most of the H-bonding with Lys551, Trp617, Tyr619, Asp618, Ser682, Asp684, Asn691, and both catalytic residues i.e. Asp760, Asp761, with a docking score of -9.24kcal/mol and ligand efficiency of -0.113 (Supplementary Figure S5) . Examorelin, Lypressin, Ornipressin, and Colistin are also common drugs in both form of RdRp. Only one H-bond with His810 and other non-covalent interactions were observed for Examorelin showed a docking score of -12.139 kcal/mol and ligand efficiency of -0.187. cache = ./cache/cord-328471-oz99upzz.txt txt = ./txt/cord-328471-oz99upzz.txt === reduce.pl bib === id = cord-328252-dk54w8z9 author = Kikkert, Marjolein title = Innate Immune Evasion by Human Respiratory RNA Viruses date = 2019-10-14 pages = extension = .txt mime = text/plain words = 11552 sentences = 550 flesch = 43 summary = Whether PA-X also degrades viral dsRNA species to prevent recognition by cytosolic RNA sensors is not entirely clear, but mutant viruses in which this PA-X protein was expressed in significantly lower amounts elicited higher levels of innate immune response; for example, IFN-beta production was much higher in these infections [71] . This indeed suggests that PA-X, besides having a role in the degradation of cellular mRNAs, may also degrade viral RNA to prevent recognition by innate immune sensors and activation of innate immune responses, similar to what was shown for the CoVs. To my knowledge, an endoribonuclease has not been identified in the RSV genome, so this virus may use alternative innate immune evasion strategies, as discussed elsewhere in this review. [91] suggested that RSV specifically targets mRNA encoding surfactant protein A, an innate immune factor with an important role in the epithelial tissue of the lung, which directly binds to virus particles to cause their destruction by host defense mechanisms. cache = ./cache/cord-328252-dk54w8z9.txt txt = ./txt/cord-328252-dk54w8z9.txt === reduce.pl bib === id = cord-328686-5ik5em5a author = Zhao, L. title = First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date = 2020-08-21 pages = extension = .txt mime = text/plain words = 1606 sentences = 110 flesch = 61 summary = In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint From the findings of this study, during the middle risk period, positive samples were detected both in 83 municipal and hospital wastewater systems. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint Although SARS-CoV-2 RNA surveillance in wastewaters is a useful WBE drive, the public health risk associated 109 with water cycle is unclear since viral particles infectivity in sewage and faeces is yet to be determined in 110 addition to its probable fecal-oral transmission. cache = ./cache/cord-328686-5ik5em5a.txt txt = ./txt/cord-328686-5ik5em5a.txt === reduce.pl bib === id = cord-328659-miujzgtd author = Mishra, Akhilesh title = Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date = 2020-07-27 pages = extension = .txt mime = text/plain words = 6064 sentences = 361 flesch = 55 summary = title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. The rapid global spread of SARS-CoV-2 in a short period of time and the availability of a large number of fully sequenced genomes provide us with a unique opportunity of understanding the short-term temporal evolution of this virus in humans in a near real-time scale. By this approach we propose the classification of the SARS-CoV-2 virus genomes into 5 mutually exclusive lineages with unique set of co-occurring mutations and geographic distribution. Our analysis revealed a total of 40 nucleotide substitutions which occurred at > 1% in the SARS-CoV-2 genomes (Table 1 and Figure 1A ). We consider a specific mutation or a set of cooccurring mutations as "lineage-defining" for SARS-CoV-2, only when they are present in at least 2% (n=30) of the sequences analysed. cache = ./cache/cord-328659-miujzgtd.txt txt = ./txt/cord-328659-miujzgtd.txt === reduce.pl bib === id = cord-328633-c31xsyeo author = Moser, Michael J. title = Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date = 2012-06-04 pages = extension = .txt mime = text/plain words = 7868 sentences = 441 flesch = 54 summary = Most RT-PCR protocols rely on two DNA polymerase (Pol) enzymes; a retroviral reverse transcriptase (RT) to copy RNA into cDNA and a thermostable DNA Pol to amplify the target sequence. Despite their wide use and general reliability, existing twoenzyme RT-PCR systems have several documented performance problems attributed to deficiencies inherent in retroviral RTs: 1) poor reagent stability, 2) low fidelity, 3) frequent rearrangements during cDNA synthesis, 4) secondary enzymatic activities (i.e. RNase H and strand switching), 5) bias for specific primers and templates, and 6) inhibition of PCR Pol enzymes [3, 4, 5, 6, 7] . We describe the discovery and biochemical attributes of one of these, 3173 Pol, its inherent RT activity and its incorporation into a single-enzyme PyroScriptH 2X RT-PCR Master Mix. The sensitivity, specificity and overall performance of this mix were compared to available one-and two-enzyme systems using a control MS2 RNA bacteriophage template, the clinically-relevant influenza A RNA and commonly used reference mRNA transcripts. cache = ./cache/cord-328633-c31xsyeo.txt txt = ./txt/cord-328633-c31xsyeo.txt === reduce.pl bib === id = cord-328737-6mcefqn5 author = Lee, Eun Yeong title = A novel nucleic acid amplification system based on nano-gap embedded active disk resonators date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4147 sentences = 181 flesch = 45 summary = We here describe for the first time a novel nucleic acid amplification system based on nano-gap active resonators that can be used for in various molecular diagnostic applications, which requires a label-free and real-time detection with rapidity and high sensitivity. First, SRSN active disk resonators were used as photoluminescence sensors for the PL peaks J o u r n a l P r e -p r o o f generated by the direct amplification of nucleic acids on the sensor surface in a label-free and real-time manner. These complexes bind to the target nucleic acids and enable the strand exchange which will begin the amplification process both on the surface of disk resonator (solid) and solution simultaneously ( Fig. 1-rectangle) , with the temperature maintained at isothermal conditions (38°C or 43°C for DNA or RNA, respectively). This photoluminescence sensor enables label-free and real-time amplification and direct detection of either bacterial DNA or viral RNA on the resonator surface. cache = ./cache/cord-328737-6mcefqn5.txt txt = ./txt/cord-328737-6mcefqn5.txt === reduce.pl bib === id = cord-328768-2qk884x2 author = Sabatier, Marina title = Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses date = 2020-10-06 pages = extension = .txt mime = text/plain words = 5361 sentences = 293 flesch = 45 summary = Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). The development of metagenomics next-generation sequencing (mNGS) has enabled the exploration of whole viral nucleic acids within a clinical sample (human virome) in order to detect pathogens not targeted by conventional PCR and to identify emerging viruses [1] [2] [3] [4] [5] [6] [7] [8] . The aim of this study was to compare two automated extraction platforms commonly used in diagnostic laboratories, the eMAG (bioMérieux, Marcy-l Étoile, France) and the MagNA Pure 24 (MP24) (Roche, Basel, Switzerland), and one manual QIAamp Viral RNA Mini Kit extraction (Qiagen, Hilden, Germany), which is among one of the most popular methods used in research laboratories. cache = ./cache/cord-328768-2qk884x2.txt txt = ./txt/cord-328768-2qk884x2.txt === reduce.pl bib === id = cord-328460-thx9zh11 author = Zanoli, Laura Maria title = Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices date = 2012-12-27 pages = extension = .txt mime = text/plain words = 8972 sentences = 407 flesch = 36 summary = Miniaturized isothermal amplification systems will be then illustrated including nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), multiple displacement amplification (MDA) and recombinase polymerase amplification (RPA). In addition, the use of droplet-based microfluidic systems for PCR enables the amplification and the analysis of individual target sequences to be performed in a significantly lower time as a consequence of a higher thermal cycling speed. These include nucleic acid sequence-based amplification (NASBA), loop-mediated amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), recombinase polymerase amplification (RPA) and multiple displacement amplification (MDA) [7] . Unlike other electrochemical techniques [56], based on the immobilization of an oligonucleotide probe onto an electrode, hybridization of a complementary target sequence, and transduction of the hybridization event [57], the microfluidic detection of LAMP amplicons [55] does not require probe immobilization and bacteria detection can be accomplished in a single chamber without DNA extraction and purification steps, since the used isothermal temperature (66 °C) provides enough thermal shock to lyse the E. cache = ./cache/cord-328460-thx9zh11.txt txt = ./txt/cord-328460-thx9zh11.txt === reduce.pl bib === id = cord-329041-coryaz2s author = Brown, Ariane J. title = Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date = 2019-09-30 pages = extension = .txt mime = text/plain words = 5934 sentences = 325 flesch = 54 summary = These data further extend the known breadth and antiviral activity of RDV to include both contemporary human and highly divergent zoonotic CoV and potentially enhance our ability to fight future emerging CoV. We previously reported the antiviral activity of RDV against a genetically diverse panel of human endemic, emerging and zoonotic CoV including HCoV-NL63 (alpha 1b), mouse hepatitis virus (MHV, beta 2a), SARS-CoV and related Bat CoVs WIV1 and SHC014 (beta 2b), as well as MERS-CoV and related Bat CoV HKU5 (beta 2c) (Agostini et al., 2018; Sheahan et al., 2017) . Inhibition of viral protease has also been evaluated with lopinavir, a protease inhibitor designed for human immunodeficiency virus, which like chloroquine exerts a moderate antiviral effect on CoV replication (EC 50 values: MERS-CoV 8 μM, SARS-CoV 17.1 μM, HCoV-229E 6.6 μM) (de Wilde et al., 2014) . cache = ./cache/cord-329041-coryaz2s.txt txt = ./txt/cord-329041-coryaz2s.txt === reduce.pl bib === id = cord-328947-3l9ydspz author = Webb, L. G. title = Chikungunya virus antagonizes cGAS-STING mediated type-I interferon responses by degrading cGAS date = 2020-10-15 pages = extension = .txt mime = text/plain words = 9857 sentences = 544 flesch = 51 summary = CHIKV is no exception, the type-I interferon (IFN) response has been demonstrated to be key in controlling CHIKV infection [21] [22] [23] [24] [25] [26] and primary sensing of the virus is via the pattern recognition receptor (PRR) retinoic acid-inducible gene I (RIG-I)-mitochondrial antiviral signaling protein (MAVS) axis [24, 26] . The lack of cGAS degradation seen in the exogenous expression system when compared to the infected cells shows that although there is a clear interaction of cGAS with nsP4, the degradation of cGAS observed is not mediated by the non-structural proteins of CHIKV, but must require other viral or host factors. Chikungunya virus inhibits DNA sensing by degrading cGAS both mock and infected cells by 4 hpi suggesting that the stress produced during the process of infection (mock or CHIKV) in HFF-1s stimulates increased translation at early timepoints ( Fig 4D, lanes 2 and 5) . cache = ./cache/cord-328947-3l9ydspz.txt txt = ./txt/cord-328947-3l9ydspz.txt === reduce.pl bib === id = cord-328960-46zui1sl author = Hillen, Hauke S. title = Structure of replicating SARS-CoV-2 polymerase date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4541 sentences = 285 flesch = 62 summary = Particle classification yielded a 3D reconstruction at a nominal resolution of 2.9 Å and led to a refined structure of the RdRp-RNA complex (Extended Data Figures 1 and 2) . The structure resembles that of the free enzyme 16 , but also reveals large additional protein regions in nsp8 that became ordered upon RNA binding and interact with RNA far outside the core enzyme (Extended Data Figure 3a ). The supernatant containing nsp12 was filtered using a 5-μm syringe filter, followed by filtration with a 0.8-µm syringe filter (Millipore) and applied onto a HisTrap HP 5 mL (GE Healthcare), preequilibrated in lysis buffer (300 mM NaCl, 50 mM Na-HEPES pH 7.4, 10 % (v/v) glycerol, 30 mM imidazole pH 8.0, 3 mM MgCl2, 5 mM β-mercaptoethanol, 0.284 µg ml-1 leupeptin, 1.37 µg ml-1 pepstatin, 0.17 mg ml-1 PMSF, and 0.33 mg ml-1 benzamidine). cache = ./cache/cord-328960-46zui1sl.txt txt = ./txt/cord-328960-46zui1sl.txt === reduce.pl bib === id = cord-329107-43e2lkht author = Pawlicka, Kamila title = Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics date = 2020-03-24 pages = extension = .txt mime = text/plain words = 6690 sentences = 377 flesch = 44 summary = Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a surveillance pathway used by cells to control the quality mRNAs and to fine-tune transcript abundance. Disturbance of this control mechanism caused by genetic mutations or dys-regulation of the NMD pathway can lead to pathologies, including neurological disorders, immune diseases and cancers. Nonsense-mediated mRNA decay (NMD) is a critical cellular surveillance mechanism that recognizes and eliminates aberrant RNAs containing premature termination codons (PTC) or abnormally long 3 untranslated regions (UTRs). Nonsense-mediated mRNA decay is a critical RNA quality control and plays a vital role in the recognition of PTCs in transcripts, as well as in the regular homeostasis of the transcriptome. Understanding the mechanism of nonsense-mediated mRNA decay might lead to new ways to use surveillance in cancer therapy or other PTC-associated genetic diseases. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon Hypoxic Inhibition of Nonsense-Mediated RNA Decay Regulates Gene Expression and the Integrated Stress Response cache = ./cache/cord-329107-43e2lkht.txt txt = ./txt/cord-329107-43e2lkht.txt === reduce.pl bib === id = cord-329102-2y49kcwu author = Lan, Tammy C. T. title = Structure of the full SARS-CoV-2 RNA genome in infected cells date = 2020-06-30 pages = extension = .txt mime = text/plain words = 9315 sentences = 507 flesch = 61 summary = We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1. cache = ./cache/cord-329102-2y49kcwu.txt txt = ./txt/cord-329102-2y49kcwu.txt === reduce.pl bib === id = cord-329361-0mpbau1b author = Bennasser, Yamina title = RNAi Therapy for HIV Infection: Principles and Practicalities date = 2012-08-16 pages = extension = .txt mime = text/plain words = 2645 sentences = 200 flesch = 56 summary = Inside eukaryotic cells, small RNA duplexes, called small interfering RNAs (siRNAs), activate a conserved RNA interference (RNAi) pathway which leads to specific degradation of complementary target mRNAs through base-pairing recognition. The practical use of RNAi therapy for HIV infection will depend on overcoming several challenges, including the ability to establish long-term expression of siRNA without off-target effects and the capacity to counteract mutant escape viruses. [4] Hence, in plants and Drosophila, when a cell they have sequence specificity for silencing mRNAs, these small is infected by a virus, an RNAi response is triggered by the foreign RNAs potentially represent a future class of antiviral drugs. [42] silencing of viral RNA and transient suppression of HIV replicaobserved that an siRNA targeted to nef rapidly elicited the emertion over a period of 3 to 4 days in single round infection of gence of siRNA-resistant viruses with point mutations in the nef cultured cells have been achieved. cache = ./cache/cord-329361-0mpbau1b.txt txt = ./txt/cord-329361-0mpbau1b.txt === reduce.pl bib === id = cord-329311-p68kr4ga author = Prebensen, Christian title = SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date = 2020-09-05 pages = extension = .txt mime = text/plain words = 1454 sentences = 111 flesch = 61 summary = title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . cache = ./cache/cord-329311-p68kr4ga.txt txt = ./txt/cord-329311-p68kr4ga.txt === reduce.pl bib === id = cord-329504-91te3nu8 author = Croll, Tristan title = Making the invisible enemy visible date = 2020-10-07 pages = extension = .txt mime = text/plain words = 4826 sentences = 219 flesch = 52 summary = A general indication of how well the atomic model fits the measurement data can be obtained by comparing the deposited R-factors to results from PDB-REDO (10) (including Whatcheck (11)) to determine the overall density fit as well as many other diagnostics. Our remodelled structure is offering a valuable structural basis for future studies, such as in-silico docking and drug design targeting at SARS-CoV-2 RdRp (34), as well as for computational modelling or simulations to investigate the molecular mechanism of viral replication (31, 35, 36) . This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. cache = ./cache/cord-329504-91te3nu8.txt txt = ./txt/cord-329504-91te3nu8.txt === reduce.pl bib === id = cord-329493-ueqlhgn0 author = Stadler, Konrad title = SARS — beginning to understand a new virus date = 2003 pages = extension = .txt mime = text/plain words = 5146 sentences = 248 flesch = 51 summary = A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection cache = ./cache/cord-329493-ueqlhgn0.txt txt = ./txt/cord-329493-ueqlhgn0.txt === reduce.pl bib === id = cord-329429-ur8g68vp author = Miłek, Justyna title = Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date = 2018-12-10 pages = extension = .txt mime = text/plain words = 3809 sentences = 187 flesch = 50 summary = Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3'UTR or 5'UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . cache = ./cache/cord-329429-ur8g68vp.txt txt = ./txt/cord-329429-ur8g68vp.txt === reduce.pl bib === id = cord-329366-xuszdrsa author = Hackbart, Matthew title = Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors date = 2020-04-07 pages = extension = .txt mime = text/plain words = 7187 sentences = 445 flesch = 57 summary = In this study, we show that CoV EndoU activity limits the abundance and length of the polyuridine (polyU) extension on 5′-polyU-containing, negative-sense (PUN) RNAs for both the beta-CoV mouse hepatitis virus strain A59 (MHV-A59) and the alpha-CoV PEDV. Overall, we propose a mechanism for EndoU, which is to cleave polyU sequences from PUN RNAs, thus limiting the formation of a PAMP and impeding the ability of MDA5 to activate the innate immune response to infection. EndoU Activity Limits Abundance and Length of PUN RNAs. Previous studies showed that the 5′ end of the CoV negative-sense RNA contains polyU extensions (35) , and that EndoU cleaves at uridine residues (22, 25, (27) (28) (29) (30) . We found that the products generated from positive-sense RNA were similar between wild-type and EndoUmut viruses, consistent with our previous results indicating that the polyA tail is not cleaved by EndoU activity (Fig. 5C ). cache = ./cache/cord-329366-xuszdrsa.txt txt = ./txt/cord-329366-xuszdrsa.txt === reduce.pl bib === id = cord-329494-cdn52epy author = Artuso, María C. title = Inhibition of Junín virus replication by small interfering RNAs date = 2009-07-08 pages = extension = .txt mime = text/plain words = 4725 sentences = 244 flesch = 51 summary = The efficacy of this Z2-siRNA against JUNV was also demonstrated in virus-infected cells, by testing infectious virus plaque formation (92.8% JUNV yield reduction), viral RNA level or antigen expression, as well as in cells transfected with Z-specific reporter plasmids (91% reduction in expression of Z-EGFP fusion protein). (E) Expression of viral antigens in Vero cells transfected with Z2-siRNA or X-siRNA and infected with JUNV was detected by immunofluorescence assay using a rabbit anti-JUNV polyclonal serum. The efficacy of this agent against JUNV was also demonstrated in virus-infected cells by testing infectious virus plaque formation, viral RNA or antigen expression, as well as in cells transfected with Z-specific reporter plasmids. The present study represents the first report of virus inhibition mediated by RNA interference for a New World arenavirus, a group in the family including four agents of severe viral hemorrhagic fevers in South America (JUNV, Machupo, Sabiá and Guanarito viruses). cache = ./cache/cord-329494-cdn52epy.txt txt = ./txt/cord-329494-cdn52epy.txt === reduce.pl bib === id = cord-329687-vhi4tbnc author = Verdugo, C. title = A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing. date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3497 sentences = 207 flesch = 61 summary = title: A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing. However, the most efficient system for massive surveillance, the pre-RNA extraction pooling approach, was obtained with the probe-based assay in test up to 10 samples adding 13.5 uL of RNA template. In this study, we compared a dye-based and probe-based real-time RT-qPCR assay for the economic and rapid detection and quantification of SARS-CoV-2 in human samples by individual and pooling testing. Our results showed that using the dye-based assay describe here, the SARS-CoV-2 can be detected up to 50 viral copies (a dilution of 10 copies/µL) of the RNA template, showing a similar analytical sensitivity obtained with the probe-based standard technique ( Table 2) showed no significant differences in CT values between pooled and individual samples, suggesting that sensitivity was not affected by pooling specimens, regardless of the viral load (Wacharapluesadee et al, 2020). cache = ./cache/cord-329687-vhi4tbnc.txt txt = ./txt/cord-329687-vhi4tbnc.txt === reduce.pl bib === id = cord-329618-kywhulpc author = Xu, Cheng title = A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells date = 2016-05-23 pages = extension = .txt mime = text/plain words = 8323 sentences = 426 flesch = 55 summary = To elucidate the effect of type I IFN on the Jak/stat pathway in salmonid alphavirus subtype 3 (SAV3) infected macrophage/dendritic like TO-cells derived from Atlantic salmon (Salmo salar L) headkidney leukocytes, we used a differential transcriptome analysis by RNA-seq and the Kyoto encyclopedia of genes and genomes (KEGGs) pathway analysis to generate a repertoire of de novo assembled genes from type I IFN treated and non-treated TO-cells infected with SAV3. CONCLUSION: Data presented in this study shows that SAV3 infection downregulates several genes of the Jak/stat pathway, which could be an immune evasion strategy, used to block the transcription of antiviral genes that would interfere with SAV3 replication in TO-cells. Hence, in this study we used the KEGG pathway analysis software which is a third generation PT based software to identify networks of genes that form the Jak/stat signaling pathway from a de novo assembled transcriptome with the aim to better understand the modulation of genes expressed by TO cells infected with SAV3. cache = ./cache/cord-329618-kywhulpc.txt txt = ./txt/cord-329618-kywhulpc.txt === reduce.pl bib === id = cord-329527-0rlotyz3 author = Bohmwald, Karen title = Neurologic Alterations Due to Respiratory Virus Infections date = 2018-10-26 pages = extension = .txt mime = text/plain words = 11036 sentences = 559 flesch = 48 summary = In addition to this, a fatal case attributed to the H1N1 pandemic infection was reported, and the clinical finding showed that the cause of death was an intracerebral thrombosis and hemorrhage with presence of the virus in the brain, but not in lungs or CSF (Simon et al., 2013 ; Figure 2) . In another approximation to understand the etiologic agent causing myelopathy post-influenza-like syndrome, CSF obtained from a patient with this disease was inoculated in several cell lines, previously reported to be permissive for the growth FIGURE 2 | Influenza virus (IV) spreads from the lungs to the CNS through the vagus nerve promoting an inflammatory state. As described so far, CoVs are respiratory viruses that exhibit neurotropic capacities that not only allows them to achieve latency and avoid the immune response of the host, but also have neurological implications that can complicate the disease associated to its infection. Although there are extensive case reports that indicate neurological manifestations associated to hMPV-infection in humans, further studies are required in mice models to characterize this disease. cache = ./cache/cord-329527-0rlotyz3.txt txt = ./txt/cord-329527-0rlotyz3.txt === reduce.pl bib === id = cord-329707-89zyu8bl author = Zhang, Xue title = Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date = 2006-11-30 pages = extension = .txt mime = text/plain words = 3212 sentences = 210 flesch = 54 summary = We constructed recombinant adenoviral vectors that can express shRNAs, which inhibited the expression of SARS-CoV genes effectively in mammalian cells. METHODS: In this study, we designed several plasmids that express small hairpin RNA molecules (shRNA) specifically targeting to the genes encoding for the SARS-CoV nucleocapsid (N) protein and envelope (E) protein, respectively. The effects of adenovirus-delivered small hairpin RNA on SARS-CoV gene expression were determined by RT-PCR, Western blot, and luciferase activity assays. RESULTS: The levels of viral mRNAs and viral proteins of the targets were significantly decreased or completely inhibited in cell lines after being infected with the recombinant adenoviruses that expressed specific shRNA molecules. CONCLUSIONS: Since many cell types can be efficiently infected by adenovirus, recombinant adenoviruses could serve as an alternative powerful tool for shRNA delivery and for gene suppression, especially when the targeted cells are resistant to transfection by DNA or RNA. cache = ./cache/cord-329707-89zyu8bl.txt txt = ./txt/cord-329707-89zyu8bl.txt === reduce.pl bib === id = cord-329710-vqorb6j7 author = Kumar, Krishna title = Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date = 2020-05-27 pages = extension = .txt mime = text/plain words = 2477 sentences = 147 flesch = 49 summary = We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. Many recent scientific reviews and essays have outlined vaccine efforts, as well as viral and host targets that are the focus of current campaigns aimed at redirecting clinically used compounds for COVID-19. The FDA-approved COVID-19 drug, remdesivir, is a nucleotide analog originally developed to treat Ebola infections (caused by another single-stranded RNA virus) and recently shown to inhibit the SARS-CoV-2 RdRP. HIV protease inhibitors lopinavir and ritonavir, included in the SOLIDARITY trial despite mixed reviews in the clinic, have been predicted to bind SARS-CoV-1 and CoV-2 3CL pro (96% sequence identity) based on computational studies. Using a recently solved crystal structure of the HR1 and HR2 domains of the SARS-CoV-2 S protein, lipidated peptide fusion inhibitors have been designed that inhibit pseudovirus infection of cells with IC 50 values in the single-digit nanomolar range. cache = ./cache/cord-329710-vqorb6j7.txt txt = ./txt/cord-329710-vqorb6j7.txt === reduce.pl bib === id = cord-330045-4gj9d181 author = Sun, Jiufeng title = Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date = 2020-08-17 pages = extension = .txt mime = text/plain words = 1541 sentences = 93 flesch = 57 summary = We recruited hospitalized patients with COVID-19 from 2 designated provincial emergency hospitals for e merging infectious diseases in Guangdong, China, and tested specimens by real-time reverse transcription PCR (rRT-PCR) to estimate the duration of the detection of SARS-CoV-2 RNA in various body fluids, using an accelerated failure time (AFT)-based modeling study. We used parametric Weibull regression models (AFT) to estimate the time until the loss of SARS-CoV-2 RNA detection in each body fluid and reported findings in medians and 95th percentiles using R software version 3.6.1 with flexsurv, survival, and survminer packages (9) . We used Weibull models to estimate the median and the 95th percentile for the time until the loss of SARS-CoV-2 RNA detection in swab, sputum, and fecal samples (Table; Figures 1, 2) . In this study, we estimated the time for COVID-19 case-patients to clear SARS-CoV-2 RNA in the acute phase of infection through an AFT-based modeling study. cache = ./cache/cord-330045-4gj9d181.txt txt = ./txt/cord-330045-4gj9d181.txt === reduce.pl bib === id = cord-330200-l6bnxi40 author = Huang, Jianping title = Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date = 2020-04-27 pages = extension = .txt mime = text/plain words = 4472 sentences = 306 flesch = 59 summary = title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. In this study, we investigated the profiles of viral RNA, IgM, and IgG in a group of patients with confirmed SARS-CoV-2 pneumonia over an 8-week period after symptom onset. Demographic data, symptom onset time, clinical features, radiological findings, routine laboratory results, and the results of SARS-CoV-2 viral RNA in throat swabs, sputum, and stool samples were recorded during hospitalization and follow-up. We investigated the serial viral load and dynamics of antibodies from patients infected with SARS-CoV-2 over an eight-week period following the onset of symptoms. cache = ./cache/cord-330200-l6bnxi40.txt txt = ./txt/cord-330200-l6bnxi40.txt === reduce.pl bib === id = cord-330131-yfhrmbvx author = Danchin, Antoine title = Cytosine drives evolution of SARS‐CoV‐2 date = 2020-04-27 pages = extension = .txt mime = text/plain words = 5318 sentences = 244 flesch = 42 summary = In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. cache = ./cache/cord-330131-yfhrmbvx.txt txt = ./txt/cord-330131-yfhrmbvx.txt === reduce.pl bib === id = cord-331066-ediowz4s author = Chechetkin, Vladimir R. title = Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date = 2020-09-09 pages = extension = .txt mime = text/plain words = 7040 sentences = 416 flesch = 57 summary = Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Therefore, the putative weakly specific assembly/packaging signals in the genomic RNA of coronaviruses should be coordinated with the parameters of the helical nucleocapsid (such as the helix pitch, inner and outer diameters) which are established by cryoelectron microscopy (cryo-EM) and other structural methods. In this article, we provide methods for the detection and comparative analysis of assembly/packaging signals in the genomic RNA of the coronaviruses SARS-CoV and SARS-CoV-2 and describe main results of our study. The abundance of quasi-periodic patterns in the genomic DNA/RNA sequences can be assessed by the spectral entropy (Balakirev et al., 2003 (Balakirev et al., , 2005 (Balakirev et al., , 2014 Chechetkin, 2011; Chechetkin & Lobzin, 1996; Chechetkin & Turygin, 1994) . cache = ./cache/cord-331066-ediowz4s.txt txt = ./txt/cord-331066-ediowz4s.txt === reduce.pl bib === id = cord-329866-io9fvy58 author = Lorusso, Eleonora title = Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis date = 2019-08-31 pages = extension = .txt mime = text/plain words = 2810 sentences = 126 flesch = 48 summary = With the aim to contribute to fill this diagnostic gap, a total of 61 effusions from cats with suspected effusive FIP were collected intra-vitam for detection of feline coronavirus (FCoV) antibodies and RNA by means of indirect immunofluorescence (IIF) assay and real-time RT-PCR (qRT-PCR), respectively. Fifty-one (48 ascitic and 3 pleuric fluids) of the 61 tested samples had FCoV antibody (Table 2 and Fig. 1 ), although only 37 positive effusions contained antibody levels ≥ 1:1600, which are considered highly suggestive of FIP diagnosis (Hartmann et al., 2003) . A recent paper (Meli et al., 2013) has investigated the agreement between FCoV antibody titres and RNA detection in the effusions of 13 cats with confirmed FIP, showing a correlation between high amounts of virus and lower signals in IIF assay, likely due to the fact that antibodies bound to viral antigens of the effusions are not able to bind to the antigens of the FCoV-infected cells used in serological tests. cache = ./cache/cord-329866-io9fvy58.txt txt = ./txt/cord-329866-io9fvy58.txt === reduce.pl bib === id = cord-330213-reb9vo7x author = Miladi, Milad title = The landscape of SARS-CoV-2 RNA modifications date = 2020-07-18 pages = extension = .txt mime = text/plain words = 3213 sentences = 210 flesch = 55 summary = From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. The long RNA sequencing reads generated for this study cover the entire SARS-CoV-2 genomic RNA as well as the different ORFs (Fig 1b,c, Fig. S1b ). Two sets of Galaxy workflows based on Tombo (16) and Nanocompore (17) tools were designed to compute the modification scores from the DRS data (Table S3) . Figure 5 : Direct RNA sequencing raw electrical signals of downsampled reads obtained from unmodified RNA (IVT, black), from samples generated for this study and from isolate from a published korean data set (Fr1-3 and Kr, red). cache = ./cache/cord-330213-reb9vo7x.txt txt = ./txt/cord-330213-reb9vo7x.txt === reduce.pl bib === id = cord-331076-ak481qew author = Eskier, Doğa title = Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date = 2020-10-12 pages = extension = .txt mime = text/plain words = 3858 sentences = 192 flesch = 52 summary = In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are under less selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020a) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors (Fig. 1) . Three of the five most common nsp14 mutations, namely 18060C>T, 18736T>C and 18877C>T are associated with increases in both genome-wide mutational load, as well as MoE status, an alternative indicator of mutational rate and virus evolution. cache = ./cache/cord-331076-ak481qew.txt txt = ./txt/cord-331076-ak481qew.txt === reduce.pl bib === id = cord-330954-ft14aa2n author = Liu, B. M. title = Epidemiological characteristics of COVID-19 patients in convalescence period date = 2020-06-03 pages = extension = .txt mime = text/plain words = 3783 sentences = 179 flesch = 54 summary = The discharged patients must meet the following criteria: (1) the body temperature returns to normal for more than 3 days; (2) respiratory symptoms improve significantly; (3) pulmonary imaging shows that the acute exudative lesions were significantly absorbed and improved; (4) the SARS-CoV-2 ribonucleic acid (RNA) detection results of two consecutive respiratory specimens are negative (sampling interval should be at least 24 h). We recorded the clinical manifestations, RNA detection results of oropharyngeal swab specimens, SARS-CoV-2 IgM−IgG antibodies detection results (data were collected on the 28th day after discharge), chest computed tomography (CT) images and medication of these patients. A case report of four mild-to-moderate COVID-19 patients (all were medical staff) showed that all convalescent patients without clinical symptoms presented RP findings of RNA detection in throat swab specimens at 5−13 days after discharge [14] . Another study found that among 62 COVID-19 convalescent medical staff, two patients without clinical symptoms showed RP findings of RNA detection in throat swab specimens at 5−6 days after discharge [15] . cache = ./cache/cord-330954-ft14aa2n.txt txt = ./txt/cord-330954-ft14aa2n.txt === reduce.pl bib === id = cord-330847-a84pcc9z author = Edwards, M. C. title = RNA recombination in the genome of Barley stripe mosaic virus date = 1992-07-31 pages = extension = .txt mime = text/plain words = 2344 sentences = 152 flesch = 67 summary = Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. A "bandaid" cloning strategy, which exploits the conservation of the 3' terminal sequence, as well as the unique nature of the 5' ends of the BSMV RNAs, has been used previously to obtain full-length cDNA clones from which infectious in vitro transcripts can be produced (3, 7). Analysis of the resulting cDNA clones suggested that CV17 RNA y is a naturally occurring chimeric recombinant, composed of a 70nucleotide (nt) a-specific leader sequence preceding a r-specific coding region. 3. ldentrfrcatron of barley stripe mosaic virus strarn CV17 LY and Type strain y-specific leader sequences In 15 putative CV17 y cDNA clones and native RNAs of strains CV17, CV42, and ND1 8. cache = ./cache/cord-330847-a84pcc9z.txt txt = ./txt/cord-330847-a84pcc9z.txt === reduce.pl bib === id = cord-330800-s91zfzfi author = Reta, Daniel Hussien title = Molecular and Immunological Diagnostic Techniques of Medical Viruses date = 2020-09-04 pages = extension = .txt mime = text/plain words = 10548 sentences = 574 flesch = 43 summary = e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens. cache = ./cache/cord-330800-s91zfzfi.txt txt = ./txt/cord-330800-s91zfzfi.txt === reduce.pl bib === id = cord-331414-i0oxm5mr author = Kautz, Tiffany F. title = A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene date = 2020-06-19 pages = extension = .txt mime = text/plain words = 5064 sentences = 241 flesch = 45 summary = To examine this, GFP was inserted into TC-83, a live-attenuated vaccine for the alphavirus Venezuelan equine encephalitis virus, as well as a low-fidelity variant of TC-83, and passaged until fluorescence was no longer observed. To examine reporter gene stability, three independent replicates of TC-83 GFP and low-fidelity TC-83 GFP were passaged 10 times on Vero cells using an approximate MOI of 0.5 ( Figure 1A ). All three TC-83 GFP replicates contained deletion variants present at a low frequency that were able to selectively remove the GFP reporter gene by passage 10 (Figure 2A) . To better understand the mechanisms underlying the conserved removal of the low-fidelity TC-83 GFP gene, M-fold was used to determine the RNA secondary structure of the virus genome ( Figure 4C-E) . To characterize the role of RNA structure of the virus genome in RNA recombination site selection, we modeled the three most common deletions that occurred at high levels during low-fidelity TC-83 GFP passaging. cache = ./cache/cord-331414-i0oxm5mr.txt txt = ./txt/cord-331414-i0oxm5mr.txt === reduce.pl bib === id = cord-329794-msxrdhb3 author = Lu, Aili title = Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date = 2004-06-20 pages = extension = .txt mime = text/plain words = 2679 sentences = 172 flesch = 61 summary = Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection. cache = ./cache/cord-329794-msxrdhb3.txt txt = ./txt/cord-329794-msxrdhb3.txt === reduce.pl bib === id = cord-331509-p19dg1jw author = Bigault, Lionel title = Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR date = 2020-05-31 pages = extension = .txt mime = text/plain words = 4317 sentences = 240 flesch = 60 summary = title: Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR In this study we described the development and validation of a SYBR™ Green one-step RT-qPCR according to the French norm NF U47-600, for the detection and quantification of PEDV viral RNA. Specificity and sensitivity, limit of detection (LoD), limit of quantification (LQ), linearity, intra and inter assay variability were evaluated using transcribed RNA and fecal and jejunum matrices spiked with virus. For a rapid, accurate and reliable diagnosis of PED in the veterinary laboratory, a method for the detection of PEDV viral RNA has been developed and more importantly validated according to the "Association Francaise de NORmalisation" (AFNOR) French NF U47-600 norm entitled "requirement and recommendation for the implementation, development and validation of PCR in animal health" (AFNOR, 2015a; AFNOR, 2015b) . This method should help harmonize detection and quantification of viral RNA from PEDV belonging to both S-non-INDEL and S-INDEL strains in both field and experimental settings. cache = ./cache/cord-331509-p19dg1jw.txt txt = ./txt/cord-331509-p19dg1jw.txt === reduce.pl bib === id = cord-331607-2h56vb0n author = Jin, Xuejiao title = Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication date = 2018-01-30 pages = extension = .txt mime = text/plain words = 10714 sentences = 488 flesch = 39 summary = reported the first 3D architecture of the membrane-bound (+) RNA viral replication compartments in FHV-infected Drosophila cells (Kopek et al., 2007) , several 3D models of cellular remodeling during plant virus infection have been characterized. Confocal microscopy analysis showed that actin patches are closely associated with large p33-containing replication organelle-like structures in yeast cells and that such patches are present throughout the large replication compartments in plant cells, suggesting that actin plays a role in recruiting viral and cellular components (e.g., lipid) for VRC assembly (Nawaz-Ul-Rehman et al., 2016; Xu and Nagy, 2016) . The examples given above provide a good illustration of a common theme in membrane remodeling and the formation of spherules/vesicles: viral proteins, sometimes with the involvement of viral RNAs, recruit host factors that are diverted from their original functions and used to create virus replication factories (Diaz and Wang, 2014; Laliberté and Zheng, 2014; Wang, 2015; Nagy, 2016) . Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulumtargeted viral protein cache = ./cache/cord-331607-2h56vb0n.txt txt = ./txt/cord-331607-2h56vb0n.txt === reduce.pl bib === id = cord-331916-n744pymd author = Liu, Jue title = Inhibition of porcine circovirus type 2 replication in mice by RNA interference date = 2006-04-10 pages = extension = .txt mime = text/plain words = 6657 sentences = 350 flesch = 52 summary = Specific inhibition of endogenous or pathogen mRNA by RNAi can be triggered by the introduction of 21 -23 nucleotide (nt) duplexes of RNA (siRNA) or by transcription of DNA precursor into short hairpin RNAs (shRNA) homologous to target sequences (Brummelkamp et al., 2002; Elbashir et al., 2001a; Paddison et al., 2002) , opening up possibilities for controlling replicative processes of pathogens. To further examine the ability of ORF1 shRNA to suppress viral gene expression in PCV2-infected PK15 cells, single nucleotide mutations were introduced into pSIR3 sequence as shown in Fig. 4A . As shown in Fig. 4B , a mutant with one nucleotide mutation in the 5V-end of the sense strand (pSIR3-m1) still had an effective reduction in the synthesis of ORF1 and ORF2 proteins, whereas with a nucleotide substitution at the center (pSIR3-m2) or 3V-end (pSIR3-m3) of the sense sequence, the resultant shRNAs failed to significantly suppress expression of PCV2 ORF1 and ORF2 in the transfected cells, further verifying the specificity of RNAi as demonstrated (Amarzguioui et al., 2003; Harborth et al., 2003) . cache = ./cache/cord-331916-n744pymd.txt txt = ./txt/cord-331916-n744pymd.txt === reduce.pl bib === id = cord-331680-qlzhtxs0 author = Goryachev, A.N. title = Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date = 2020-11-03 pages = extension = .txt mime = text/plain words = 4106 sentences = 200 flesch = 51 summary = In accordance with the purpose of the study, the following tasks were set: -to select the nucleotide sequence of the virus that is supposed to be inhibited, -to carry out the synthesis of oligonucleotide, -to determine cytotoxicity and antiviral activity in an in vitro experiment on cell culture. The assessment of antiviral activity of the drug in addition to cytopathic action was also taken into account by reducing the infectious titer of the virus in the culture of Vero cells E6 according to PCR RNA SARS-CoV-2, determined by the threshold of the number of reaction cycles (cycle treshold, Ct) in various dilutions of the study drug. Determination of the antiviral efficacy of the antisense oligonucleotide according to the treatment scheme (administration of the drug 24 hours after infection) was taken into account by the decrease in the infectious titer of the virus in the culture of Vero E6 cells by the cytopathic effect. cache = ./cache/cord-331680-qlzhtxs0.txt txt = ./txt/cord-331680-qlzhtxs0.txt === reduce.pl bib === id = cord-331802-wo462anq author = Xia, Hongjie title = Human Enterovirus Nonstructural Protein 2C(ATPase) Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone date = 2015-07-28 pages = extension = .txt mime = text/plain words = 9410 sentences = 440 flesch = 50 summary = Herein, we report that the nonstructural protein 2C(ATPase) of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. Herein, we report that although bacterially expressed EV71 2C ATPase did not exhibit any RNA remodeling activity, eukaryotically expressed EV71 2C ATPase functions not only as an RNA helicase that unwinds RNA helices from 3 0 to 5 0 in an ATP-dependent manner but also as an RNA chaperone that destabilizes helices from either direction and facilitates strand annealing and complex RNA structure formation independently of ATP. cache = ./cache/cord-331802-wo462anq.txt txt = ./txt/cord-331802-wo462anq.txt === reduce.pl bib === id = cord-332270-fusfdkjw author = Lukiw, Walter J. title = Biomarkers for Alzheimer’s Disease (AD) and the Application of Precision Medicine date = 2020-09-21 pages = extension = .txt mime = text/plain words = 5193 sentences = 198 flesch = 29 summary = The ongoing search for valid biomarkers for AD is being carried out globally in at least a dozen major geriatric, bioinformatic, neurobiological, neuro-genetic and neurological bioscience arenas: (i) those involving the age, gender, and geriatrics of the 'prospectiveAD patient'; (ii) in the genetics and epigenetics of the AD patient including messenger RNA (mRNA) and microRNA (miRNA) signaling patterns, complexity and genomic methylation research; (iii) in multiple biofluids from AD patients including the blood (plasma/serum) of the systemic circulation, the glymphatic system, the cerebrospinal fluid (CSF) and/or urine; (iv); through the detailed analysis of molecular cargos from both biofluids and tissue-compartmentalized exosomes and extracellular microvesicles (EXs and EMVs); (v) throughout the peripheral nervous system (PNS; typically using skin biopsies); (vi) via clinically-based geriatric, psychiatric, and neurological assessment and testing; (vii) via advances in neuro-radiological labeling techniques and neuroimaging technologies including CAT, PET, PET-SN, MRI, fMRI; UHF-MRI, DOT, MEG, SPECT, cranial ultrasound, functional ultrasound (fUS) imaging, and immunohistochemistry involving confocal laser scanning microscopy and other advanced microscopic and neuroimaging techniques; (viii) from the quantitation and characterization of the load of microbial and microbial-derived components in the AD-affected brain; (ix) via the identification, quantitation, and characterization of AD-specific lesions including amyloid peptide-enriched SPs and NFTs; (x) after post-mortem examination and biopsies of AD cases, again matched up against those same biomarkers in age-and gender-matched neurologically normal controls to corroborate the prospective diagnosis of AD; (xi) via the comprehensive analysis of the potential contribution of overlapping progressive, age-related neurological disorders to AD-type change; and lastly (xii), through the assessment of the socioeconomic, environmental, and lifestyle factors of the 'prospectiveAD patient' ( Table 1 ). cache = ./cache/cord-332270-fusfdkjw.txt txt = ./txt/cord-332270-fusfdkjw.txt === reduce.pl bib === id = cord-332003-67e9fchy author = Boisguérin, Prisca title = Delivery of therapeutic oligonucleotides with cell penetrating peptides() date = 2015-06-29 pages = extension = .txt mime = text/plain words = 13067 sentences = 636 flesch = 42 summary = Although challenged later on as detailed in Section 7, this mechanism and the possibility to use such so called cell-penetrating peptides (CPPs) as non-viral delivery vectors for biomolecules, fostered a very large interest. Since the chemical conjugation and purification of negatively charged ONs with the most popular cationic CPPs has turned out to be difficult, most applications have concerned chargeneutral ON analogues such as Peptide Nucleic Acids (PNAs) and PMO (see Section 3). Unexpectedly, in a well-characterized HeLa 705 cell assay with a positive read-out ( Fig. 1) , splicing redirection using PNA or PMO oligomers conjugated to various standard CPPs (Tat, Penetratin or oligo-arginines) was not achieved in our research groups [57] . This led to the development of several arginine-rich peptides as PMO conjugates for use in muscle cells and in vivo mouse models of DMD as outlined in Section 4. cache = ./cache/cord-332003-67e9fchy.txt txt = ./txt/cord-332003-67e9fchy.txt === reduce.pl bib === id = cord-332006-if46jycd author = Whitehead, Kathryn A. title = Knocking down barriers: advances in siRNA delivery date = 2009 pages = extension = .txt mime = text/plain words = 6655 sentences = 391 flesch = 42 summary = Three years later, Tuschl and co-workers published their celebrated proof-of-principle experiment demonstrating that synthetic small interfering RNA (siRNA) could achieve sequence-specific gene knockdown in a mammalian cell line 2 . Toxicity of certain cationic lipid particles has been reported both in vitro and in vivo [76] [77] [78] , and certain synthetic agents have been found to induce a gene signature of their own that might increase the off-target effects of siRNA 79, 80 . Tumour growth in a mouse model of metastatic Ewing's sarcoma was shown to be inhibited by the systemic delivery of nanoparticles formed by cyclodextrin, the targeting ligand transferrin, and siRNA specific for the EWS-FLI1 fusion gene commonly associated with the condition. Toxicogenomics of non-viral drug delivery systems for RNAi: potential impact on siRNA-mediated gene silencing activity and specificity cache = ./cache/cord-332006-if46jycd.txt txt = ./txt/cord-332006-if46jycd.txt === reduce.pl bib === id = cord-332356-au7s3dmp author = Strandin, Tomas title = The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date = 2011-09-15 pages = extension = .txt mime = text/plain words = 6554 sentences = 329 flesch = 53 summary = The results indicate that the binding ability of Gn-CT towards nucleic acids is rather unspecific since in addition to genomic RNA, also unrelated RNA as well as single-stranded DNA was able to interact with Gn-CTs of PUUV and TULV. Purified, lysed and micrococcal nuclease (MNase)-treated virus preparation and in vitro transcribed and radiolabeled genomic PUUV S segment were allowed to form RNA-protein complexes prior to UV cross-linking. The capability of structural proteins to bind RNA was analyzed by incubating purified, lysed and micrococcal nuclease (MNase)-treated virus preparations with radioactive PUUV S segment RNA in the case of PUUV ( The samples were immunoprecipitated with MAbs or PAbs specific to N, Gn or Gc and retained radioactivity on protein G beads after washing was measured by scintillation counting. The mapping indicated that the same peptides that were previously shown to interact with RNP and N protein (Hepojoki et al., 2010b) were capable of binding also nucleic acids (Fig. 5A ). cache = ./cache/cord-332356-au7s3dmp.txt txt = ./txt/cord-332356-au7s3dmp.txt === reduce.pl bib === id = cord-332024-jk983q4p author = Briese, Thomas title = Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date = 2005-02-17 pages = extension = .txt mime = text/plain words = 1738 sentences = 84 flesch = 36 summary = We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. To address the need for sensitive multiplex assays in diagnostic molecular microbiology, we created a polymerase chain reaction (PCR) platform in which microbial gene targets are coded by a library of 64 distinct Masscode tags (Qiagen Masscode technology, Qiagen, Hilden, Germany). Multiplex primer sets were designed to identify up to 22 respiratory pathogens in a single Mass Tag PCR reaction; sensitivity was established by using synthetic DNA and RNA standards as well as titered viral stocks; the utility of Mass Tag PCR was determined in blinded analysis of previously diagnosed clinical specimens. cache = ./cache/cord-332024-jk983q4p.txt txt = ./txt/cord-332024-jk983q4p.txt === reduce.pl bib === id = cord-333261-knj2rrut author = Albright, Catherine J. title = An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date = 2011-11-11 pages = extension = .txt mime = text/plain words = 3408 sentences = 205 flesch = 59 summary = To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. The extensive data available on HRV genomes enables many bioinformatics opportunities for students, including alignment of genome sequences to look for mutations at the RNA level and differences among protein sequences. Students can examine differences in the HRV serotypes over several years of data regarding a university population to identify HRV mutations that have occurred and their severity in causing symptoms in the host. In this inquiry-based laboratory project, students use a variety of techniques, including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis to look for the presence of HRV in nasal lavage samples from human subjects. By analyzing surveys in which subjects indicate severity of their symptoms, stress factors, and average hours of rest per night, students can identify possible contributors to HRV infection. cache = ./cache/cord-333261-knj2rrut.txt txt = ./txt/cord-333261-knj2rrut.txt === reduce.pl bib === id = cord-332632-u2ud0vmq author = Lussi, Carmela title = What can pestiviral endonucleases teach us about innate immunotolerance? date = 2016-03-17 pages = extension = .txt mime = text/plain words = 8703 sentences = 394 flesch = 44 summary = In particular, the unique extension of 'self' to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host's own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. Thus, the survival strategy of BVDV consists of being non-cytopathogenic and producing less dsRNA than its cp counterpart, and expressing the IFN antagonists N pro as the first protein in order to reduce or even avoid IFN production in infected cells and E rns to degrade immunostimulatory viral RNA before they might activate the host's PRRs. Notably, both pestiviral IFN antagonists are not only required to constantly maintain innate immunotolerance during persistent infections, but they also play an important role in acute infections [25] . cache = ./cache/cord-332632-u2ud0vmq.txt txt = ./txt/cord-332632-u2ud0vmq.txt === reduce.pl bib === id = cord-332992-8rmqg4rf author = de Vries, A. A. F. title = SARS-CoV-2/COVID-19: a primer for cardiologists date = 2020-07-15 pages = extension = .txt mime = text/plain words = 9182 sentences = 433 flesch = 39 summary = Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . cache = ./cache/cord-332992-8rmqg4rf.txt txt = ./txt/cord-332992-8rmqg4rf.txt === reduce.pl bib === id = cord-333429-bq7kfpby author = Shi, Ding title = Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date = 2020-07-02 pages = extension = .txt mime = text/plain words = 3513 sentences = 251 flesch = 57 summary = title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. We identified that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV A c c e p t e d M a n u s c r i p t combination therapy and corticosteroid treatment were not independent factors. In conclusion, we found that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV combination therapy and corticosteroid treatment were not. cache = ./cache/cord-333429-bq7kfpby.txt txt = ./txt/cord-333429-bq7kfpby.txt === reduce.pl bib === id = cord-333636-h2sg6shp author = Kochan, G. title = Characterization of the RNA-binding activity of VP3, a major structural protein of Infectious bursal disease virus date = 2003 pages = extension = .txt mime = text/plain words = 5975 sentences = 334 flesch = 53 summary = The histidine-tagged VP3 was affinity-purified and used to study its ability to bind RNA molecules using three complementary methods: (i) Northwestern blotting; (ii) binding of VP3 protein-RNA complexes to nitrocellulose membranes; and (iii) electrophoretic mobility shift assays. Briefly, increasing amounts (from 5 × 10 −2 mM to 5 × 10 −6 mM) of purified VP3 or BSA, used as a control for non-specific interaction, were mixed with 10 6 cpm of 32 P-labeled ssRNA probe B (5 × 10 −6 mM) in binding reaction buffer (50 mM Tris, 150 mM KCl, 150 mM NaCl 10% Glycerol, 0,01% Triton X 100), in 16 µl final volume, so the VP3/RNA molar ratio in these experiments varied from 10 4 to 1. Competition assays based on nitrocellulose binding were carried out using virus-derived radiolabeled ssRNA probes together with increasing concentrations of non-radioactive competitor RNA and DNA probes. cache = ./cache/cord-333636-h2sg6shp.txt txt = ./txt/cord-333636-h2sg6shp.txt === reduce.pl bib === id = cord-333473-c1lykari author = Irigoyen, Nerea title = High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling date = 2016-02-26 pages = extension = .txt mime = text/plain words = 18258 sentences = 844 flesch = 56 summary = Also, it has been employed in the study of the replication of large DNA viruses; namely, human cytomegalovirus [17] [18] , Kaposi's sarcoma-associated herpesvirus [19] , herpes simplex virus 1 [20] , vaccinia virus [21] , and bacteriophage lambda [22] , providing insights into the temporal regulation of gene expression in these viruses and identifying numerous previously unrecognized translated ORFs, including novel protein-coding ORFs and short regulatory uORFs. In this paper, we describe the first analysis of RNA virus replication and gene expression by ribosome profiling (and parallel RNASeq), using MHV as a model system. The latter are calculated on a per gene (rather than per transcript) basis, using RNASeq and RiboSeq reads contained entirely within annotated CDS regions (i.e. excluding 5 0 and 3 0 UTRs and also RPFs accumulating at or near to initiation or termination sites), and, like the virus values, are expressed relative to the mean levels for the cell (due to normalization by library size). cache = ./cache/cord-333473-c1lykari.txt txt = ./txt/cord-333473-c1lykari.txt === reduce.pl bib === id = cord-333547-88dkh6xd author = Hasan, Shadi W. title = Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date = 2020-10-19 pages = extension = .txt mime = text/plain words = 3980 sentences = 220 flesch = 54 summary = Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. A limited number of studies have shown that the shedding period of SARS-CoV-2 in stool samples varies considerably, and can still be detected up to 27.9 ± 10.7 days after infection in some cases [9, 11] . Consequently, the main objectives of this study were: (i) to detect the presence of SARS-CoV-2 virus in municipal (untreated) wastewater and treated effluents of wastewater treatment plants (WWTPs) in the UAE; (ii) to quantify the viral concentration in viral gene copies per liter; and (iii) to explore whether these measurements mirror infections in the population in order to comment on the utility of this method to track the epidemiology of the disease. cache = ./cache/cord-333547-88dkh6xd.txt txt = ./txt/cord-333547-88dkh6xd.txt === reduce.pl bib === id = cord-333524-a6p6ma8r author = Khan, Pavana title = Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date = 2020-09-23 pages = extension = .txt mime = text/plain words = 8841 sentences = 603 flesch = 50 summary = 19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ). cache = ./cache/cord-333524-a6p6ma8r.txt txt = ./txt/cord-333524-a6p6ma8r.txt === reduce.pl bib === id = cord-333979-bx2xspbe author = Kalikiri, Mahesh K R title = High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads date = 2020-04-11 pages = extension = .txt mime = text/plain words = 2029 sentences = 102 flesch = 52 summary = title: High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads We developed a method using a widely available lysis buffer coupled with solid-phase reverse immobilization (SPRI) beads to extract viral RNA from swabs collected in viral transport medium (VTM) which can be performed manually or on a Hamilton STAR liquid-handling robot. Retrospective, residual nasopharyngeal specimens that previously tested positive or negative for respiratory syncytial virus (RSV) using the Cepheid GeneXpert Flu/RSV kit or the Fast Track Diagnostics Respiratory Pathogens 21 PCR (FTD-RESP21) were extracted with our new approach on a Hamilton STAR liquid handling robot with 8 CO-RE channels. When applying these conditions to 204 clinical samples, we only observed a 2.5% inhibition of the RT-qPCR, indicating that our method is suitable for large-scale use in testing laboratories. In this manuscript, we demonstrate the feasibility of using reagents commonly available in molecular biology and next-generation sequencing laboratories for the extraction of SARS-CoV-2 viral RNA for the diagnosis of COVID-19. cache = ./cache/cord-333979-bx2xspbe.txt txt = ./txt/cord-333979-bx2xspbe.txt === reduce.pl bib === id = cord-334082-fyxn0g3v author = O’Carroll, I.P. title = Viral Nucleic Acids date = 2015-08-20 pages = extension = .txt mime = text/plain words = 5495 sentences = 271 flesch = 54 summary = This scheme in turn places two requirements on the nucleic acid: it must be replicated in the virus-producing cell, to provide the genetic material encased in the progeny virus particles; and it must encode the proteins needed for the production of the progeny particles, including at a minimum the structural proteins from which the particles will be assembled. The DNAs of ssDNA viruses are replicated by a mechanism similar to 'rolling circle' replication, involving synthesis of dsDNA intermediates containing multiple tandem copies of the viral genome. These viruses are unique in that their genomic RNA is translated immediately upon infection; that is, the virus particle is simply a package that introduces an mRNA molecule into the cell. When the particle infects a new host cell, the RNA-dependent DNA polymerase or 'reverse transcriptase' in the virus copies this RNA into dsDNA. cache = ./cache/cord-334082-fyxn0g3v.txt txt = ./txt/cord-334082-fyxn0g3v.txt === reduce.pl bib === id = cord-333515-llqpfhwg author = Zhao, Juanjuan title = Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date = 2020-03-03 pages = extension = .txt mime = text/plain words = 3575 sentences = 230 flesch = 56 summary = Their serial plasma samples (n = 535) collected during the hospitalization period were tested for total antibodies (Ab), IgM and IgG against SARS-CoV-2 using immunoassays. To mitigate this knowledge gap, and to provide scientific analysis on the benefit of antibody testing when used in combination with the current RNA testing, this study investigates the dynamics of total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 in serial blood samples collected from 173 confirmed COVID-19 patients and provides discussion on the clinical value of antibody testing. A total of 535 plasma samples collected during the hospitalization period of the 173 patients were tested for antibodies against SARS-CoV-2. In addition to the diagnosis value of Ab test, our study revealed a strong positive correlation between clinical severity and antibody titer since 2-week after illness onset, for the first time in COVID-19 patients. cache = ./cache/cord-333515-llqpfhwg.txt txt = ./txt/cord-333515-llqpfhwg.txt === reduce.pl bib === id = cord-332747-u46xryoo author = Mingorance, Lidia title = Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date = 2018-09-18 pages = extension = .txt mime = text/plain words = 10355 sentences = 485 flesch = 37 summary = To determine which aspects of the HCV replication cycle are limited by lipin1 silencing, single cycle infection experiments were conducted by inoculating control and lipin1-deficient cell cultures at MOI 10 with genotype 2a D183 virus. Once cultures reached >95% of HCV-positive cells, they were transduced with lentiviral vectors expressing control, HCV RNA-targeting or LPIN1-specific shRNAs. At day 7 post-transduction, cells were split and samples of the cells and supernatants were collected 24 hours later to determine infectious virus production rate by infectivity titration HCV (C) and RNA levels by RT-qPCR (D). This reduced abundance is illustrated by a significant reduction in the fraction of cells displaying vesicular structures in lipin1-deficient cell cultures (Fig 7H) despite comparable transfection efficiency and viral protein expression levels, indicating that lipin1 may be required in a critical step leading to formation of the HCV-induced vesicular compartment. cache = ./cache/cord-332747-u46xryoo.txt txt = ./txt/cord-332747-u46xryoo.txt === reduce.pl bib === id = cord-334123-wb45ww7f author = Schimmel, Paul title = RNA pseudoknots that interact with components of the translation apparatus date = 1989-07-14 pages = extension = .txt mime = text/plain words = 3334 sentences = 169 flesch = 60 summary = A third and earlier study proposed that an RNA pseudoknot is recognized by a DNA binding protein that autogenously regulates translation of its mRNA (McPheeters et al., 1988) . The tRNA-like structures at the 3' ends of plant viral RNAs provide one example where the pseudoknot format may be necessary to form a substrate that is specifically recognized by an enzyme. Previous structural mapping experiments by Draper and co-workers suggested a model for the 5' region of the mRNA which constitutes the S4 binding site; it envisions a hairpin helix and loop that encompasses nucleotides 19 to 72. The second study provides evidence that pseudoknot formation in a viral mRNA is required for frameshift suppression of a termination codon that, in turn, allows a fusion protein to be synthesized from two overlapping reading frames. This element encodes a stem-loop structure that starts six nucleotides downstream from the proposed site of frameshifting, near the end of the first reading frame. cache = ./cache/cord-334123-wb45ww7f.txt txt = ./txt/cord-334123-wb45ww7f.txt === reduce.pl bib === id = cord-333080-qytwbsne author = Alahari, Suresh K. title = SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date = 2020-07-28 pages = extension = .txt mime = text/plain words = 2244 sentences = 123 flesch = 49 summary = Altogether, TGF-beta signaling pathway as well as hub miRNAs, and LncRNAs involve during SARS-CoV pathogenesis can be considered as potential therapeutic targets. Developing functional computational models and networks to predict potential SARS-CoV -miRNA/lncRNA association may benefit not only the understanding of COVID-19 mechanism at the noncoding RNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis, and prevention. Since multiple ways of interaction between miRNAs, lncRNAs, and mRNA have been reported to play key roles in determining the cellular functions during viral infection, it is essential to discover these interactions in an integrated fashion to comprehensively decipher the networks and key regulatory noncoding-RNA hubs underpinning the pathology of SARS-CoV. Our in-silico analysis has built a network of protein-protein interaction between the Human SARS coronavirus (SARS-CoV) and host proteome (Figure 1) , as well as strong miRNA-mRNA-lncRNA crosstalk ( Figure 4 and Table 2 ) possibly modulating the human response to the viral infection. cache = ./cache/cord-333080-qytwbsne.txt txt = ./txt/cord-333080-qytwbsne.txt === reduce.pl bib === id = cord-332484-qy8vj6uu author = Pierini, Roberto title = Modulation of membrane traffic between endoplasmic reticulum, ERGIC and Golgi to generate compartments for the replication of bacteria and viruses date = 2009-04-01 pages = extension = .txt mime = text/plain words = 4247 sentences = 239 flesch = 42 summary = This review describes examples where both intracellular bacteria (Salmonella, Chlamydia and Legionella) and viruses (picornaviruses and hepatitis C) recruit membrane vesicles to sites of replication by modulating proteins that control the secretory pathway. Intracellular bacteria remain within membrane-bound vacuoles to avoid delivery to lysosomes and then recruit vesicles from the secretory pathway to provide nutrients necessary for microbial growth and cell division. Many viruses generate densely packed membrane vesicles to shield them from recognition by cellular defence pathways that recognise double-stranded RNA, and at the same time the membranes provide a platform to recruit viral and host proteins required for replication [3] [4] [5] . This review describes how recent work on intracellular bacteria such as Salmonella, Chlamydia and Leigionella draws parallels with studies on (+) strand RNA viruses where microbial proteins recruit membranes by modulating proteins that control the secretory pathway. cache = ./cache/cord-332484-qy8vj6uu.txt txt = ./txt/cord-332484-qy8vj6uu.txt === reduce.pl bib === id = cord-334771-uy3s6443 author = Rao, BL title = A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date = 2004-09-09 pages = extension = .txt mime = text/plain words = 3672 sentences = 187 flesch = 49 summary = Samples obtained were: 54 blood samples, 22 throat swabs, ten CSF samples, and one brain aspirate from 55 patients with encephalitis; five blood samples and nine throat swabs from 13 fever cases; and ten blood samples and one throat swab from ten family contacts (including specimens from the brother and mother of a patient who Methods Cell lines and peripheral blood lymphocyte co-cultures were used to isolate the causative agent from clinical samples. The confirmed Chandipura virus encephalitis group consisted of individuals from whose samples we isolated the virus, viral RNA, or reactive IgM antibodies. The viruses isolated in different cell lines from clinical samples from patients with encephalitis were confirmed as Chandipura virus with various techniques including complement fixation, neutralisation test, and immunofluorescence assay. Moreover, the presence of Chandipura virus RNA in nine patients with encephalitis, all from samples obtained before day 4 after onset of illness, suggests an early viraemic phase of the infection process. cache = ./cache/cord-334771-uy3s6443.txt txt = ./txt/cord-334771-uy3s6443.txt === reduce.pl bib === id = cord-332844-2se4d1yp author = Yun, Sang-Im title = Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses date = 2015-12-29 pages = extension = .txt mime = text/plain words = 4793 sentences = 233 flesch = 52 summary = Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase. Generation of an infectious cDNA clone is a key step in developing a reverse genetics system for RNA viruses, especially for positive-strand RNA viruses, because its genome acts as viral mRNA that is translated into proteins by host cell ribosomes. cache = ./cache/cord-332844-2se4d1yp.txt txt = ./txt/cord-332844-2se4d1yp.txt === reduce.pl bib === id = cord-335443-iv2gs3kg author = Kim, Youngchang title = Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date = 2020-06-28 pages = extension = .txt mime = text/plain words = 5464 sentences = 333 flesch = 57 summary = Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme's active site, providing basis for the uracil scaffold-based drug development. For SARS-CoV it was reported that Nsp15 cleaves highly conserved non-translated RNA on (+) sense strand showing that both RNA sequence and structure are important for cleavage 6, 7 . The enzyme cleaves efficiently eicosamer 5'GAACU¯CAU¯GGACCU¯U¯GGCAG3' at all four uridine sites (Fig. 1) , as well as synthetic EndoU substrate ( 5′-6-FAM-dArU¯dAdA -6-TAMRA-3′ ) 8 in the presence of Mn 2+ and the reaction rate increases with metal ion concentration. SARS-CoV-2 Nsp15 protein was crystallized with 5'UMP, 3'UMP, 5'GpU and Tipiracil using methods described previously 8 and the structures were determined at 1.82 Å, 1.85 Å, 1.97 Å and 1.85 Å, respectively. In the crystal structure of Nsp15/5'GpU, the dinucleoside monophosphate binds to the active site with uracil interacting with Tyr343 and Ser294 (Fig. 4B ), as seen in the Nsp15/5'UMP complex. cache = ./cache/cord-335443-iv2gs3kg.txt txt = ./txt/cord-335443-iv2gs3kg.txt === reduce.pl bib === id = cord-335482-nx7odchj author = Makino, Shinji title = Defective interfering particles of mouse hepatitis virus date = 1984-02-29 pages = extension = .txt mime = text/plain words = 3840 sentences = 210 flesch = 60 summary = We have observed marked reduction of infectivity in the course od serial undiluted passages of JHM virus in DBT cell culture. To avoid contamination of the standard virus stock with DI particles, plaque purified MHV (JHM strain) (Hirano et aL, 1981; Makino et al, 1983) was propagated on DBT cells at a multiplicity of infection (m.o.i.) of 0.0002 and at 15 hr postinfection (p.i.) culture fluid was harvested and clarified by low speed centrifugation. Preparation of the Standard JHM Virus for Interference Assay JHM virus was propagated on DBT cells after infection at an m.o.i. of 1.0 and was harvested at 14 hr p.i. The culture fluid was clarified by centrifugation at 8000 rpm for 30 min. To determine if the reduction in the yield of infectious virus was due to the presence of DI particles, a'n interference analysis was performed with several culture fluid samples at different passage levels. cache = ./cache/cord-335482-nx7odchj.txt txt = ./txt/cord-335482-nx7odchj.txt === reduce.pl bib === id = cord-335040-1qa6pe4v author = Rogstam, Annika title = Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date = 2020-10-06 pages = extension = .txt mime = text/plain words = 7408 sentences = 385 flesch = 59 summary = The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication. observed SARS nsp10 in the same space group as reported here, I213, reporting a monomer in the asymmetric unit but a dimer in solution, as was determined by size exclusion Residues shaded in red are fully conserved, while residues with text in red indicate a change to a similar residue. We determined the crystal structure and behaviour in solution of SARS-CoV-2 nsp10 in its unbound form. cache = ./cache/cord-335040-1qa6pe4v.txt txt = ./txt/cord-335040-1qa6pe4v.txt === reduce.pl bib === id = cord-332710-2s14knw6 author = Lai, Michael M.C. title = Recombination in large RNA viruses: Coronaviruses date = 1996-12-31 pages = extension = .txt mime = text/plain words = 4204 sentences = 236 flesch = 42 summary = The capacity of coronaviruses to undergo recombination may be related to its mRNA transcription mechanism, which involves discontinuous RNA synthesis, suggesting the nonprocessive nature of the viral polymerase. The first coronavirus recombinant was isolated by coinfecting temperature-sensitive (ts) mutants of two mouse hepatitis virus (MHV) strains, A59 and JHM, and selecting progeny viruses which grew at the nonpermissive temperature. In contrast, clear-cut evidence of recombination has been obtained for natural isolates of avian infectious bronchitis virus (IBV), many of which have recombination between different strains in the spike protein gene or the 3'-end of viral RNA. 33 In this case, the viral RNA containing the sequence of the transfected RNA fragments was detected by reverse transcription-polymerase chain reaction (RT-PCR), although the actual recombinants could not be isolated because of lack of selection markers. cache = ./cache/cord-332710-2s14knw6.txt txt = ./txt/cord-332710-2s14knw6.txt === reduce.pl bib === id = cord-335614-qh98622y author = Xu, Puzhi title = A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date = 2019-11-16 pages = extension = .txt mime = text/plain words = 6543 sentences = 352 flesch = 41 summary = These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout. The results of PCA and OPLA-DA analysis showed that there was an obvious separation between the content of the Con and Dis groups, revealing significant changes in the concentrations of metabolites in the kidney induced by NIBV infection. In addition, the transcriptomic analysis showed that NIBV infection also activated the RIG-I-like receptor signalling pathway (Figure 3f , signal 2), which included the transcriptional upregulation of genes such as MDA5, IPS-1, TRAF3, and IκB. In the present study, the ABCG2 mRNA was downregulated in the model group chicken kidneys, partially explaining the significantly increased uric acid levels caused by NIBV infection. cache = ./cache/cord-335614-qh98622y.txt txt = ./txt/cord-335614-qh98622y.txt === reduce.pl bib === id = cord-335864-392xmrq0 author = Sun, Yu-Meng title = Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application date = 2020-08-10 pages = extension = .txt mime = text/plain words = 13942 sentences = 786 flesch = 45 summary = With recent developments in sequencing methods and information analysis, an increasing number of novel ncRNAs have been identified, including long noncoding RNAs (lncRNAs) [5, 6] , circular RNAs (circRNAs) [7, 8] , and novel small ncRNAs [9] [10] [11] . Most circRNAs derived from mRNA back-splicing lose translational capacity because of the lack of effective ORFs or ribosome entry approaches, while a few circRNAs from coding or Sno-lncRNAs maintain their stability by their classical stem-loop structures of snoRNAs. c Alternative splicing within circRNAs. d A number of novel small ncRNAs derived from rRNAs (rRFs), tRNAs (tsRNAs), and snoRNAs (sdRNAs) have also been found to be enriched in RNA-induced silencing complexes (RISCs) and function in a miRNA-like pathway This approach can provide in-depth analysis of transcripts from target regions of genome. cache = ./cache/cord-335864-392xmrq0.txt txt = ./txt/cord-335864-392xmrq0.txt === reduce.pl bib === id = cord-334463-nvu5tqxb author = Kim, Chonsaeng title = Echovirus 7 Entry into Polarized Intestinal Epithelial Cells Requires Clathrin and Rab7 date = 2012-04-10 pages = extension = .txt mime = text/plain words = 6207 sentences = 325 flesch = 48 summary = We found that drugs, small interfering RNAs (siRNAs), and dominant negative mutants that target factors required for clathrin-mediated endocytosis, including clathrin and dynamin, inhibited both EV7 infection and internalization of virions from the cell surface. We previously (19) observed that, to infect polarized epithelium, CVB3 binds DAF on the cell surface, moves to the tight junction, and then enters the cell by an unusual mechanism that is independent of both dynamin and clathrin but which requires caveolin; contact with CAR in the tight junction leads to an essential conformational change in the CVB3 virion, but disruption of the capsid does not appear to occur until the virus has moved to an unidentified intracellular compartment. We had previously observed that CVB3 infection of Caco-2 cells occurs by a complex process that depends on caveolin but not dynamin-2, appears to be independent of clathrin-mediated endocytosis, and is inhibited by depletion of membrane cholesterol (19) . cache = ./cache/cord-334463-nvu5tqxb.txt txt = ./txt/cord-334463-nvu5tqxb.txt === reduce.pl bib === id = cord-334394-qgyzk7th author = Edgar, Robert C. title = Petabase-scale sequence alignment catalyses viral discovery date = 2020-08-10 pages = extension = .txt mime = text/plain words = 8134 sentences = 423 flesch = 51 summary = To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To expand the known repertoire of viruses and catalyse global virus discovery, in particular for Coronaviridae (CoV) family, we developed the Serratus cloud computing architecture for ultra-high throughput sequence alignment. We aligned 3,837,755 public RNA-seq, meta-genome, meta-virome and meta-transcriptome datasets (termed a sequencing run [5] ) against a collection of viral family pangenomes comprising all GenBank CoV records clustered at 99% identity plus all non-retroviral RefSeq records for vertebrate viruses (see Methods and Extended Table 1 ). We performed de novo assembly on 52,772 runs potentially containing CoV sequencing reads by combining 37,131 SRA accessions identified by the Serratus search with 18,584 identified by an ongoing cataloguing initiative of the SRA called STAT [5] . cache = ./cache/cord-334394-qgyzk7th.txt txt = ./txt/cord-334394-qgyzk7th.txt === reduce.pl bib === id = cord-334299-0zn1z7rc author = Ahmed, Warish title = Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date = 2020-09-30 pages = extension = .txt mime = text/plain words = 1373 sentences = 73 flesch = 47 summary = title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information However, in order to reliably interpret data produced from these efforts for informing public health interventions, additional quality control information and standardization in sampling design, sample processing, and data interpretation and reporting is needed. The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. In view of this need, we recommend methodological and quality assurance approaches for SARS-CoV-2 RNA detection in 158 wastewater using molecular methods. cache = ./cache/cord-334299-0zn1z7rc.txt txt = ./txt/cord-334299-0zn1z7rc.txt === reduce.pl bib === id = cord-336093-ic6q6ke8 author = Sun, Ying title = Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date = 2014-02-11 pages = extension = .txt mime = text/plain words = 6321 sentences = 361 flesch = 57 summary = Abbreviations: SARS, severe acute respiratory syndrome; SARS-CoV, SARS coronavirus; nsp, nonstructural protein; N7-MTase, guanine-N7-methyltransferase; 2 0 -O-MTase, 2 0 -O-methyltransferase; AdoMet, S-adenosyl-L-methionine; AdoHcy, S-adenosyl-L-homocysteine; ATA, aurintricarboxylic acid; IC 50 , inhibitory concentration at 50% activity. A single transformed colony of the YBS40 strain containing plasmids expressing human N7-MTase (MT-Human), SARS-CoV N7-MTase (MT-SARS), N7-MTases of other coronaviruses (MT-MHV, MT-TGEV, and MT-IBV), and the pMceK294A vector as control (representing the yeast N7-MTase [MT-Yeast]), were inoculated separately into 5 ml of a basic medium (Min SD Base) lacking tryptophan and incubated at 30°C for 21-24 h until reaching a similar final cell density in the stationary phase (0.5-1.0  10 8 cells/ml) (Chrebet et al., 2005) . Although AdoHcy, ATA and sinefungin, were previously reported to be inhibitors of coronavirus RNA MTases in vitro , only sinefungin significantly suppressed the growth of the MT-yeast, MT-human, and MT-SARS yeast cells (Fig. 3 ). cache = ./cache/cord-336093-ic6q6ke8.txt txt = ./txt/cord-336093-ic6q6ke8.txt === reduce.pl bib === id = cord-336319-8068s9a3 author = Graci, Jason D. title = Mechanisms of action of ribavirin against distinct viruses date = 2005-11-15 pages = extension = .txt mime = text/plain words = 6460 sentences = 343 flesch = 36 summary = Indirect mechanisms include reduction in cellular guanosine triphosphate (GTP) pools via inosine monophosphate dehydrogenase (IMPDH) inhibition, and an immunomodulatory effect in which a T-helper type 1 (antiviral) immune response is maintained. Direct mechanisms include inhibition of RNA capping activity, direct inhibition of viral polymerases, and increased mutation frequency via incorporation of ribavirin into newly synthesised genomes leading to error catastrophe. For all three compounds, a linear correlation was noted between GTP pool inhibition and antiviral activity as measured by viral RNA synthesis, as well as antiviral effect measured by reduction in CPE, suggesting that IMPDH inhibition is the primary mechanism of antiviral activity for all three compounds. Although direct biochemical evidence was not obtained, this finding suggested that ribavirin inhibits the capping of RNA genomes, either by interfering with the guanylyltransferase or methyltransferase activities (both of which are thought to be encoded by nsP1) or potentially by being incorporated as a cap analogue, which may impact translation of the RNA. cache = ./cache/cord-336319-8068s9a3.txt txt = ./txt/cord-336319-8068s9a3.txt === reduce.pl bib === id = cord-336560-m5u6ryy9 author = Boudewijns, Robbert title = STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date = 2020-07-02 pages = extension = .txt mime = text/plain words = 5019 sentences = 308 flesch = 51 summary = Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 . Similar as in humans 37 , semiquantitative lung pathology scores were obtained from high-resolution chest micro-CT scans of freebreathing animals 38 The increase in replication of SARS-CoV-2 seen in IL28R-a -/hamsters, on one hand, combined with a tempered inflammatory response and lung injury as compared to WT hamsters, on the other hand, is in line with the role of type III IFN plays during respiratory virus infections, including SARS-CoV-1 53 . cache = ./cache/cord-336560-m5u6ryy9.txt txt = ./txt/cord-336560-m5u6ryy9.txt === reduce.pl bib === id = cord-335067-tg66h99q author = Woolhouse, Mark E.J. title = Ecological and taxonomic variation among human RNA viruses date = 2013-03-19 pages = extension = .txt mime = text/plain words = 1395 sentences = 88 flesch = 59 summary = The realisation that many newly discovered and/or emerging pathogens have zoonotic origins has prompted much interest in the nature of the non-human reservoirs and biological characteristics that enable pathogens to jump between host species. 1 Here, we focus on an important group of pathogens -RNA viruses -and consider how taxonomic diversity and various aspects of ecological diversity -host range, route of infection and transmissibility -are related to one another. 2 We catalogue ICTV-recognised RNA virus species for which we can find convincing evidence of natural human infection in the peer-reviewed scientific literature (see Ref. 3 for more methodological details). Our procedure reveals a total of 158 human infective RNA virus species from 47 genera and 17 families (with one genus unassigned to a family). The overlap is also illustrated in that 47 out of 60 recognised mammal virus genera contain human infective species, as do 17 out of 19 families. There are 68 species of vector-borne RNA virus that can infect humans. cache = ./cache/cord-335067-tg66h99q.txt txt = ./txt/cord-335067-tg66h99q.txt === reduce.pl bib === id = cord-334315-ymkrgj0h author = Moon, Stephanie L. title = Cytoplasmic Viruses: Rage against the (Cellular RNA Decay) Machine date = 2013-12-05 pages = extension = .txt mime = text/plain words = 1995 sentences = 100 flesch = 43 summary = This review describes the myriad ways that viruses deal with the general host RNA decay machinery that is active in the cell immediately upon viral infection-turning what, at first, appears to be very hostile territory for a foreign transcript into a sort of ''promised land'' for viral gene expression. Disparate RNA viruses have, therefore, evolved unique mechanisms by which they disarm host RNA decay pathways by inactivating or proteolytically degrading important nucleases to promote productive viral infections. In addition, to make a cell more amenable to virus production, these virally encoded nucleases may also create a new ''sandbox'' in the cytoplasm for viral RNAs by initiating the large-scale decay of cellular mRNAs and dramatically altering the landscape of host gene expression. Considering the importance of RNA stability in regulating transcript abundance, the inactivation or commandeering of cellular RNA decay factors by viruses is likely to significantly alter host gene expression. cache = ./cache/cord-334315-ymkrgj0h.txt txt = ./txt/cord-334315-ymkrgj0h.txt === reduce.pl bib === id = cord-336012-8klkojpo author = Harilal, Divinlal title = SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date = 2020-06-18 pages = extension = .txt mime = text/plain words = 3040 sentences = 144 flesch = 45 summary = Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. Here we show that cWGS is cost-effective and is highly scalable when using a target enrichment sequencing method, and we also demonstrate its utility in tracking the origin of SARS-CoV-2 transmission. cache = ./cache/cord-336012-8klkojpo.txt txt = ./txt/cord-336012-8klkojpo.txt === reduce.pl bib === id = cord-335377-zrbn637z author = Ishimaru, Daniella title = RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date = 2012-12-26 pages = extension = .txt mime = text/plain words = 7699 sentences = 376 flesch = 52 summary = Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. We further show that kissing dimer formation plays a role in frameshift-stimulation and modulates the relative abundance of full-length and subgenomic viral RNAs. Plasmids containing wild-type pseudoknot as well as the ÁS3 pk mutant were described in Plant et al (1) . Our previous NMR analysis of exchangeable imino protons of the SARS-CoV pseudoknot ( Figure 1A , wild-type pk) provided unequivocal evidence for the existence of Stem 3 (1). Surprisingly, in the context of the SARS-CoV Stem 3 sequence, 5 0 -cuug-3 0 tetraloop-capped mutants readily formed extended duplex structures as revealed by native gel and NMR analysis. cache = ./cache/cord-335377-zrbn637z.txt txt = ./txt/cord-335377-zrbn637z.txt === reduce.pl bib === id = cord-335441-bj3me7p8 author = Jourdain, Elsa title = Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data date = 2010-01-28 pages = extension = .txt mime = text/plain words = 6354 sentences = 311 flesch = 52 summary = Five of the six ducks excreted viral RNA in their feces on the first day post-inoculation (PI) and all samples (feces, cloacal and oral swabs) from all birds were positive on the second day PI (Figures 4 and S1 ). Intermittent and moderate (high ct-values) viral RNA shedding was detected for all birds in water, fecal or cloacal samples between day 1 and 7 after H7N7 re-inoculation ( Figure 4 ). Active H5 infection was confirmed only in one duck, by expression of H5-specific antibodies and detection of viral RNA in the various sample types (feces, water, oral and cloacal swabs) with a pattern similar to the H5-inoculated control bird. Eight 3-month-old male wild-type mallards (Anas platyrhynchos) of approximately the same body mass and size (measurement of the left wing, the right tarsus length and the distance from bill tip to back of the skull) were selected from a Swedish duck farm known from previous successive sampling to be free from IAV infection. cache = ./cache/cord-335441-bj3me7p8.txt txt = ./txt/cord-335441-bj3me7p8.txt === reduce.pl bib === id = cord-337339-0vkigjv2 author = Osterrieder, Nikolaus title = Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date = 2020-07-20 pages = extension = .txt mime = text/plain words = 4327 sentences = 220 flesch = 47 summary = We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. Moreover, transgenic mice expressing human ACE2 represent a lethal SARS-CoV-2 infection model resulting in significant weight loss and permitting robust virus replication in the respiratory tract including the lungs [20] . In contrast to SARS-CoV-2 titers, histopathological changes differed markedly between young and aged Syrian hamsters over time: younger animals launched more severe reactions at early time points after infection, while lesions and inflammation in the lungs became more pronounced and widespread at later time points in the elderly. Based on the data presented here, we propose that comparative preclinical assessments of SARS-CoV-2 vaccines and other treatment options in young versus aged hamsters may yield valuable and relevant results, as this small animal model appears to mimic age-dependent differences in humans. cache = ./cache/cord-337339-0vkigjv2.txt txt = ./txt/cord-337339-0vkigjv2.txt === reduce.pl bib === id = cord-336554-n8n5ii5k author = Singh, Thakur Uttam title = Drug repurposing approach to fight COVID-19 date = 2020-09-05 pages = extension = .txt mime = text/plain words = 13032 sentences = 690 flesch = 44 summary = Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . cache = ./cache/cord-336554-n8n5ii5k.txt txt = ./txt/cord-336554-n8n5ii5k.txt === reduce.pl bib === id = cord-336775-d4hi9myk author = Kirtipal, Nikhil title = From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date = 2020-08-13 pages = extension = .txt mime = text/plain words = 8606 sentences = 442 flesch = 46 summary = Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Hence, acute respiratory distress syndrome (ARDS) is caused by cytokine storm that triggers a destruction in host cells via immune system and subsequently results into multiple organs failure or death as stated in case of SARS-CoV-2 outbreak; similar observations were noted in case of SARS-CoV infection (Kumar et al., 2020) . When developing novel therapeutic strategies to check the immunoregulatory cytokines such as TNFβ and IL6, investigation should be considered on the viral strain and targeted organ specificity; for example, SARS-CoV-2 has more affinity to ACE2 which are scattering on different organs like lung and kidney while MERS-like CoV can even infect T-cells. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) cache = ./cache/cord-336775-d4hi9myk.txt txt = ./txt/cord-336775-d4hi9myk.txt === reduce.pl bib === id = cord-337026-osgi06o4 author = Panoutsopoulos, Alexios A. title = Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date = 2020-06-19 pages = extension = .txt mime = text/plain words = 3174 sentences = 171 flesch = 48 summary = Given the uprising number of publications and case reports of COVID-19 patients showing conjunctivitis [61, 62] and the history of other coronaviruses that are found in tears, we have to consider the possibility of a separate, alternative viral mechanism through which the virus can enter the patient's organism through epithelial cells of the eye [63] . The growing evidence on COVID-19 and its ocular implications and manifestations, in both animals and humans, is covered by many interesting reviews, all published 5 to 6 months after the novel coronavirus' outbreak [64] [65] [66] [67] [68] , something that reveals the need to understand the virus from different perspectiveswhich at first may have seemed secondary in priority-in order to be able to reach a treatment. cache = ./cache/cord-337026-osgi06o4.txt txt = ./txt/cord-337026-osgi06o4.txt === reduce.pl bib === id = cord-334947-pa0p5dif author = Rozen-Gagnon, Kathryn title = Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date = 2014-01-16 pages = extension = .txt mime = text/plain words = 8887 sentences = 415 flesch = 44 summary = Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. To estimate the population diversity of variants by deep sequencing, cDNA libraries were prepared by Superscript III from RNA extracted from virus generated in BHK-21 or C6/36 cells, and the viral genome was amplified using a high fidelity polymerase (Phusion) to generate 5 overlapping amplicons 2-3 kb in length. To address the possibility that the fitness cost of defective replication, observed in mosquito cell culture, would favor the reversion of these mutant polymerases to wildtype, we deep sequenced virus from the body of an individual mosquito that presented the median titer from each group. cache = ./cache/cord-334947-pa0p5dif.txt txt = ./txt/cord-334947-pa0p5dif.txt === reduce.pl bib === id = cord-336447-hpnkou41 author = Pitlik, Silvio Daniel title = COVID-19 Compared to Other Pandemic Diseases date = 2020-07-31 pages = extension = .txt mime = text/plain words = 6148 sentences = 396 flesch = 49 summary = Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. cache = ./cache/cord-336447-hpnkou41.txt txt = ./txt/cord-336447-hpnkou41.txt === reduce.pl bib === id = cord-337673-1nau263l author = Wu, Chang-Jer title = Antiviral applications of RNAi for coronavirus date = 2006-01-24 pages = extension = .txt mime = text/plain words = 4329 sentences = 253 flesch = 52 summary = Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . cache = ./cache/cord-337673-1nau263l.txt txt = ./txt/cord-337673-1nau263l.txt === reduce.pl bib === id = cord-337879-liqhbqxl author = Kriesel, John D. title = Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain date = 2012-03-08 pages = extension = .txt mime = text/plain words = 5060 sentences = 296 flesch = 54 summary = Sequences from GB virus C (GBV-C), a flavivirus not previously isolated from brain, were enriched in one of the MS samples. This study shows the feasibility of deep sequencing for the detection of occult viral infections in the brains of deceased persons with MS. Multiple sclerosis (MS) is a chronic demyelinating disease of unknown cause, which affects the brain and spinal cord of about 400,000 individuals in the U.S. A number of viral infections of the CNS can lead to demyelination, including distemper (dogs), measles (SSPE, humans), and influenza (humans). To enhance the detection of non-human sequences, RNA samples that passed the quality control step above were subjected to rRNA removal using the RiboMinus kit (Invitrogen Inc., Carlsbad, CA). One subject who died with primary-progressive MS had .1000 36 bp sequences detected that mapped to GBV-C virus (hepatitis G), a human flavivirus not known to cause any persistent disease and never before detected in human brain. cache = ./cache/cord-337879-liqhbqxl.txt txt = ./txt/cord-337879-liqhbqxl.txt === reduce.pl bib === id = cord-337361-salby0fu author = Bujarski, Jozef J. title = Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date = 2013-03-26 pages = extension = .txt mime = text/plain words = 6863 sentences = 335 flesch = 39 summary = In some viruses, the frequency of homologous crossing-over is very high and practically every replicated viral RNA molecule can be considered as chimerical in nature, as we have demonstrated for brome mosaic virus (BMV) RNAs (Urbanowicz et al., 2005) . The generally accepted mechanism of RNA recombination is currently explained by a copy-choice model where the viral RNA polymerase (RdRp) complex in mRNA viruses [reverse transcriptase (RT) in retroviruses] changes templates during synthesis of the nascent strand (Galetto et al., 2006) . Among the factors known to promote replicase to switch are sequence homologies between recombination substrates along with secondary structures at the crossover sites, as demonstrated with the BMV and other systems (Figlerowicz and Bujarski, 1998; Nagy et al., 1999b) . Comparison among three plant RNA virus replication systems (TBSV, BMV, and dianthoviruses) reveals general patterns within the stepwise process of viral replicase complex assembly which requires concerted involvement of protein-protein, RNA-protein, and protein-lipid interactions (Mine and Okuno, 2012) . cache = ./cache/cord-337361-salby0fu.txt txt = ./txt/cord-337361-salby0fu.txt === reduce.pl bib === id = cord-337199-mbv8kd1k author = Ballarín-González, Borja title = Clinical translation of RNAi-based treatments for respiratory diseases date = 2012-09-07 pages = extension = .txt mime = text/plain words = 10541 sentences = 571 flesch = 41 summary = This review outlines the essential steps required for the clinical translation of RNAi-based respiratory therapies including disease and RNA target selection, siRNA design, respiratory barriers, and delivery solutions. 1 In vitro screening and selection of siRNA candidates against potential targets such as pathogenic or host factors; 2 optimize siRNA designs with high silencing activity and avoid immune recognition, increase stability, and reduce off-target effects; 3 evaluation of cytokine profile and gene silencing efficiency in preclinical disease models using either naked or a suitable delivery system; and 4 clinical trials to evaluate toxicity and biological activity of lead formulations Considerable efforts have attempted to harness the "exogenous" or "endogenous" branches of the RNAi pathway for therapeutic purposes. The authors suggested that the observed therapeutic effect reported in early studies was most likely due to activation of the innate immune response by the recognition of viral-specific nonmodified siRNA sequences by toll-like receptors (TLRs) instead of an RNAi-mediated effect. cache = ./cache/cord-337199-mbv8kd1k.txt txt = ./txt/cord-337199-mbv8kd1k.txt === reduce.pl bib === id = cord-337998-08tknscm author = Sztuba-Solinska, Joanna title = A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8 date = 2016-11-16 pages = extension = .txt mime = text/plain words = 8269 sentences = 434 flesch = 51 summary = Selective 2′-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3′ stem-loop (nucleotides 1868–1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. 3E-5E-GFP minigenome RNA secondary structure and host protein interactions were examined using selective 2 -hydroxyl acylation analyzed by primer extension (SHAPE) (38, 39) , antisense-interfered SHAPE (aiSHAPE) (40) , electrophoretic mobility shift assays (EMSA), siRNA, and mutational analysis, using both the 3E-5E-GFP minigenome system and EBOV reverse genetics. The secondary structure of the EBOV 3E-5E-GFP minigenome RNA predicted by RNAstructure software version 5.7 (48) and chemical probing data from SHAPE were used to generate 10 three-dimensional (3D) models for the trailer-to-leader panhandle interaction in the wt-EBOV genome and variants, A30U and A26U/A30U, using open-source RNAComposer, version 1.0 (http://rnacomposer.cs.put.poznan.pl/). cache = ./cache/cord-337998-08tknscm.txt txt = ./txt/cord-337998-08tknscm.txt === reduce.pl bib === id = cord-337508-nfzaw8gg author = Kirkland, P.D. title = The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 date = 2020-10-05 pages = extension = .txt mime = text/plain words = 2708 sentences = 134 flesch = 54 summary = authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 With the widespread introduction of molecular based diagnostic assays, especially real time PCR (qPCR), studies have been undertaken to evaluate the stability of viruses in VTMs, particularly in commercially prepared products, while being held at a range of temperatures. After becoming aware of concerns of variable results for the same samples in different assays, we initiated a study to compare the stability of SARS-CoV-2 RNA in several commercially manufactured VTMs and an in-house product. The results of these studies clearly indicate that the commercially prepared VTM solutions have had an adverse impact on the ability to detect both SARS-CoV-2 and influenza RNA. The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses cache = ./cache/cord-337508-nfzaw8gg.txt txt = ./txt/cord-337508-nfzaw8gg.txt === reduce.pl bib === id = cord-337976-c2auspti author = Weiss, Susan R. title = Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date = 1983-04-30 pages = extension = .txt mime = text/plain words = 3818 sentences = 267 flesch = 61 summary = A cDNA probe representing the genome of mouse hepatitis virus (MHV) strain A59 (MHV-A59) was used to measure nucleotide sequence homologies among murine and human coronaviruses and the SD and SK coronaviruses isolated by Burks et al. Since SD and SK were isolated by inoculation of multiple sclerosis (MS) central nervous system (CNS) tissue into mice or cultured mouse cells, it is important to determine their relationships to other murine and human coronavirus isolates. Some strains of HCV such as 0C43, are antigenically related to murine coronaviruses such as MHV strain JHM (McIntosh, 1974; Gerdes et al., 1981a, b) and may be grown in the brains of suckling mice (McIntosh et al., 1967) . We have further compared murine and human coronaviruses and SD and SK by using molecular hybridization of virus-specific RNA with cDNA probes. RNA extracted either from brain homogenates of OC43-infected suckling mice or from HRT cells infected with OC43 shows homology with A59 cDNA when assayed by blot hybridization. cache = ./cache/cord-337976-c2auspti.txt txt = ./txt/cord-337976-c2auspti.txt === reduce.pl bib === id = cord-334891-4jgtxg07 author = Choudhury, Abhigyan title = In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date = 2020-11-11 pages = extension = .txt mime = text/plain words = 2926 sentences = 169 flesch = 54 summary = This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. The binding of Spike protein with the human ACE2 receptor triggers the pathogenesis 3 of the SARS-CoV-2, leading to the activation of TLRs to activate the proliferation and 4 production of pro-inflammatory cytokines causing cytokine storm, those results in 5 inflammations. cache = ./cache/cord-334891-4jgtxg07.txt txt = ./txt/cord-334891-4jgtxg07.txt === reduce.pl bib === id = cord-338083-77re4l0w author = Bolin, Steven R. title = Origination and consequences of bovine viral diarrhea virus diversity date = 2005-03-04 pages = extension = .txt mime = text/plain words = 6748 sentences = 329 flesch = 43 summary = The genetic diversity that occurs among isolates of BVDV is characteristic of RNA viruses that exist in nature as quasispecies (a swarm of viral mutants). However, altered base sequence in this region of the viral genome has been identified after passage of the virus in cell culture, and has been detected in viral RNA that was extracted from tissues of an infected animal [20, 21] . The selection of the antigenic variants likely occurred during the acute infection of the dams of those PI cattle and resulted in transplacental transmission of slightly different BVDV to a group of fetuses. Genetic and antigenic variability in bovine viral diarrhea virus (BVDV) isolates from Belgium Pathogenesis of primary respiratory disease induced by isolates from a new genetic cluster of bovine viral diarrhea virus type I Clinical and immunologic responses of vaccinated and unvaccinated calves to infection with a virulent type-II isolate of bovine viral diarrhea virus cache = ./cache/cord-338083-77re4l0w.txt txt = ./txt/cord-338083-77re4l0w.txt === reduce.pl bib === id = cord-336986-rmxin1da author = De Clercq, Erik title = New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date = 2019-08-07 pages = extension = .txt mime = text/plain words = 2711 sentences = 221 flesch = 57 summary = Eight different compounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/or other hemorrhagic fever virus (HFV) infections. Abstract: Eight differentc ompounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/oro ther hemorrhagic fever virus (HFV) infections.T hey can be considered as either (i)adenine analogues (3-deazaneplanocin A, galidesivir,G S-6620 andr emdesivir) or (ii)guanine analogues containing the carboxamide entity (ribavirin, EICAR, pyrazofurin and favipiravir). [26] It wasa lso found active against other emerging viruses such as respiratory syncytial virus (RSV) and hepatitis Cv irus (HCV),a nd the presence of the 1'-cyano group in remdesivir wasf ound to be critical in providing selectivity toward the viral (RNA) polymerases. cache = ./cache/cord-336986-rmxin1da.txt txt = ./txt/cord-336986-rmxin1da.txt === reduce.pl bib === id = cord-337285-t6qr41wc author = Ikeda, Masanori title = Modulation of host metabolism as a target of new antivirals() date = 2007-10-10 pages = extension = .txt mime = text/plain words = 8180 sentences = 466 flesch = 46 summary = Using cell culture systems, several cellular proteins have been identified as effective molecules for HCV RNA replication (Table 1) . [66] reported that lovastatin (LOV), one of the HMG-CoA reductase inhibitors, inhibited HCV RNA replication in HCV replicon-harboring cells. Depletion of the GGPP by statins may inhibit the geranylgeranylation of cellular proteins such as FBL2 and cause the anti-HCV effect in the cells. During the development of IFN therapy for patients with CH-C, the lack of a robust method of HCV RNA replication in cell culture has hampered research into the HCV life cycle and the discovery of potent new anti-HCV reagents. VX-950, a novel hepatitis C virus (HCV) NS3-4A protease inhibitor, exhibits potent antiviral activities in HCV replicon cells Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells cache = ./cache/cord-337285-t6qr41wc.txt txt = ./txt/cord-337285-t6qr41wc.txt === reduce.pl bib === id = cord-338345-mr1orklo author = Adedeji, Adeyemi O. title = Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase date = 2016-09-07 pages = extension = .txt mime = text/plain words = 4253 sentences = 233 flesch = 57 summary = Unless stated otherwise, for this specific experiment, we used the 5=-RNA-20 partially duplex substrate (see Fig. S1 in the supplemental material), since previous coronavirus helicase, i.e., SARS-CoV nsp13, was shown to have a 5=-to-3= directionality (29) . To determine whether nucleic acid unwinding by M-nsp13 depends on the loading strand length and to determine the minimum length of the 5= singlestranded overhang required for efficient helicase activity, we designed five partially duplex RNA substrates with single-stranded 5= ends of various lengths (between 0 and 20 bases) (see Fig. S1 in the supplemental material; Fig. 6 ) but with dsRNA duplex regions of the same length. Overall, these results suggest that M-nsp13's ability to unwind the 5=-RNA-20 partially duplex substrate is likely due to residual cellular ATP purified with the helicase as well as to a long overhang length, which enhances M-nsp13's unwinding activity. cache = ./cache/cord-338345-mr1orklo.txt txt = ./txt/cord-338345-mr1orklo.txt === reduce.pl bib === id = cord-335231-617e5dcy author = Pettersson, Lisa title = Hantavirus RNA in Saliva from Patients with Hemorrhagic Fever with Renal Syndrome date = 2008-03-17 pages = extension = .txt mime = text/plain words = 3332 sentences = 178 flesch = 54 summary = During an outbreak in northern Sweden of nephropathia epidemica (NE), a milder form of hemorrhagic fever with renal syndrome, we collected saliva and plasma from 14 hospitalized NE patients with verifi ed Puumala virus (PUUV) infection. During an outbreak in northern Sweden of nephropathia epidemica (NE), a milder form of hemorrhagic fever with renal syndrome, we collected saliva and plasma from 14 hospitalized NE patients with verifi ed Puumala virus (PUUV) infection. For this reason, we collected saliva from patients during an NE outbreak in northern Sweden and analyzed the samples for the presence and levels of PUUV RNA by using a real-time reverse transcription-PCR (RT-PCR) assay. Furthermore, we detected no inhibition of real-time RT-PCR in saliva or plasma when we analyzed our patient samples by using an internal positive control (data not shown). cache = ./cache/cord-335231-617e5dcy.txt txt = ./txt/cord-335231-617e5dcy.txt === reduce.pl bib === id = cord-337899-w5zh40gv author = Bissoyi, Akalabya title = Alphavirus Nonstructural Proteases and Their Inhibitors date = 2017-07-14 pages = extension = .txt mime = text/plain words = 7294 sentences = 399 flesch = 48 summary = Recently, several protease inhibitors have been developed using computeraided drug design methodologies (Gupta, 2013; Gupta et al., 1983; Wlodawer and Vondrasek, 1998) , synthetic approaches, high-throughput screening method (Mayr and Bojanic, 2009) , and drug reposition-based approaches (Sundberg, 2000) , which could possibly target the NSPs responsible for virus replication. The former ligand is therefore supposed to be a promising inhibitor of NSP2 protease of CHIKV virus, and has been emerged as one of the promising antiviral drug candidates with potential symptomatic and disease-modifying effects. Exploring the polymerase activity of Chikungunya viral non structural protein 4 (nsP4) using molecular modeling, epharmacophore and docking studies. Molecular modeling and docking study to elucidate novel Chikungunya virus nsP2 protease inhibitors Exploring the polymerase activity of Chikungunya viral nonstructural protein 4 (nsP4) using molecular modeling, e-pharmacophore and docking studies cache = ./cache/cord-337899-w5zh40gv.txt txt = ./txt/cord-337899-w5zh40gv.txt === reduce.pl bib === id = cord-338307-vfutmwxq author = Sturman, Lawrence S. title = The Molecular Biology of Coronaviruses date = 1983-12-31 pages = extension = .txt mime = text/plain words = 21959 sentences = 1287 flesch = 52 summary = The pattern of three major structural proteins and their organization in the virion as shown for MHV-A59 in Fig. 3 is generally applicable to most other species of coronaviruses (reviewed in detail by Siddell et al., 1982) . (1981b) , using a cDNA probe prepared against the mRNA of MHV-A59 which coded for the nucleocapsid protein, obtained evidence of 7 0 4 0 % homology by analysis of hybridization kinetics of viral RNA from cells infected with MHV-1, -3, -S, and -JHM. t 1980) demonstrated that different size classes of poly(A)containing intracellular MHV-JHM RNAs fractionated on sucroseformamide gradients directed the synthesis of different structural proteins in cell-free translation systems. The studies showed that, like avian coronaviruses, for the murine coronavirus MHV-A59, the oligonucleotides of each of the subgenomic RNAs were included within the next larger species, starting from the 3' end of the genome. cache = ./cache/cord-338307-vfutmwxq.txt txt = ./txt/cord-338307-vfutmwxq.txt === reduce.pl bib === id = cord-338680-wwlttymp author = Khonyongwa, K. title = Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date = 2020-07-30 pages = extension = .txt mime = text/plain words = 4839 sentences = 288 flesch = 53 summary = Due to the high prevalence of infection during the peak of the outbreak, one of the suggested strategies to prevent healthcare transmission was to screen all patients on admission by a single combined nose and throat swab assessed for SARS-CoV-2 RNA to allow segregation into COVID-19 positive and non COVID-19 cohort wards. The latter included assessment of the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity, COVID-19 patients as sources of infection, self-reported COVID-19 sickness absence among hospital staff hospital bed occupancy, community incidence, and the incidence of other significant hospital-acquired infections. NHS England released its reporting criteria in May 2020 (written communication described in supplementary data) following which cases were also classified as per date of the SARS-CoV-2 RNA detection. Correlation between weekly incidence of HA-COVID-19 (including late indeterminate cases) and staff self-reported sickness absence, delayed RNA positive cases, community incidence and Trust COVID-19 bed occupancy is displayed in figure 3. cache = ./cache/cord-338680-wwlttymp.txt txt = ./txt/cord-338680-wwlttymp.txt === reduce.pl bib === id = cord-339456-82iks0xf author = Mikel, P. title = Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date = 2015-02-25 pages = extension = .txt mime = text/plain words = 10033 sentences = 499 flesch = 53 summary = title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Also MS2 phage-like particles have been used as the process control virus for the detection of pathogenic RNA viruses in clinical samples. prepared MS2 phage-like particles, also called armored RNA (aRNA), that carried the consensus RNA sequence from human immunodeficiency virus type 1 (HIV-1) packaged in the capsid which can serve as quantitative standard in detection of HIV-1 (Pasloske et al. MS2 phage-like particles carrying the plant-specific ribulose-1,5-bisphosphate carboxyl small subunit (rbcs) gene fragment were used as the process control virus in qRT-PCR detection of severe acute respiratory syndrome coronavirus (SARS-CoV) . cache = ./cache/cord-339456-82iks0xf.txt txt = ./txt/cord-339456-82iks0xf.txt === reduce.pl bib === id = cord-338727-1kodz527 author = Ilinskaya, O. N. title = Ribonucleases as antiviral agents date = 2014-10-11 pages = extension = .txt mime = text/plain words = 4605 sentences = 227 flesch = 44 summary = Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. Therefore, the formation of RNA fragments enhanced by RNase L, followed by their interaction with RIG I and MDA5, activates transcription factor NF κB and triggers transcription of interferon β gene, which prevents virus replication and stimulates the growth of immune system cells [9] . Previously, onconase, an RNases from oocytes of the leopard frog Rana pipiens, efficiently suppresses the replication of HIV 1 due to the selective degrada tion of viral RNA, which exhibits no pronounced cytotoxic effect on infected human cells [22] . At the first stage, when binase meets the virus outside cell, its catalytic activity is not inhibited by the natural RNase and it may destroy viral RNA (Fig. 3, C) . Ribonucleases in HIV type 1 inhibition: Effect of recombinant RNases on infection of primary T cells and immune activation induced RNase gene and protein expression cache = ./cache/cord-338727-1kodz527.txt txt = ./txt/cord-338727-1kodz527.txt === reduce.pl bib === id = cord-338358-ppjxo2di author = Whitworth, Kristin M. title = Zygote injection of CRISPR/Cas9 RNA successfully modifies the target gene without delaying blastocyst development or altering the sex ratio in pigs date = 2016-10-15 pages = extension = .txt mime = text/plain words = 4959 sentences = 267 flesch = 55 summary = title: Zygote injection of CRISPR/Cas9 RNA successfully modifies the target gene without delaying blastocyst development or altering the sex ratio in pigs Pairs of CRISPR guide RNAs that flanked the start codon and polyadenylated Cas9 were co-injected into the cytoplasm of zygotes and cultured in vitro to the blastocyst stage. In a previous study, CRISPR/Cas9 RNA injection of pig zygotes resulted in 100 % of the piglets having biallelic DNA edits of the targeted CD163 or CD1D gene (Whitworth et al. Zygote injection with CRISPR/Cas9 guide RNA was used to efficiently (100 %) create pigs with a biallelic edit of the TMPRSS2 gene for use as a biomedical model (Fig. 2e, f) . The sex ratio measured in the resulting blastocysts and piglets was not significantly affected by in vitro culture or CRISPR/Cas9 RNA injection. cache = ./cache/cord-338358-ppjxo2di.txt txt = ./txt/cord-338358-ppjxo2di.txt === reduce.pl bib === id = cord-338901-1kzy7rts author = Li, Heng title = Overview of therapeutic drug research for COVID-19 in China date = 2020-06-17 pages = extension = .txt mime = text/plain words = 5098 sentences = 253 flesch = 48 summary = According to the information that we have collected so far, this article provides an overview of potential therapeutic drugs and compounds with much attention, including favipiravir and hydroxychloroquine, as well as traditional Chinese medicine, which have been reported with good clinical treatment effects. In these 155 pooled clinical trials, a number of approved chemical and biomacromolecule drugs have been used in COVID-19 treatment clinical trials for drug repurposing, most of which are nucleotide analogs and protease inhibitors against other viral pathogens, including influenza virus, HIV and HCV. In vitro studies have shown that lopinavir/ritonavir can inhibit the replication of MERS-CoV and SARS-CoV and exert antiviral effects [22] [23] [24] [25] . In the latest "Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia", it is recommended to use ribavirin at a dose of 500 mg each time for adults and in combination with interferon or lopinavir/ritonavir, with 2-3 intravenous infusions daily. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) cache = ./cache/cord-338901-1kzy7rts.txt txt = ./txt/cord-338901-1kzy7rts.txt === reduce.pl bib === id = cord-339288-y8woqsii author = Tews, Birke Andrea title = Self-Replicating RNA date = 2016-06-11 pages = extension = .txt mime = text/plain words = 7567 sentences = 338 flesch = 44 summary = Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. Three years later, the performance of poliovirus cDNA clones could be significantly ameliorated through the introduction of SV40 transcription and replication signals and transfection of the resulting construct into cells expressing the SV40 large T antigen [14] , thus ensuring replication of the DNA-plasmid in eukaryotic cells leading to a higher yield of viral RNA and recovered virus (Fig. 2, left part) . The resulting virus CP7_E2alf was only able to infect pigs and thus displayed the Fig. 3 Generation of a chimeric viral genome from two parental RNAs. On the level of a cDNA construct, one protein-coding sequence is replaced by the corresponding gene of the other virus (principle used for the pestivirus vaccine CP7_E2alf [58] ). cache = ./cache/cord-339288-y8woqsii.txt txt = ./txt/cord-339288-y8woqsii.txt === reduce.pl bib === id = cord-339782-rybjc58j author = Carmo, Anália title = Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1844 sentences = 106 flesch = 52 summary = The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead. In men, the first negative test took 24 ± 9 days (range: 7 -46) and in women it took 25 ± 9 days (range: 9 -44), P>0.05, In an attempt to understand why some patients maintained positive tests for longer, we correlated the detection of SARS-CoV-2 RNA with the host immune response to virus infection. The lack of information regarding persistence of virus RNA and infectivity, disease severity and immune response, supports the current guidance of viral clearance confirmation prior to patient transference out of dedicated COVID-19 wards and of ending isolation in mild illness patients. cache = ./cache/cord-339782-rybjc58j.txt txt = ./txt/cord-339782-rybjc58j.txt === reduce.pl bib === id = cord-338582-o976nab9 author = Dahlhausen, Bob title = Future Veterinary Diagnostics date = 2010-09-19 pages = extension = .txt mime = text/plain words = 9199 sentences = 511 flesch = 35 summary = Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. PCR uses the highly specific molecular recognition ability of Watson-Crick base pairing to provide the selectivity needed for a nucleic acid probe to bind to a targeted DNA sequence and allow for its exponential amplification. It has been used to develop rapid diagnostic tests for several pathogenic viruses with singlestranded RNA genomes, including influenza A, 13 footand-mouth disease virus, 14 and severe acute respiratory syndrome (SARS)-associated coronavirus. DNA microarrays also permit relatively rapid interrogation of a clinical sample against thousands of genetic targets, allowing for simultaneous detection and discrimination among hundreds of pathogenic agents of veterinary interest. Unlike PCR technology where the target agent must be known to use specific test primers, microarrays can allow for the rapid diagnosis of multiple pathogenic agents in disease outbreaks and epidemics of unknown etiology. cache = ./cache/cord-338582-o976nab9.txt txt = ./txt/cord-338582-o976nab9.txt === reduce.pl bib === id = cord-340189-jo38hjqa author = Bar-On, Yinon M title = SARS-CoV-2 (COVID-19) by the numbers date = 2020-04-02 pages = extension = .txt mime = text/plain words = 7246 sentences = 458 flesch = 58 summary = If you are infectious for 4 days, then you will infect four others on average, which is on the high end of the R 0 values for SARS-CoV-2 in the absence of physical distancing. Assuming entry of the virus to the cells is rapid (we estimate 10 min for SARS-CoV-2), the time it takes to produce progeny can be estimated by quantifying the lag between inoculation and the appearance of new intracellular virions, also known as the 'eclipse period'. While both the time to complete a replication cycle and the burst size may vary significantly in an animal host due to factors including the type of cell infected or the action of the immune system, these numbers provide us with an approximate quantitative view of the viral life-cycle at the cellular level. (Hirano et al., 1976) : "The average per-cell yield of active virus was estimated to be about 6-7  10 2 plaque-forming units." This data is for MHV, so more research is needed to verify these values for SARS-CoV-2. cache = ./cache/cord-340189-jo38hjqa.txt txt = ./txt/cord-340189-jo38hjqa.txt === reduce.pl bib === id = cord-336628-0evl3wnd author = Neufeldt, Christopher J. title = SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date = 2020-07-21 pages = extension = .txt mime = text/plain words = 5880 sentences = 362 flesch = 49 summary = Consistently, secreted cytokine profiles from both severe COVID-19 patients and SARS-CoV-2 infected lung epithelial cells, were enriched for pro-inflammatory cytokines and lacked type I/III IFNs. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells. To confirm that the lack of IFN response in Calu-3 or A549-ACE2 cells infected with SARS-CoV-2 was not due to defects in the activation of innate immune pathways, we To test if IFNs could limit virus replication even after establishment of infection, A549-ACE2 cells were treated with high levels of various IFNs at the time point of infection or 6 h thereafter. these results indicate that SARS-CoV2-infection triggers the cGAS-STING pathway, leading to NF-κB-mediated induction of pro-inflammatory cytokines, and that this response can be controlled with STING inhibitors. cache = ./cache/cord-336628-0evl3wnd.txt txt = ./txt/cord-336628-0evl3wnd.txt === reduce.pl bib === id = cord-339976-tg2jkss7 author = Wang, Haibin title = Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date = 2004-07-01 pages = extension = .txt mime = text/plain words = 2579 sentences = 120 flesch = 50 summary = title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome Reliable and sensitive determination of the SARS CoV load would aid in the early identification of infected individuals, provide guidance for treatment (especially the use of steroid hormones and antiviral agents), and aid in monitoring of a patient's clinical course and outcome. The method could detect the CoV load during the SARS course, as demonstrated in Fig. 1B , representative data from the 44 patients tested. High frequency of point mutations clustered within the adenosine triphosphatebinding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome cache = ./cache/cord-339976-tg2jkss7.txt txt = ./txt/cord-339976-tg2jkss7.txt === reduce.pl bib === id = cord-339431-kyr5lv15 author = Saçar Demirci, Müşerref Duygu title = Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date = 2020-03-17 pages = extension = .txt mime = text/plain words = 2323 sentences = 163 flesch = 52 summary = In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Although there are studies regarding to the viral replication and their interaction with host innate immune system, the role of miRNA-mediated RNA-silencing in SARS-CoV-2 infection has not been enlightened yet. In this study, SARS-CoV-2 genome was searched for miRNA-like sequences and potential host-virus interactions based on miRNA actions were analyzed. In our study, we have also identified possible miRNA like small RNAs from SARS-CoV-2 genome which target important human genes. cache = ./cache/cord-339431-kyr5lv15.txt txt = ./txt/cord-339431-kyr5lv15.txt === reduce.pl bib === id = cord-338812-q24jycgk author = Zakaryan, H. title = Nuclear remodelling during viral infections date = 2011-04-28 pages = extension = .txt mime = text/plain words = 4462 sentences = 226 flesch = 37 summary = At present, we know that the nucleus contains the chromatin territories that mainly consist of DNA-protein complexes, as well as several distinct interchromosomal compartments (bodies) that support molecular activities, including replication, transcription and processing of nucleic acids (Fig. 1) . For many years the classical view of these components focused on their crucial role for the biogenesis of ribosomal subunits, but proteomic analysis of human nucleoli showed the presence of about 4500 nucleolar proteins with different functions, thus revealing the multifunctional nature of the nucleolus (Ahmad et al., 2009) . The previous decade of extensive studies implicated PML NBs in stress response (Maul et al., 1995) , gene regulation (Zhong et al., 2000) , oncogenesis (Salomoni and Pandolfi, 2002) , cell senescence (Bischof et al., 2002) , DNA damage repair (Dellaire and Bazett-Jones, 2004) , apoptosis (Takahashi et al., 2004) as well as in antiviral defence mechanisms (Everett and Chelbi-Alix, 2007) . cache = ./cache/cord-338812-q24jycgk.txt txt = ./txt/cord-338812-q24jycgk.txt === reduce.pl bib === id = cord-339209-oe8onyr9 author = Vasilakis, Nikos title = Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date = 2014-05-20 pages = extension = .txt mime = text/plain words = 5817 sentences = 272 flesch = 46 summary = The organization of each genome was similar to that described previously for the mesoniviruses (NDiV, CavV, HanaV, NseV and MenoV), featuring a long 5'-untranslated region (5'-UTR) of 359 to 370 nt, six major long open reading frames (ORFs), and a long terminal region of 1780 to 1804 nt preceding the poly[A] tail ( Figure 2 ). To determine the phylogenetic relationships of the newly identified insect viruses, maximum likelihood (ML) phylogenetic trees were constructed based on the amino acid alignments of ORF2a (unprocessed S protein) and a concatenated region of the highly conserved domains within ORF1ab (3CL pro , RdRp and ZnHel1). A Clustal X alignment of the mesonivirus ORF3a proteins and individual structural analyses using SignalP and TMHMM and NetNGlyc (www.expasy.org) indicated that each is a class I transmembrane glycoprotein with a predicted N-termimal signal peptide, an ectodomain containing a conserved set of 6 cysteine residues and a single conserved N-glycosylation site, a transmembrane domain and a C-terminal cytoplasmic domain ( Figure 4A, 4D) . cache = ./cache/cord-339209-oe8onyr9.txt txt = ./txt/cord-339209-oe8onyr9.txt === reduce.pl bib === id = cord-339172-210dwhgj author = Knoops, Kèvin title = SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date = 2008-09-16 pages = extension = .txt mime = text/plain words = 9930 sentences = 411 flesch = 43 summary = Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''inner vesicles,'' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. cache = ./cache/cord-339172-210dwhgj.txt txt = ./txt/cord-339172-210dwhgj.txt === reduce.pl bib === id = cord-340046-kgbvld0y author = Houspie, Lieselot title = Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date = 2011-03-04 pages = extension = .txt mime = text/plain words = 4081 sentences = 219 flesch = 53 summary = BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms (defined in Table 1 ), using a commercially available condenser (RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA). Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. cache = ./cache/cord-340046-kgbvld0y.txt txt = ./txt/cord-340046-kgbvld0y.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-340489-yo3cp5vs author = nan title = KAPITEL 13 Infektionskrankheiten date = 2008-12-31 pages = extension = .txt mime = text/plain words = 26536 sentences = 3917 flesch = 45 summary = Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. cache = ./cache/cord-340489-yo3cp5vs.txt txt = ./txt/cord-340489-yo3cp5vs.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-341034-2oigu75k author = Moser, Theresa S. title = AMP-Activated Kinase Restricts Rift Valley Fever Virus Infection by Inhibiting Fatty Acid Synthesis date = 2012-04-19 pages = extension = .txt mime = text/plain words = 9932 sentences = 511 flesch = 45 summary = We found that the energy regulator AMPK, which potently inhibits fatty acid synthesis, restricts infection of the Bunyavirus, Rift Valley Fever Virus (RVFV), an important re-emerging arthropod-borne human pathogen for which there are no effective vaccines or therapeutics. Furthermore, we found that AMPK is activated during RVFV infection, leading to the phosphorylation and inhibition of acetyl-CoA carboxylase, the first rate-limiting enzyme in fatty acid synthesis. Consistent with a role for AMPK both in early events during viral replication and in spread as measured by plaque assay Figure 1A ), we observed an increase in viral infection at early time points before virus spread, as well as increased spread in cells lacking AMPK by monitoring the production of RVFV N protein over time by microscopy ( Figure S1A-B) . We have found that energy-mediated activation of AMPK restricts infection of the Bunyavirus Rift Valley fever virus by decreasing levels of fatty acid synthesis. cache = ./cache/cord-341034-2oigu75k.txt txt = ./txt/cord-341034-2oigu75k.txt === reduce.pl bib === id = cord-341541-3l6tjf3t author = Hajijafari Anaraki, Mozafar title = Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene date = 2020-05-26 pages = extension = .txt mime = text/plain words = 1276 sentences = 87 flesch = 49 summary = title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene Extensive rate of variations in in spike glycoprotein subunit gene of infectious bronchitis virus (IBV) caused challenges for counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. The study aimed at investigating the possibility use of RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area. Using RdRp, as a genetic marker eliminates the challenges arise from the enormous variations that making difficult the discrimination between field and vaccine strains as well as affiliation of certain variants to various geographical areas. Based on the RT-PCR detection and sequence analysis of IBV RdRp gene, an overall prevalence of field strains estimated as 44.2%. cache = ./cache/cord-341541-3l6tjf3t.txt txt = ./txt/cord-341541-3l6tjf3t.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-340475-h0q1m3ed author = Carnero, Elena title = Type I Interferon Regulates the Expression of Long Non-Coding RNAs date = 2014-11-06 pages = extension = .txt mime = text/plain words = 10164 sentences = 544 flesch = 55 summary = Further validation showed that ISR2, 8, and 12 expression mimics that of their neighboring genes GBP1, IRF1, and IL6, respectively, all related to the IFN response.These genes are induced in response to different doses of IFNα2 in different cell lines at early (ISR2 or 8) or later (ISR12) time points. HuH7 cells were treated for 6, 24, 48, or 72 h with increasing doses of IFNα2 up to 10,000 units/ml, and the expression levels of GBP1, IRF1, BST2, OAS, IL6, and ISG15 were evaluated by qRT-PCR (Figure 1) . cache = ./cache/cord-340475-h0q1m3ed.txt txt = ./txt/cord-340475-h0q1m3ed.txt === reduce.pl bib === id = cord-341324-f9g9gitn author = Rojas, José M. title = Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date = 2020-10-21 pages = extension = .txt mime = text/plain words = 10837 sentences = 595 flesch = 42 summary = This includes for instance cooperating in PRR recognition of viral PAMPs, stabilizing signaling complexes to improve their resistance to degradation, stopping virus entry, blocking viral capsid formation, impairing trafficking and budding of virions from the infected cells, but also modulating the IFN response to avoid the toxicity of these potent immune mediators. The phosphorylated STAT1/STAT2 heterodimer associates with interferon regulatory factor 9 (IRF9) to form the transcriptional factor complex ISGF3, which translocate to the nucleus and binds the IFN-response elements (ISRE) in ISG promoters leading to the expression of ISG products [36] (Fig. 2 The oligoadenylate synthetase (OAS)-latent RNase (RNase L) pathway is another IFN-inducible pathway that provides the cell with an effector mechanism upon recognition of viral dsRNA (reviewed in [44] ). cache = ./cache/cord-341324-f9g9gitn.txt txt = ./txt/cord-341324-f9g9gitn.txt === reduce.pl bib === id = cord-341342-kyavg4vu author = Masters, P. S. title = Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date = 1992 pages = extension = .txt mime = text/plain words = 5901 sentences = 279 flesch = 57 summary = The RNase sensitivity of the ability of N protein to migrate into nondenaturing gels was not due to possible contaminating protease activity in the RNase preparations, since the same RNase-treated samples of translated N 148 P.S. Masters protein showed no degradation when analyzed by SDS-PAGE (Fig. 3, lanes an, lower) . Since the N mRNAs synthesized from the transcription vectors shown in Fig. 1 contained this portion of the leader sequence, it seemed possible that the N-RNA complex observed in nondenaturing PAGE was that of translated N protein binding to its own mRNA. That the observed complex was not due to translated N protein binding to the leader portion of its own mRNA was also supported by the observation that full-length N protein translated from a construct in which the MHV leader sequence was entirely deleted was also able to migrate into nondenaturing gels (data not shown). cache = ./cache/cord-341342-kyavg4vu.txt txt = ./txt/cord-341342-kyavg4vu.txt === reduce.pl bib === === reduce.pl bib === id = cord-340422-8f5xe4zc author = Rowland, R. R. R. title = Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine date = 2001 pages = extension = .txt mime = text/plain words = 4715 sentences = 283 flesch = 50 summary = Porcine reproductive and respiratory syndrome virus (PRRSV) belongs to a group of RNA viruses that establish persistent infections. IFN-γ mRNA expression was observed in the lymph nodes and lungs of pigs infected with wild-type PRRSV strain SDSU-23983. The purpose of this study was to evaluate the production of IFN-␥ in pigs following infection with PRRSV and to characterize the mechanism of IFN-␥ action following infection of MARC-145 cells with wild-type and culture adapted PRRSV isolates. The results show that IFN-␥ efficiently inhibits PRRSV replication in MARC-145 cells, and at least part of the antiviral activity may be through PKR. IFN-␥ mRNA expression was detected in the lymph nodes from two of the 3 pigs infected with the wild-type P6 virus (Fig. 1) . Consistent with other reports describing the presence of cell-mediated immunity during PRRSV infection [4, 31] , we observed IFN-␥ mRNA expression in lymph nodes and lungs of PRRSV-infected pigs (Fig. 1) . IFN gamma inhibits porcine reproductive and respiratory syndrome virus replication in macrophages cache = ./cache/cord-340422-8f5xe4zc.txt txt = ./txt/cord-340422-8f5xe4zc.txt === reduce.pl bib === id = cord-341502-jlzufa28 author = Lee, Sungyul title = The SARS-CoV-2 RNA interactome date = 2020-11-02 pages = extension = .txt mime = text/plain words = 5845 sentences = 362 flesch = 51 summary = The second pool of 275 oligos ("Probe II") covers the remaining region (21563:29872, NC_045512.2) which is shared by both the gRNA and sgRNAs. To first check whether our method specifically captures the viral RNP complexes, we compared the resulting purification from Vero cells infected with SARS-CoV-2 (BetaCoV/Korea/KCDC03/2020) at MOI 0.1 for 24 hours (Kim et al., 2020b ) by either Probe I or Probe II. In combination, we define these 109 proteins as the "SARS-CoV-2 RNA interactome." 37 host proteins such as CSDE1 (Unr), EIF4H, FUBP3, G3BP2, PABPC1, ZC3HAV1 were enriched in both the Probe I and Probe II RNP capture experiments on infected cells ( Figure 1F ), thus identifying a robust set of the "core SARS-CoV-2 RNA interactome." Gene ontology (GO) term enrichment analysis revealed that these host factors are involved in RNA stability control, mRNA function, and viral process ( Figure S1F ). To measure the impact of these host proteins on coronavirus RNAs, we conducted knockdown experiments and infected Calu-3 cells with SARS-CoV-2 ( Figure 5A and 5B). cache = ./cache/cord-341502-jlzufa28.txt txt = ./txt/cord-341502-jlzufa28.txt === reduce.pl bib === id = cord-342117-r2chpw7y author = Wu, Xinwei title = Inhibitory effect of small interfering RNA on dengue virus replication in mosquito cells date = 2010-10-14 pages = extension = .txt mime = text/plain words = 2928 sentences = 191 flesch = 59 summary = The antiviral effect of siRNA was evaluated by measurement of cell survival rate using the MTT method and viral RNA was quantitated with real-time RT-PCR. CONCLUSIONS: Our data showed that synthetic siRNA against the DEN-1 membrane glycoprotein precursor gene effectively inhibited DEN-1 viral RNA replication and increased C6/36 cell survival rate. Therefore, in this study, we designed and synthesized 21 nt siRNAs against the DEN-I viral PrM gene, and investigated their inhibition effects of dengue virus replication in transfected C6/36 cells. These data indicate that siRNA against DEN viral genome can effectively inhibit viral RNA replication in the C6/36 cells, protect host cell from viral attack, suggesting its potential role in prevention and treatment of dengue fever. Our data showed that synthetic siRNA against the DEN membrane glycoprotein precursor gene effectively inhibited DEN viral RNA replication and increased C6/36 cell survival rate. Inhibition of viral gene expression and replication in mosquito cells by dsRNA-triggered RNA interference cache = ./cache/cord-342117-r2chpw7y.txt txt = ./txt/cord-342117-r2chpw7y.txt === reduce.pl bib === id = cord-342189-ya05m58o author = Banerjee, Abhik K. title = SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date = 2020-10-08 pages = extension = .txt mime = text/plain words = 11469 sentences = 647 flesch = 55 summary = Here, we comprehensively define the interactions between each SARS-CoV-2 protein and human RNAs. We show that 10 viral proteins form highly specific interactions with mRNAs or ncRNAs, including those involved in progressive steps of host cell protein production. We show J o u r n a l P r e -p r o o f 5 that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We identified several pathogenic functions of SARS-CoV-2 in human cells -including global inhibition of host mRNA splicing, protein translation, and membrane protein trafficking -and described the molecular mechanisms by which the virus acts to disrupt these essential cell processes. cache = ./cache/cord-342189-ya05m58o.txt txt = ./txt/cord-342189-ya05m58o.txt === reduce.pl bib === id = cord-342456-5gp3cry0 author = Hoagland, Daisy A. title = Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date = 2020-07-13 pages = extension = .txt mime = text/plain words = 4511 sentences = 240 flesch = 48 summary = Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. These signatures were then used as queries against the LINCS L1000 dataset, a collection of gene expression profiles generated following the administration of >20,000 bioactive compounds including >1,000 FDA-approved drugs to human cell lines at a variety of different times and concentrations (Subramanian et al., 2017) With L1000FWD , we could identify reciprocal transcriptional signatures generated between SARS-CoV-2 infection and a given compound. Overall, based on the L1000 data, these seven compounds influence the same pharmacological high-dimensional gene expression signature space and are predicted to disrupt key cellular processes that are modulated in response to SARS-CoV-2 infection. cache = ./cache/cord-342456-5gp3cry0.txt txt = ./txt/cord-342456-5gp3cry0.txt === reduce.pl bib === id = cord-341804-rnj3wtg4 author = Jin, Zhe title = Drug treatment of coronavirus disease 2019 (COVID-19) in China. date = 2020-06-27 pages = extension = .txt mime = text/plain words = 2048 sentences = 136 flesch = 43 summary = This article reviewed the clinical use, mechanism and efficacy of the clinically approved drugs recommended in the Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (DTPNCP) released by National Health Commission of P.R.China, and the novel therapeutic agents now undergoing clinical trials approved by China National Medical Products Administration (NMPA) to evaluate experimental treatment for COVID-19. However, more evidence is needed either for 4 supporting or opposing the systemic therapeutic administration of glucocorticoids in 5 patients with SARS-CoV-2 infection (Qin et al., 2020 a variety of immune cells 20 and improves the immunity, while IFN-β takes effect by inhibiting the adsorption of certain 1 viruses, enhancing phagocytosis of natural killer cells and mononuclear macrophages Tocilizumab is a recombinant humanized anti-IL-6 receptor (IL-6R) monoclonal antibody, 21 13 which can specifically bind to soluble and membrane-bound IL-6 receptors and inhibit 1 signal transduction mediated by IL-6, thereby reducing inflammation and blocking cytokine 2 storm caused by COVID-19 (Scheinecker et al., 2009) . cache = ./cache/cord-341804-rnj3wtg4.txt txt = ./txt/cord-341804-rnj3wtg4.txt === reduce.pl bib === id = cord-342344-jjnf4yje author = Mello, C. J. title = Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3122 sentences = 190 flesch = 55 summary = Diagnostic assays for the presence of SARS-CoV-2 currently use real-time reverse transcriptase PCR (RT-qPCR) to yield a binary (positive or negative) result based on an amplification cycle threshold (Ct) value 9-12 . Current PCR-based assays can detect the presence of very short SARS-CoV-2 RNA sequences but do not distinguish whether these sequences are derived from longer molecules present in the sample at the time of collection. To address these issues, we explored using droplet digital PCR (ddPCR) 19, 20 to more precisely quantify SARS-CoV-2 RNA in biological samples and evaluate the extent to which positive results reflect larger, intact viral nucleic acids. The results yielded definitive evidence of linkage: although only 822 of the 12,220 droplets (6.7%) were positive for either N1 or N2, 75% of the droplets that were positive for N2 (HEX) were also positive for N1 (FAM) (Fig. 2a, Table 1 ); we estimate (using a formula we previously described 21 , which accounts for chance co-encapsulation) that 71% of the detected RNA sequences were physically linked. cache = ./cache/cord-342344-jjnf4yje.txt txt = ./txt/cord-342344-jjnf4yje.txt === reduce.pl bib === id = cord-342412-azkamnpa author = Ecker, David J title = The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date = 2005-04-25 pages = extension = .txt mime = text/plain words = 7206 sentences = 409 flesch = 42 summary = This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. For example, the Centers for Disease Control and Prevention (CDC) maintains an ever-changing list of notifiable diseases, the National Institute of Allergy and Infectious Disease (NIAID) lists agents with potential for use in bioterrorist attacks, and the Department of Health and Human Services (HHS) maintains a list of critical human pathogens. This article focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. It provides a compilation of lists, taken from the database, of important and/or regulated biological agents from a number of agencies including HHS, the United States Department of Agriculture (USDA), the CDC, the World Health Organization (WHO), the NIAID, and other sources. cache = ./cache/cord-342412-azkamnpa.txt txt = ./txt/cord-342412-azkamnpa.txt === reduce.pl bib === id = cord-343470-w215pzdc author = Tsai, Kevin title = Epigenetic and epitranscriptomic regulation of viral replication date = 2020-06-12 pages = extension = .txt mime = text/plain words = 9761 sentences = 452 flesch = 41 summary = Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. First, the viral protein VP16, which is packaged into the tegument layer of incoming virions, recruits host proteins, including host-cell factor 1 (HCF-1) and octamer-binding factor (Oct-1), in order to form a complex that recruits the histone demethylases lysine-specific demethylase 1 (LSD1) and Jumonji domain 2 (JMJD2) family members as a means to remove repressive H3K9 marks from viral immediate early promoters 42 Upon entry into the cell nucleus, the DNA of many viruses initiates the replication process adjacent to subnuclear structures called pro-myelocytic leukaemia nuclear bodies (PML-NBs). cache = ./cache/cord-343470-w215pzdc.txt txt = ./txt/cord-343470-w215pzdc.txt === reduce.pl bib === id = cord-342676-ykog278j author = Stewart, H. title = Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging date = 2016-03-14 pages = extension = .txt mime = text/plain words = 6858 sentences = 338 flesch = 46 summary = To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We wished to investigate the possibility that similar specific secondary structures are present within HCV RNAs destined for packaging, and whether their interactions with Core cooperatively drive the RNA encapsidation and nucleocapsid assembly processes. A mutant genome unable to form such structures displays impaired viral infectivity whilst RNA replication is unaffected, indicating these motifs may interact specifically with Core. Role of RNA structures in genome terminal sequences of the hepatitis C virus for replication and assembly cache = ./cache/cord-342676-ykog278j.txt txt = ./txt/cord-342676-ykog278j.txt === reduce.pl bib === id = cord-342145-cq6xe5r7 author = Dao Thi, Viet Loan title = A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date = 2020-08-12 pages = extension = .txt mime = text/plain words = 9311 sentences = 507 flesch = 58 summary = The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital's diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ). cache = ./cache/cord-342145-cq6xe5r7.txt txt = ./txt/cord-342145-cq6xe5r7.txt === reduce.pl bib === id = cord-342649-ysossker author = Scagnolari, Carolina title = Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus date = 2012-03-10 pages = extension = .txt mime = text/plain words = 3759 sentences = 161 flesch = 42 summary = The relationship between viral load, disease severity and antiviral immune activation in infants suffering from respiratory syncytial virus (RSV)-associated bronchiolitis has not been well identified. The main objective of this study was to determine the existence of a correlation between RSV load and disease severity and also between different clinical markers and mRNA levels of the interferon stimulated gene (ISG)56 in infants hospitalized for bronchiolitis. Results indicated that viral load was positively related to the clinical severity of bronchiolitis, the length of hospital stay, the levels of glycemia and the relative gene expression of ISG56, whereas an inverse correlation was observed with the levels of hemoglobin. In the framework of a study aimed at understanding the pathogenesis of RSV infection and at further characterizing viral and host factors involved in determining the severity of bronchiolitis, we addressed whether any diVerences in RSV-RNA levels in the airway tracts of infants with bronchiolitis might explain the broad clinical spectrum of RSVassociated bronchiolitis. cache = ./cache/cord-342649-ysossker.txt txt = ./txt/cord-342649-ysossker.txt === reduce.pl bib === id = cord-343448-xhm97wy2 author = Rinaldi, Andrea title = RNA to the rescue: RNA is one of the most promising targets for drug development given its wide variety of uses date = 2020-06-26 pages = extension = .txt mime = text/plain words = 2934 sentences = 167 flesch = 49 summary = In brief, RNAi works through gene silencing, degrading the mRNA for a specific protein through the coordinated action of double-stranded RNA and a complex biochemical machinery it activates (Fig 1) . The spearhead is mRNA-1273, which encodes a prefusion-stabilized form of the spike (S) protein of SARS-CoV-2, developed at an unusually fast rate (first volunteer injected on Mach 16, only 65 days after the publication of the virus sequence) by Moderna, a biotech based in Cambridge, Massachusetts (https://www.modernatx.c om/). Multi-component proteins that would be impossible to target with other systems are accessible with RNA technology, as recently demonstrated by the generation of a multi-antigenic mRNA vaccine encoding human cytomegalovirus glycoproteins gB and pentameric complex (John et al, 2018) . CV9202, for example, is a mRNA encoding six antigens usually expressed in non-small-cell lung cancer (NSCLC), developed by CureVac, a biotech based in Tübingen, Germany (https://www.curevac.com/), in collaboration with Boehringer Ingelheim. cache = ./cache/cord-343448-xhm97wy2.txt txt = ./txt/cord-343448-xhm97wy2.txt === reduce.pl bib === id = cord-342681-pqzcy9wu author = Pongpirul, Wannarat A. title = Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date = 2020-07-17 pages = extension = .txt mime = text/plain words = 1740 sentences = 117 flesch = 41 summary = Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. During the study period, Thailand's discharge criteria for hospitalized COV-ID-19 patients required resolution of clinical signs and symptoms and 2 respiratory specimens without detectable SARS-CoV-2 RNA collected >24 hours apart. Clinical resolution occurred a median of 12 (9-13.5 ) days after illness onset, and these patients had detectable SARS-CoV-2 RNA in upper respiratory tract specimens for a median of 14 (9-26) days after illness onset (Table 2) . However, patients became afebrile 6 days after illness onset, with a median of 9 (3-19.75 ) additional days of detectable SARS-CoV-2 RNA in respiratory specimens after resolution of fever ( Table 2 ). Other studies have described asymptomatic patients with upper respiratory specimens positive for SARS-CoV-2 (9), and evidence suggests such cases pose a risk for transmission (10) (11) (12) . cache = ./cache/cord-342681-pqzcy9wu.txt txt = ./txt/cord-342681-pqzcy9wu.txt === reduce.pl bib === id = cord-343963-99rd3o79 author = Wong, Mun-Teng title = Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date = 2014-12-29 pages = extension = .txt mime = text/plain words = 17253 sentences = 1074 flesch = 42 summary = 13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production. cache = ./cache/cord-343963-99rd3o79.txt txt = ./txt/cord-343963-99rd3o79.txt === reduce.pl bib === id = cord-342902-y1v8wzxq author = Yuan, Shuofeng title = Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date = 2020-10-07 pages = extension = .txt mime = text/plain words = 5692 sentences = 291 flesch = 45 summary = Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. We found that co-application of clofazimine and remdesivir impacts SARS-CoV-2 replication in a manner that extends beyond the additive combinatorial activity predicted by the Bliss independence model (maximal Bliss Synergy Score of 44.28; Figure 5a , Extended Data Figure 2) , and indicates these two drugs harbor a synergistic antiviral relationship. cache = ./cache/cord-342902-y1v8wzxq.txt txt = ./txt/cord-342902-y1v8wzxq.txt === reduce.pl bib === id = cord-343350-04e6wvov author = Liu, Haipeng title = Antiviral immunity in crustaceans date = 2009-02-15 pages = extension = .txt mime = text/plain words = 8002 sentences = 441 flesch = 43 summary = White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis Preliminary study on haemocyte response to white spot syndrome virus infection in black tiger shrimp Penaeus monodon Time-course and levels of apoptosis in various tissues of black tiger shrimp Penaeus monodon infected with white-spot syndrome virus Protein expression profiling of the shrimp cellular response to white spot syndrome virus infection Cloning and characterization of a caspase gene from black tiger shrimp (Penaeus monodon)-infected with white spot syndrome virus (WSSV) Immunological responses of Penaeus monodon to DNA vaccine and its efficacy to protect shrimp against white spot syndrome virus (WSSV) Multiple envelope proteins are involved in white spot syndrome virus (WSSV) infection in crayfish Identification of white spot syndrome virus (WSSV) envelope proteins involved in shrimp infection DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV) cache = ./cache/cord-343350-04e6wvov.txt txt = ./txt/cord-343350-04e6wvov.txt === reduce.pl bib === id = cord-342901-ca2xxkb2 author = Lloyd, Richard E. title = Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses date = 2015-05-31 pages = extension = .txt mime = text/plain words = 16221 sentences = 823 flesch = 50 summary = Though PTB was the first, a wide spectrum of factors, largely nuclear RBPs, have also been proposed as poliovirus ITAFs, including Lupus autoantigen (La) (Meerovitch et al., 1993 (Meerovitch et al., , 1989 , poly(rC)binding proteins (PCBPs) (Blyn et al., 1996; Gamarnik and Andino, 1997) , upstream of N-ras (UNR) (Anderson et al., 2007; Boussadia et al., 2003; Hunt et al., 1999) , SRp20 (Bedard et al., 2007) and glycyl-tRNA synthetase (GARS) (Andreev et al., 2012) (Table 1 ). In addition, certain ITAFs play crucial roles in regulating the conversion of translation-competent genomic RNAs into replicationcompetent RNAs. PTB was known as a nuclear splicing factor when its role as an ITAF of poliovirus and EMCV was discovered; a classic hijacked nuclear protein pressed into a new role required for the virus. cache = ./cache/cord-342901-ca2xxkb2.txt txt = ./txt/cord-342901-ca2xxkb2.txt === reduce.pl bib === id = cord-344714-0cam9ipf author = Russo, Maria title = Roles of flavonoids against coronavirus infection date = 2020-07-28 pages = extension = .txt mime = text/plain words = 8395 sentences = 394 flesch = 46 summary = Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL(pro), 3CL(pro), NTPase/helicase. Inhibition of TMPRSS2 and Furin protease activities can be considered an interesting therapeutic option against coronavirus infection, especially COVID-19, allowing the block and/or prevention of SARS-CoV-2 infection, as recently reported [28] . Based on these observations, it is not surprising that molecular docking approach, summarized in Fig. 3 , supports the role of flavonoids in the inhibition of SARS-CoV 3CL pro by binding His41 and Cys145 of the catalytic site and other active site residues (e.g., Met49, Gly143, His163, His164, Glu166, Pro168, and Gln89), stimulating their validation by in vitro and in vivo studies. cache = ./cache/cord-344714-0cam9ipf.txt txt = ./txt/cord-344714-0cam9ipf.txt === reduce.pl bib === id = cord-343221-e29of29o author = Kindler, Eveline title = Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication date = 2017-02-03 pages = extension = .txt mime = text/plain words = 7896 sentences = 423 flesch = 51 summary = Specifically, we show that genetically engineered mutants of mouse hepatitis virus (MHV) and human coronavirus 229E (HCoV-229E), respectively, that encode an EndoU active-site substitution known to abolish nucleolytic activity, were severely attenuated and elicited an immediate and simultaneous activation of host cell dsRNA sensors. The severe attenuation of MHV H277A and HCoV-229E H250A replication in wild-type murine and human macrophages, respectively, precluded the use of primary macrophages to assess the sensitivity of EndoU-deficient coronaviruses to IFN-I pre-treatment. Our data suggest that direct restriction of replication of EndoU-deficient coronaviruses is mediated by RNase L-mediated RNA degradation and inhibition of host cell translation through activation of PKR. Notably, also in this case Xrn1 is required to further process the de-capped mRNAs. Our data show that early during coronavirus infection the EndoU activity conceptually fulfils the same task, namely the removal of dsRNA that would otherwise trigger host cell dsRNA responses, such as IFN-β expression and activation of PKR and OAS/RNase L. cache = ./cache/cord-343221-e29of29o.txt txt = ./txt/cord-343221-e29of29o.txt === reduce.pl bib === id = cord-342653-bpyc2gbl author = Wang, Hai-Tao title = Substrate recognition by TRIM and TRIM-like proteins in innate immunity date = 2020-10-20 pages = extension = .txt mime = text/plain words = 8560 sentences = 478 flesch = 49 summary = While E3 ligases are often thought to negatively regulate the stability of the target molecule by Ub-mediated proteasomal targeting, many TRIMs have been shown to enhance innate immune signaling pathways [15] , through both proteasome-dependent and -independent mechanisms. The study of RIG-I and RIPLET interaction provides a detailed example of how TRIM-like proteins utilize bivalency and CC for regulating substrate selectivity, higher-order oligomerization and innate immune function. Given that an increasing number of receptors and signaling molecules in the innate immune system are shown to multimerize upon activation [77] , it is tempting to speculate that TRIM/TRIM-like proteins may utilize multimer-specific substrate recognition as a common mechanism for regulating their immune functions. The avidity-driven substrate recognition mechanism of TRIM/TRIM-like proteins would thus ensure more precise control of innate immune signaling and restriction functions. cache = ./cache/cord-342653-bpyc2gbl.txt txt = ./txt/cord-342653-bpyc2gbl.txt === reduce.pl bib === id = cord-344006-0iq9s94n author = Atzrodt, Cassandra L. title = A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date = 2020-05-23 pages = extension = .txt mime = text/plain words = 7283 sentences = 428 flesch = 54 summary = All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . cache = ./cache/cord-344006-0iq9s94n.txt txt = ./txt/cord-344006-0iq9s94n.txt === reduce.pl bib === id = cord-343632-cv3qgno3 author = Zhang, Yinhua title = Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP date = 2020-02-29 pages = extension = .txt mime = text/plain words = 2344 sentences = 143 flesch = 49 summary = Here we report a method to identify SARS-CoV-2 (COVID-19) virus RNA from purified RNA or cell lysis using loop-mediated isothermal amplification (LAMP) using a visual, colorimetric detection. Here we describe a molecular diagnostic approach for SARS-CoV-2 RNA detection using loop-mediated isothermal amplification (LAMP) and simple visual detection of amplification for potential use in rapid, field applications. This study describes testing and validation of 5 sets LAMP primers targeting two fragments of the SARS-CoV-2 genome using short (~300bp) RNA fragments made with in vitro transcription and RNA samples from patients. https://doi.org/10.1101/2020.02.26.20028373 doi: medRxiv preprint With current diagnostic methods, e.g. RT-qPCR, purified RNA is used in the input. Although a small number of samples were tested here, the colorimetric LAMP assay enables reliable SARS-CoV-2 detection without sophisticated instrumentation, matching the RT-qPCR performance in field and point-of-care settings. /2020 In conclusion, colorimetric LAMP provides a simple, rapid method for SARS-CoV-2 RNA detection. cache = ./cache/cord-343632-cv3qgno3.txt txt = ./txt/cord-343632-cv3qgno3.txt === reduce.pl bib === id = cord-344464-if6js43s author = Cowley, J. A. title = The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date = 2002 pages = extension = .txt mime = text/plain words = 3523 sentences = 183 flesch = 54 summary = title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report We report here a 5596 nt sequence comprising the 3′-end of the (+) ssRNA genome of gill-associated virus (GAV), an invertebrate nidovirus of Penaeus monodon prawns. The sequence extends from a subgenomic RNA start site 35 nt upstream of the 4923 nt ORF3 gene to a 3′-poly(A) tail of the 26235 nt genome of GAV. Completion of the genome sequence of GAV has revealed a gene organisation unique among nidoviruses in there is no discrete membrane protein gene and that the putative ORF3 spike glycoprotein gene resides downstream of a gene (ORF2) encoding a structural protein associated with nucleocapsids. A contig of a 5596 nt sequence from the GAV genomic 3 -poly(A) tail to an intergenic 5 -sgRNA start site 35 nt upstream of the ORF3 start codon [10] was deduced from overlapping cDNA clones (Figs. cache = ./cache/cord-344464-if6js43s.txt txt = ./txt/cord-344464-if6js43s.txt === reduce.pl bib === id = cord-344410-yo9libo0 author = Zhou, Yan title = Mutational analysis of the SDD sequence motif of a PRRSV RNA-dependent RNA polymerase date = 2011-09-16 pages = extension = .txt mime = text/plain words = 5856 sentences = 295 flesch = 57 summary = A core palm structure containing the four motifs (A-D) found in all classes of polymerases [1] is present in the C-terminal region of nsp9; therefore, it is possible to identify RdRp catalytic activity by testing whether the conserved SDD motif (at residues 3050 to 3052 of nsp9) itself is essential for virus replication (Figure 1) . To study the impact of mutations in the SDD motif on PRRSV transcription, RT-PCR analysis of the sg mRNA7s was performed on the total RNAs obtained from mock-transfected BHK-21 cells and cells transfected with pMDD, pSAD, pSED, pSND, pSGD, pSDA, pSDE, pSDN, pSGA, pGND, pGDD, and pAPRRS, using a forward primer located in the leader region and a reverse primer in ORF7. The mutant PRRSV full-length cDNA clones pMDD, pSAD, pSED, pSND, pSGD, pSDA, pSDE, pSDN, pGDN, and pSGA carrying mutations specifying the SDD motif in the viral replicase (Table 1) , were transfected into BHK-21 cells and failed to produce sg mRNA7s (Figure 2) . cache = ./cache/cord-344410-yo9libo0.txt txt = ./txt/cord-344410-yo9libo0.txt === reduce.pl bib === id = cord-342756-rgm9ffpk author = Senger, Mario Roberto title = COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date = 2020-10-02 pages = extension = .txt mime = text/plain words = 16108 sentences = 1024 flesch = 51 summary = Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. In the following topic, we will review SARS-CoV-2 structure and mechanism of infection in order to discuss molecular targets from the virus or its human host that are being considered for drug repurposing and perhaps future development of new drugs. (128) Its role as a functional receptor of SARS-CoV-2 S protein in host cells makes this protein a potential drug target to treat COVID-19. (138) TMPRSS2 has a major role in SARS-CoV-2 cell entry and replication, and thus represents an interesting therapeutic target since its inhibitors could potentially block virus infection in its initial stages. (199) A robust preclinical drug discovery pipeline comprising in vitro, and in vivo models of SARS-CoV-2 infection is particularly important to identify new antivirals for human COVID-19 treatment. cache = ./cache/cord-342756-rgm9ffpk.txt txt = ./txt/cord-342756-rgm9ffpk.txt === reduce.pl bib === id = cord-343604-v986m9jd author = Vijayakumar, Balaji Gowrivel title = In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date = 2020-08-06 pages = extension = .txt mime = text/plain words = 1258 sentences = 90 flesch = 47 summary = title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential. Coronavirus main 403 proteinase (3CLpro) structure: basis for design of anti-SARS drugs Structural basis for inhibition 675 of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir cache = ./cache/cord-343604-v986m9jd.txt txt = ./txt/cord-343604-v986m9jd.txt === reduce.pl bib === id = cord-341513-e6p3lrlf author = Li, Yunchuan title = Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection date = 2017-09-29 pages = extension = .txt mime = text/plain words = 6136 sentences = 341 flesch = 47 summary = title: Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection To determine the role of lncRNAs in inflammatory cytokine production, the cells were transfected with siE52329, siN54010 or non-specific control siRNA, and then infected with JEV. To examine the role of lncRNA E52329 and N54010 in regulating the kinase activity of MKK4/JNK pathway, BV2 cells were transfected with siE52329, siN54010 or non-specific control siRNA, and then infected with JEV. The results of our study reveal the first experimental evidence demonstrating the complex regulation of lncRNAs by JEV infection in mice brain and microglial cells. Third, the integration of microarray platform, quantitative real-time PCR, GO analysis, pathways analysis, and lncRNA-mRNA coexpression network analysis has allowed us to conduct an active comparative genomics and bioinformatics study to reveal host lncRNAs expression patterns associated with JEV infection. cache = ./cache/cord-341513-e6p3lrlf.txt txt = ./txt/cord-341513-e6p3lrlf.txt === reduce.pl bib === id = cord-344749-omzhhr0k author = Kaya, Sariye Irem title = Electrochemical virus detections with nanobiosensors date = 2020-02-14 pages = extension = .txt mime = text/plain words = 8402 sentences = 508 flesch = 37 summary = Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen cache = ./cache/cord-344749-omzhhr0k.txt txt = ./txt/cord-344749-omzhhr0k.txt === reduce.pl bib === id = cord-344782-ond1ziu5 author = Zhang, Jing title = Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date = 2018-10-24 pages = extension = .txt mime = text/plain words = 6003 sentences = 280 flesch = 49 summary = Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. cache = ./cache/cord-344782-ond1ziu5.txt txt = ./txt/cord-344782-ond1ziu5.txt === reduce.pl bib === id = cord-344636-go5cw92q author = Huang, Wei E. title = RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date = 2020-04-25 pages = extension = .txt mime = text/plain words = 4771 sentences = 253 flesch = 61 summary = In this work, we developed a COVID-19 diagnosis kit for the rapid detection of SARS-CoV-2, using one-step reverse transcription and loop-mediated isothermal amplification (RT-LAMP). Positive amplification products were obtained even for 2 copies of the synthetic viral DNA fragment template in 30 min when using the S17 primers (lane 4 in Fig. 1D ), demonstrating that the LAMP reaction was rapid and sensitive. To assess the potential of RT-LAMP in detecting RNA virus of SARS-CoV-2, we then tested the performance of these primers with synthesized RNA fragments of the N gene, S gene and Orf1ab gene obtained from in vitro transcription (Appendix S1). The ultimate aim is to develop an enclosed device that integrates RNA extraction, purification, reverse transcription (RT) and loop-mediated isothermal amplification (LAMP) to detect the SARS-CoV-2 virus directly from a throat swab sample. cache = ./cache/cord-344636-go5cw92q.txt txt = ./txt/cord-344636-go5cw92q.txt === reduce.pl bib === id = cord-342800-62jklwiy author = Xu, Shuqin title = mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection date = 2020-09-09 pages = extension = .txt mime = text/plain words = 13579 sentences = 706 flesch = 43 summary = The RNActive ® vaccine platform designed by CureVac used co-delivered RNA and protamine complex as the adjuvant to induce Th1 T cell responses, and naked, unmodified, and sequence-optimized mRNA as the antigen to develop mRNA vaccines [54] . used LNP to deliver self-amplified RNA vaccines, which caused the mRNA expression level in mice to be significantly higher than that of naked mRNA, CD4 + , and CD8 + T cell immune responses were also effectively induced. Overall development steps of those vaccines are (1) constructing the core antigen-encoding mRNA sequence optimized or combined based on selected antigen(s) from the target pathogen; (2) trying and choosing a proper combination of mRNA construction type, adjuvants, carrier materials and the route of administration; (3) detecting in vivo expression of the encoded antigen and the level of elicited immune responses; (4) providing research and demonstrations of immune induction mechanisms. cache = ./cache/cord-342800-62jklwiy.txt txt = ./txt/cord-342800-62jklwiy.txt === reduce.pl bib === id = cord-345647-h3imwhss author = Gao, Wen-Hua title = Newly identified viral genomes in pangolins with fatal disease date = 2020-04-12 pages = extension = .txt mime = text/plain words = 5018 sentences = 287 flesch = 53 summary = To identify the possible etiologic agents of disease in the four pangolins, eight meta-transcriptomic libraries from blood, liver, spleen, lung, kidney, and fecal samples were constructed, generating a total of 306,908,179 paired-end sequence reads. De novo assembly revealed the high abundance of a pestivirusand coltivirus-like virus in all the meta-transcriptomic libraries of the pangolin 1-Dongyang and 2-Lishui, representing 6-80 and 1-29 per cent of total viral contigs, respectively (Supplementary Table S2 ). Considering that they are related, yet clearly genetically distinct, from known members of Pestivirus and Coltivirus (see below), we designated these two newly identified viruses as Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV), respectively, reflecting their hosts species and the geographic location of sampling. Consequently, DYPV was identified in the heart, liver, spleen, lung, kidney, brain, blood, throat swab, and fecal sampled from pangolin 1-Dongyang, as well as the nymph ticks (Amblyomma javanense) collected from this animal. cache = ./cache/cord-345647-h3imwhss.txt txt = ./txt/cord-345647-h3imwhss.txt === reduce.pl bib === id = cord-345204-ch0e6lzl author = Scarlata, S. title = Design Of A Rapid And Reversible Fluorescence Assay To Detect COVID-19 And Other Pathogens date = 2020-10-05 pages = extension = .txt mime = text/plain words = 2917 sentences = 172 flesch = 59 summary = The method uses fluorescent sensors (i.e. molecular beacons) designed to detect COVID-19 RNA or any RNA of interest, concurrent with an internal control without the need for amplification. The molecular beacons are stem-loop structures in which a ~10 nucleotide loop region has the complementary sequence of a region of the target RNA, and a fluorophore and quencher are placed on the 5' and 3' ends of the stem. Here, we designed a COVID-19 beacon that is completely quenched in its native form and undergoes a 50-fold increase in fluorescence when exposed to nanomolar amounts of synthetic viral oligonucleotide. Fluorescence increases from beacon responses signals are rapid and can be reversed by the addition of inexpensive ssDNA with a sequence identical to the loop region, or high salt if attached to a matrix. cache = ./cache/cord-345204-ch0e6lzl.txt txt = ./txt/cord-345204-ch0e6lzl.txt === reduce.pl bib === id = cord-344321-fjer281d author = Ning, Yi title = Aptamers used for biosensors and targeted therapy date = 2020-10-20 pages = extension = .txt mime = text/plain words = 16947 sentences = 1045 flesch = 49 summary = Aptamers, first raised by two research groups independently in 1990 [1, 2] , are single-stranded DNA (ssDNA) or RNA sequences obtained through systematic evolution of ligands by exponential enrichment (SELEX) that can fold into secondary and three-dimensional shapes, enabling them to recognize various target molecules with high specificity and affinity, including proteins [3, 4] , small molecules [5, 6] , metal ions [7, 8] , bacterial cells [9, 10] , viruses [11, 12] , cancer cells [13, 14] , and even tissues [15] . developed a novel QD-Apt conjugate to be loaded with Dox for the targeted delivery of drugs to PC cells based on the mechanism of binary (Bi)-FRET (Fig. 15A) [215] . The Apt-Dox-Lip complex showed selective internalization and enhanced cytotoxicity to MCF-7 breast cancer cells and xenograft MCF-7 breast tumors in nude mice, suggesting that AS1411 aptamer-functionalized liposomes can specifically bind nucleolin overexpressed on the MCF-7 cell surface, and implement drug delivery with high selectivity. cache = ./cache/cord-344321-fjer281d.txt txt = ./txt/cord-344321-fjer281d.txt === reduce.pl bib === id = cord-345302-wbkfjz8r author = Devaney, Ryan title = A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date = 2016-10-04 pages = extension = .txt mime = text/plain words = 7869 sentences = 352 flesch = 41 summary = This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Of specific interest is the enteric viral population associated with RSS of which many RNA and DNA viruses have been implicated and co-infections of multiple viruses such as rotavirus, chicken astrovirus (CAstV), avian nephritis virus (ANV), and reoviruses have been detected in birds affected with RSS or with poor performance (Reynolds et al., 1986; Guy, 1998; Kang et al., 2012) . Other enteric pathogens associated with avian malabsorption diseases include reoviruses, parvoviruses, and members of the family Caliciviridae; many of which have also been observed in broiler chickens Smyth et al., 2007; Pantin-Jackwood et al., 2008 , Wolf et al., 2011 . cache = ./cache/cord-345302-wbkfjz8r.txt txt = ./txt/cord-345302-wbkfjz8r.txt === reduce.pl bib === id = cord-345863-j01l71dh author = Drechsler, Yvonne title = Host Gene Expression of Macrophages in Response to Feline Coronavirus Infection date = 2020-06-09 pages = extension = .txt mime = text/plain words = 5530 sentences = 259 flesch = 43 summary = Considering the importance of genetics and host immune responses in viral infections, the goal of this study was to elucidate host gene expression in macrophages using RNA sequencing. Our results highlight individual host responses playing an important role, consistent with the fact that few cats develop feline infectious peritonitis despite a common presence of enteric FCoV. Cultured macrophages were infected with the FIPV 79-1146 for 2 and 17 h before RNA was collected for the expression analysis of host genes and viral reads. Viral RNA load per sample in both raw read count summation and normalized fragments per kilobase million (FPKM) average from all virus' genes combined, obtained in cellular extracts of either macrophages or CRFK cells infected with FIPV, at 2 and 17 h post-infection. In contrast to the macrophages exposed to the virus, RNA sequencing showed several log-fold increases of viral isolates in the CRFK cells used as replication controls from 2 to 17 h (Table 1 ). cache = ./cache/cord-345863-j01l71dh.txt txt = ./txt/cord-345863-j01l71dh.txt === reduce.pl bib === id = cord-345157-fhmhpobi author = Qi, Dan title = Virus infection-induced host mRNA degradation and potential application of live cell imaging date = 2018-12-12 pages = extension = .txt mime = text/plain words = 2619 sentences = 158 flesch = 49 summary = Herein, we focus on several possible mechanisms of infection-induced host RNA turnover, which seems to be a common strategy for both prokaryotic and eukaryotic viruses during the very early stage of infection and a potential application of live cell imaging on its visualization. Many viruses also impair the translation of cellular mRNA [1e3], one of the mechanisms during the shift of gene expression from host to virus, a process termed "host shutoff", in order to prevent the production of anti-viral, host protecting proteins [4] . Moreover, Gaglia et al.'s work showed that viral encoded proteins trigger host mRNA degradation by a primary endonucleolytic cleavage causing shutoff of host gene expression and a host exonuclease such as Xrn1, an important 5 0 to 3 0 exonuclease in human cells, were required in subsequent completion of host mRNA turnover [5] . cache = ./cache/cord-345157-fhmhpobi.txt txt = ./txt/cord-345157-fhmhpobi.txt === reduce.pl bib === id = cord-343662-scn7b4c6 author = Delli Ponti, Riccardo title = A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs date = 2018-12-03 pages = extension = .txt mime = text/plain words = 6568 sentences = 336 flesch = 51 summary = CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. CROSSalign, available at our webpages http://service.tartaglialab.com//new_submission/ crossalign, is based on the combination of two methods: (1) Computational Recognition Of Secondary Structure (CROSS), which is an algorithm trained on experimental data to predict RNA secondary structure profiles without sequence length restrictions and at single-nucleotide resolution (Delli Ponti et al., 2017) ; (2) the Dynamic Time Warping (DTW) algorithm to assess the similarity of two profiles of different lengths (Giorgino, 2009) . We developed the CROSSalign method based on the combination of the CROSS algorithm to predict the RNA secondary structure at single-nucleotide resolution (Delli Ponti et al., 2017) and the DTW algorithm to align profiles of different lengths (Giorgino, 2009 ). cache = ./cache/cord-343662-scn7b4c6.txt txt = ./txt/cord-343662-scn7b4c6.txt === reduce.pl bib === id = cord-345898-a6vt8kso author = Ren, Linzhu title = Live Cell Reporter Systems for Positive-Sense Single Strand RNA Viruses date = 2016-01-04 pages = extension = .txt mime = text/plain words = 6000 sentences = 289 flesch = 38 summary = There are three types of cell-based reporter systems that express certain reporter protein for positive-sense single strand RNA virus infections. An RVP is a type of virus-like particle (VLP) composed of viral structural proteins and a self-replicating replicon RNA containing a reporter gene [17, 63] . However, when the cells were infected with the specific virus, the viral RdRp was provided by the virus and the defective replicon was activated, resulting in high-level expression of the reporter gene, which could be easily examined [44] . However, when the cells were infected with the specific virus, the viral RdRp was provided by the virus and the defective replicon was activated, resulting in high-level expression of the reporter gene, which could be easily examined [44] . Development of Dengue type-2 virus replicons expressing GFP reporter gene in study of viral RNA replication cache = ./cache/cord-345898-a6vt8kso.txt txt = ./txt/cord-345898-a6vt8kso.txt === reduce.pl bib === id = cord-345654-vyz6f3he author = Dennehy, John J. title = Evolutionary ecology of virus emergence date = 2016-12-30 pages = extension = .txt mime = text/plain words = 11475 sentences = 701 flesch = 43 summary = Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between‐host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between‐host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead‐end spillover infections. Virus quasispecies may facilitate host range expansion Viruses are among the smallest nucleic acid-based replicating entities and possess characteristics associated with exceptionally fast evolutionary change: small genomes, short generation times, high mutation rates, large population sizes, high levels of genetic diversity, and strong selection pressures. cache = ./cache/cord-345654-vyz6f3he.txt txt = ./txt/cord-345654-vyz6f3he.txt === reduce.pl bib === id = cord-342634-4ouhdjsr author = Semrad, Katharina title = Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding date = 2010-12-26 pages = extension = .txt mime = text/plain words = 7141 sentences = 399 flesch = 52 summary = In brief, the group of proteins with RNA chaperone activity includes proteins that, first, open up misfolded structures without requirement of ATP and that, second, are dispensable once the RNA has been folded. coli showed that 1/3 of the tested proteins possesses strong RNA chaperone activity in vitro in the trans-splicing assay [21] . E. coli contains nine members of the csp family and CspA, the major cold-shock protein and CspE were identified to interact non-specifically with RNA molecules and to possess nucleic acid melting activities [44] [45] [46] . Later, a detailed study on possible functions of Ro RNPs, which are Ro ribonucleoprotein complexes, composed of a small noncoding cytoplasmic RNA, termed Y RNA and its protein partners was conducted: besides the permanently associated proteins Ro60 and La, subpopulations of Ro-RNPs also contain hnRNP I and hnRNP K, both of which exhibited strong RNA chaperone activity in vitro in the transsplicing and the cis-splicing assay [22] . cache = ./cache/cord-342634-4ouhdjsr.txt txt = ./txt/cord-342634-4ouhdjsr.txt === reduce.pl bib === id = cord-343918-5yk1j4ms author = Gorbalenya, A.E. title = Phylogeny of Viruses date = 2008-07-30 pages = extension = .txt mime = text/plain words = 3892 sentences = 182 flesch = 40 summary = For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Phylogenetic analysis is used in a wide range of studies to address both applied and fundamental issues of virus research, including epidemiology, diagnostics, forensic studies, phylogeography, origin, evolution, and taxonomy of viruses. With the latter virus, poor sampling of the coronavirus diversity in the SARS-CoV lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. cache = ./cache/cord-343918-5yk1j4ms.txt txt = ./txt/cord-343918-5yk1j4ms.txt === reduce.pl bib === id = cord-345957-wuk2arf9 author = Mohamed, Fakry F. title = Detection and genetic characterization of bovine kobuvirus from calves in Egypt date = 2018-02-08 pages = extension = .txt mime = text/plain words = 4245 sentences = 219 flesch = 61 summary = When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Initially, kobuviruses included Aichivirus (AiV), bovine kobuvirus (BKoV), and porcine kobuvirus (PKoV) based on the hosts infected e.g. humans, cattle, 1 3 and swine, respectively. In this study, we report BKoV infections among cattle populations of Egypt, the full-length genome of one Egyptian strain (BKoV/ Egy-1/ KY407744) as well as the phylogenetic analysis of BKoV strains from Cairo and Sharkia provinces. The RNA samples (n = 36) were subjected to RT-PCR for the detection of BKoV using degenerate primers (Univ-Kobu-F and Univ-Kobu-R), which amplify a conserved region in the 3D (RdRp) gene of all kobuviruses [12] ( Table 1 ). cache = ./cache/cord-345957-wuk2arf9.txt txt = ./txt/cord-345957-wuk2arf9.txt === reduce.pl bib === id = cord-346544-kk7qyn4w author = Andersson, M. title = SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date = 2020-05-26 pages = extension = .txt mime = text/plain words = 4992 sentences = 305 flesch = 53 summary = Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. . https://doi.org/10.1101/2020.05.21.20105486 doi: medRxiv preprint prevalence of vRNA detection in blood, serum or plasma, noting whether this attribute was correlated with clinical or laboratory phenotypes of disease, and recording Ct values when these were reported. We collected 212 serum samples through the microbiology department at Oxford University Hospitals NHS Foundation Trust, OUH NHSFT, comprising adults with a diagnosis of COVID-19, confirmed by SARS-CoV-2 detection by a clinical diagnostic microbiology laboratory using RT-PCR on a respiratory swab, classified in three groups as follows: Based on a systematic review of the literature, together with our own data, we estimate that SARS-CoV-2 RNA may be present at low copy numbers in ~10% of blood samples obtained from individuals with COVID-19 prior to day 28, most of which arise at earlier timepoints and in the setting of more severe disease. cache = ./cache/cord-346544-kk7qyn4w.txt txt = ./txt/cord-346544-kk7qyn4w.txt === reduce.pl bib === id = cord-345413-bsd32j8r author = Terada, Yutaka title = Establishment of a Virulent Full-Length cDNA Clone for Type I Feline Coronavirus Strain C3663 date = 2019-08-02 pages = extension = .txt mime = text/plain words = 7979 sentences = 438 flesch = 56 summary = To determine viral RNA replication in A72 cells, A72, MDCK, DH82, and Fcwf-4 cells were infected with rC3663-Nluc virus at an MOI of 0.01, followed by real-time RT-PCR analysis of RNA extracted at 24, 48, and 72 hpi. Next, we determined the levels of production of infectious virus particles from rC3663-Nluc-infected A72 cells by collecting the culture supernatants at 24, 48, and 72 hpi and measuring viral titers by plaque assays with Fcwf-4 cells (Fig. 3E ). Thus, to determine expression levels of sg N mRNA (sg mRNA6), total RNAs extracted from rC3663 virus-infected or mock-infected Fcwf-4 and A72 cells at 48 and 72 hpi were subjected to Northern blot analysis with a specific type I FCoV 3= untranslated region (3=UTR) probe (Fig. 5A) . We further examined the expression levels of viral sg mRNAs in cells infected with the parental C3663 strain or type I FCoV strain Yayoi using Northern blot analysis with specific RNA probes against the 3=-UTR. cache = ./cache/cord-345413-bsd32j8r.txt txt = ./txt/cord-345413-bsd32j8r.txt === reduce.pl bib === id = cord-346267-l08ld2cy author = Wertheim, Joel O. title = Purifying Selection Can Obscure the Ancient Age of Viral Lineages date = 2011-06-24 pages = extension = .txt mime = text/plain words = 6414 sentences = 327 flesch = 47 summary = Over longer periods of evolutionary time (i.e., along long internal branches on a phylogenetic tree), evidence of evolution at the nucleotide level could be lost, which could bias tMRCA estimates towards younger dates (i.e., underestimate the length of these branches). The results presented here demonstrate that not accounting for purifying selection may bias tMRCA estimation in RNA viruses towards more recent dates, and a degree of correction can be realized by employing more realistic codon-based substitution models, capable of partially accounting for the biasing effect of purifying selection. Using BMCMC analysis, we inferred the substitution rate and root age under a standard nucleotide substitution model (GTR + Γ 4 ) for each of our three viral data sets: MeV/RPV/PPRV nucleoprotein, EBOV glycoprotein, and AIV neuraminidase (table 1) . The nucleotide substitution model (GTR + Γ 4 ) underestimated the length of branches simulated under empirical (IFEL) selection regimes inferred from the three viral data sets ( fig. cache = ./cache/cord-346267-l08ld2cy.txt txt = ./txt/cord-346267-l08ld2cy.txt === reduce.pl bib === id = cord-345630-bam3pa70 author = Lee, Han-Jung title = The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date = 1991-02-28 pages = extension = .txt mime = text/plain words = 5973 sentences = 418 flesch = 65 summary = authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase Third, the 3'-half of the gene 1 sequences of IBV and MHV-A59 contains the sequence motifs for RNA polymerase and helicase, which are the activities expected to be involved in RNA synthesis Gorbalenya et a/., 198913; Bredenbeek et a/., 1990) . The alignment of amino acids in ORF la of MHV-JHM and IBV showed that there are four possible stretches of moderate homology which are separated by highly diverged sequences (Fig. 8) . Although ORF la is highly diverged between MHV-JHM and IBV, common functional domains could be identified in this ORF of both viruses by detailed amino acid sequence analysis (see Materials and Methods) (Fig. 9 ). cache = ./cache/cord-345630-bam3pa70.txt txt = ./txt/cord-345630-bam3pa70.txt === reduce.pl bib === id = cord-344421-rmnck42f author = Theuns, Sebastiaan title = Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus date = 2018-06-29 pages = extension = .txt mime = text/plain words = 8648 sentences = 453 flesch = 50 summary = Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (10(6.42)–10(7.01) copies/swab) and diarrheic signs was not observed during a follow-up study. Third-generation sequencing using MinION (Oxford Nanopore Technologies, ONT) might be a useful and affordable diagnostic tool for swine veterinary medicine as it allows rapid sample preparation and real-time sequence analysis. The shedding of porcine kobuvirus, RVA and rotavirus C (RVC) was quantitatively investigated in 5 suckling pigs of the same farm from which the diarrheic feces originated. The third-generation sequencing device MinION (ONT), holds promise as a diagnostic platform, as it allows real-time sequencing and analyses of all DNA/RNA in a sample, theoretically without needing pre-amplification of viral nucleic acids. In the present study, a novel RT-qPCR assay, targeting the conserved 3D gene encoding the RNA-dependent-RNA-polymerase, was developed and used to assess, for the first time, longitudinal quantitative shedding kinetics of porcine kobuvirus in pigs under field conditions. cache = ./cache/cord-344421-rmnck42f.txt txt = ./txt/cord-344421-rmnck42f.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-346930-gl573ip9 author = Hussain, Azhar title = Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date = 2020-05-24 pages = extension = .txt mime = text/plain words = 4177 sentences = 207 flesch = 45 summary = Although multiple drugs show promise in the treatment of COVID-19 via either inhibiting viral replication or preventing fusion of the virus to the ACE2 receptors, further investigation is still warranted and necessary before the admission of any type of pharmaceutical agent. This review explores various drugs and their mechanism of action which are either currently being used in clinical trials or may be used in the future for the treatment of COVID-19. Since the emergence of the virus in China in December of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across the globe resulting in the current global pandemic. Arbidol (also known as Umifenovir) is a promising repurposed antiviral agent with a unique mechanism of action targeting the S protein/ACE2 interaction and inhibiting membrane fusion of the viral envelope to the host cell [7] . cache = ./cache/cord-346930-gl573ip9.txt txt = ./txt/cord-346930-gl573ip9.txt === reduce.pl bib === id = cord-347302-ylnb6qfl author = van der Schaar, Hilde M. title = Fat(al) attraction: Picornaviruses Usurp Lipid Transfer at Membrane Contact Sites to Create Replication Organelles date = 2016-03-22 pages = extension = .txt mime = text/plain words = 5330 sentences = 266 flesch = 36 summary = Replication organelles (ROs) are membranous structures that not only harbor viral proteins but also contain a specific array of hijacked host factors that create a unique lipid microenvironment optimal for genome replication. Whatever function GBF1 plays in enterovirus replication, it might be related to the functioning rather than the formation of ROs, because poliovirus proteins expressed in the presence of BFA induced membrane rearrangements indistinguishable from those found in infected cells [43] . The Importance of MCSs for Controlling the Metabolism of Other Lipids in Infected Cells Besides mediating cholesterol/PI4P exchange, OSBP regulates the homeostasis of other lipids via MCSs. Notably, OSBP regulates the ceramide transfer protein (CERT)-dependent shuttling of ceramide (a precursor of sphingomyelin, a lipid that associates with cholesterol in membrane microdomains) from ER to trans-Golgi [70] . Since RO membranes are enriched in PI4P, ORP5 and/or ORP8 may also be recruited to ER-RO MCSs and transport phosphatidylserine to ROs, from where it may transition to the autophagosome-like DMVs. Enterovirus replication has been associated with alterations of other lipid metabolic pathways as well. cache = ./cache/cord-347302-ylnb6qfl.txt txt = ./txt/cord-347302-ylnb6qfl.txt === reduce.pl bib === id = cord-346514-vyo8l14p author = Chen, I-Hsuan title = Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date = 2013-06-13 pages = extension = .txt mime = text/plain words = 5141 sentences = 304 flesch = 60 summary = The polyadenylation signal in the 3′ UTR of BaMV was shown to be involved in the synthesis of minus-strand viral RNA and regulating the length of the poly(A) tail (Chen et al., 2005) . To test whether the replicase preparation could polyadenylate exogenous plus-strand RNA templates, 5′ end-labeled radioactive BaMV plus-strand RNA substrate containing the entire 3′-UTR and 7, 15, or 40 adenylates (r138/7A, r138/15A, or r138/40A, respectively), were subjected to the polyadenylation activity assay. BaMV minigenomes were demonstrated to be suitable templates for an in vitro replication assays (Huang et al., 2009) ; therefore, the exogenous plus-strand or minus-strand BaMV minigenome was added to the reaction to help determine whether the poly(A) tail could be added to the 3′ end of preformed or newly transcribed plus-strand RNA, respectively. cache = ./cache/cord-346514-vyo8l14p.txt txt = ./txt/cord-346514-vyo8l14p.txt === reduce.pl bib === id = cord-346138-ip42zcld author = Zhurakivska, Khrystyna title = An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date = 2020-08-20 pages = extension = .txt mime = text/plain words = 3947 sentences = 211 flesch = 56 summary = The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. Several authors therefore suppose an infection of the gastrointestinal tract by the virus (11, 24) , with its continuous elimination with the feces which has been reported to last from 1 to 12 days (24) and in some cases, viral RNA were detected in feces or anal swabs even after the respiratory tests became negative (11, 22, 24) . The reference method for testing positivity to SARS-CoV-2 infection is represented by the pharyngeal swab that is taken from the patient's nasopharynx or oropharynx and, through an RT-PCR analyzed for the presence of viral RNA (8) . cache = ./cache/cord-346138-ip42zcld.txt txt = ./txt/cord-346138-ip42zcld.txt === reduce.pl bib === id = cord-345371-pjbviagq author = Lisi, Lucia title = Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date = 2020-07-23 pages = extension = .txt mime = text/plain words = 10648 sentences = 512 flesch = 37 summary = The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. Here, we review the recently published literature on the pharmacological treatments used so far and/or undergoing evaluation in clinical trials, with focus on the biochemical mechanisms of action of repurposed or investigational drugs, classified as agents directly targeting the virus ( Figure 1 and Table 1 ) and those used to treat the respiratory distress and inflammation associated with the cytokine release syndrome ( Figure 2 and Table 2 ). cache = ./cache/cord-345371-pjbviagq.txt txt = ./txt/cord-345371-pjbviagq.txt === reduce.pl bib === id = cord-348669-mizygp4j author = Beall, Anne title = Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date = 2016-01-05 pages = extension = .txt mime = text/plain words = 6021 sentences = 293 flesch = 43 summary = title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. While the recombinant icPEDV replicated the clinical phenotypes of parental PC22A in vivo, icPEDV-⌬ORF3-RFP infection resulted in a partial attenuation in pigs based on lower diarrhea scores. Both the parental PEDV PC22A strain and its derivative recombinant cloned virus were genetically stable and fully pathogenic in neonatal gnotobiotic pigs, demonstrating that icPEDV provides not only a strategy that allows for the systematic evaluation of the role of viral genes in pathogenesis, tropism, and virulence but also a translational platform for the development of rationally attenuated live virus vaccines. cache = ./cache/cord-348669-mizygp4j.txt txt = ./txt/cord-348669-mizygp4j.txt === reduce.pl bib === id = cord-348204-365z3qxz author = Harun, Mohammad Syamsul Reza title = Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats date = 2013-11-09 pages = extension = .txt mime = text/plain words = 4691 sentences = 235 flesch = 52 summary = Real time RT-qPCR developed focusing on 2 up-regulated genes (PD-L1 and A3H) together with an apoptosis associated gene PD-1 expressions in FIPV infected CRFK cells and in PBMCs from healthy and FIP diagnosed cats produced concordant results with transcriptome data. FIPV infected cells also showed high up-regulation of PD-1 expression at 3 h.p.i. and moderately up-regulated at 12 h.p.i but were being down-regulated at 6, 9, 24 and 48 h.p.i. Meanwhile, PD-L1 gene was consistently down-regulated from 3 hours to 48 h.p.i. Peripheral Blood Mononuclear Cells (PBMCs), obtained from cats with clinical signs associated with FIP (Table 4) , were purified and analysed with real-time PCR. The reference feline genome sequence assembly of transcriptome analysis of early infection (3 h.p.i.) of CRFK cells with FIPV 79-1146 showed that the expressions of 215 transcripts (0.8% of the trimmed annotated) were statistically significant, based on Kal's Z test. cache = ./cache/cord-348204-365z3qxz.txt txt = ./txt/cord-348204-365z3qxz.txt === reduce.pl bib === id = cord-347221-g98q9cga author = Piyush, Ravikant title = Nucleic acid-based therapy for coronavirus disease 2019 date = 2020-09-19 pages = extension = .txt mime = text/plain words = 4217 sentences = 246 flesch = 50 summary = This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This phenomenon of producing an effective immunity is particularly important in their use against the development of nucleic acid based therapeutic drugs for the treatment of SARS-CoV-2. Nucleic acid-based therapies, especially, RNA therapies including RNAi (RNA interference), siRNAs (small interfering RNA) and RNA aptamers, Ribozymes and ASOs (antisense oligonucleotides) target and neutralize the crucial components of the virus-like specific mRNA molecules, viral proteins like E (envelope), M (membrane), or N (nucleocapsid), or SARS helicase, etc. The nucleic acid-based vaccination technologies involve the use of RNA (mRNA) [34] or plasmid DNA, which encodes for antigen. cache = ./cache/cord-347221-g98q9cga.txt txt = ./txt/cord-347221-g98q9cga.txt === reduce.pl bib === === reduce.pl bib === id = cord-347532-n51qv9pp author = Wacharapluesadee, Supaporn title = Group C Betacoronavirus in Bat Guano Fertilizer, Thailand date = 2013-08-17 pages = extension = .txt mime = text/plain words = 1191 sentences = 71 flesch = 54 summary = To the Editor: Bats play a critical role in the transmission and origin of zoonotic diseases, primarily viral zoonoses associated with high casefatality rates, including those caused by Nipah virus (NiV) and severe acute respiratory syndrome (SARS)-like coronavirus (CoV) infections (1) . To assess pathogens in bat guano, we examined bat guano from a cave in the Khao Chong Phran Non-hunting Area (KCP-NHA) in Ratchaburi Province, Thailand, where bat guano was sold as agricultural fertilizer, for the presence of NiV, CoV, and H. The detection of CoVs in bat guano from the KCP-NHA cave in Ratchaburi was consistent with the previous finding of alphacoronavirus from Hipposideros armiger bats from the same province in 2007, but those researchers tested fresh bat feces (9) . Duplex nested RT-PCR for detection of Nipah virus RNA from urine specimens of bats cache = ./cache/cord-347532-n51qv9pp.txt txt = ./txt/cord-347532-n51qv9pp.txt === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === === reduce.pl bib === id = cord-347128-6lyoz8nn author = Kim, Cheorl-Ho title = SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date = 2020-06-26 pages = extension = .txt mime = text/plain words = 15413 sentences = 988 flesch = 53 summary = O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. In RNA viruses, the S glycoprotein (PDB: 6VSB) is the biggest protein, heavily glycosylated and its N-terminal domain (NTD) sequence binds to the host receptor to enter the ER of host cells. However, MERS-CoV does not have a similar enzyme and thus MER-CoV binding to SA receptors is mediated by energetically reversible interactions of the lipid rafts with increased SA receptors [75] , thus enhancing dipeptidyl peptidase 4 (DPP4) or carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) recognition power and viral entry [76] and membrane-associated 78-kDa glucose-regulated protein (GRP78) [77] . Entry of host cells needs binding of S glycoproteins to the CEACAM receptor, forming S-protein-mediated membrane fusion. For example, impairment of ACE2 receptor glycosylation does not influence S-glycoprotein-ACE2 interaction, however, SARS-CoV-2 virus entry into respiratory epithelial host cells was downregulated [133] . cache = ./cache/cord-347128-6lyoz8nn.txt txt = ./txt/cord-347128-6lyoz8nn.txt === reduce.pl bib === id = cord-348799-qu4zin3o author = Wu, Nannan title = The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation date = 2019-10-10 pages = extension = .txt mime = text/plain words = 11391 sentences = 520 flesch = 48 summary = This lack of specificity was not present in cells however, given that the ectopic expression of ISG20 did not lead to the indiscriminate degradation of cellular RNAs (ribosomal as well as small nucleolar RNAs previously shown to be associated to ISG20 [2] ), nor of an Hepatitis C virus (HCV)-derived Luciferase reporter mRNA produced in vitro and then transfected into cells (S4C and S4D Fig) , suggesting that in cells the RNase activity of ISG20 is tightly controlled. Self mimicry allows the escape of target genes' mRNAs from the effects of ISG20 VSV infection and ectopic DNA or RNA transfection do not bear much in common apart from the fact that both represent artificial injections into the cell of non-self genetic material from without. To further determine whether ISG20 acted on translation initiation and more specifically through specific initiation factors (eIFs), capped and polyadenylated mRNAs coding luciferase under the control of several 5' untranslated regions (5' UTRs) were generated in vitro and directly transfected in ISG20-expressing cells (Fig 3D) . cache = ./cache/cord-348799-qu4zin3o.txt txt = ./txt/cord-348799-qu4zin3o.txt === reduce.pl bib === id = cord-347710-ff64y6ef author = Wan, Qianya title = Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date = 2020-07-13 pages = extension = .txt mime = text/plain words = 36567 sentences = 2487 flesch = 46 summary = hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. cache = ./cache/cord-347710-ff64y6ef.txt txt = ./txt/cord-347710-ff64y6ef.txt === reduce.pl bib === id = cord-348243-e5tdb08v author = Schermer, Bernhard title = Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date = 2020-11-02 pages = extension = .txt mime = text/plain words = 3958 sentences = 236 flesch = 56 summary = METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). To allow for the comparison of different nucleic acid detection methods for SARS-CoV-2 we collected redundant material from nasopharyngeal swabs obtained for qPCR testing in clinical routine due to suspected COVID-19. We first tested two recently described assays for SARS-CoV-2 detection on isolated RNA from patient samples. In summary, our multiplex RT-LAMP protocol is a simple and sensitive way to detect SARS-CoV-2 RNA from clinical samples. Currently, a test based on our multiplexed RT-LAMP assay would-in contrast to a good specificity-most likely miss to identify those infected patients with very low amounts of viral RNA in the nose or throat and would not yet reach the sensitivity of the gold-standard qPCR assays. cache = ./cache/cord-348243-e5tdb08v.txt txt = ./txt/cord-348243-e5tdb08v.txt === reduce.pl bib === id = cord-349684-2tioh80m author = Pezzotti, Giuseppe title = Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date = 2020-06-20 pages = extension = .txt mime = text/plain words = 5388 sentences = 338 flesch = 51 summary = The present study compared the effects of exposing SARS-CoV-2 to aqueous suspensions of Si3N4 and aluminum nitride (AlN) particles and two controls, (i.e., a suspension of copper (Cu) particles (positive control) and a sham treatment (negative control)). In (c) and (d), results of RT-PCR tests for supernatants after 10 min exposure of virus suspension to Cu, AlN, and Si3N4 powders for viral N gene "set 1" and "set 2" primers are shown, respectively. The present work is the first to show that compounds capable of endogenous nitrogen-release, such as Si3N4 and AlN, can inactivate the SARS-CoV-2 virus at least as effectively as Cu. These results suggest that multiple antiviral mechanisms may be operative, such as RNA fragmentation, and in the case of Cu, direct metal ion toxicity; but while Cu and AlN supernatants demonstrated strong and partial cellular lysis, respectively, Si3N4 provoked no metabolic alterations. cache = ./cache/cord-349684-2tioh80m.txt txt = ./txt/cord-349684-2tioh80m.txt === reduce.pl bib === id = cord-349839-s32d3di2 author = Westhof, Eric title = RNA pseudoknots date = 1992-06-30 pages = extension = .txt mime = text/plain words = 3427 sentences = 185 flesch = 59 summary = In the folding of a single-stranded RNA molecule, there are only three ways in which two base-paired segments can be related to each other: two consecutive hairpins; two helices separated by an internal bulge; and, pseudoknots [1]. The first two motifs can be represented as two-dimensional graphs without self-intersections whereas pseudoknots cannot, as they are fundamentally three-dimensional structures in which the four base-paired strands alternate along the sequence of the RNA molecule. The three types of 'classic' pseudoknots with co-axial stacking of the two base-paired helices and with single-stranded segments crossing the RNA grooves. The third pseudoknot involves the 530 stem-loop structure [19] , which is known to be important for the binding of tRNA to the ribosomal A site [20] , and was recently shown to be essential for ribosomal function [21.o] . cache = ./cache/cord-349839-s32d3di2.txt txt = ./txt/cord-349839-s32d3di2.txt === reduce.pl bib === id = cord-349042-u9svz7pf author = Li, Jifen title = The successes and future prospects of the linear antisense RNA amplification methodology date = 2018-03-29 pages = extension = .txt mime = text/plain words = 5015 sentences = 253 flesch = 42 summary = The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. Examination of expression profiles of single live cells has shown that linear aRNA amplification neither results in occurs after synthesis of double-stranded cDNA, when T7 RNA polymerase is added and aRNA is transcribed from the cDNA template. 45 developed a method to facilitate aRNA detection of antibody-antigen interactions by covalently attaching a double-stranded cDNA that contains a T7 RNA polymerase promoter in front of a reporter sequence to a specific antibody. cache = ./cache/cord-349042-u9svz7pf.txt txt = ./txt/cord-349042-u9svz7pf.txt === reduce.pl bib === id = cord-349341-ap5n6ijl author = Kopek, Benjamin G title = Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle date = 2007-08-14 pages = extension = .txt mime = text/plain words = 8539 sentences = 431 flesch = 44 summary = The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5'-triphosphate incorporation localized between inner and outer mitochondrial membranes inside ∼50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. To localize more precisely FHV RNA synthesis in relation to spherules, we incubated mitochondria isolated from uninfected and FHV-infected Drosophila cells with a nucleotide mix including 5-bromouridine 5'-triphosphate (BrUTP) and performed immunogold labeling EM with an antibody recognizing BrU incorporated into RNA, but not unincorporated BrUTP. To generate 3-D surface maps of the virus-induced membrane rearrangements associated with FHV RNA replication, we manually traced the inner and outer mitochondrial membranes (including spherules) over ;100 adjacent, 2.2nm-spaced virtual sections of selected tomographic reconstructions, and we used a computer-generated mesh overlay to join these tracings into continuous surfaces ( Figure 4 ). cache = ./cache/cord-349341-ap5n6ijl.txt txt = ./txt/cord-349341-ap5n6ijl.txt === reduce.pl bib === id = cord-350342-j4p8235a author = Brocato, Rebecca L. title = Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date = 2020-10-27 pages = extension = .txt mime = text/plain words = 5265 sentences = 283 flesch = 49 summary = All of the SARS-CoV-2-challenged hamsters had detectable viral RNA in pharyngeal swabs at the first time point assayed, 3 dpi, and remained consistent (10 3 to 10 5 molecules of nucleocapsid using a second primer set [N2] per 100 ng RNA) throughout the duration of CyP treatment (Fig. 1C) . Viral RNA and infectious virus were detected in lung tissue from a subset of hamsters collected 13 dpi, on the day of euthanasia of moribund animals (14 to 34 dpi), or after euthanasia at 35 dpi (end of study) ( Fig. 1E and F). Electron microscopy studies were performed on lung sections of SARS-CoV-2infected, CyP-treated hamsters with various lung viral loads (Fig. 1) . Similarly, lung tissue collected at 13 dpi (end of study) indicate comparable levels of viral RNA detected (Fig. 6D ) but significantly reduced infectious virus in Centi-F1 MAb-treated animals (P ϭ 0.0002; unpaired t test) (Fig. 6E) . cache = ./cache/cord-350342-j4p8235a.txt txt = ./txt/cord-350342-j4p8235a.txt === reduce.pl bib === id = cord-348147-leni23pa author = Müller, B. title = Genetic diversity and recombination of murine noroviruses in immunocompromised mice date = 2007-05-29 pages = extension = .txt mime = text/plain words = 3482 sentences = 203 flesch = 52 summary = Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. These specimens were obtained from 28 different mouse lines, including immunocompetent mice, lines with muta(4), b-TCR À=À (2), RAG2=gChain À=À (5), B6 Casp À=À (2), CD36=SRA À=À (2), CCL3 À=À (2), LFA À=À (2), LyZ À=À (2), PSEN tg (2), Bl6 wt (4) a GE genome equivalents; for more than one positive sample the mean was calculated b Includes partial sequences of the ORFs (underlined isolates; ORF1, RNA polymerase gene; ORF2, capsid gene) Ã Contains both regions tions in a number of immune effector molecules, and transgenic mouse lines (Table 1) . Like human noroviruses, the present sequence data indicate that murine norovirus strains are also genetically diverse and can, therefore, be subdivided in genetic clusters. cache = ./cache/cord-348147-leni23pa.txt txt = ./txt/cord-348147-leni23pa.txt === reduce.pl bib === id = cord-350189-2su7oqbz author = Elmén, Joacim title = Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date = 2005-01-14 pages = extension = .txt mime = text/plain words = 5415 sentences = 322 flesch = 55 summary = A priori, this suggests that LNA may be used to increase the functional half-life of siRNA in vivo by two different mechanisms, e.g. by enhancing the resistance of the constituent RNA strands against degradation by single-stranded RNases and by stabilizing the siRNA duplex structure that is critical for activity. Next, we examined the effect of making single RNA to LNA exchanges at base-paired positions in the antisense strand of the firefly luciferase siLNA1. Although we cannot exclude that these modifications somehow prevent loading of the antisense strand into RISC, we believe this to be unlikely given the functionality of many significantly more modified siLNAs. Rather, as these positions are all close to the site where RNA target cleavage occurs [between pos. The SARS siRNA (Table 1) has identical closing base-pairs at both ends (A:U) making it likely that enough of both the antisense and sense strand would be incorporated into RISC to observe activity on the respective targets. cache = ./cache/cord-350189-2su7oqbz.txt txt = ./txt/cord-350189-2su7oqbz.txt === reduce.pl bib === id = cord-348860-zaimorg0 author = Ratra, Ruchi title = Functional genomics as a tool in virus research date = 2008-06-01 pages = extension = .txt mime = text/plain words = 3379 sentences = 171 flesch = 39 summary = The genomics era has revolutionized the biological sciences and has heralded the emergence of new 'omics' methodologies such as transcriptomics (study of the gene expression and expression levels of mRNAs at a given time and condition), proteomics (study of the entire protein content of a cell/tissue under various conditions, their structure and functions), metabolomics (study of the metabolite profi le of different cellular processes), phosphoproteomics (a branch of proteomics that characterizes proteins that are phosphorylated), interactomics/system biology (a science that unifi es transcriptomics, proteomics and metabolomics to look at the organism as a whole) and so on. DNA microarrays, proteomics and bioinformatic analysis are routinely used to analyze changes in host and viral gene and protein expression that occur in a virus infected cell [25] . cache = ./cache/cord-348860-zaimorg0.txt txt = ./txt/cord-348860-zaimorg0.txt === reduce.pl bib === id = cord-350906-ew04zzh6 author = Khambhati, Khushal title = Current progress in CRISPR‐based diagnostic platforms date = 2018-10-26 pages = extension = .txt mime = text/plain words = 2266 sentences = 136 flesch = 49 summary = 10 East-Seletsky et al 10 have taken the advantage and demonstrated the use of Cas13 for the detection of 0.01 nM of λRNA with high specificity, using the signals generated from fluorophore-quencher based reporter RNA molecule ( Figure 1 ). The resultant amplified DNA sequence is then subjected to in vitro T7 transcription, and produced RNA molecule is detected by Cas13-guided reporter assay. 11 For improved multiplexed detection, Cas12a has been used along with Cas13 RNAse. 11 F I G U R E 1 Schematic representation of CRISPR-based diagnostic tool, in the presence of the appropriate gRNA, Cas13 recognizes the target RNA sequence that is complementary. The produced RNA molecule can be recognized via fluorescence signals that are generated by the reporter molecule upon target recognition by the Cas13 RNAse. 4 The cleaved reporter molecule can also be detected in the form of bands through a lateral flow assay. cache = ./cache/cord-350906-ew04zzh6.txt txt = ./txt/cord-350906-ew04zzh6.txt === reduce.pl bib === id = cord-349623-dw5o9i59 author = Miranda, José P. title = Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date = 2020-10-15 pages = extension = .txt mime = text/plain words = 3813 sentences = 174 flesch = 48 summary = Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise's buffer pH 7.2. For the standard protocol, routinely used in the laboratory for the detection of SARS-CoV-2, an aliquot of 180 ul of the sample from the nasopharyngeal swab, including 10 ul of extraction control, was used to extract RNA with the MagNA Pure 96 DNA and Viral NA LV Kit (Roche Diagnostics, Cat. No. For the standardization of the direct SARS-CoV-2 detection protocol without RNA extraction steps, 50 ul aliquots from the primary sample (nasopharyngeal swabs) of 5 anonymized patients were subjected to heat shock (65, 70, or 95 • C) during different incubation times (5, 10, or 30 min), and then were quickly placed at 4 • C until the moment of amplification. cache = ./cache/cord-349623-dw5o9i59.txt txt = ./txt/cord-349623-dw5o9i59.txt === reduce.pl bib === id = cord-348815-lthz75oc author = Kurreck, Jens title = RNA Interference: From Basic Research to Therapeutic Applications date = 2009-01-19 pages = extension = .txt mime = text/plain words = 14116 sentences = 846 flesch = 56 summary = Successful applications in animal models have already led to the initiation of RNAi‐based clinical trials as a new therapeutic option.[Image: see text] Only ten years ago Andrew Fire and Craig Mello were able to show that double‐stranded RNA molecules could inhibit the expression of homologous genes in eukaryotes. This Review provides an overview of the molecular processes involved, with a particular focus on the posttranscriptional inhibition of gene expression in mammalian cells, the possible applications in research, and the results of the first clinical studies. Antisense and RNAi strategies have many things in common, such as the necessity to identify suitable binding sequences on the target RNA, the stabilization of the oligonucleotide by chemical modification, or the transport of the negatively charged polymer across the cell membrane. [19] There are, however, important differences between the two technologies: Antisense oligonucleotides are single-stranded (modified) DNA molecules, which primarily induce the cleavage of the target RNA in the cell nucleus by activation of RNase H. cache = ./cache/cord-348815-lthz75oc.txt txt = ./txt/cord-348815-lthz75oc.txt === reduce.pl bib === id = cord-346916-jj4l9ydl author = Girardi, Erika title = Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date = 2020-08-23 pages = extension = .txt mime = text/plain words = 13119 sentences = 728 flesch = 45 summary = Moreover, despite the molecular mimicry set by RNA viruses to resemble cellular mRNAs and escape host recognition, the viral nucleic acid still needs to embark on a long journey through a hostile cell environment and must overcome the obstacles put in place by the host antiviral system in order to be translated and replicated. Another example, is the zinc-finger antiviral protein (ZAP), which binds vRNAs containing a ZAP response element (ZRE) and induces RNA degradation via interaction of its N-terminal domain with host decay machinery mediated [75] (Fig. 1 ). In fact, IRES elements present in the genome of different families of RNA viruses lack overall conserved features [146, 147] .The classification of viral IRESs in four types stems from their structural organization, their respective dependence on sets of translation initiation factors, and whether they use scanning or instead directly recruit ribosomes to the start codon [148] (Fig. 2) . cache = ./cache/cord-346916-jj4l9ydl.txt txt = ./txt/cord-346916-jj4l9ydl.txt === reduce.pl bib === id = cord-351864-zozrj7w5 author = Chappleboim, A. title = ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date = 2020-08-13 pages = extension = .txt mime = text/plain words = 5782 sentences = 321 flesch = 57 summary = Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Briefly, we show ( Figure 1 ) that we can introduce barcoded and target-specific reverse transcription primers to the samples, allowing them to hybridize to target RNA molecules already in the lysis buffer, or after a brief RNA cleanup step. Observing the target sequence directly allowed us to identify viral sequence variations in some cases ( Figure 2D ).Cross-Sample Contamination is minimal When pooling samples early on in the protocol, the main concern is that RNA molecules will be erroneously tagged due to residual free primers, or due to other artifacts during RT, PCR, or sequencing. cache = ./cache/cord-351864-zozrj7w5.txt txt = ./txt/cord-351864-zozrj7w5.txt === reduce.pl bib === id = cord-347472-n6811ens author = Rosebrock, Adam P. title = Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date = 2020-05-15 pages = extension = .txt mime = text/plain words = 6252 sentences = 344 flesch = 51 summary = The US Centers for Disease Control and Prevention (CDC) have specified and given emergency use authorization (EUA) for a SARS-CoV-2 molecular diagnostic used to detect viral RNA in clinical samples (2) . Genomic DNA is co-purified in quantities sufficient to generate strong positive signals for the CDC-specified extraction control during work-up of clinical RNA specimens. To test for the presence of control-affecting DNA, qPCR reactions lacking reverse transcriptase were performed on SARS-CoV-2-positive clinical samples using the CDC-specified RP primer and probe. All clinical samples tested generated unambiguous extraction control positive signals in the absence of reverse transcription, a reaction context that could not have detected virus an RNA virus ( Fig. 2A) Single-digit copies of genomic DNA are sufficient to generate a positive control signal using the CDC-designed assay. Due to the presence of co-purifying genomic DNA in clinical samples, loss of RNA integrity leads to false-negative results using the CDC-specified control. cache = ./cache/cord-347472-n6811ens.txt txt = ./txt/cord-347472-n6811ens.txt === reduce.pl bib === id = cord-347351-emdj66vj author = Kampf, Günter title = Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date = 2020-09-18 pages = extension = .txt mime = text/plain words = 10283 sentences = 592 flesch = 50 summary = Originating from a single travel-associated primary case from China, the first documented chain of multiple human-to-human transmissions of SARS-CoV-2 outside of Asia allowed a detailed study of transmission events and identified several factors (e.g. cumulative face-toface contact, direct contact with secretions or body fluids of a patient, personal protective equipment) to classify contacts as low or high risk [32] . In the close surrounding of COVID-19 patients in hospitals SARS-CoV-2 RNA is detected more frequently compared to surfaces outside the patient rooms but samples were so far consistently negative for infectious virus. General disinfection of frequently touched surfaces in the public such as shopping carts or door handles is, however, unlikely to add any protective value because even in COVID-19 wards inanimate surfaces were mainly contaminated in the permanent and immediate surrounding of symptomatic patients (detection of viral RNA, not of infectious virus) and only rarely one room away [138] suggesting that the risk to find SARS-CoV-2 on frequently touched surfaces in the public is low. cache = ./cache/cord-347351-emdj66vj.txt txt = ./txt/cord-347351-emdj66vj.txt === reduce.pl bib === id = cord-350040-e8q7wq0h author = Aronin, N title = Target selectivity in mRNA silencing date = 2006-02-16 pages = extension = .txt mime = text/plain words = 6614 sentences = 503 flesch = 58 summary = Here is limned a roadmap to explain RISC assemblyhow there are two types of RNAi, one of which is applicable to humans; how thermodynamic properties of siRNA direct strand selection to confer full RNAi activity; how RISC proteins direct siRNA presentation to its target mRNA; and how these principles can be used to design selective and functional siRNAs. Innate mRNA silencing in mammals is currently the province of microRNAs, single stranded, small RNAs that block translation with short-term survival of target mRNA. Not all siRNAs are active, however, even when their guide strands have perfect complementarity to target mRNAs. Designing siRNAs with single nucleotide specificity requires the guide strand to be incorporated into RISC, in preference to the passenger strand. The complexity of siRNA design is that small changes in siRNA:mRNA complementarity can have profound effects on RNAi effectiveness; mismatches might have few consequences or, as shown above, improve silencing by strand selection. cache = ./cache/cord-350040-e8q7wq0h.txt txt = ./txt/cord-350040-e8q7wq0h.txt === reduce.pl bib === id = cord-350747-5t5xthk6 author = Gmyl, A. P. title = Diverse Mechanisms of RNA Recombination date = 2005 pages = extension = .txt mime = text/plain words = 8187 sentences = 463 flesch = 41 summary = It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. An illustrative example of deletions is provided by defective interfering (DI) genomes, which accumulate in a virus population upon high-multiplicity infections and lack a fragment of the sequence coding for viral proteins [5] [6] [7] . A special role in the variation of RNA viruses is played by recombination, the generation of new genomes from two or more parental RNAs. Recombination between viral RNA molecules was observed for the first time as early as in the 1960s in the poliovirus [14, 15] . In other words, it is possible to assume that some of the mechanisms of nonreplicative RNA recombination play an important role in the evolution of not only viral, but also cell genomes [51, 90] . cache = ./cache/cord-350747-5t5xthk6.txt txt = ./txt/cord-350747-5t5xthk6.txt === reduce.pl bib === id = cord-350019-4nlbu54e author = Robinson, Elektra K. title = The how and why of lncRNA function: An innate immune perspective() date = 2019-09-02 pages = extension = .txt mime = text/plain words = 13173 sentences = 715 flesch = 44 summary = Using this extensively studied biological system, we identified the first example of a TLR-stimulated lncRNA, lincRNA-Cox2, which was capable of positively and negatively regulating distinct types of innate immune genes [42] [43] [44] [45] [46] . The majority of lncRNAs studied in immunity were initially identified following RNA-sequencing to examine their expression profiles in specific cell lines or tissues during inflammatory activation. Hence future studies may opt to target TF binding sites, secondary structure and/or polyadenylation sites as a way to more finely dissect the functional portions of lncRNAs. The ease in which Cas9 can be targeted to specific genomic regions sparked the development of a modified (catalytically inactivated) version of the protein fused to the KRAB (Krüppel associated box) chromatin-silencing domain termed CRISPRi [174, 175] (Fig. 3C) . Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites cache = ./cache/cord-350019-4nlbu54e.txt txt = ./txt/cord-350019-4nlbu54e.txt === reduce.pl bib === id = cord-348777-pk9y6vfp author = Ding, Cheng title = Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date = 2020-09-28 pages = extension = .txt mime = text/plain words = 3609 sentences = 190 flesch = 46 summary = title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. Our observational results revealed that corticosteroid therapy had no positive effect on the durations of SARS-CoV-2 RNA clearance among patients with mild COVID-19. Results from this study suggested that patients with mild COVID-19 may not benefit from corticosteroid therapy in terms of the duration of SARS-CoV-2 clearance. cache = ./cache/cord-348777-pk9y6vfp.txt txt = ./txt/cord-348777-pk9y6vfp.txt === reduce.pl bib === id = cord-350533-fp1ctpax author = Tchesnokov, Egor P. title = Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein date = 2020-06-04 pages = extension = .txt mime = text/plain words = 6033 sentences = 346 flesch = 50 summary = Moreover, we identified 2'-deoxy-2'-amino-CTP as a novel inhibitor of CCHFV RdRp. We further show that CC.4 inhibits the CCHFV-associated DUB activity of the full-length L protein and the isolated DUB domain to a similar extent. Inhibition of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein ribavirin-TP or favipiravir-TP are also used as substrates opposite template C (Fig 3, middle) . Inhibition of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein CCHFV L full-length protein and the isolated OTU domain cleave ubiquitin-AMC in a time dependent manner with similar velocities illustrated by the slopes of the initial linear portion of product formation (Fig 8B) . The identification of small molecule compounds that inhibit viral RNA synthesis relies on the availability of recombinant L protein, which is a multifunctional protein with a high molecular weight of~450 kDa. Here we report the expression of full-length CCHFV L protein that possess active RdRp and DUB domains. cache = ./cache/cord-350533-fp1ctpax.txt txt = ./txt/cord-350533-fp1ctpax.txt === reduce.pl bib === id = cord-350836-1enteev7 author = Brisse, Morgan title = Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date = 2019-07-17 pages = extension = .txt mime = text/plain words = 16347 sentences = 859 flesch = 47 summary = RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. For the former, siRNA-mediated knock-down (110, 111) , cellular knockout (112) and inhibition by viral protein (109, (113) (114) (115) (116) conditions for TRIM25 in multiple cell types have been shown to change RIG-I cellular localization (110) and to negatively affect RIG-I K63 ubiquitination, association with MAVS and IFN signaling [when the constitutively active RIG-I CARD domain was overexpressed (109, (112) (113) (114) (115) (116) or during viral infection (109, 111, 114) ]. cache = ./cache/cord-350836-1enteev7.txt txt = ./txt/cord-350836-1enteev7.txt === reduce.pl bib === id = cord-350600-73q8mve4 author = Myint, S. title = Detection of human coronavirus 229E in nasal washings using RNA:RNA hybridization date = 2005-12-09 pages = extension = .txt mime = text/plain words = 1996 sentences = 126 flesch = 61 summary = A method is described for the detection of human coronavirus 229E (HCV 229E) in nasal washings using RNA:RNA filter hybridization. In this paper we describe a specific and sensitive test to detect one of these major groups, HCV 2293, in nasal washings. Briefly, using a method based on that of Gubler and Hoffmann [19831, cDNAs were generated from HCV 2293 RNA isolated from infected C16 cells [Phillpotts, 19831. The results of virus titration and probing of nasal washings from seven volunteers are presented in Table I . Three of the seven volunteers suffered a cold, and all three volunteers had detectable coronavirus RNA in their nasal washings. The results we have obtained show that the detection of HCV 2293 infection by nucleic acid hybridisation is a reliable and specific method. Hybridisation to known quantities of HCV 2293 RNA showed that less than 1 ng of virus-specific RNA from C16 cells infected with HCV 2293 could be detected. cache = ./cache/cord-350600-73q8mve4.txt txt = ./txt/cord-350600-73q8mve4.txt === reduce.pl bib === id = cord-350697-u032yk0z author = Roy, Anupam title = Can concomitant use of zinc and curcumin with other immunity‐boosting nutraceuticals be the arsenal against COVID‐19? date = 2020-06-02 pages = extension = .txt mime = text/plain words = 1110 sentences = 68 flesch = 44 summary = Lack of effective prophylaxis against COVID-19 has prompted regulatory authorities to propose boosting of immunity of individuals via nutritional supplements. While modern medicine directly confronts an antigen (via vaccination or antibiotic), in comparison nutraceuticals, food supplements, and traditional medicines activate the overall immunity of the human body. Both molecules have a proven history of antiviral activity in both in vitro and in vivo trials thus could be leadings in developing new prophylactic candidates against COVID-19. Thus, these supplements as a part of the food, nutraceutical, or traditional medicines may pave the way towards developing a therapeutic strategy against the COVID-19 pandemic. The success story of TCM is continuously inspiring us to test food supplements and raise individual immunity. Potential mechanisms by which Curcumin and Zinc can exert therapeutic effects against COVID-19. Curcumin inhibits SARS-CoV-2 entry by binding directly to the receptorbinding domain (RBD) of Spike (S) protein of the virus. cache = ./cache/cord-350697-u032yk0z.txt txt = ./txt/cord-350697-u032yk0z.txt === reduce.pl bib === id = cord-350640-sz6xj5o3 author = Menzel, Nicolas title = MAP-Kinase Regulated Cytosolic Phospholipase A2 Activity Is Essential for Production of Infectious Hepatitis C Virus Particles date = 2012-07-26 pages = extension = .txt mime = text/plain words = 10059 sentences = 549 flesch = 49 summary = When transfecting our infectious firefly luciferase reporter virus genome Luc-Jc1 [14] into highly permissive Huh-7.5 human hepatoma cells [15] cultured in the presence or absence of serum, we measured comparable levels of luciferase activity 4 to 48 h after transfection ( Figure S1A ). Among the inhibitors tested, U0126 a selective inhibitor of the MAPK/ERK pathway, substantially decreased the production of infectious virus particles as is evident from the dose-dependent reduction of luciferase activity in the inoculated cells ( Figure 1B) . To investigate if PLA2G4A activity is relevant for the production of infectious HCV particles we treated Luc-Jc1 transfected cells with pyrrolidine-2 (Py-2), a specific inhibitor of this type of phospholipase [22, 23] . Irrespective of culturing these cells in the presence or absence of serum, we observed a strong and dose-dependent inhibition of production of infectious particles resulting in a more than 100-fold reduction of luciferase transduction at 5 and 20 mM of Py-2, respectively ( Figure 2B ). cache = ./cache/cord-350640-sz6xj5o3.txt txt = ./txt/cord-350640-sz6xj5o3.txt === reduce.pl bib === id = cord-349417-vn7q8wc4 author = Ziebuhr, John title = The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date = 2006 pages = extension = .txt mime = text/plain words = 3379 sentences = 179 flesch = 45 summary = Activation of the coronavirus replication complex involves extensive proteolytic processing of the replicase polyproteins to produce 16 (in IBV: 15) mature products called nonstructural proteins (nsp) 1 to 16 (reviewed in Refs. The N-terminal regions of the coronavirus polyproteins, which are poorly conserved among the coronavirus groups I, II, and III, are cleaved at two (in IBV) or three sites (in all other coronaviruses) by one (IBV and SARS-CoV) or two zinc-finger-containing papain-like cysteine proteases called PL1 pro and PL2 pro . The observed pattern of conservation in different nidovirus families suggests a functional hierarchy for the newly identified RNA-processing activities, with the manganese ion-dependent uridylate-specific endoribonuclease, NendoU, playing a central role. Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication cache = ./cache/cord-349417-vn7q8wc4.txt txt = ./txt/cord-349417-vn7q8wc4.txt === reduce.pl bib === id = cord-349762-f5no10eq author = Nagura-Ikeda, Mayu title = Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date = 2020-08-24 pages = extension = .txt mime = text/plain words = 4270 sentences = 233 flesch = 54 summary = The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription–loop-mediated isothermal amplification (RT-LAMP). Here, we describe the clinical performance of various molecular diagnostic methods, including the RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, 3 direct RT-qPCR kits, and RT-LAMP, and a commercial SARS-CoV-2 RAT used on self-collected saliva specimens in diagnosing COVID-19. The RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed different sensitivities for detecting viral RNA in saliva specimens, but each can be selectively used according to the clinical setting and facilities if close attention is paid to any false-negative results. cache = ./cache/cord-349762-f5no10eq.txt txt = ./txt/cord-349762-f5no10eq.txt === reduce.pl bib === id = cord-350762-rh4zbehk author = Hutcheson, Jessica M. title = Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date = 2015-06-04 pages = extension = .txt mime = text/plain words = 4301 sentences = 229 flesch = 52 summary = In this study, we utilize microRNA (miRNA)-expressing constructs (a type of RNA interference) in an attempt to target and knockdown five NDV structural RNAs for nucleoprotein (NP), phosphoprotein (P), matrix (M), fusion (F), and large (L) protein genes. Using pre-miRNA to activate the cellular RNAi pathway, a miRNA can be used to target the messenger RNA of NDV structural proteins, leading to the degradation of the transcripts and inhibiting viral replication [11] . In this study, we attempted to determine if constitutive expression of miRNA sequences targeting the mRNA of five of the structural NDV proteins in chicken embryo fibroblast cells (DF-1) would lead to decreased viral yield after infection, and/or resistance against NDV cytopathic effects. Inhibition of Newcastle disease virus replication by RNA interference targeting the matrix protein gene in chicken embryo fibroblasts cache = ./cache/cord-350762-rh4zbehk.txt txt = ./txt/cord-350762-rh4zbehk.txt === reduce.pl bib === id = cord-351377-xorj8tnz author = Kao, Chi-Fei title = The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date = 2018-10-04 pages = extension = .txt mime = text/plain words = 5936 sentences = 234 flesch = 48 summary = Moreover, inoculation with iPEDVPT-P96 elicited comparable levels of anti-PEDV specific plasma IgG and fecal/salivary IgA, neutralizing antibody titers, and similar but less effective immunoprotection against the virulent PEDVPT-P5 challenge compared to the parental PEDVPT-P96. In the present study, an infectious cDNA clone of an attenuated G2b PEDV strain was successfully generated for the first time, and the in vitro and in vivo data indicate that iPEDVPT-P96 is further attenuated but remains immunogenic compared to its parental PEDVPT-P96 viral stock. While one piglet in the PEDVPT-P96 group showed intermittent loose diarrhea (score = 1) and viral shedding at 6 to 11 days post-inoculation (DPI) with the peak viral titer of 1.45 ± 3.24 log 10 RNA copies/mL at 8 DPI (Figure 4) , no evidence of PEDV-associated clinical signs and fecal viral shedding were demonstrated in both iPEDVPT-P96 and mock groups. cache = ./cache/cord-351377-xorj8tnz.txt txt = ./txt/cord-351377-xorj8tnz.txt === reduce.pl bib === id = cord-349358-leicos9j author = Ketzinel‐Gilad, Mali title = RNA interference for antiviral therapy date = 2006-06-16 pages = extension = .txt mime = text/plain words = 12734 sentences = 684 flesch = 44 summary = During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Likewise, expression vectors of siRNAs specific for two different regions of the WNV genome protected 293T cells from WNV infection, and significantly reduced viral RNA replication and virus production [35] . From the reports on the use of siRNA against human viral pathogens causing acute disease, we could learn that for each specific pathogen infecting a specific cell lineage or tissue, we would probably need to perform an indepth assessment, with proper in vitro and in vivo models, and develop specific delivery systems. The most challenging part of RNAi approaches for chronic viral infections is to design the best delivery method that would facilitate the targeting of the specific organ/cells with the appropriate expression system, for durable intracellular levels of gene-silencing effect. cache = ./cache/cord-349358-leicos9j.txt txt = ./txt/cord-349358-leicos9j.txt === reduce.pl bib === id = cord-351489-tzmev77c author = Yuan, Shuofeng title = Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date = 2020-06-10 pages = extension = .txt mime = text/plain words = 5002 sentences = 238 flesch = 40 summary = They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. In this primary screening, chloroquine, lopinavir, and remdesivir which were recently reported to have anti-SARS-CoV-2 activity, exhibited about 1.3-2.0 log10 copies/mL reduction in viral RNA load ( Figure 1 ). In comparison, recombinant IFN-β demonstrated the most potent anti-SARS-CoV-2 activity, with Avonex (IFN-β1a), Rebif (IFN-β1a), and Betaferon (IFN-β1b) each achieving about 3 log10 copies/mL reduction in viral load. In our primary screening using a fixed antiviral agent concentration and virus inoculum, we identified recombinant IFNs and lipogenesis modulators to be the most potent anti-SARS-CoV-2 agents among 22 broad-spectrum antivirals. cache = ./cache/cord-351489-tzmev77c.txt txt = ./txt/cord-351489-tzmev77c.txt === reduce.pl bib === id = cord-350083-kldu8q8x author = Oany, Arafat Rahman title = Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date = 2015-08-08 pages = extension = .txt mime = text/plain words = 5019 sentences = 315 flesch = 51 summary = title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. To date, information regarding the processing, structure and functions of Ebola virus (EBOV) protein L (EBOL) demonstrates that it is an RNA-dependent RNA polymerase, with the assistance of VP35. In the present study, we have followed immunoinformatics approaches for designing potential conserved epitope candidate for the utility of vaccine development against the deadly Ebola virus, with an expectation of further wet lab validation. Protein variability server predicted the variability of the conserved region of the RNA-dependent RNA polymerase-L ( Fig. 10) to ensure that the proposed epitope is within the invariable region. Design of an epitope-based peptide vaccine against spike protein of human corona virus: an in silico approach cache = ./cache/cord-350083-kldu8q8x.txt txt = ./txt/cord-350083-kldu8q8x.txt === reduce.pl bib === id = cord-351482-hzh5tyoo author = Peng, Xinxia title = Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date = 2011-11-15 pages = extension = .txt mime = text/plain words = 7697 sentences = 348 flesch = 49 summary = The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). cache = ./cache/cord-351482-hzh5tyoo.txt txt = ./txt/cord-351482-hzh5tyoo.txt === reduce.pl bib === id = cord-351837-vasuu70k author = Shannon, Ashleigh title = Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date = 2020-09-17 pages = extension = .txt mime = text/plain words = 6507 sentences = 349 flesch = 50 summary = title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. This enzyme readily incorporates T-705-ribose-5′-phosphate into viral RNA in vitro, and cell culture based infectious virus studies show an increase in mutations in the presence of Favipiravir. To determine the efficacy and MoA of T-705 against SARS-CoV we first characterised nsp12 primerdependent activity using traditional annealed primer-template (PT) and self-priming hairpin (HP) RNAs that may confer additional stability on the elongation complex ( Supplementary Fig. 1c) . These data reveal that the SARS-CoV nsp12 is the fastest viral RdRp known, with rates significantly faster than the 5-20 s −1 observed for picornaviral polymerases at room temperature [33] [34] [35] and 4-18 s −1 for hepatitis C and dengue virus polymerases at 30 and 37°C 36, 37 . cache = ./cache/cord-351837-vasuu70k.txt txt = ./txt/cord-351837-vasuu70k.txt === reduce.pl bib === id = cord-349672-2kt7xw8i author = Dasgupta, Tumpa title = Mechanism of Type IA Topoisomerases date = 2020-10-17 pages = extension = .txt mime = text/plain words = 8538 sentences = 463 flesch = 53 summary = Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. In type IA topoisomerases, the hydroxyl group in the side chain of the active site tyrosine residue is responsible for the first nucleophilic attack on the scissile phosphate of a single-stranded DNA resulting in the cleavage of the G-strand and the formation of the transient 5 -phospho-tyrosyl covalent linkage [66] . Though the type IA topoisomerase core domain that forms the characteristic torus structure contains all the highly conserved motifs responsible for G-strand binding and cleavage religation, the C-terminal domains of bacterial topoisomerase I have been shown to be required for removing negative supercoils from DNA rapidly in a processive mechanism [61, 72, [84] [85] [86] [87] . cache = ./cache/cord-349672-2kt7xw8i.txt txt = ./txt/cord-349672-2kt7xw8i.txt === reduce.pl bib === id = cord-351115-dy81dtnk author = Wang, Chen title = Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date = 2020-10-20 pages = extension = .txt mime = text/plain words = 6133 sentences = 310 flesch = 50 summary = This study addresses both by utilizing evolutionary information from SARS-CoV-2 sequence and structural data to search for actionable functional sites for each protein in the SARS-CoV-2 genome. Here we systematically suggest potential drug target sites for most SARS-CoV-2 proteins based on evolutionary information. This relative ranking re ects the variation entropy of each sequence position within and across the branches of an associated phylogenetic tree, revealing evolutionary pressure points that correspond to functional and structural determinants, and the protein sites at which they often cluster (30) . As in our approach to discover ET drug sites, we combined ET residue ranking information with sequencing data from SARS-CoV-2 isolates to arrive at linear peptides along the proteome that are evolutionarily important and also show little variation in the current outbreak ( Figure S6 , Dataset S5). The data include, for example, multiple sequence alignments, precalculated ET ranks, and predicted epitopes (both linear and structural) for all SARS-CoV-2 proteins. cache = ./cache/cord-351115-dy81dtnk.txt txt = ./txt/cord-351115-dy81dtnk.txt === reduce.pl bib === id = cord-351520-c5fi2uoh author = Zhong, Bo title = Regulation of virus-triggered type I interferon signaling by cellular and viral proteins date = 2010-02-01 pages = extension = .txt mime = text/plain words = 10571 sentences = 637 flesch = 46 summary = Recently, we and others identified a new adapter protein called mediator of IRF3 activation (MITA, also known as STING), which plays a critical role in virus-induced type I IFN expression (Ishikawa and Barber, 2008; Zhong et al., 2008) . cache = ./cache/cord-351520-c5fi2uoh.txt txt = ./txt/cord-351520-c5fi2uoh.txt === reduce.pl bib === id = cord-352178-irjhmxsg author = Saxton-Shaw, Kali D. title = O'nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date = 2013-01-24 pages = extension = .txt mime = text/plain words = 5953 sentences = 299 flesch = 49 summary = Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Our study analyzed both structural and non-structural regions of the ONNV genome using chimeric viruses and artificially infected Anopheles gambiae mosquitoes. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from chikungunya virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Six additional non-structural chimeric viruses were also constructed using a novel type II restriction enzyme cloning strategy to examine the broader genome with respect to ONNV's unique vector specificity for An. gambiae mosquitoes (Figure 2) . cache = ./cache/cord-352178-irjhmxsg.txt txt = ./txt/cord-352178-irjhmxsg.txt === reduce.pl bib === id = cord-352088-9k01ej6l author = Saiz, Juan-Carlos title = Vaccines against RNA Viruses date = 2020-08-27 pages = extension = .txt mime = text/plain words = 2330 sentences = 94 flesch = 39 summary = The authors show that vaccination with the GP5-Mosaic-based vaccines resulted in cellular reactivity and higher levels of neutralizing antibodies to both VR2332 and MN184C PRRSV strains, whilst vaccination with the GP5-WT vaccines only induced response against the heterologous challenging virus (VR2332). Another important disease in pigs is that caused by the porcine epidemic diarrhea virus (PEDV), a coronavirus responsible of highly contagious intestinal infections that may result in the death of newborn piglets and weight loss in pigs of all ages, and that seriously damages the swine industry. López-Gil and coworkers [7] , by using an approach based on the modified vaccinia Ankara (MVA) encoding the RVFV glycoproteins (rMVAGnGc), extend their previous observations that a single inoculation was sufficient to induce a protective immune response in mice after a lethal viral challenge, which was related to the presence of glycoprotein specific CD8+ cells and a low-level detection of in vitro neutralizing antibodies. cache = ./cache/cord-352088-9k01ej6l.txt txt = ./txt/cord-352088-9k01ej6l.txt === reduce.pl bib === id = cord-352361-jh31omg2 author = Nobach, Daniel title = No evidence for European bats serving as reservoir for Borna disease virus 1 or other known mammalian orthobornaviruses date = 2020-01-30 pages = extension = .txt mime = text/plain words = 3751 sentences = 209 flesch = 41 summary = Although several rodents and other small mammals are known as important reservoirs for many viruses, bats (order: Chiroptera) represent the vast majority of identified natural reservoirs of several virus families/species to date [1, 14] . In conclusion, due to the continuous detection of new viruses in bats, the unclear situation regarding additional potential BoDV-1-reservoirs and molecular evidence for co-evolution of bats and bornaviruses, this study was conducted to investigate the potential presence of the most common orthobornaviruses in bats from endemic and non-endemic areas in Germany. Although the bicolored white-toothed shrew has been identified as indigenous reservoir of BoDV-1, other potential reservoirs or animal carriers are still unknown so that further investigations of small mammals including bat species are urgently needed. Distribution of Borna disease virus antigen and RNA in tissues of naturally infected bicolored white-toothed shrews, Crocidura leucodon, supporting their role as reservoir host species cache = ./cache/cord-352361-jh31omg2.txt txt = ./txt/cord-352361-jh31omg2.txt === reduce.pl bib === id = cord-351559-az4pgi9k author = Turjya, Rafeed Rahman title = Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date = 2020-06-29 pages = extension = .txt mime = text/plain words = 2438 sentences = 173 flesch = 48 summary = Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. cache = ./cache/cord-351559-az4pgi9k.txt txt = ./txt/cord-351559-az4pgi9k.txt === reduce.pl bib === id = cord-351920-igmb2yfe author = Oma, Veslemøy Sunniva title = Bovine coronavirus in naturally and experimentally exposed calves; viral shedding and the potential for transmission date = 2016-06-13 pages = extension = .txt mime = text/plain words = 5526 sentences = 317 flesch = 57 summary = The aims of the study were to investigate the duration and quantity of BCoV shedding in feces and nasal secretions related to clinical signs, the presence of virus in blood and tissues and to test the hypothesis that seropositive calves are not infectious to naïve in-contact calves three weeks after BCoV infection. In two experimental studies, infected calves were not protected against reinfection with a different BCoV strain three weeks after the first challenge, but did not develop clinical signs [19, 20] . The majority of experimental studies have used BCoV inoculation as challenge procedure, which may influence clinical signs and viral shedding, and thereby the transmission potential compared to natural infection. The present study showed that calves infected with BCoV shed viral RNA for five weeks, and harbored viral RNA in intestinal tissues and lymph nodes even longer. cache = ./cache/cord-351920-igmb2yfe.txt txt = ./txt/cord-351920-igmb2yfe.txt === reduce.pl bib === id = cord-351854-5s03f0pp author = Ben-Ami, Roni title = Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date = 2020-04-22 pages = extension = .txt mime = text/plain words = 3316 sentences = 197 flesch = 54 summary = title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. Three such limitations might be: (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; (3) favorability of simple algorithms which may minimize human error in a laboratory setting. . https://doi.org/10.1101/2020.04.17.20069062 doi: medRxiv preprint probability of a sample to be positive by p (prevalence of detectable COVID-19 patients in the relevant population) and the pool size by n. This allows for reliable and efficient screening of large asymptomatic populations for the presence of SARS-CoV-2 infection, even when RNA extraction and RT-PCR reagents are in short supply. cache = ./cache/cord-351854-5s03f0pp.txt txt = ./txt/cord-351854-5s03f0pp.txt === reduce.pl bib === id = cord-350286-n7ylgqfu author = Giri, Rajanish title = When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date = 2020-04-03 pages = extension = .txt mime = text/plain words = 15827 sentences = 874 flesch = 56 summary = The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . cache = ./cache/cord-350286-n7ylgqfu.txt txt = ./txt/cord-350286-n7ylgqfu.txt === reduce.pl bib === id = cord-351365-dc9t3vh3 author = Todt, Daniel title = Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date = 2016-10-13 pages = extension = .txt mime = text/plain words = 6318 sentences = 320 flesch = 40 summary = Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis. Figure 1 provides an overview of a selection of RNA viruses against which RBV was shown to be active: hepatitis C virus (HCV, Flaviviridae), dengue virus (DENV, Flaviviridae), respiratory syncytial virus (RSV, Paramyxoviridae), influenza A and B virus (Orthomyxoviridae), chikungunya virus (CHIKV, Togaviridae), poliovirus (Picornaviridae), Hantaan virus (Bunyaviridae), and Lassa virus (Arenaviridae) [28, 29] ( Figure 1 ). Furthermore, mechanisms on the virus itself were described by inhibition of the capping efficiency, the viral polymerase, and a mutagenic effect on newly synthesized RNA genomes. A Mutation in the hepatitis E virus RNA polymerase promotes its replication and associates with ribavirin treatment failure in organ transplant recipients cache = ./cache/cord-351365-dc9t3vh3.txt txt = ./txt/cord-351365-dc9t3vh3.txt === reduce.pl bib === id = cord-352768-16vgnq14 author = Tang, Qingquan title = Application of siRNA Against SARS in the Rhesus Macaque Model date = 2008 pages = extension = .txt mime = text/plain words = 4389 sentences = 274 flesch = 48 summary = Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen's genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. A pair of siRNAs showing prominent prophylactic and therapeutic activities in the cell culture study (29), referred to as siSC2 and siSC5, were further evaluated in vivo, first in mice using a reporter gene assay and subsequently using a clinically acceptable intranasal administration in the recently established rhesus macaque SARS model (23-26). cache = ./cache/cord-352768-16vgnq14.txt txt = ./txt/cord-352768-16vgnq14.txt === reduce.pl bib === id = cord-353640-giznbcpd author = Barza, Ruby title = Use of a Simplified Sample Processing step without RNA Extraction for direct SARS-CoV-2 RT-PCR Detection date = 2020-08-11 pages = extension = .txt mime = text/plain words = 1204 sentences = 59 flesch = 55 summary = RT-PCR results using the ChromaCode HDPCR™ SARS-CoV-2 were compared using the heat-RNA release method and an automated RNA extraction system (EMAG). We compared the diagnostic sensitivity of the heat-RNA release method for detection of SARS-CoV-2 using NP swabs in viral transport media (VTM) to results obtained using an automated RNA extraction system (EMAG ® , bioMerieux, Durham, NC). A total of 174 COVID-19 positive samples were used for the study comprising 87 unique COVID-19 NP including Ct values using the heat-RNA release method were compared to the results obtained using the automated RNA-extraction method with both the LDT and ChromaCode SARS-CoV-2 assays. Comparison of the heat-RNA release method to EMAG ® using the ChromaCode SARS-CoV-2 RUO alone yielded a 94% agreement (81/86 positive samples). We found that the direct detection of SARS-CoV-2 using a 65°C heat inactivation and release step for 20minutes without RNA extraction and purification performed very well compared to the use of an automated RNA extraction instrument. cache = ./cache/cord-353640-giznbcpd.txt txt = ./txt/cord-353640-giznbcpd.txt === reduce.pl bib === id = cord-351548-jvl63652 author = Juranic Lisnic, Vanda title = Dual Analysis of the Murine Cytomegalovirus and Host Cell Transcriptomes Reveal New Aspects of the Virus-Host Cell Interface date = 2013-09-26 pages = extension = .txt mime = text/plain words = 11978 sentences = 623 flesch = 49 summary = Finally, a recent transcriptomic analysis of newly synthesized RNA in MCMV infected fibroblasts [15] applied RNA-Seq technology to study regulation of viral gene expression and identified a very early peak of viral gene transcriptional activity at 1-2 hours post infection followed by rapid cellular countermeasures but did not attempt to re-annotate MCMV genome. The MCMV transcripts identified through our classical cDNA cloning and sequencing (green arrows) and the RNA-Seq expression profiles (gray histograms), showed complementary results to each other but diverged dramatically from current annotations. Because cDNA cloning and RNA-Seq identified significant differences between the MCMV transcriptome and current annotations, we performed an in depth analysis of several genomic regions by northern analyses ( Figure 5 , Figures S2, S3 , S4, S5) using our cDNA clones to generate strand specific riboprobes ( Table 1) . cache = ./cache/cord-351548-jvl63652.txt txt = ./txt/cord-351548-jvl63652.txt === reduce.pl bib === id = cord-352664-heoj8ji8 author = Hubbard, Amelia title = Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date = 2015-02-25 pages = extension = .txt mime = text/plain words = 9181 sentences = 460 flesch = 45 summary = In this study, we developed a robust and rapid 'field pathogenomics' strategy, using transcriptome sequencing of PST-infected wheat leaves to gain insight into the population structure of an emerging pathogen. To characterize the genotypic diversity of PST at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the UK in the spring and summer of 2013 ( Figure 1a ; Table S1 in Additional file 1). To determine the relationship between the 2013 PST field isolates and previously prevalent PST populations, the genomes of 14 UK and 7 French purified PST isolates collected between 1978 and 2011 were sequenced using an Illumina whole-genome shotgun approach Figure 2 Identification of wheat varieties using transcriptome data generated directly from PST-infected field samples. We used multivariate discriminant analysis of principal components (DAPC) with the 34,764 biallelic SNP sites to define the population structure and identify groups of genetically related PST isolates. cache = ./cache/cord-352664-heoj8ji8.txt txt = ./txt/cord-352664-heoj8ji8.txt === reduce.pl bib === id = cord-352891-ljmkqdzx author = Parang, Keykavous title = Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date = 2020-05-17 pages = extension = .txt mime = text/plain words = 3165 sentences = 182 flesch = 52 summary = title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. Therefore, HCoV-229E may be a good initial model for the evaluation of antiviral compounds that could have potential applications against other coronaviruses, such as SARS-COV-2, the coronavirus that causes COVID-19. We have previously shown that the conjugation of certain fatty acids to the anti-HIV NRTIs, such as FLT, 3TC and FTC, enhanced activity against X4, R5, cell-associated, and/or multi-drug resistant virus when compared with their parent nucleosides [24] [25] [26] [27] . A series of anti-HIV nucleosides and their fatty acyl derivatives were compared with remdesivir for antiviral activity against HCoV-229E in MRC-5 cells. cache = ./cache/cord-352891-ljmkqdzx.txt txt = ./txt/cord-352891-ljmkqdzx.txt === reduce.pl bib === id = cord-354465-5nqrrnqr author = Haslinger, Christian title = RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties date = 1999 pages = extension = .txt mime = text/plain words = 10341 sentences = 756 flesch = 67 summary = Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. In case of one particular class of biopolymers, the ribonucleic acid (RNA) molecules, decoding of information stored in the sequence can be properly decomposed into two steps: (i) formation of the secondary structure, that is, of the pattern of Watson-Crick (and GU) base pairs, and (ii) the embedding of the contact structure in three-dimensional space. On the other hand, an increasing number of experimental findings, as well as results from comparative sequence analysis, suggest that pseudo-knots are important structural elements in many RNA molecules (Westhof and Jaeger, 1992) . cache = ./cache/cord-354465-5nqrrnqr.txt txt = ./txt/cord-354465-5nqrrnqr.txt === reduce.pl bib === id = cord-354536-c9v9kbw8 author = Han, Yan-Jie title = Advances and challenges in the prevention and treatment of COVID-19 date = 2020-07-09 pages = extension = .txt mime = text/plain words = 5268 sentences = 330 flesch = 48 summary = This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. cache = ./cache/cord-354536-c9v9kbw8.txt txt = ./txt/cord-354536-c9v9kbw8.txt === reduce.pl bib === id = cord-352465-n746e8qt author = Wang, Fei title = Targeting stress granules: A novel therapeutic strategy for human diseases date = 2020-08-16 pages = extension = .txt mime = text/plain words = 9128 sentences = 555 flesch = 40 summary = Chronic stress might even induce formation of cytotoxic pathological SGs. SGs participate in various biological functions including response to apoptosis, inflammation, immune modulation, and signalling pathways; moreover, SGs are involved in pathogenesis of neurodegenerative diseases, viral infection, aging, cancers and many other diseases. One of the most studied mRNP granules is SGs. SGs are a type of dynamic granular substance formed of mRNA of stagnant translation and RBPs in the cytoplasm of eukaryotic cells, the formation of which is stimulated by various stresses including oxidative stress, heat shock, hypoxia, or viral infection (Fig. 1) . For example, eIF2α phosphorylation-dependent SGs (Type I) induced by sodium arsenite (SA) and bortezomib [40] may protect cells in the stress response, inhibit apoptosis and promote cell survival by the sequestration of signalling molecules, such as RACK1 [41] , ROCK1 [42] and Raptor [43] . cache = ./cache/cord-352465-n746e8qt.txt txt = ./txt/cord-352465-n746e8qt.txt === reduce.pl bib === id = cord-354394-zojhdnlu author = Wang, Wei-Kung title = Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date = 2004-07-17 pages = extension = .txt mime = text/plain words = 3972 sentences = 175 flesch = 56 summary = We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 10(2) to 5.93 x 10(6) copies/mL) and saliva (7.08 x 10(3) to 6.38 x 10(8) copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four patients, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis. Using a quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) assay and fractionation experiment, we investigated the load of SARS-CoV in these samples and different components of the throat wash. As shown in Table 1 , SARS-CoV RNA was detected in the cell-associated component of the throat wash from all 16 specimens examined. cache = ./cache/cord-354394-zojhdnlu.txt txt = ./txt/cord-354394-zojhdnlu.txt === reduce.pl bib === id = cord-352814-fcl2g5wr author = Balboni, Andrea title = A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date = 2011-11-22 pages = extension = .txt mime = text/plain words = 3998 sentences = 177 flesch = 49 summary = In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The aim of this work was to develop a real-time PCR assay for diagnosing infection with SARS-related coronaviruses from bat guano in order to use it as a screening tool in epidemiological surveys for the detection of the viruses. The developed SYBR Green real-time PCR techniques were applied to an SARS-like coronavirus survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) which were sampled in Italy in 2009, resulting in a prevalence of coronavirus infection of 42%. After optimisation of the SYBR Green real-time PCR assay, for each run, duplicates of six 10-fold dilutions of the standard plasmid, triplicates of the viral reverse-transcribed RNA of the bat samples, and a no template control were simultaneously subjected to analysis. cache = ./cache/cord-352814-fcl2g5wr.txt txt = ./txt/cord-352814-fcl2g5wr.txt === reduce.pl bib === id = cord-353524-3w970ycx author = Dömling, Alexander title = Chemistry and Biology of SARS-CoV-2 date = 2020-05-22 pages = extension = .txt mime = text/plain words = 3942 sentences = 237 flesch = 52 summary = Given that SARS-CoV-2 and SARS-CoV share very high identical sequence in their 3CLpro, these HIV protease inhibitors are currently again repurposed for the treatment of COVID-19 (Chinese Clinical Trial Registry: ChiCTR2000029539). 30, 31 The interplay of the ACE receptor in cardiovascular diseases (with the well-known drug class of ACE inhibitors) and as the docking point for SARS-CoV-2 cellular infection is a current point of intense debate and research. For example, the crystal structure of SARS-CoV-2 N protein RNA-binding domain was just published and will give structural insight as a potential drug target. Potential broad spectrum inhibitors of the coronavirus 3CLpro: A virtual screening and structure-based drug design study Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites cache = ./cache/cord-353524-3w970ycx.txt txt = ./txt/cord-353524-3w970ycx.txt === reduce.pl bib === id = cord-354510-jlg5je0s author = de Carvalho, A. F. title = THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date = 2020-06-20 pages = extension = .txt mime = text/plain words = 4112 sentences = 234 flesch = 58 summary = Methods Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. 13 Here we describe the use of a simple, virus-inactivating and denaturing solution as part of a swab collection kit, aiming to decrease the infectious potential of the clinical sample and, at the same time, to preserve highly frail RNA molecules during transportation and short-term storage before testing. In order to increase personnel safety, to avoid losing collaborators due to infections by SARS-CoV-2, and at the same time to increase preservation of the RNA contained in clinical samples, we introduced the use of the guanidinecontaining solution as collection and transport media instead of commonly used viral transport media (VTM). cache = ./cache/cord-354510-jlg5je0s.txt txt = ./txt/cord-354510-jlg5je0s.txt === reduce.pl bib === id = cord-352379-q5inrxcm author = Lai, Michael M. C. title = SARS virus: The beginning of the unraveling of a new coronavirus date = 2003-10-17 pages = extension = .txt mime = text/plain words = 7004 sentences = 376 flesch = 49 summary = Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public's interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection cache = ./cache/cord-352379-q5inrxcm.txt txt = ./txt/cord-352379-q5inrxcm.txt === reduce.pl bib === id = cord-356013-pl3tmky8 author = Brian, D. A. title = Coronavirus Genome Structure and Replication date = 2005 pages = extension = .txt mime = text/plain words = 8382 sentences = 446 flesch = 53 summary = In addition to the SARS coronavirus (treated separately elsewhere in this volume), the complete genome sequences of six species in the coronavirus genus of the coronavirus family [avian infectious bronchitis virus-Beaudette strain (IBV-Beaudette), bovine coronavirus-ENT strain (BCoV-ENT), human coronavirus-229E strain (HCoV-229E), murine hepatitis virus-A59 strain (MHV-A59), porcine transmissible gastroenteritis-Purdue 115 strain (TGEV-Purdue 115), and porcine epidemic diarrhea virus-CV777 strain (PEDV-CV777)] have now been reported. With regard to the 5 0 UTR it is known that the 5 0 -terminal sequence is required for DI RNA replication ) and at least two stem-loops (stem-loops III and IV in Fig. 4 ) function as higher-order cis-acting signaling elements (Raman et al. cis-Acting sequences required for coronavirus infectious bronchitis virus defective-RNA replication and packaging cache = ./cache/cord-356013-pl3tmky8.txt txt = ./txt/cord-356013-pl3tmky8.txt === reduce.pl bib === id = cord-354824-7fdcu2f0 author = Wu, Renyi title = An Update on Current Therapeutic Drugs Treating COVID-19 date = 2020-05-11 pages = extension = .txt mime = text/plain words = 9652 sentences = 504 flesch = 42 summary = Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients. This estimated 20% of patients developing more severe disease with SARS-CoV-2 infection are most likely due to genetics, epigenetics, and or other factors, with dampened innate immune response to fight the virus coupled with enhanced viral load leading to cytokine storm, severe inflammatory/oxidative stress response, and severe lung injury secondary to ARDS. Chloroquine can inhibit the entry of SARS-CoV-2 and prevent virus-cell fusion by interfering with glycosylation of ACE2 receptor and its binding with spike protein, suggesting that chloroquine treatment might be more effective in the early stage of infection, before COVID-19 reduces ACE2 expression and activity [30, 38, 39] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, doubleblinded, phase IIb clinical trial (CloroCovid-19 Study) cache = ./cache/cord-354824-7fdcu2f0.txt txt = ./txt/cord-354824-7fdcu2f0.txt === reduce.pl bib === id = cord-353576-f29kmtot author = Maricic, T. title = A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date = 2020-06-26 pages = extension = .txt mime = text/plain words = 3499 sentences = 200 flesch = 60 summary = We then tested 1 l of mouthwash from each of the 20 individuals using two RT-qPCR kits advertised to allow direct detection of SARS-CoV-2 from nasopharyngeal swabs: Luna Universal Probe (NEB, Ipswich, USA) and PrimeDirect (Takara, Kyoto, Japan) as well as another kit, SuperScript III with Platinum Taq (Invitrogen, Waltham, USA). To systematically investigate how the NEB Luna assay performs compared to RNA extraction followed by the Roche assay for mouthwash samples, we investigated 62 gargle lavages from patients that were either negative or presented with various viral loads based on previous investigations. In the first scheme, the samples were tested individually using the direct RT-qPCR protocol and the results were evaluated and reported back to the facility by 7 p.m. To detect any inhibition that the mouthwash samples may introduce into the RT-qPCR reactions, we added a synthesized control RNA that was quantified in parallel with SARS-CoV-2 by a probe . cache = ./cache/cord-353576-f29kmtot.txt txt = ./txt/cord-353576-f29kmtot.txt === reduce.pl bib === id = cord-354051-ro3o27pv author = Peccia, J. title = SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date = 2020-05-22 pages = extension = .txt mime = text/plain words = 1244 sentences = 101 flesch = 57 summary = title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant. SARS-CoV-2 viral RNA concentrations were quantitatively compared with local hospital admission data and community COVID-19 compiled testing data. SARS-CoV-2 RNA sludge concentrations were quantitatively compared with data that are commonly used to track the community progression of COVID-19 including hospital admissions (Figure 2A This study uniquely utilized primary sewage sludge instead of raw wastewater for virus RNA measurements. cache = ./cache/cord-354051-ro3o27pv.txt txt = ./txt/cord-354051-ro3o27pv.txt === reduce.pl bib === id = cord-355676-2y8vowbi author = Liu, Pinghua title = A Previously Unrecognized Unr Stem-Loop Structure in the Coronavirus 5’ Untranslated Region Plays a Functional role in Replication date = 2006 pages = extension = .txt mime = text/plain words = 1329 sentences = 76 flesch = 62 summary = The RNA secondary structure prediction algorithm Vienna RNA 1.5 4 was used to predict the secondary structures of group 1 and group 2 coronavirus 5' UTRs. A reverse genetic system based on in vitro assembly of cloned cDNAs (A-G) was used to recover wild-type MHV-A59 1000 and mutant viruses. The assembled fragment containing either the wild-type sequence, or with mutations in SL2, was ligated into MHV-A59-1000 RNA was electroporated into BHK-R cells to recover infectious virus as described. Analysis of the entire 30 kb MHV and SARS-CoV genomes reveals that SL2-like stem loops are extremely rare (appearing just 3 and 5 other times, respectively); this suggests an important role in coronavirus replication. Consistent with the predicted structure of the UNR loop, the U49A mutant was viable and produced a virus with a near normal plaque size (Figs 4A-B) . cache = ./cache/cord-355676-2y8vowbi.txt txt = ./txt/cord-355676-2y8vowbi.txt === reduce.pl bib === id = cord-355743-vjiecd4k author = Ghosh, Sabyasachi title = Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date = 2020-04-29 pages = extension = .txt mime = text/plain words = 4826 sentences = 279 flesch = 63 summary = The decoding algorithm takes as input cycle threshold values from qPCR tests on the pools, and returns a result for each sample, along with an estimate of viral load if positive. Once pooled tests are run, the cycle threshold values can be entered into the app which solves for and displays the list of positive and negative samples along with an estimate of viral loads. 16 × 40 pooling matrix: Table 2 shows the emulated cycle threshold (Ct) values for the 16 RT-qPCR tests corresponding to five different trials (0, 1, 2, 3 or 4 positive samples out of a total of 40 samples). 24 × 60 pooling matrix: Table 3 shows the cycle threshold (Ct) values obtained for the 24 RT-qPCR tests corresponding to a trial with 2 positive samples out of a total of 60 samples. cache = ./cache/cord-355743-vjiecd4k.txt txt = ./txt/cord-355743-vjiecd4k.txt === reduce.pl bib === id = cord-353274-wozwpvpq author = Borremans, B. title = Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date = 2020-05-20 pages = extension = .txt mime = text/plain words = 6160 sentences = 362 flesch = 50 summary = In this study we quantified IgG and IgM antibody kinetics and RNA shedding probability during SARS-CoV-2 infection (up to 60 days post symptom onset) by drawing on published data. This formal integration approach enabled us to leverage 3,214 data points from 516 individuals with symptoms ranging from asymptomatic to critical, published in 22 studies, resulting in a quantitative synthesis of diverse data on anti-SARS-CoV-2 antibody patterns and RNA shedding during the early phase of infection. One of the goals of this study is to estimate the means and variation of IgG and IgM seroconversion times (time between symptom onset and first antibody detection) for different assays, antigens, and disease severity. . https://doi.org/10.1101/2020.05.15.20103275 doi: medRxiv preprint weighted bootstrapping procedure integrates all types of data that contain useful information about the timing of seroconversion of different antibodies in day(s) post symptom onset (dpo). The probability of detecting SARS-CoV-2 specific IgG or IgM in plasma or serum samples was estimated by integrating data on whether an individual tested positive or negative on a given dpo. cache = ./cache/cord-353274-wozwpvpq.txt txt = ./txt/cord-353274-wozwpvpq.txt === reduce.pl bib === id = cord-354096-x2skguz8 author = Ray, Pradipta R. title = A pharmacological interactome between COVID-19 patient samples and human sensory neurons reveals potential drivers of neurogenic pulmonary dysfunction date = 2020-06-01 pages = extension = .txt mime = text/plain words = 6354 sentences = 328 flesch = 46 summary = We hypothesized that SARS-CoV-2 infection drives changes in immune cell-derived factors that then interact with receptors expressed by the sensory neuronal innervation of the lung to further promote important aspects of disease severity, including ARDS. We sought to quantify how immune cells might interact with sensory innervation of the lung in COVID-19 using published data from patients, existing RNA sequencing datasets from human dorsal root ganglion neurons and other sources, and a genome-wide ligand-receptor pair database curated for pharmacological interactions relevant for neuro-immune interactions. Additionally, we found that upregulation of transcription factor genes in COVID-19 samples identifies transcription factors associated with alveolar cell types (EHF, PAX9, ELF3, GHRL2) and immune cells (RFX3, SOX5, TP63, HOPX) with functions including regulation of antiviral pathways (NR3C2), based on ARCHS4 database (Lachmann et al., 2018) and the Enrichr gene set enrichment analysis tool (Kuleshov et al., 2016) (Supplementary Table 2 ). cache = ./cache/cord-354096-x2skguz8.txt txt = ./txt/cord-354096-x2skguz8.txt === reduce.pl bib === id = cord-355499-5vj3oasa author = Song, Xiangjun title = Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date = 2015-06-07 pages = extension = .txt mime = text/plain words = 4223 sentences = 275 flesch = 53 summary = title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 In this study, we performed microRNA microarray assay and predicted targets of altered miRNAs. The results showed TGEV infection caused the change of miRNAs profile. In conclusion, differentially expressed miR-4331 that is caused by TGEV infection can suppress transcription of TGEV gene 7 via targeting cellular CDCA7. Overall, we observed that TGEV infection caused the change of miRNA profile and miR-4331 suppressed transcription of TGEV gene 7 via directly targeting CDCA7. The major findings in this study are that TGEV infection leads to the change of cellular miRNAs expression profile, and altered miRNAs regulate transcription of TGEV gene 7 through targeting cellular CDCA7. In conclusion, the results of the present study provide evidence that TGEV infection resulted in altered profiles of miRNAs in PK-15 cells and the differentially expressed miR-4331 was involved in regulation of TGEV transcription by targeting cellular CDCA7. cache = ./cache/cord-355499-5vj3oasa.txt txt = ./txt/cord-355499-5vj3oasa.txt === reduce.pl bib === id = cord-353810-mf753ae9 author = Tan, Cedric Chih Shen title = A novel method for the capture-based purification of whole viral native RNA genomes date = 2019-04-08 pages = extension = .txt mime = text/plain words = 5929 sentences = 352 flesch = 54 summary = This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes. Based on the mapping rates to human and DENV1 reference genomes for pre and post-capture groups, shown in Table 2 , purification factor was calculated to be 272-fold. The minimum coverage required for variant calling was, as described above, benchmarked to that of Illumina reads so that the effectiveness of our capture-based purification method could be more accurately evaluated based on the higher error read rates of direct RNA sequencing technology. Indeed, after comparison of the postcapture and concentrated post-capture sequencing runs (Table 2) , the 2.5-fold increase in the percentage of reads mapping to DENV1 suggests that scaling our method greatly improved the signal-to-noise ratio of this particular downstream RNA assay. cache = ./cache/cord-353810-mf753ae9.txt txt = ./txt/cord-353810-mf753ae9.txt === reduce.pl bib === id = cord-354733-qxivrhj8 author = Gniazdowski, V. title = Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date = 2020-08-06 pages = extension = .txt mime = text/plain words = 3924 sentences = 251 flesch = 56 summary = Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Prolonged viral RNA shedding was associated with recovery of infectious 31 virus in specimens collected up to 20 days after the first positive result in patients who were 32 symptomatic at the time of specimen collection. Infection control personnel and physicians managing COVID-19 patients and patients under 43 investigation (PUI) continue to face several diagnostic dilemmas related to a lack of 44 understanding of the clinical sensitivities of SARS-CoV-2 molecular diagnostics and the 45 correlation between viral RNA detection and shedding of infectious virus. cache = ./cache/cord-354733-qxivrhj8.txt txt = ./txt/cord-354733-qxivrhj8.txt === reduce.pl bib === id = cord-354829-god79qzw author = Mao, Kaimin title = Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets date = 2020-09-23 pages = extension = .txt mime = text/plain words = 6328 sentences = 315 flesch = 45 summary = title: Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets Here we performed a statistical meta-analysis of five publicly available gene expression datasets from LPS-induced ALI mouse models, conducted RNA-sequencing (RNA-seq) to screen differentially expressed genes (DEGs) in response to LPS administration and AST treatment, and integrative analysis to determine robust genetic signatures associated with LPS-induced ALI onset and AST administration. We subsequently integrated the RNA-seq and microarray meta-analysis data, and 11 core DEGs (Timp1, Ly6i, Cxcl13, Irf7, Cxcl5, Ccl7, Isg15, Saa3, Saa1, Tgtp1, and Gbp11) that were upregulated in ALI models and downregulated significantly after AST treatment were identified ( Table 2) . To further identify the robust expression signature related to LPS-induced ALI and investigate the transcriptional changes in response to the treatment of ALI by AST, we performed RNA-seq on three groups of mice and integrated the data with the results of the above mentioned meta-analysis. cache = ./cache/cord-354829-god79qzw.txt txt = ./txt/cord-354829-god79qzw.txt === reduce.pl bib === id = cord-353475-dtn7h1gj author = Haddad, Hazem title = miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date = 2020-08-20 pages = extension = .txt mime = text/plain words = 1462 sentences = 103 flesch = 64 summary = In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. To understand the early steps of COVID-19 infection, we predicted miRNAs sequences targeting the submitted 29903bp of viral ss-RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 complete genomic RNA sequence) from the isolate of Wuhan-Hu-J o u r n a l P r e -p r o o f 1. cache = ./cache/cord-353475-dtn7h1gj.txt txt = ./txt/cord-353475-dtn7h1gj.txt === reduce.pl bib === id = cord-354003-ko45l1qv author = Scarpin, M Regina title = Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation date = 2020-10-15 pages = extension = .txt mime = text/plain words = 16822 sentences = 829 flesch = 46 summary = Pioneering efforts to identify the mechanisms regulating translation of 5 0 TOP mRNAs, however, did show that wheat germ extracts contain a repressor that specifically limits translation of 5 0 TOP mRNAs in cell-free translation assays (Biberman and Meyuhas, 1999; Shama and Meyuhas, 1996) , suggesting that plants also discriminately regulate translation of 5 0 TOP mRNAs. Here, we show that the TOR-LARP1-5 0 TOP signaling axis regulates translation in Arabidopsis, impacting expression of a set of deeply conserved 5 0 TOP genes, including translation elongation factors, polyA-binding proteins, karyopherins/importins, and the translationally-controlled tumor protein. TOR-LARP1-5 0 TOP signaling in Arabidopsis seedlings regulates translation of mRNAs that encode deeply conserved eukaryotic proteins, plant lineage-specific proteins, and diverse proteins involved in ribosome biogenesis. cache = ./cache/cord-354003-ko45l1qv.txt txt = ./txt/cord-354003-ko45l1qv.txt === reduce.pl bib === id = cord-355179-wmfwl2bh author = Jung, Eunhye title = Neutralization of Acidic Intracellular Vesicles by Niclosamide Inhibits Multiple Steps of the Dengue Virus Life Cycle In Vitro date = 2019-06-18 pages = extension = .txt mime = text/plain words = 5305 sentences = 271 flesch = 44 summary = Overall, the data indicate that the antiviral activity of niclosamide during the early stage of the DENV life cycle correlates with the neutralization profile of the low-pH compartments, suggesting that blocking endosomal acidification results in the inhibition of viral genome replication and polyprotein processing, which further impedes viral protein expression and virus production. In this study, we found that neutralization of low-pH intracellular compartments by niclosamide not only inhibited the early stage of the DENV viral life cycle, such as viral RNA replication, independent of the entry step but also the late stage, specifically, the maturation of virus particles into infectious virions. Indeed, niclosamide treatment www.nature.com/scientificreports www.nature.com/scientificreports/ during the first 6 h of infection reduced DENV replication in BHK-21 cells harbouring dengue replicons to a level comparable to that of ribavirin, suggesting that the drug affects viral RNA replication and/or translation independent of its effect on entry, membrane fusion and genome release. cache = ./cache/cord-355179-wmfwl2bh.txt txt = ./txt/cord-355179-wmfwl2bh.txt === reduce.pl bib === id = cord-353484-q7d0ysbo author = Liu, Xue title = COVID-19: Progress in diagnostics, therapy and vaccination date = 2020-06-19 pages = extension = .txt mime = text/plain words = 8557 sentences = 465 flesch = 41 summary = Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. Another type of rapid diagnostic test (RDT) that detects the presence of viral antigens expressed by SARS-CoV-2 virus in a respiratory tract sample is of low complexity and may provide results typically within 30 minutes [68, 69] . Studies in Vero E6 cells have suggested that favipiravir can cripple the SARS-CoV-2 virus (EC50 = 61.88 μM) [88] , and patients with COVID-19 are being recruited in randomized trials to evaluate the efficacy of favipiravir plus other antivirals (e.g., ClinicalTrials.gov: ChiCTR2000029600, ChiCTR2000029544). As no specific therapeutic agents or vaccines are available for COVID-19, this therapy is the only strategy that is immediately available for use to prevent and treat a novel, emerging infectious disease such as SARS-CoV-2 infection [121, 122] . cache = ./cache/cord-353484-q7d0ysbo.txt txt = ./txt/cord-353484-q7d0ysbo.txt === reduce.pl bib === id = cord-355758-tk7eturq author = Berrio, Alejandro title = Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date = 2020-09-22 pages = extension = .txt mime = text/plain words = 2175 sentences = 156 flesch = 49 summary = Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. In Importantly, we also detected signals of positive selection in two additional regions of the 414 SARS-CoV-2 genome, specifically within the genes encoding Nsp4 and Nsp16 (Fig 1A) . Comparative analysis of coronavirus genomic RNA structure reveals 718 conservation in SARS-like coronaviruses. cache = ./cache/cord-355758-tk7eturq.txt txt = ./txt/cord-355758-tk7eturq.txt === reduce.pl bib === id = cord-355397-y69bk5jc author = Caruso, Ícaro P. title = Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism date = 2020-09-06 pages = extension = .txt mime = text/plain words = 5105 sentences = 297 flesch = 55 summary = Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs' Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. We calculated the structural model of the N-NTD:dsTRS complex based on the experimental data for the N-NTD interaction with a non-specific dsRNA (5'-CACUGAC-3') (dsNS) (16) using the HADDOCK 2.2 server (20) . In contrast to the decrease in the number of intramolecular hydrogen bonds between the sense and anti-sense strands of dsRNAs (WC base-pairing) due to N-NTD binding, we observed an increase in the average number of intermolecular hydrogen bonds formed between the nitrogenous bases of dsTRS and N-NTD (protein-RNA interaction) along the 100 ns MD simulation, whereas for dsNS, this average value was constant ( Figure 3B top). cache = ./cache/cord-355397-y69bk5jc.txt txt = ./txt/cord-355397-y69bk5jc.txt === reduce.pl bib === id = cord-355075-ieb35upi author = Papenfuss, Anthony T title = The immune gene repertoire of an important viral reservoir, the Australian black flying fox date = 2012-06-20 pages = extension = .txt mime = text/plain words = 8952 sentences = 480 flesch = 54 summary = alecto transcriptome provides information on a variety of immune genes not previously identified in any bat species and represents an important starting point for examining the antiviral activity of these molecules. To enrich for sequences corresponding to cytokines and innate immune genes, the second dataset was derived from pooled total RNA obtained from mitogen-stimulated spleen, white blood cells and lymph node and unstimulated thymus and bone marrow obtained from one pregnant female and one adult male flying fox. A full length transcript, encoding a 667 amino acid protein was identified in our bat transcriptome datasets and found to be orthologous to Mx1 based on comparison with known mammalian Mx1 and Mx2 family members (Figure 4a and data not shown). Genes involved in the adaptive immune system, including MHC class I and II genes and T and B cell receptors and co-receptors were highly represented in both the thymus and pooled datasets providing evidence that bats have all of the components necessary to mount an adaptive immune response. cache = ./cache/cord-355075-ieb35upi.txt txt = ./txt/cord-355075-ieb35upi.txt === reduce.pl bib === id = cord-355477-7xd93aqv author = SATIJA, NAMITA title = The Molecular Biology of SARS Coronavirus date = 2007-04-23 pages = extension = .txt mime = text/plain words = 4946 sentences = 279 flesch = 52 summary = abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells cache = ./cache/cord-355477-7xd93aqv.txt txt = ./txt/cord-355477-7xd93aqv.txt === reduce.pl bib === id = cord-356009-emn2w8if author = Roshandel, M. R. title = What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date = 2020-10-13 pages = extension = .txt mime = text/plain words = 4687 sentences = 292 flesch = 49 summary = Conclusions: Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight ?percent of patients but also its incidence may have associations with the severity of the ?systemic disease, ICU admission, and fatality rates. The searches included medical subject headings (MeSH) and keywords for SARS-CoV-2, COVID, Corona, together with shedding, persistence, urine, urinary, specimen, viral load, or RNA body fluids. We completed the data abstraction process using created forms to record study characteristics, clinical data, and laboratory data including study year and design, country of study origin, total initial population size, test type for disease diagnosis, test type for samples (urine/stool/rectal swab/blood), patients age (including mean and range), number of positive and total patients and/or (wherever applicable) number of positive and total specimens collected for each test category, disease severity, ICU admission, and fatality rate. cache = ./cache/cord-356009-emn2w8if.txt txt = ./txt/cord-356009-emn2w8if.txt === reduce.pl bib === id = cord-355357-b6aklh44 author = Stapleford, Kenneth A. title = Viral Polymerase-Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion date = 2015-08-26 pages = extension = .txt mime = text/plain words = 7650 sentences = 342 flesch = 43 summary = IMPORTANCE Previous studies using the RNA mutagen ribavirin to select for drug-resistant variants have highlighted the essential role of the viral RNA-dependent RNA polymerase in regulating replication fidelity. Similar to other studies, we previously utilized the RNA mutagens ribavirin and 5-fluorouracil to study drug-resistant mutations in alphaviruses (CHIKV and SINV) and identified residue 483 of the RdRp nsP4 as a key determinant of polymerase fidelity (10, 11) . Furthermore, given that both the CHIKV high-fidelity polymerase variant nsP4 (C483Y) and the novel nsP2 (G641D) variants were isolated in the same antiviral treatment, we addressed their additive roles in resistance to the RNA mutagens ribavirin and 5-fluorouracil (Fig. 1B) . By treating cells during viral infection with each compound, we found that the high-fidelity nsP2 variant and double mutant were more resistant to both nucleotide-depleting compounds ( Fig. 7B and C) , similar to what we observed with ribavirin treatment. cache = ./cache/cord-355357-b6aklh44.txt txt = ./txt/cord-355357-b6aklh44.txt === reduce.pl bib === id = cord-356115-vblgotjn author = Sawicki, Stanley G title = Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins date = 2005-12-09 pages = extension = .txt mime = text/plain words = 10631 sentences = 458 flesch = 52 summary = The coronavirus replicase-transcriptase complex is an assembly of viral and cellular proteins that mediate the synthesis of genome and subgenome-sized mRNAs in the virus-infected cell. Here, we report a genetic and functional analysis of 19 temperature-sensitive (ts) mutants of Murine hepatitis virus MHV-A59 that are unable to synthesize viral RNA when the infection is initiated and maintained at the non-permissive temperature. We focused our phenotypic analysis on the eight MHV-A59 ts mutants that had been genotyped and began by measuring ''total'' viral RNA synthesis in infected cells prior to and following shift from the permissive to the non-permissive temperature. This phenotype resembled that seen with MHV-A59-infected cells treated with CH, and we conclude that the complementation group I mutants are defective in their ability to form active replicase-transcriptase complexes at 40 8C but retain the positive-strand synthesis activity of the complexes formed at the permissive temperature. cache = ./cache/cord-356115-vblgotjn.txt txt = ./txt/cord-356115-vblgotjn.txt === reduce.pl bib === id = cord-354529-k8p2u7iq author = Wu, Yongran title = Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date = 2020-08-31 pages = extension = .txt mime = text/plain words = 3753 sentences = 223 flesch = 57 summary = Clinical information of patients was collected from the electronic medical information system of Jinyintan Hospital, including the following factors: demographic data; date of symptom onset, admission, first CP infusion and discharge; laboratory data before and after infusion of CP, including white blood cell count, neutrophil count, lymphocyte count, liver and kidney function test, and inflammatory factors such as high sensitive C-reaction protein (HsCRP); results of SARS-CoV-2 test and cycle threshold value (Ct value) of quantitative reverse transcription-polymerase chain reaction; patients' status and treatments before or after the CP therapy, including the vital signs, anti-virus therapy, oxygen therapy, and other treatments; total volume dose of CP; pulmonary imaging examination data; information on complications such as transfusion-related adverse reactions. Clinical Benefit and Outcome of Patients with Prolonged Positivity of SARS-CoV-2 RNA after CP Therapy As shown in Table 3 , the median and interquartile ranged total volume of CP transfusion was 400 (200-400) mL in EN group and 400 (400-800) mL in LN group. cache = ./cache/cord-354529-k8p2u7iq.txt txt = ./txt/cord-354529-k8p2u7iq.txt === reduce.pl bib === id = cord-352200-i05h8csb author = Xu, Yi title = Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date = 2012-04-27 pages = extension = .txt mime = text/plain words = 5286 sentences = 278 flesch = 47 summary = title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. As a whole, 81388 distinct unigenes have been identified and the results indicated that SRBSDV infection can potentially perturb primary metabolism and the ubiquitin-proteasome pathway of WBPH and activate immune regulatory systems, such as RNA interfering, autophagy and antimicrobial peptide production. However, some unigenes were obtained only from viruliferous or non-viruliferous samples (data not shown) and we believe these differences may be caused by distinctions that arise from long-term ecological adaptation to virus infection. In addition, GO analysis also showed a similar distribution of gene functions for non-viruliferous and viruliferous WBPH (Figure 4 ), indicating that the number of genes expressed in each GO category was not significantly affected by SRBSDV infection. cache = ./cache/cord-352200-i05h8csb.txt txt = ./txt/cord-352200-i05h8csb.txt === reduce.pl bib === id = cord-353703-u86ggw11 author = Gao, Peng title = Reprogramming the unfolded protein response for replication by porcine reproductive and respiratory syndrome virus date = 2019-11-18 pages = extension = .txt mime = text/plain words = 8258 sentences = 412 flesch = 49 summary = We provide evidence that the virus targets the UPR central regulator GRP78 for proteasomal degradation via a mechanism that requires viral glycoprotein GP2a, while both IRE1-XBP1s and PERK-eIF2α-ATF4 signaling branches of the UPR are turned on at early stage of infection. In support of our hypothesis, antibodies to ATF4, but not the isotype control (IgG), could immunoprecipitate viral RNA from infected MARC-145 cells, as detected by RT-qPCR of the PRRSV 5'UTR region ( Fig 7D) . Because GRP78 is the master regulator, its reduced accumulation likely prevents any modulation of the UPR, keeping the ER stress pathways induced for The abundance of viral RNA was assessed by RT-PCR of ORF7, normalized against the house-keeping gene GAPDH, and then compared the benefit of the virus. cache = ./cache/cord-353703-u86ggw11.txt txt = ./txt/cord-353703-u86ggw11.txt === reduce.pl bib === id = cord-355913-fhvt1ht1 author = Burrell, Christopher J. title = Virus Replication date = 2016-11-11 pages = extension = .txt mime = text/plain words = 9861 sentences = 405 flesch = 42 summary = Little is known about what determines whether a given picornavirus positive-sense RNA molecule will be directed (1) to a replication complex (a structure bound to smooth endoplasmic reticulum), where it serves as template for transcription by RNA-dependent RNA polymerase into negative-sense RNA, or (2) to a ribosome, where it serves as mRNA for translation into protein, or (3) to a procapsid, with which it associates to form a virion. In the case of positive-sense single-stranded RNA viruses, the incoming RNA genome can bind directly to ribosomes and be translated in full or in part without the need for any prior transcription; all other forms of incoming viral RNA must first be transcribed to produce mRNA, in order to begin the process of expression of the infecting viral genome. cache = ./cache/cord-355913-fhvt1ht1.txt txt = ./txt/cord-355913-fhvt1ht1.txt === reduce.pl bib === id = cord-353342-2n6kqyeo author = Corman, Victor M. title = Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date = 2016-02-15 pages = extension = .txt mime = text/plain words = 4046 sentences = 223 flesch = 52 summary = title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays cache = ./cache/cord-353342-2n6kqyeo.txt txt = ./txt/cord-353342-2n6kqyeo.txt === reduce.pl bib === id = cord-353290-1wi1dhv6 author = Kustin, Talia title = Biased mutation and selection in RNA viruses date = 2020-09-28 pages = extension = .txt mime = text/plain words = 7611 sentences = 402 flesch = 52 summary = We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses. Nevertheless, RNA viruses do share several common features that drive their evolution: (a) their ultimate dependence on the cell, (b) their high mutation rates, (c) strong purifying selection derived from constraints operating on a small and densely coding genome, and (d) sporadic but powerful positive selection driven by an evolutionary arms race with the host they infect. Two non-mutually exclusive hypotheses may be put forth to explain the consistent pattern of A-richness that we observe: there is selection for more A in viral sequences, and/or there is a mutational bias that leads to more A in genomes of viruses. cache = ./cache/cord-353290-1wi1dhv6.txt txt = ./txt/cord-353290-1wi1dhv6.txt === reduce.pl bib === id = cord-354398-f3cg8gi1 author = Al-Saud, Haya title = Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date = 2020-09-20 pages = extension = .txt mime = text/plain words = 4018 sentences = 199 flesch = 55 summary = The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. We validated the modified Invitrogen Forensic DNA Purification kit in extracting in-laboratory propagated SARS-COV-2 RNA by conducting manual and automated extractions on titrations from 15 000 copies to 60 copies of SARS-COV-2 followed by RT-qPCR methods: the commercially available TaqPath One-Step qRT-QP-CR kit (using the N, S, and ORF1b genes) and primers and probes from Metabion, Germany to establish an inhouse RT-qPCR assay based on E, RdRp2 and RdRp4 gene detection as per recommended SARS-COV-2 testing from CDC and WHO. cache = ./cache/cord-354398-f3cg8gi1.txt txt = ./txt/cord-354398-f3cg8gi1.txt === reduce.pl bib === id = cord-352991-duqkpkll author = Waghmare, Alpana title = Respiratory Syncytial Virus Lower Respiratory Disease in Hematopoietic Cell Transplant Recipients: Viral RNA Detection in Blood, Antiviral Treatment, and Clinical Outcomes date = 2013-09-24 pages = extension = .txt mime = text/plain words = 5112 sentences = 245 flesch = 43 summary = Although RSV RNA has been detected in serum from patients with RSV lower respiratory disease (LRD) after HCT, the association with clinical outcomes has not been well established in multivariable models. Univariate analysis at day 90 following RSV LRD revealed several factors that were statistically significantly associated with overall mortality and pulmonary death including transplant year, cell source, conditioning regimen, WBC count, monocyte count, platelet count, oxygen requirement at diagnosis, steroid use at diagnosis, palivizumab treatment, and ribavirin treatment following LRD (Supplementary Table 1 ). Hazard ratios and 95% confidence intervals from multivariable models evaluating respiratory syncytial virus (RSV) RNA detection in blood as a risk factor for overall mortality and pulmonary death by day 90 following RSV lower respiratory disease (LRD; n = 92), including P values. cache = ./cache/cord-352991-duqkpkll.txt txt = ./txt/cord-352991-duqkpkll.txt === reduce.pl bib === id = cord-354407-zzxjv666 author = Campanacci, Valérie title = Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date = 2004-06-07 pages = extension = .txt mime = text/plain words = 2338 sentences = 137 flesch = 60 summary = title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive‐stranded RNA virus (SARS‐CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. The crystal structure of the main (or 3CL) protease of transmissible gastroenteritis virus, a related coronavirus, has been determined and was used to construct a model of the SARS-CoV 3CL protease, facilitating future drug design against this important target (Anand et al., 2003) . In the related mouse hepatitis virus, which is a group 2 coronavirus, the SARS-CoV Nsp9 corresponds to a 12 kDa cleavage product (P1a-12) that is found preferentially in the perinuclear region of infected cells, where it co-localizes with other components of the viral replication complex (Bost et al., 2000) . cache = ./cache/cord-354407-zzxjv666.txt txt = ./txt/cord-354407-zzxjv666.txt === reduce.pl bib === id = cord-354114-frdsct44 author = Vogel, Liesbeth title = Pathogenic characteristics of persistent feline enteric coronavirus infection in cats date = 2010-07-23 pages = extension = .txt mime = text/plain words = 5339 sentences = 266 flesch = 53 summary = FECV is associated with asymptomatic persistent enteric infections, while FIPV causes feline infectious peritonitis (FIP), a usually fatal systemic disease in domestic cats and some wild Felidae. Faecal virus, i.e. genomic RNA, was detected during persistent FECV infection only in the large intestine, downstream of the appendix, and could occasionally be observed also in the blood. The cats were monitored for clinical signs, body weight, faecal virus shedding and serum antibody titres for 70 days post inoculation. In all animals, the amount of virus in the faeces subsequently increased within two days to peak levels of 10 6 -10 8 genomes/lL faeces, after which shedding remained high for an extended period until day 16 and day 23 post inoculation in FECV UCD and FECV RM infected cats, respectively. In order to determine in which part(s) of the gut virus was present during viral persistence, we screened the contents of the entire intestines of two FECV UCD infected cats. cache = ./cache/cord-354114-frdsct44.txt txt = ./txt/cord-354114-frdsct44.txt === reduce.pl bib === id = cord-354582-fniymnmf author = Ma, Zhiqian title = Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date = 2020-06-30 pages = extension = .txt mime = text/plain words = 8373 sentences = 423 flesch = 44 summary = In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . cache = ./cache/cord-354582-fniymnmf.txt txt = ./txt/cord-354582-fniymnmf.txt ===== Reducing email addresses cord-000128-t74b5j2j cord-000830-jiy4cp4n cord-000822-iuglkdcp cord-000881-s90geszi cord-003254-yiqdsf9z cord-001835-0s7ok4uw cord-003707-fbe47bgi cord-006960-9pho3hk6 cord-004584-bcw90f5b cord-004534-jqm1hxps cord-027975-77544sed cord-035067-ic843wr9 cord-023608-w2g7v7g1 cord-020010-q58x6xb0 cord-048327-xgwbl8em cord-048222-1pq6dkl5 cord-103015-3dxwbmd2 cord-103377-j1mmx7k7 cord-122092-gdyt02er cord-259593-shrd1s7r cord-260422-z22t57ju cord-264051-ps0x2es1 cord-263987-ff6kor0c cord-268337-o6lo55o8 cord-271188-ewlxy5po cord-273609-whm2ce4u cord-275602-cog4nma0 cord-272702-7uc4ozjy cord-272576-ez731lif 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cord-352200-i05h8csb cord-355075-ieb35upi cord-354407-zzxjv666 cord-353342-2n6kqyeo cord-354398-f3cg8gi1 cord-355357-b6aklh44 cord-352991-duqkpkll cord-353703-u86ggw11 cord-354114-frdsct44 cord-353290-1wi1dhv6 cord-356115-vblgotjn cord-354003-ko45l1qv cord-355913-fhvt1ht1 cord-354582-fniymnmf Creating transaction Updating pos table Building ./etc/reader.txt cord-001521-l36f1gp7 cord-022889-lv6fy6e6 cord-256444-grw5s2pf cord-327660-p1b07b4t cord-318551-c1qr27lg cord-346916-jj4l9ydl number of items: 1,349 sum of words: 11,763,802 average size in words: 8,911 average readability score: 49 nouns: virus; cells; protein; cell; viruses; infection; proteins; replication; expression; patients; gene; results; sequence; study; analysis; genome; host; activity; dna; blood; data; samples; coronavirus; disease; structure; genes; studies; type; time; sequences; treatment; detection; response; role; system; levels; influenza; acid; transcription; control; group; number; membrane; methods; translation; rnas; synthesis; effect; site; polymerase verbs: used; showed; binding; including; based; induce; contains; identifying; found; infected; associated; suggests; increasing; detect; comparing; follows; observed; determining; require; performed; indicate; provides; reported; expressed; involved; targeting; inhibit; mediating; described; causing; resulting; reveal; known; demonstrated; reduced; led; develop; obtained; produced; encoded; generates; test; occurs; regulate; form; treated; derive; allowed; made; relates adjectives: viral; human; specific; different; high; antiviral; clinical; respiratory; positive; immune; cellular; non; new; molecular; anti; several; single; structural; important; small; similar; dependent; negative; first; many; low; severe; significant; like; novel; infectious; acute; higher; present; large; genetic; potential; multiple; genomic; possible; infected; functional; major; nucleic; available; early; common; various; recent; active adverbs: also; however; well; highly; respectively; therefore; previously; significantly; recently; even; still; directly; furthermore; moreover; together; first; currently; often; approximately; interestingly; specifically; nt; less; especially; now; double; finally; yet; rather; prior; relatively; subsequently; mainly; particularly; indeed; much; similarly; additionally; generally; likely; potentially; rapidly; far; usually; probably; later; strongly; single; efficiently; fully pronouns: we; it; their; its; our; i; they; them; us; his; itself; he; one; her; she; themselves; you; your; mrnas; my; nsp15; nsp10; me; him; ourselves; ns3/4a; imagej; himself; nsp7; iosns; isg20; mg; s; ifit5; 2h5-a14; nsp1; isgf3; p~; ours; eef1a; u; pdcs; p210bcr; em; rss1gfp; rad5; nsps; irfibv32; ifit1; herself proper nouns: RNA; SARS; CoV-2; Fig; PCR; C; HCV; IFN; CoV; RT; mRNA; T; M; DNA; COVID-19; siRNA; HIV-1; A; N; B; S; HIV; MHV; II; University; Table; L; HBV; USA; RdRp; MERS; ⁄; miRNA; G; miRNAs; Coronavirus; China; mg; Figure; I; IBV; D; siRNAs; RNase; Virus; ORF; pH; E.; ACE2; K keywords: rna; sars; virus; dna; pcr; cell; protein; ifn; covid-19; hcv; viral; gene; hiv-1; cov-2; mhv; patient; infection; mers; rig; sequence; hiv; study; structure; human; ibv; ace2; hbv; china; result; expression; university; sirna; prrsv; genome; disease; vero; target; coronavirus; bat; atp; sample; orf; method; lamp; delivery; vaccine; rsv; replication; mutation; chikv one topic; one dimension: rna file(s): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956653/ titles(s): Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics three topics; one dimension: rna; sars; cells file(s): https://api.elsevier.com/content/article/pii/S0065352708602869, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/, https://doi.org/10.1038/s41392-020-00311-7 titles(s): The Molecular Biology of Coronaviruses | EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS | NAD(+) metabolism: pathophysiologic mechanisms and therapeutic potential five topics; three dimensions: rna virus protein; virus rna viruses; cov sars blood; cells cell patients; protein cells cell file(s): https://api.elsevier.com/content/article/pii/S1877117309900096, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435362/, https://api.elsevier.com/content/article/pii/B9783437428319100130, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104449/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120058/ titles(s): Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery | Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus | KAPITEL 13 Infektionskrankheiten | Scientific Abstracts | 1 Micro-organismen, de mens en het ontstaan van infectieziekten: algemene principes Type: cord title: keyword-rna-cord date: 2021-05-25 time: 16:19 username: emorgan patron: Eric Morgan email: emorgan@nd.edu input: keywords:rna ==== make-pages.sh htm files ==== make-pages.sh complex files ==== make-pages.sh named enities ==== making bibliographics id: cord-022084-hap7flng author: ARRUDA, EURICO title: Respiratory Tract Viral Infections date: 2009-05-15 words: 19181.0 sentences: 1041.0 pages: flesch: 43.0 cache: ./cache/cord-022084-hap7flng.txt txt: ./txt/cord-022084-hap7flng.txt summary: The Centers for Disease Control and Prevention (CDC) recommends the immunization of persons aged 50 years and older; residents of nursing homes; children and adults with chronic cardiovascular or pulmonary disease, including asthma; persons chronically ill with diabetes mellitus, renal dysfunction, or hemoglobinopathies; immunosuppressed patients including those with HIV infection; children and adolescents on chronic aspirin therapy who may develop postinfluenza Reye'' s syndrome; women who will be pregnant during the influenza season; children aged 6 to 23 months; those who can transmit influenza to persons at high risk, such as health-care workers and household contacts of those at high risk including children 0 to 23 months of age; crew members of cruise ships; providers of essential services; and unimmunized travelers to areas where influenza may be circulating, including the tropics, the southern hemisphere between April and September, and those traveling in large organized tourist groups. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152450/ doi: 10.1016/b978-0-443-06668-9.50064-8 id: cord-303319-v3iyur78 author: Abe, Takayuki title: Cytosolic DNA‐sensing immune response and viral infection date: 2019-02-26 words: 7788.0 sentences: 355.0 pages: flesch: 38.0 cache: ./cache/cord-303319-v3iyur78.txt txt: ./txt/cord-303319-v3iyur78.txt summary: The findings of these studies have suggested that antiviral responses are mediated by cytosolic or intracellular compartment sensors and their adaptor molecules (e.g., TLR, myeloid differentiation primary response 88, retinoic acid inducible gene‐I, IFN‐β promoter stimulator‐1, cyclic GMP‐AMP synthase and stimulator of IFN genes axis) for the primary sensing of virus‐derived nucleic acids, leading to production of type I IFNs, pro‐inflammatory cytokines and chemokines by the host cells. Thus far, many different immune evasion strategies employed by various viruses have been identified, including: (i) interference with the functions of the host innate immune response via physical interactions with viral antagonistic proteins targeted to sensors, adaptors, related intracellular kinases and transcription factors; (ii) inducing degradation or specific cleavage at the protein level; and (iii) sequestration of signal transduction molecules targeting the PTM systems. abstract: How host cells recognize many kinds of RNA and DNA viruses and initiate innate antiviral responses against them has not yet been fully elucidated. Over the past decade, investigations into the mechanisms underlying these antiviral responses have focused extensively on immune surveillance sensors that recognize virus‐derived components (such as lipids, sugars and nucleic acids). The findings of these studies have suggested that antiviral responses are mediated by cytosolic or intracellular compartment sensors and their adaptor molecules (e.g., TLR, myeloid differentiation primary response 88, retinoic acid inducible gene‐I, IFN‐β promoter stimulator‐1, cyclic GMP‐AMP synthase and stimulator of IFN genes axis) for the primary sensing of virus‐derived nucleic acids, leading to production of type I IFNs, pro‐inflammatory cytokines and chemokines by the host cells. Thus, host cells have evolved an elaborate host defense machinery to recognize and eliminate virus infections. In turn, to achieve sustained viral infection and induce pathogenesis, viruses have also evolved several counteracting strategies for achieving immune escape by targeting immune sensors, adaptor molecules, intracellular kinases and transcription factors. In this review, we discuss recent discoveries concerning the role of the cytosolic nucleic acid‐sensing immune response in viral recognition and control of viral infection. In addition, we consider the regulatory machinery of the cytosolic nucleic acid‐sensing immune response because these immune surveillance systems must be tightly regulated to prevent aberrant immune responses to self and non‐self‐nucleic acids. url: https://doi.org/10.1111/1348-0421.12669 doi: 10.1111/1348-0421.12669 id: cord-307354-dkwcheu0 author: Abernathy, Emma title: Emerging roles for RNA degradation in viral replication and antiviral defense date: 2015-05-31 words: 7160.0 sentences: 359.0 pages: flesch: 45.0 cache: ./cache/cord-307354-dkwcheu0.txt txt: ./txt/cord-307354-dkwcheu0.txt summary: Alpha-herpesviruses such as herpes simplex-1 (HSV-1) express a FEN1-like nuclease termed virion host shutoff protein (vhs) that is directed to mRNAs through interactions with the translation Fig. 1 . Quality control decay pathways such as NMD recognize aberrant mRNAs during translation, including the presence of premature termination codons (PTC), and induce endonucleolytic cleavage, whereupon the fragments are degraded by exonucleases. The RNAi pathway restricts gene expression by processing the long double stranded RNAs frequently generated during viral replication into short interfering RNAs (siR-NAs), which guide endonucleolytic cleavage of complementary target mRNAs. Although mammalian cells possess the RNAi machinery, in most cases RNAi does not appear to play a significant antiviral role, and has instead been supplanted by the protein-based interferon response (Cullen, 2014) . Small interfering RNAs that deplete the cellular translation factor eIF4H impede mRNA degradation by the virion host shutoff protein of herpes simplex virus abstract: Abstract Viral replication significantly alters the gene expression landscape of infected cells. Many of these changes are driven by viral manipulation of host transcription or translation machinery. Several mammalian viruses encode factors that broadly dampen gene expression by directly targeting messenger RNA (mRNA). Here, we highlight how these factors promote mRNA degradation to globally regulate both host and viral gene expression. Although these viral factors are not homologous and use distinct mechanisms to target mRNA, many of them display striking parallels in their strategies for executing RNA degradation and invoke key features of cellular RNA quality control pathways. In some cases, there is a lack of selectivity for degradation of host versus viral mRNA, indicating that the purposes of virus-induced mRNA degradation extend beyond redirecting cellular resources towards viral gene expression. In addition, several antiviral pathways use RNA degradation as a viral restriction mechanism, and we will summarize new findings related to how these host-encoded ribonucleases target and destroy viral RNA. url: https://doi.org/10.1016/j.virol.2015.02.007 doi: 10.1016/j.virol.2015.02.007 id: cord-341050-hnuogpqn author: Acharya, Dhiraj title: An Overview of Current Approaches Toward the Treatment and Prevention of West Nile Virus Infection date: 2016-05-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The persistence of West Nile virus (WNV) infections throughout the USA since its inception in 1999 and its continuous spread throughout the globe calls for an urgent need of effective treatments and prevention measures. Although the licensing of several WNV vaccines for veterinary use provides a proof of concept, similar efforts on the development of an effective vaccine for humans remain still unsuccessful. Increased understanding of biology and pathogenesis of WNV together with recent technological advancements have raised hope that an effective WNV vaccine may be available in the near future. In addition, rapid progress in the structural and functional characterization of WNV and other flaviviral proteins have provided a solid base for the design and development of several classes of inhibitors as potential WNV therapeutics. Moreover, the therapeutic monoclonal antibodies demonstrate an excellent efficacy against WNV in animal models and represent a promising class of WNV therapeutics. However, there are some challenges as to the design and development of a safe and efficient WNV vaccine or therapeutic. In this chapter, we discuss the current approaches, progress, and challenges toward the development of WNV vaccines, therapeutic antibodies, and antiviral drugs. url: https://doi.org/10.1007/978-1-4939-3670-0_19 doi: 10.1007/978-1-4939-3670-0_19 id: cord-271419-v6dfel3l author: Adachi, Shun title: Commentary: Origin and evolution of pathogenic coronaviruses date: 2020-04-21 words: 1211.0 sentences: 77.0 pages: flesch: 51.0 cache: ./cache/cord-271419-v6dfel3l.txt txt: ./txt/cord-271419-v6dfel3l.txt summary: Among viruses, some coronaviruses (CoVs) are notorious for causing the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The said article has successfully predicted today''s COVID-19 outbreak by pointing out that novel pathogenic variants will readily emerge from very diversified severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs) of the bat origin through their close coexistence and high genetic recombination ability (Figure 1) . Since RNA viruses are easy to mutate and coronaviruses have high potentials for recombination, we can easily see the track of mutations and evolutions of the viruses, especially for SARS-CoV and MERS-CoV. Thus, to consider the origin of new pathogens and the prevention of their transmission to humans, and control of the viruses, not only studies on SARS-CoV, MERS-CoV, and SARS-CoV-2, but also those on their relatives SARSr-CoVs and MERSr-CoVs are recommendable for bats tracked for the ecology and evolution. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32373134/ doi: 10.3389/fimmu.2020.00811 id: cord-312461-5qzpo6l1 author: Adalja, Amesh A. title: Characteristics of Microbes Most Likely to Cause Pandemics and Global Catastrophes date: 2019-08-30 words: 6830.0 sentences: 290.0 pages: flesch: 40.0 cache: ./cache/cord-312461-5qzpo6l1.txt txt: ./txt/cord-312461-5qzpo6l1.txt summary: A substantial proportion of pandemic and biological threat preparedness activities have focused on list-based approaches that were in part based on pandemic influenzas of the past, historical biological weapon development programs, or recent outbreaks of emerging infectious diseases (e.g., SARS, MERS, Ebola) (Centers for Disease Control and Prevention 2017; Casadevall and Relman 2010) . Cultivating and maintaining expertise in the epidemiology, surveillance, and pathogenicity of all classes of microbes, with explicit incorporation of a One Health approach-which incorporates and integrates information from infectious diseases of plants, amphibians, and reptiles-will help foster the broad capacities needed for emerging pandemic and global catastrophic biological risks. Pathogen-based lists, both USA and global, based on influenza precedents, historical biological weapon programs, and emerging infectious diseases were responsible for galvanizing early activities in the field of pandemic preparedness and have helped drive many important contributions. abstract: Predicting which pathogen will confer the highest global catastrophic biological risk (GCBR) of a pandemic is a difficult task. Many approaches are retrospective and premised on prior pandemics; however, such an approach may fail to appreciate novel threats that do not have exact historical precedent. In this paper, based on a study and project we undertook, a new paradigm for pandemic preparedness is presented. This paradigm seeks to root pandemic risk in actual attributes possessed by specific classes of microbial organisms and leads to specific recommendations to augment preparedness activities. url: https://www.ncbi.nlm.nih.gov/pubmed/31463536/ doi: 10.1007/82_2019_176 id: cord-338345-mr1orklo author: Adedeji, Adeyemi O. title: Biochemical Characterization of Middle East Respiratory Syndrome Coronavirus Helicase date: 2016-09-07 words: 4253.0 sentences: 233.0 pages: flesch: 57.0 cache: ./cache/cord-338345-mr1orklo.txt txt: ./txt/cord-338345-mr1orklo.txt summary: Unless stated otherwise, for this specific experiment, we used the 5=-RNA-20 partially duplex substrate (see Fig. S1 in the supplemental material), since previous coronavirus helicase, i.e., SARS-CoV nsp13, was shown to have a 5=-to-3= directionality (29) . To determine whether nucleic acid unwinding by M-nsp13 depends on the loading strand length and to determine the minimum length of the 5= singlestranded overhang required for efficient helicase activity, we designed five partially duplex RNA substrates with single-stranded 5= ends of various lengths (between 0 and 20 bases) (see Fig. S1 in the supplemental material; Fig. 6 ) but with dsRNA duplex regions of the same length. Overall, these results suggest that M-nsp13''s ability to unwind the 5=-RNA-20 partially duplex substrate is likely due to residual cellular ATP purified with the helicase as well as to a long overhang length, which enhances M-nsp13''s unwinding activity. abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) helicase is a superfamily 1 helicase containing seven conserved motifs. We have cloned, expressed, and purified a Strep-fused recombinant MERS-CoV nonstructural protein 13 (M-nsp13) helicase. Characterization of its biochemical properties showed that it unwound DNA and RNA similarly to severe acute respiratory syndrome CoV nsp13 (S-nsp13) helicase. We showed that M-nsp13 unwound in a 5′-to-3′ direction and efficiently unwound the partially duplex RNA substrates with a long loading strand relative to those of the RNA substrates with a short or no loading strand. Moreover, the K(m) of ATP for M-nsp13 is inversely proportional to the length of the 5′ loading strand of the partially duplex RNA substrates. Finally, we also showed that the rate of unwinding (ku) of M-nsp13 is directly proportional to the length of the 5′ loading strand of the partially duplex RNA substrate. These results provide insights that enhance our understanding of the biochemical properties of M-nsp13. IMPORTANCE Coronaviruses are known to cause a wide range of diseases in humans and animals. Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel coronavirus discovered in 2012 and is responsible for acute respiratory syndrome in humans in the Middle East, Europe, North Africa, and the United States of America. Helicases are motor proteins that catalyze the processive separation of double-stranded nucleic acids into two single-stranded nucleic acids by utilizing the energy derived from ATP hydrolysis. MERS-CoV helicase is one of the most important viral replication enzymes of this coronavirus. Herein, we report the first bacterial expression, enzyme purification, and biochemical characterization of MERS-CoV helicase. The knowledge obtained from this study might be used to identify an inhibitor of MERS-CoV replication, and the helicase might be used as a therapeutic target. url: https://www.ncbi.nlm.nih.gov/pubmed/27631026/ doi: 10.1128/msphere.00235-16 id: cord-269466-9hnal9ad author: Agbeci, Maxime title: Contribution of Host Intracellular Transport Machineries to Intercellular Movement of Turnip Mosaic Virus date: 2013-10-03 words: 7184.0 sentences: 391.0 pages: flesch: 49.0 cache: ./cache/cord-269466-9hnal9ad.txt txt: ./txt/cord-269466-9hnal9ad.txt summary: In this study, we used a novel dual gene cassette construct that differentiated primary infected cells from cells infected after virus intercellular movement to show that the early as well as the late secretory pathway, but not endocytosis, was important for TuMV transport. By using a dual cassette of genes encoding fluorescent proteins that can differentiate between primary infected cells and cells infected after intercellular transport, we provide evidence that turnip mosaic virus (TuMV) needs a functional secretory pathway where pre-and post-Golgi trafficking and the actomyosin network are important for its movement. Fig. 2E shows that that there was no significant difference in the ratio of red over green fluorescence during BFA and CMA treatments compared with the no inhibitor treatment (TuMV alone) at 4 dpinf, indicating that viral protein production in the primary infected cells was not affected by the drug treatments. abstract: The contribution of different host cell transport systems in the intercellular movement of turnip mosaic virus (TuMV) was investigated. To discriminate between primary infections and secondary infections associated with the virus intercellular movement, a gene cassette expressing GFP-HDEL was inserted adjacent to a TuMV infectious cassette expressing 6K(2):mCherry, both within the T-DNA borders of the binary vector pCambia. In this system, both gene cassettes were delivered to the same cell by a single binary vector and primary infection foci emitted green and red fluorescence while secondarily infected cells emitted only red fluorescence. Intercellular movement was measured at 72 hours post infiltration and was estimated to proceed at an average rate of one cell being infected every three hours over an observation period of 17 hours. To determine if the secretory pathway were important for TuMV intercellular movement, chemical and protein inhibitors that blocked both early and late secretory pathways were used. Treatment with Brefeldin A or Concanamycin A or expression of ARF1 or RAB-E1d dominant negative mutants, all of which inhibit pre- or post-Golgi transport, reduced intercellular movement by the virus. These treatments, however, did not inhibit virus replication in primary infected cells. Pharmacological interference assays using Tyrphostin A23 or Wortmannin showed that endocytosis was not important for TuMV intercellular movement. Lack of co-localization by endocytosed FM4-64 and Ara7 (AtRabF2b) with TuMV-induced 6K(2)-tagged vesicles further supported this conclusion. Microfilament depolymerizing drugs and silencing expression of myosin XI-2 gene, but not myosin VIII genes, also inhibited TuMV intercellular movement. Expression of dominant negative myosin mutants confirmed the role played by myosin XI-2 as well as by myosin XI-K in TuMV intercellular movement. Using this dual gene cassette expression system and transport inhibitors, components of the secretory and actomyosin machinery were shown to be important for TuMV intercellular spread. url: https://www.ncbi.nlm.nih.gov/pubmed/24098128/ doi: 10.1371/journal.ppat.1003683 id: cord-016808-gy8d8285 author: Agol, Vadim I. title: The Origin and Evolution of Viruses date: 2008 words: 3255.0 sentences: 172.0 pages: flesch: 44.0 cache: ./cache/cord-016808-gy8d8285.txt txt: ./txt/cord-016808-gy8d8285.txt summary: Modern hypotheses of viral origin are based on two major developments of the molecular biology: discovery of ribozymes (RNA-based enzymes) and formulation of the "RNA World" theory (RNA had been "invented" before proteins and DNA), on the one hand, and achievements of genomics (determination of the nucleotide sequences of a great number of cellular and viral genomes), on the other. Three distinct DNA viruses, which had infected RNA genome-containing cells, gave rise to the three distinct domains of life, bacteria, archea, and eukarya (Forterre, 2006) . To infect a human, an avian flu virus should change its receptor specificity, which depends on the interaction of viral hemagglutinin (HA) with a cellular membrane glycoprotein receptor. Such a change in the host range may be achieved by either mutations in the avian HA or acquisition by an avian virus of the HA gene from human influenza virus as a result of genetic exchange (reassortment) between these viruses during mixed infections. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain abstract: The lecture covers three main topics: (i) Viruses: properties, place in the living world, and possible origin; (ii) Molecular basis of viral variability and evolution; and (iii) Evolution of viral pathogenicity and emerging viral infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121209/ doi: 10.1007/978-1-4020-8761-5_7 id: cord-325230-3kg4oe4g author: Agol, Vadim I. title: Viral security proteins: counteracting host defences date: 2010-11-09 words: 8716.0 sentences: 426.0 pages: flesch: 41.0 cache: ./cache/cord-325230-3kg4oe4g.txt txt: ./txt/cord-325230-3kg4oe4g.txt summary: These proteins include: capsid proteins; an RNA-dependent RNA polymerase (3D pol ); a protein (VPg, or 3B) that serves as a primer for the initiation of RNA synthesis; an ATPase with a conserved superfamily 3 helicase motif (2C ATPase ) and an essential but poorly defined role in viral RNA replication; a chymotrypsin-like protease (3C pro ), which, as the mature protein or as a precursor, is a major factor in polyprotein processing; two hydrophobic membrane-binding proteins (2B and 3A) that participate in the generation of a virus-friendly environment; and, flanking the precursor of the capsid proteins, one or two highly variable proteins (L and 2A), the structure and functions of which are the subject of this Review. abstract: Interactions with host defences are key aspects of viral infection. Various viral proteins perform counter-defensive functions, but a distinct class, called security proteins, is dedicated specifically to counteracting host defences. Here, the properties of the picornavirus security proteins L and 2A are discussed. These proteins have well-defined positions in the viral polyprotein, flanking the capsid precursor, but they are structurally and biochemically unrelated. Here, we consider the impact of these two proteins, as well as that of a third security protein, L(*), on viral reproduction, pathogenicity and evolution. The concept of security proteins could serve as a paradigm for the dedicated counter-defensive proteins of other viruses. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro2452) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro2452 doi: 10.1038/nrmicro2452 id: cord-253539-0kcujnfa author: Agranovsky, A. A. title: Principles of Molecular Organization, Expression, and Evolution of Closteroviruses: Over The Barriers date: 1996-12-31 words: 10620.0 sentences: 481.0 pages: flesch: 55.0 cache: ./cache/cord-253539-0kcujnfa.txt txt: ./txt/cord-253539-0kcujnfa.txt summary: It has been suggested that the genes for CP homologues arose by gene duplication that probably occurred in a common closterovirus ancestor; it is noteworthy that, despite significant divergence, the CP homologues of BYV and CTV have retained the profile of conserved amino acid residues that are believed to ensure the characteristic fold of the filamentous plant virus CPs (Boyko et al., 1992 , Dolja et al., 1991 . L I W RNA-2 contains genes for the small hydrophobic protein, the HSP7O homologue, the 59-kDa protein distantly related to the B W 64-kDa and CTV 61-kDa products, the 9-kDa protein, the 28-kDa CP, the 52-kDa protein whose C-terminal domain is homologous to the CP, and the 26-kDa protein The monopartite genome of another whitefly-transmissible closterovirus, cucumber chlorotic spot virus (CCSW, has a size of approximately 15.5 kb (Woudt et al., 1993a,b) . abstract: Publisher Summary This chapter focuses on the molecular organization, evolution, and expression of closterovirus genomes, as well as on their unique particle structure. The closterovirus group combines several positive-strand RNA viruses with very flexuous filamentous particles, of which beet yellows virus (BYV) is the type virus. Closteroviruses are distinct from other RNA viruses of plants in some important phenomenological aspects. They have genomes of up to 20 kilobases (kb), a value comparable only to those of the animal coronaviruses and toroviruses, which have the largest RNA genomes of all positive-strand RNA viruses. The existence of such genomes having a coding capacity several times that of an average RNA virus genome raises questions as to the trend whereby the long genomes have evolved and the possible novel functions they have acquired. The dramatic increase in the closterovirus genome coding capacity may be linked to the distinct ecological niche they occupy. Thus, closteroviruses are the only elongated plant viruses known so far to cause phloem-limited infections in plants and to persist in their insect vectors for many hours, in contrast to only minutes. url: https://www.ncbi.nlm.nih.gov/pubmed/8895832/ doi: 10.1016/s0065-3527(08)60735-6 id: cord-293355-0v71xwqy author: Aguiar, Eric Roberto Guimarães Rocha title: Virus‐derived small RNAs: molecular footprints of host–pathogen interactions date: 2016-05-12 words: 6830.0 sentences: 446.0 pages: flesch: 50.0 cache: ./cache/cord-293355-0v71xwqy.txt txt: ./txt/cord-293355-0v71xwqy.txt summary: Thus, the pattern of small RNAs generated in infected cells can be used as a molecular footprint to identify and characterize viruses independent on sequence homology searches against known references. Different RNAi mechanisms can generate vsRNAs during viral infection including the mammalian miRNA pathway, Drosophila small interfering RNA (siRNA) pathway, and mosquito piRNA pathway. 22, 23 In animals, there are at least three separate RNAi mechanisms that can generate vsRNAs during viral infection: the microRNA (miRNA), piwi-interacting RNA (piRNA), and small interfering RNA (siRNA) pathways ( Figure 1 ). Interestingly, EVEs seemed to favor the generation of small RNAs with molecular characteristics of piRNAs rather than siRNAs. Second, some viruses have developed viral suppressors of the siRNA pathway (VSRs) that can significantly affect the pattern of vsRNAs. VSRs allow for accumulation of viral RNA that can be degraded by other host mechanisms. abstract: Viruses are obligatory intracellular parasites that require the host machinery to replicate. During their replication cycle, viral RNA intermediates can be recognized and degraded by different antiviral mechanisms that include RNA decay, RNA interference, and RNase L pathways. As a consequence of viral RNA degradation, infected cells can accumulate virus‐derived small RNAs at high levels compared to cellular molecules. These small RNAs are imprinted with molecular characteristics that reflect their origin. First, small RNAs can be used to reconstruct viral sequences and identify the virus from which they originated. Second, other molecular features of small RNAs such as size, polarity, and base preferences depend on the type of viral substrate and host mechanism of degradation. Thus, the pattern of small RNAs generated in infected cells can be used as a molecular footprint to identify and characterize viruses independent on sequence homology searches against known references. Hence, sequencing of small RNAs obtained from infected cells enables virus discovery and characterization using both sequence‐dependent strategies and novel pattern‐based approaches. Recent studies are helping unlock the full application of small RNA sequencing for virus discovery and characterization. WIREs RNA 2016, 7:824–837. doi: 10.1002/wrna.1361 1.. RNA Processing > Processing of Small RNAs; 2.. RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms; 3.. RNA Methods > RNA Analyses In Vitro and In Silico. url: https://doi.org/10.1002/wrna.1361 doi: 10.1002/wrna.1361 id: cord-279841-oq25o4qr author: Ahlquist, Paul title: Viral and host determinants of RNA virus vector replication and expression date: 2005-03-07 words: 2269.0 sentences: 99.0 pages: flesch: 36.0 cache: ./cache/cord-279841-oq25o4qr.txt txt: ./txt/cord-279841-oq25o4qr.txt summary: Further insights into RNA virus vector design and optimization are emerging from recent advances on the function of viral RNA replication factors, the nature of the viral RNA replication complex as a membrane-bounded compartment sequestering replication components from competing processes and host defenses, and identification of surprisingly diverse host genes contributing to many virus replication steps. An unusual feature of BMV for identifying and characterizing host functions in viral replication is that BMV directs RNA replication, gene expression and virion formation in the genetic model yeast, Saccharomyces cerevisiae [13] . In recent years, classical yeast genetics have been used to identify host genes that function in controlling BMV translation [14, 15] , selecting BMV RNAs as replication templates [16] , activating the viral RNA replication complex [17] , maintaining a lipid composition required for membrane-associated RNA replication [18, 19] , and other steps. abstract: Positive-strand RNA viruses have proven to be valuable vectors for delivery and expression of antigens for direct vaccination of animals and vaccine production in plants. However, optimal use of these viruses as vectors for vaccine and other purposes is limited by incomplete understanding of their replication pathways and associated constraints on inserted foreign genes. Further insights into RNA virus vector design and optimization are emerging from recent advances on the function of viral RNA replication factors, the nature of the viral RNA replication complex as a membrane-bounded compartment sequestering replication components from competing processes and host defenses, and identification of surprisingly diverse host genes contributing to many virus replication steps. url: https://www.ncbi.nlm.nih.gov/pubmed/15734041/ doi: 10.1016/j.vaccine.2004.11.005 id: cord-328471-oz99upzz author: Ahmad, Jamshaid title: SARS-CoV-2 RNA Dependent RNA Polymerase (RdRp) – A drug repurposing study date: 2020-07-23 words: 5089.0 sentences: 282.0 pages: flesch: 55.0 cache: ./cache/cord-328471-oz99upzz.txt txt: ./txt/cord-328471-oz99upzz.txt summary: In this global health emergency, drug repurposing (or repositioning) is one of the fast track option that involves screening of existing FDA approved drugs for the identification of potential molecules that can disrupt the function of key proteins of the SARS-CoV-2 and can be used for treatment against COVID-19. Whereas, Demoxytocin showed ten H-bonds with both active site Asp760 and Asp761 and other key residues e.g. Trp617, Tyr619, Lys621, Ser682, Glu811, Lys621, Tyr619, Trp617, Ser682 and Glu811 with dock score -9.68kcal/mol and ligand efficiency of -0.142 (Supplementary Figure S3) . Colistin (polymyxin E, polypeptide antibiotics) showed most of the H-bonding with Lys551, Trp617, Tyr619, Asp618, Ser682, Asp684, Asn691, and both catalytic residues i.e. Asp760, Asp761, with a docking score of -9.24kcal/mol and ligand efficiency of -0.113 (Supplementary Figure S5) . Examorelin, Lypressin, Ornipressin, and Colistin are also common drugs in both form of RdRp. Only one H-bond with His810 and other non-covalent interactions were observed for Examorelin showed a docking score of -12.139 kcal/mol and ligand efficiency of -0.187. abstract: The outbreak of SARS-CoV-2 in December 2019 in China subsequently lead to a pandemic. Lack of vaccine and specific anti-viral drugs started a global health disaster. For a sustained control and protection, development of potential anti-viral drugs is one of the targeted approach. Although, designing and developing a panel of new drugs molecules are always encouraged. However, in the current emergency, drug repurposing study is one of the most effective and fast track option. The crystal structure of a SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) RNA Dependent RNA Polymerase (RdRp) has recently been deciphered through X-ray crystallography. The single-chain of core RNA Dependent RNA Polymerase relies on virus-encoded cofactors nsp7 and two units of nsp8 for its optimum function. This study explored the FDA approved database of 7922 molecules and screened against the core polymerase along with cofactors. Here we report a panel of FDA approved drugs that show substantial interactions with key amino acid residues of the active site. Interestingly, some of the identified drugs (Ornipressin, Lypressin, Examorelin, Polymyxin B1) bind strongly within the binding pockets of both forms of RdRp. Besides, we found strong candidates for the complex form as well which include Nacortocin, Cistinexine, Cisatracurium (among others). These drugs have the potential to be considered while contriving therapeutic options. url: https://doi.org/10.1016/j.heliyon.2020.e04502 doi: 10.1016/j.heliyon.2020.e04502 id: cord-315611-xbj41ekc author: Ahmad, Mohammed title: Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase date: 2020-07-14 words: 5038.0 sentences: 301.0 pages: flesch: 49.0 cache: ./cache/cord-315611-xbj41ekc.txt txt: ./txt/cord-315611-xbj41ekc.txt summary: Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. 20−22 In this report, using computer-aided homology modeling, docking, and molecular simulations, we have predicted the protein structure and probable small-molecule inhibitors against SARS-CoV2 RdRp (CoV2-RdRp). Taking together the aforementioned interaction and comparison of the model and experimentally determined structures, we propose the probable initiation complex of CoV2-RdRp bound to RNA and GTP molecules in Figure 2D . Molecular Dynamics simulation studies of the native and ligand-bound complexes of CoV2-RdRp. MD (Molecular dynamics) simulations were performed for the modelled structure of the RdRp protein and docked complexes for the GTP, lead optimized, and FIH compounds for a 50 ns time period. abstract: [Image: see text] The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2. url: https://www.ncbi.nlm.nih.gov/pubmed/32743211/ doi: 10.1021/acsomega.0c02096 id: cord-334299-0zn1z7rc author: Ahmed, Warish title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information date: 2020-09-30 words: 1373.0 sentences: 73.0 pages: flesch: 47.0 cache: ./cache/cord-334299-0zn1z7rc.txt txt: ./txt/cord-334299-0zn1z7rc.txt summary: title: Surveillance of SARS-CoV-2 RNA in wastewater: Methods optimisation and quality control are crucial for generating reliable public health information However, in order to reliably interpret data produced from these efforts for informing public health interventions, additional quality control information and standardization in sampling design, sample processing, and data interpretation and reporting is needed. The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. In view of this need, we recommend methodological and quality assurance approaches for SARS-CoV-2 RNA detection in 158 wastewater using molecular methods. abstract: Monitoring for SARS-CoV-2 RNA in wastewater through the process of wastewater-based epidemiology (WBE) provides an additional surveillance tool, contributing to community-based screening and prevention efforts as these measurements have preceded disease cases in some instances. Numerous detections of SARS-CoV-2 RNA have been reported globally using various methods, demonstrating the technical feasibility of routine monitoring. However, in order to reliably interpret data produced from these efforts for informing public health interventions, additional quality control information and standardization in sampling design, sample processing, and data interpretation and reporting is needed. This review summarizes published studies of SARS-CoV-2 RNA detection in wastewater as well as available information regarding concentration, extraction, and detection methods. The review highlights areas for potential standardization including considerations related to sampling timing and frequency relative to peak fecal loading times; inclusion of appropriate information on sample volume collected; sample collection points; transport and storage conditions; sample concentration and processing; RNA extraction process and performance; effective volumes; PCR inhibition; process controls throughout sample collection and processing; PCR standard curve performance; and recovery efficiency testing. Researchers are recommended to follow the Minimum Information for Publication of Quantitative Real-Time PCR (MIQE) guidelines. Adhering to these recommendations will enable robust interpretation of wastewater monitoring results and improved inferences regarding the relationship between monitoring results and disease cases. url: https://www.ncbi.nlm.nih.gov/pubmed/33052320/ doi: 10.1016/j.coesh.2020.09.003 id: cord-017167-8cdbcrh7 author: Ahola, Tero title: Functions of Chikungunya Virus Nonstructural Proteins date: 2016-12-03 words: 10491.0 sentences: 530.0 pages: flesch: 49.0 cache: ./cache/cord-017167-8cdbcrh7.txt txt: ./txt/cord-017167-8cdbcrh7.txt summary: The nonstructural proteins (nsPs) of chikungunya virus (CHIKV) are expressed as one or two polyprotein precursors, which are translated directly from the viral genomic RNA. Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis. However, recent studies of SFV P1234 processing reveal that a second mechanism, the presentation of cleavage sequences via long-range interactions between different domains of the polyprotein, Processing of CHIKV ns polyprotein P1234 and RNA synthesis. The main interaction appears to be mediated by a membrane-binding peptide located in the central part of the protein (approximately residues 244-263 in CHIKV nsP1; Fig. 2 ), which forms an amphipathic alpha helix, as characterized for the corresponding peptide from SFV (Ahola et al. However, the effects of mutations introduced into the NTPase/helicase active site were different for these viruses: in SINV such a mutation strongly reduced the nsP2-dependent degradation of Rpb1 whereas CHIKV nsP2 mostly retained its ability to block host gene expression. abstract: The nonstructural proteins (nsPs) of chikungunya virus (CHIKV) are expressed as one or two polyprotein precursors, which are translated directly from the viral genomic RNA. Mature nsPs are generated by precise processing of these polyproteins. Both the precursors and mature nsPs are essential for CHIKV replication. Similar to other alphaviruses, CHIKV nsPs not only perform virus RNA replication but are also crucial for other activities essential for virus infection and pathogenesis. Thus far the best-studied CHIKV ns-protein is nsP2, for which protease, NTPase, RNA triphosphatase, and RNA helicase activities have been demonstrated. In addition, nsP2 is crucial for shut-off of host cell transcription and translation and it counteracts cellular antiviral responses. Compared to their homologues from the well-studied Sindbis and Semliki Forest viruses, CHIKV nsP1, nsP3, and nsP4 have been subjected to only few studies. Nevertheless, there are strong indirect pieces of evidence indicating that these CHIKV proteins have the same enzymatic activities as their counterparts in the other alphaviruses. Information concerning the specific interaction of CHIKV nsPs with host components is beginning to emerge. All the nsPs are involved in the functioning of membrane-bound replication complexes also called spherules, but the finer details of the structure and assembly of these complexes are currently poorly understood. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121661/ doi: 10.1007/978-3-319-42958-8_6 id: cord-048322-5eqdrd52 author: Aigner, Achim title: Delivery Systems for the Direct Application of siRNAs to Induce RNA Interference (RNAi) In Vivo date: 2006-05-18 words: 7333.0 sentences: 363.0 pages: flesch: 41.0 cache: ./cache/cord-048322-5eqdrd52.txt txt: ./txt/cord-048322-5eqdrd52.txt summary: The antitumorigenic effects of PEI/siRNA-mediated in vivo gene-targeting of tumor-relevant proteins like in mouse tumor xenograft models are described. The efficient protection against enzymatic or nonenzymatic degradation is particularly important for RNA molecules including siRNAs. In fact, while the therapeutic potential of siRNAs for the treatment of various diseases is in principle very promising, limitations of transfer vectors may turn out to be rate-limiting in the development of RNAi-based therapeutic strategies. Their ultimate success, however, will Figure 4 : Systemic treatment of mice with PEI-complexed HER-2-specific siRNAs leads to reduced growth of subcutaneous SKOV-3 tumor xenografts due to decreased HER-2 expression. RNAi-mediated gene-targeting through systemic application of polyethylenimine (PEI)-complexed siRNA in vivo Atelocollagenmediated synthetic small interfering RNA delivery for effective gene silencing in vitro and in vivo abstract: RNA interference (RNAi) is a powerful method for specific gene silencing which may also lead to promising novel therapeutic strategies. It is mediated through small interfering RNAs (siRNAs) which sequence-specifically trigger the cleavage and subsequent degradation of their target mRNA. One critical factor is the ability to deliver intact siRNAs into target cells/organs in vivo. This review highlights the mechanism of RNAi and the guidelines for the design of optimal siRNAs. It gives an overview of studies based on the systemic or local application of naked siRNAs or the use of various nonviral siRNA delivery systems. One promising avenue is the the complexation of siRNAs with the polyethylenimine (PEI), which efficiently stabilizes siRNAs and, upon systemic administration, leads to the delivery of the intact siRNAs into different organs. The antitumorigenic effects of PEI/siRNA-mediated in vivo gene-targeting of tumor-relevant proteins like in mouse tumor xenograft models are described. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1559929/ doi: 10.1155/jbb/2006/71659 id: cord-276575-jfug80yu author: Aigner, Achim title: Applications of RNA interference: current state and prospects for siRNA-based strategies in vivo date: 2007-04-25 words: 5251.0 sentences: 325.0 pages: flesch: 47.0 cache: ./cache/cord-276575-jfug80yu.txt txt: ./txt/cord-276575-jfug80yu.txt summary: From the mechanism, it becomes clear that small interfering RNAs (siRNAs) play a pivotal role in triggering RNAi. Thus, the efficient delivery of target gene-specific siRNAs is one major challenge in the establishment of therapeutic RNAi. Numerous studies, based on different modes of administration and various siRNA formulations and/or modifications, have already accumulated promising results. While the inhibition of the activity of (aberrant) gene products, e.g., through small molecule inhibitors or inhibitory antibodies is one major focus in therapy, much attention has now shifted to an earlier step, i.e., the initial knockdown of the specific gene of interest through RNAi. However, for the in vivo application of RNAi in mammals as a therapeutic approach for reversing a pathological condition as well as for the study of particular gene functions, sophisticated strategies for the induction of RNAi are needed. RNAi-mediated gene-targeting through systemic application of polyethylenimine (PEI)-complexed siRNA in vivo abstract: Within the recent years, RNA interference (RNAi) has become an almost-standard method for in vitro knockdown of any target gene of interest. Now, one major focus is to further explore its potential in vivo, including the development of novel therapeutic strategies. From the mechanism, it becomes clear that small interfering RNAs (siRNAs) play a pivotal role in triggering RNAi. Thus, the efficient delivery of target gene-specific siRNAs is one major challenge in the establishment of therapeutic RNAi. Numerous studies, based on different modes of administration and various siRNA formulations and/or modifications, have already accumulated promising results. This applies to various animal models covering viral infections, cancer and multiple other diseases. Continuing efforts will lead to the development of efficient and “double-specific” drugs, comprising of siRNAs with high target gene specificity and of nanoparticles enhancing siRNA delivery and target organ specificity. url: https://www.ncbi.nlm.nih.gov/pubmed/17457539/ doi: 10.1007/s00253-007-0984-y id: cord-009943-fzynh14x author: Ai‐Nakib, W. title: Detection of Human Rhinoviruses and Their Molecular Relationship Using cDNA Probes date: 2005-12-11 words: 2879.0 sentences: 158.0 pages: flesch: 58.0 cache: ./cache/cord-009943-fzynh14x.txt txt: ./txt/cord-009943-fzynh14x.txt summary: Further, evidence is provided in this study that indicates that it would be feasible to use cDNA probes to detect human rhinoviruses in nasal washings. In a preliminary study we found that this probe does indeed cross-hybridize with a number of human rhinoviruses indicating the feasibility of cDNA:RNA hybridization for rhinovirus detection [Al-Nakib et al, 19861 . We have now extended these studies to include a larger series of human rhinoviruses (totalling some 56 viruses) and looked in more detail at the molecular relationship between these viruses, the limits of detection, and the feasibility of applying these procedures for the direct detection of viral RNA in nasal washings. However, in addition to detecting virus at lower titres, the strength of the hybridization signals obtained with 20 x SSC-37 % formaldehyde were particularly strong at all virus dilutions in nasal washings compared with phenol/chloroform extraction, indicating that more viral RNA has been immobilised onto the nitrocellulose filters. abstract: We describe here a cDNA: RNA hybridization system for the study of human rhinoviruses. We have constructed an M13 probe from the 5′ end of the genome of rhinovirus 14 (HRV‐14) and used this to detect directly viral RNA. Of the 56 human rhinoviruses so far investigated 54 or 96.4% gave clearly positive hybridization signals. However, the strength of this signal depended very much on the molecular relationship of these viruses. Thus, HRV‐3, 4, 17, 72, and, to a slightly lesser extent, HRV‐2, 6, 9, 13, 19, 31, 42, 49, 64, and 69 appear to be closely related to HRV‐14 whereas HRV‐5, 7, 8, 16, 32, 40, 45, 55, 56, 63, 80, 82, and 85 appear to be relatively divergent. Further, evidence is provided in this study that indicates that it would be feasible to use cDNA probes to detect human rhinoviruses in nasal washings. However, the sensitivity of detection was clearly affected by both the inclusion of inhibitors of endogenous RNase activity in the RNA extraction mixture and also in the method of extracting the viral RNA. From reconstruction experiments in nasal washings and under optimal conditions, we can detect virus at 10(2.8) TCID(50)/ml. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167088/ doi: 10.1002/jmv.1890200311 id: cord-280272-mn596x1p author: Akhrymuk, Ivan title: Magnetic Nanotrap Particles Preserve the Stability of Venezuelan Equine Encephalitis Virus in Blood for Laboratory Detection date: 2020-01-28 words: 6551.0 sentences: 300.0 pages: flesch: 51.0 cache: ./cache/cord-280272-mn596x1p.txt txt: ./txt/cord-280272-mn596x1p.txt summary: We have tested the ability of magnetic Nanotrap® (NT) particles to improve stability and detection of Venezuelan equine encephalitis virus (VEEV), viral capsid protein, and viral genomic RNA in whole human blood at elevated temperature and prolonged storage conditions. We have tested the ability of magnetic Nanotrap ® (NT) particles to improve stability and detection of Venezuelan equine encephalitis virus (VEEV), viral capsid protein, and viral genomic RNA in whole human blood at elevated temperature and prolonged storage conditions. In this study, we sought to apply new magnetic NT particles that consist of NIPAm copolymers functionalized with reactive red 120 to evaluate the efficacy of preservation of infectious VEEV, viral RNA, and VEEV capsid protein in whole blood samples at ambient and elevated temperature as well as at low and high humidity conditions. abstract: Most of the modern techniques used for identification of viral-induced disease are based on identification of viral antigens and/or nucleic acids in patient's blood. Diagnosis in the field or in remote locations can be challenging and alternatively samples are shipped to diagnostic labs for testing. Shipments must occur under controlled temperature conditions to prevent loss of sample integrity. We have tested the ability of magnetic Nanotrap® (NT) particles to improve stability and detection of Venezuelan equine encephalitis virus (VEEV), viral capsid protein, and viral genomic RNA in whole human blood at elevated temperature and prolonged storage conditions. NT particles have previously been shown to capture and enrich multiple pathogens including respiratory syncytial virus, influenza virus, coronavirus, and Rift Valley fever virus. Our study indicates that samples incubated with NT particles had detectable levels of infectious VEEV in blood equal to or greater than samples without NT treatment across all temperatures. Viral RNA detection was increased in the presence of NT particles at later time points (72 h) and higher temperature (40°C) conditions. Likewise, detection of VEEV capsid protein was enhanced in the presence of NT particles up to 72 h at 40°C. Finally, we intranasally infected C3H mice with TC-83, the live attenuated vaccine strain of VEEV, and demonstrated that NT particles could substantially increase the detection of VEEV capsid in infected blood incubated up to 72 h at 40°C. Samples without NT particles had undetectable capsid protein levels. Taken together, our data demonstrate the ability of NT particles to preserve and enable detection of VEEV in human and mouse blood samples over time and at elevated temperatures. url: https://www.ncbi.nlm.nih.gov/pubmed/32064269/ doi: 10.3389/fvets.2019.00509 id: cord-302195-25gjbyi1 author: Al Huraimel, Khalid title: SARS-CoV-2 in the environment: Modes of transmission, early detection and potential role of pollutions date: 2020-07-15 words: 7089.0 sentences: 386.0 pages: flesch: 50.0 cache: ./cache/cord-302195-25gjbyi1.txt txt: ./txt/cord-302195-25gjbyi1.txt summary: This article aims to examine the latest investigations on SARS-CoV-2 plausible environmental transmission modes, employment of wastewater surveillance for early detection of COVID-19, and elucidating the role of solid waste, water, and atmospheric quality on viral infectivity. There is no conclusive evidence for aerosol or faecal-oral transmission of SARS-CoV-2 despite several researchers considering them as plausible routes that may explain the high infectivity and global spread of COVID-19 (Chen et al., 2020; van Doremalen et al., 2020; Wang et al., 2020a) . From the literature studied, concerns of COVID-19 infection through environmental contact pertain mainly to areas that lack proper sanitation and wastewater treatment, lack adequate solid waste management infrastructure, in areas where raw sewage is discharged directly into natural water bodies, and in cities where air pollution is problematic.  Robust evidence is needed to assess impact of air pollution, solid waste management, and sewage contamination of water bodies on COVID-19 spread and infectivity. abstract: Abstract The coronavirus disease 2019 (COVID-19) is spreading globally having a profound effect on lives of millions of people, causing worldwide economic disruption. Curbing the spread of COVID-19 and future pandemics may be accomplished through understanding the environmental context of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and adoption of effective detection tools and mitigation policies. This article aims to examine the latest investigations on SARS-CoV-2 plausible environmental transmission modes, employment of wastewater surveillance for early detection of COVID-19, and elucidating the role of solid waste, water, and atmospheric quality on viral infectivity. Transmission of SARS-CoV-2 via faecal-oral or bio-aerosols lacks robust evidence and remains debatable. However, improper disinfection and defected plumbing systems in indoor environments such as hospitals and high-rise towers may facilitate the transport of virus-laden droplets of wastewater causing infection. Clinical and epidemiological studies are needed to present robust evidence that SARS-CoV-2 is transmissible via aerosols, though quantification of virus-laden aerosols at low concentrations presents a challenge. Wastewater surveillance of SARS-CoV-2 can be an effective tool in early detection of outbreak and determination of COVID-19 prevalence within a population, complementing clinical testing and providing decision makers guidance on restricting or relaxing movement. While poor air quality increases susceptibility to diseases, evidence for air pollution impact on COVID-19 infectivity is not available as infections are dynamically changing worldwide. Solid waste generated by households with infected individuals during the lockdown period may facilitate the spread of COVID-19 via fomite transmission route but has received little attention from the scientific community. Water bodies receiving raw sewage may pose risk of infection but this has not been investigated to date. Overall, our understanding of the environmental perspective of SARS-CoV-2 is imperative to detecting outbreak and predicting pandemic severity, allowing us to be equipped with the right tools to curb any future pandemic. url: https://www.sciencedirect.com/science/article/pii/S0048969720344752?v=s5 doi: 10.1016/j.scitotenv.2020.140946 id: cord-354398-f3cg8gi1 author: Al-Saud, Haya title: Automated SARS-COV-2 RNA extraction from patient nasopharyngeal samples using a modified DNA extraction kit for high throughput testing date: 2020-09-20 words: 4018.0 sentences: 199.0 pages: flesch: 55.0 cache: ./cache/cord-354398-f3cg8gi1.txt txt: ./txt/cord-354398-f3cg8gi1.txt summary: The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. We validated the modified Invitrogen Forensic DNA Purification kit in extracting in-laboratory propagated SARS-COV-2 RNA by conducting manual and automated extractions on titrations from 15 000 copies to 60 copies of SARS-COV-2 followed by RT-qPCR methods: the commercially available TaqPath One-Step qRT-QP-CR kit (using the N, S, and ORF1b genes) and primers and probes from Metabion, Germany to establish an inhouse RT-qPCR assay based on E, RdRp2 and RdRp4 gene detection as per recommended SARS-COV-2 testing from CDC and WHO. abstract: BACKGROUND: The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has prompted a need for mass testing to identify patients with viral infection. The high demand has created a global bottleneck in testing capacity, which prompted us to modify available resources to extract viral RNA and perform reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) to detect SARS-COV-2. OBJECTIVES: Report on the use of a DNA extraction kit, after modifications, to extract viral RNA that could then be detected using an FDA-approved SARS-COV-2 RT-qPCR assay. MATERIALS AND METHODS: Initially, automated RNA extraction was performed using a modified DNA kit on samples from control subjects, a bacteriophage, and an RNA virus. We then verified the automated extraction using the modified kit to detect in-lab propagated SARSCOV-2 titrations using an FDA approved commercial kit (S, N, and ORF1b genes) and an in-house primer-probe based assay (E, RdRp2 and RdRp4 genes). RESULTS: Automated RNA extraction on serial dilutions SARS-COV-2 achieved successful one-step RT-qPCR detection down to 60 copies using the commercial kit assay and less than 30 copies using the in-house primer-probe assay. Moreover, RT-qPCR detection was successful after automated RNA extraction using this modified protocol on 12 patient samples of SARS-COV-2 collected by nasopharyngeal swabs and stored in viral transport media. CONCLUSIONS: We demonstrated the capacity of a modified DNA extraction kit for automated viral RNA extraction and detection using a platform that is suitable for mass testing. LIMITATIONS: Small patient sample size. CONFLICT OF INTEREST: None. url: https://doi.org/10.5144/0256-4947.2020.373 doi: 10.5144/0256-4947.2020.373 id: cord-333080-qytwbsne author: Alahari, Suresh K. title: SARS-CoV infection crosstalk with human host cell noncoding-RNA machinery: An in-silico approach date: 2020-07-28 words: 2244.0 sentences: 123.0 pages: flesch: 49.0 cache: ./cache/cord-333080-qytwbsne.txt txt: ./txt/cord-333080-qytwbsne.txt summary: Altogether, TGF-beta signaling pathway as well as hub miRNAs, and LncRNAs involve during SARS-CoV pathogenesis can be considered as potential therapeutic targets. Developing functional computational models and networks to predict potential SARS-CoV -miRNA/lncRNA association may benefit not only the understanding of COVID-19 mechanism at the noncoding RNA level, but also the detection of disease biomarkers for disease diagnosis, treatment, prognosis, and prevention. Since multiple ways of interaction between miRNAs, lncRNAs, and mRNA have been reported to play key roles in determining the cellular functions during viral infection, it is essential to discover these interactions in an integrated fashion to comprehensively decipher the networks and key regulatory noncoding-RNA hubs underpinning the pathology of SARS-CoV. Our in-silico analysis has built a network of protein-protein interaction between the Human SARS coronavirus (SARS-CoV) and host proteome (Figure 1) , as well as strong miRNA-mRNA-lncRNA crosstalk ( Figure 4 and Table 2 ) possibly modulating the human response to the viral infection. abstract: Although 70% of the genome is transcribed to RNA in humans, only ∼2% of these transcripts are translated into proteins. The rest of the transcripts are defined as noncoding RNAs, including Long noncoding RNAs (LncRNAs) and MicroRNAs (miRNAs) that mostly function post-transcriptionally to regulate the gene expression. The outbreak of a novel coronavirus (SARS-CoV) has caused a major public health concern across the globe. The SARS-CoV is the seventh coronavirus that is known to cause human disease. There are currently no promising antiviral drugs with proven efficacy nor are there vaccines for its prevention. As of July 13, 2020, SARS-CoV has been infected more than 13 million cases in more than 213 countries, with an estimated mortality rate of ∼3%. Thus, it is of utmost important priority to develop novel therapies for COVID-19. It is not fully investigated whether noncoding RNAs regulate signaling pathways that SARS-CoV involved in. Hence, computational analysis of the noncoding RNA interactions and determining importance of key regulatory noncoding RNAs in antiviral defense mechanisms will likely be helpful in developing new drugs to attack SARS-CoV infection.. To elucidate this, we utilized bioinformatic approaches to find the interaction network of SARS-CoV/human proteins, miRNAs, and lncRNAs. We found TGF-beta signaling pathway as one of the potential interactive pathways. Furthermore, potential miRNAs/lncRNAs networks that the virus might engage during infection in human host cells have been shown. Altogether, TGF-beta signaling pathway as well as hub miRNAs, and LncRNAs involve during SARS-CoV pathogenesis can be considered as potential therapeutic targets. url: https://www.sciencedirect.com/science/article/pii/S0753332220307411?v=s5 doi: 10.1016/j.biopha.2020.110548 id: cord-102766-n6mpdhyu author: Alam, Md. Nafis Ul title: Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses date: 2020-06-25 words: 3193.0 sentences: 192.0 pages: flesch: 56.0 cache: ./cache/cord-102766-n6mpdhyu.txt txt: ./txt/cord-102766-n6mpdhyu.txt summary: title: Short k-mer Abundance Profiles Yield Robust Machine Learning Features and Accurate Classifiers for RNA Viruses Machine Learning methods are becoming more reliable for characterizing sequence data, but virus genomes are more variable than all forms of life and viruses with RNA-based genomes have gone overlooked in previous machine learning attempts. We designed a novel short k-mer based scoring criteria whereby a large number of highly robust numerical feature sets can be derived from sequence data. Here, we present a novel short k-mer based sequence 28 scoring method that generates robust sequence information for training machine learning 29 classifiers. Here, we present a novel short k-mer based sequence 28 scoring method that generates robust sequence information for training machine learning 29 classifiers. VirFinder: a novel k-mer based tool for identifying viral sequences from 558 assembled metagenomic data. abstract: High throughout sequencing technologies have greatly enabled the study of genomics, transcriptomics and metagenomics. Automated annotation and classification of the vast amounts of generated sequence data has become paramount for facilitating biological sciences. Genomes of viruses can be radically different from all life, both in terms of molecular structure and primary sequence. Alignment-based and profile-based searches are commonly employed for characterization of assembled viral contigs from high-throughput sequencing data. Recent attempts have highlighted the use of machine learning models for the task but these models rely entirely on DNA genomes and owing to the intrinsic genomic complexity of viruses, RNA viruses have gone completely overlooked. Here, we present a novel short k-mer based sequence scoring method that generates robust sequence information for training machine learning classifiers. We trained 18 classifiers for the task of distinguishing viral RNA from human transcripts. We challenged our models with very stringent testing protocols across different species and evaluated performance against BLASTn, BLASTx and HMMER3 searches. For clean sequence data retrieved from curated databases, our models display near perfect accuracy, outperforming all similar attempts previously reported. On de-novo assemblies of raw RNA-Seq data from cells subjected to Ebola virus, the area under the ROC curve varied from 0.6 to 0.86 depending on the software used for assembly. Our classifier was able to properly classify the majority of the false hits generated by BLAST and HMMER3 searches on the same data. The outstanding performance metrics of our model lays the groundwork for robust machine learning methods for the automated annotation of sequence data. Author Summary In this age of high-throughput sequencing, proper classification of copious amounts of sequence data remains to be a daunting challenge. Presently, sequence alignment methods are immediately assigned to the task. Owing to the selection forces of nature, there is considerable homology even between the sequences of different species which draws ambiguity to the results of alignment-based searches. Machine Learning methods are becoming more reliable for characterizing sequence data, but virus genomes are more variable than all forms of life and viruses with RNA-based genomes have gone overlooked in previous machine learning attempts. We designed a novel short k-mer based scoring criteria whereby a large number of highly robust numerical feature sets can be derived from sequence data. These features were able to accurately distinguish virus RNA from human transcripts with performance scores better than all previous reports. Our models were able to generalize well to distant species of viruses and mouse transcripts. The model correctly classifies the majority of false hits generated by current standard alignment tools. These findings strongly imply that this k-mer score based computational pipeline forges a highly informative, rich set of numerical machine learning features and similar pipelines can greatly advance the field of computational biology. url: https://doi.org/10.1101/2020.06.25.170779 doi: 10.1101/2020.06.25.170779 id: cord-333261-knj2rrut author: Albright, Catherine J. title: An exercise in molecular epidemiology: Human rhinovirus prevalence and genetics date: 2011-11-11 words: 3408.0 sentences: 205.0 pages: flesch: 59.0 cache: ./cache/cord-333261-knj2rrut.txt txt: ./txt/cord-333261-knj2rrut.txt summary: To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. The extensive data available on HRV genomes enables many bioinformatics opportunities for students, including alignment of genome sequences to look for mutations at the RNA level and differences among protein sequences. Students can examine differences in the HRV serotypes over several years of data regarding a university population to identify HRV mutations that have occurred and their severity in causing symptoms in the host. In this inquiry-based laboratory project, students use a variety of techniques, including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis to look for the presence of HRV in nasal lavage samples from human subjects. By analyzing surveys in which subjects indicate severity of their symptoms, stress factors, and average hours of rest per night, students can identify possible contributors to HRV infection. abstract: Human rhinovirus (HRV) is one of the most common human respiratory pathogens and is responsible for the majority of upper respiratory illnesses. Recently, a phylogeny was constructed from all known American Type Culture Collection (ATCC) HRV sequences. From this study, three HRV classifications (HRVA, HRVB, and HRVC) were determined and techniques for classifying new isolates of HRV were reported. The genetic change of this virus in specific populations over time is of great interest to understand the evolution and epidemiology of viruses. To facilitate the collections of HRV sequences over a number of years, a virology experiment was designed in which students test nasal lavage samples to look for HRV infection. Students will learn a variety of techniques including RNA isolation, cDNA synthesis, qPCR, and agarose gel electrophoresis as well as bioinformatic skills though examination of sequences from the HRV‐field isolates. Furthermore, students can look at symptom data from subjects to investigate correlations between symptom severity and factors such as stress and sleep patterns. Such information can be used to examine hypotheses regarding HRV mutation, symptom severity and epidemiology. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 6, pp. 457–458, 2011 url: https://doi.org/10.1002/bmb.20530 doi: 10.1002/bmb.20530 id: cord-274569-jh0dyyz7 author: Alenquer, Marta title: Exosome Biogenesis, Regulation, and Function in Viral Infection date: 2015-09-17 words: 7844.0 sentences: 447.0 pages: flesch: 43.0 cache: ./cache/cord-274569-jh0dyyz7.txt txt: ./txt/cord-274569-jh0dyyz7.txt summary: These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. These routes require maturation of the EE into recycling endosomes or multivesicular bodies (MVBs), which can either fuse with lysosomes (L) to generate endolysosomes (EL) or with the plasma membrane to release intraluminal vesicles to the milieu as exosomes. This mechanism was recently reported for HCV [113] , where exosomes derived from infected human hepatoma cells containing full-length viral RNA, along with core and envelope proteins [115] , were shown to be infectious and a major route of transmission. demonstrated that B lymphocytes infected with Epstein-Barr virus (EBV), a human gammaherpesvirus associated with a variety of lymphoblastoid and epithelial cancers, released exosomes containing MHC II molecules, and that these vesicles were capable of activating specific CD4 + T cell clones in vitro [122] . abstract: Exosomes are extracellular vesicles released upon fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. They originate as intraluminal vesicles (ILVs) during the process of MVB formation. Exosomes were shown to contain selectively sorted functional proteins, lipids, and RNAs, mediating cell-to-cell communications and hence playing a role in the physiology of the healthy and diseased organism. Challenges in the field include the identification of mechanisms sustaining packaging of membrane-bound and soluble material to these vesicles and the understanding of the underlying processes directing MVBs for degradation or fusion with the plasma membrane. The investigation into the formation and roles of exosomes in viral infection is in its early years. Although still controversial, exosomes can, in principle, incorporate any functional factor, provided they have an appropriate sorting signal, and thus are prone to viral exploitation. This review initially focuses on the composition and biogenesis of exosomes. It then explores the regulatory mechanisms underlying their biogenesis. Exosomes are part of the endocytic system, which is tightly regulated and able to respond to several stimuli that lead to alterations in the composition of its sub-compartments. We discuss the current knowledge of how these changes affect exosomal release. We then summarize how different viruses exploit specific proteins of endocytic sub-compartments and speculate that it could interfere with exosome function, although no direct link between viral usage of the endocytic system and exosome release has yet been reported. Many recent reports have ascribed functions to exosomes released from cells infected with a variety of animal viruses, including viral spread, host immunity, and manipulation of the microenvironment, which are discussed. Given the ever-growing roles and importance of exosomes in viral infections, understanding what regulates their composition and levels, and defining their functions will ultimately provide additional insights into the virulence and persistence of infections. url: https://doi.org/10.3390/v7092862 doi: 10.3390/v7092862 id: cord-319780-rfj9t99r author: Alexander, S.P.H. title: A rational roadmap for SARS‐CoV‐2/COVID‐19 pharmacotherapeutic research and development. IUPHAR Review 29 date: 2020-05-01 words: 15196.0 sentences: 814.0 pages: flesch: 47.0 cache: ./cache/cord-319780-rfj9t99r.txt txt: ./txt/cord-319780-rfj9t99r.txt summary: Analysis of the co-crystal structure suggested that the SARS spike protein binds to the active site of angiotensin converting enzyme 2 (ACE2, Li et al., 2005) . A truncated version of human recombinant ACE2, lacking the transmembrane domain, mitigated against SARS-CoV infection of cells (Li et al., 2003) and has been used in animal models to reduce symptoms of severe acute lung failure , diabetic nephropathy (Oudit et al., 2010) and cardiac hypertrophy and fibrosis . A recent cryo-EM structure suggested that ACE2 and B 0 AT1/SLC6A19 form a heterodimer which pairs up through interfaces between the two ACE2 partners (Figure 1) , with the RBD of SARS-CoV-2 spike protein binding to the peptidase active site of ACE2 suggesting that B 0 AT1/SLC6A19 may facilitate entry of the novel coronavirus. Tumor necrosis factor- convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) abstract: In this review, we identify opportunities for drug discovery in the treatment of COVID‐19 and in so doing, provide a rational roadmap whereby pharmacology and pharmacologists can mitigate against the global pandemic. We assess the scope for targetting key host and viral targets in the mid‐term, by first screening these targets against drugs already licensed; an agenda for drug re‐purposing, which should allow rapid translation to clinical trials. A simultaneous, multi‐pronged approach using conventional drug discovery methodologies aimed at discovering novel chemical and biological means targetting a short‐list of host and viral entities should extend the arsenal of anti‐SARS‐CoV‐2 agents. This longer‐term strategy would provide a deeper pool of drug choices for future‐proofing against acquired drug resistance. Second, there will be further viral threats, which will inevitably evade existing vaccines. This will require a coherent therapeutic strategy which pharmacology and pharmacologists are best placed to provide. url: https://www.ncbi.nlm.nih.gov/pubmed/32358833/ doi: 10.1111/bph.15094 id: cord-103735-nil1vv6h author: Alfano, Niccolo title: Non-invasive surveys of mammalian viruses using environmental DNA date: 2020-03-29 words: 5829.0 sentences: 373.0 pages: flesch: 53.0 cache: ./cache/cord-103735-nil1vv6h.txt txt: ./txt/cord-103735-nil1vv6h.txt summary: Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. We provide evidence that environmental and invertebrate-derived DNA samples including waterhole water, sediment and wild haematophagous terrestrial leeches can be used to survey known and unknown viruses. abstract: Environmental DNA (eDNA) and its subdiscipline, invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively [1,2]. Water is ubiquitous in most ecosystems, and, among invertebrates, terrestrial haematophagous leeches are abundant and can be easily collected in many tropical rainforests [3,4]. Such non-invasive nucleic acid sources can mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA sources have been applied to monitoring specific wildlife pathogens [5,6]. However, previous studies have focused on known pathogens, whereas most wildlife pathogens are uncharacterized and unknown. Non-invasive approaches to monitoring known and novel pathogens may be of particular benefit in ecosystems prone to viral emergence, many of which occur in areas where invasive sampling is challenging, such as tropical rainforests. Here, we show that both eDNA from natural waterholes, and iDNA from terrestrial haematophagous leeches, can be used to detect unknown viruses circulating in mammalian hosts (Figure 1). Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Congruence was found between host DNA assignment and viruses identified in leeches, and between animals observed visiting the waterholes and the viruses detected. Our results demonstrate that eDNA/iDNA samples may represent an effective non-invasive resource for studying wildlife viral diversity. Several of the detected viruses were novel, highlighting the potential of eDNA/iDNA for epidemiological analysis of emerging viruses prior to their emergence. Highlights Environmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for viruses A comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversity Leech blood meal host determination and viruses identified were congruent Viruses determined from water correlated with known and observed species visiting the water sources In brief Alfano, Dayaram, et al. demonstrate that environmental DNA from southeast Asian leech bloodmeals and waterholes from Africa and Mongolia can be used as to detect viruses circulating in wildlife. These nucleic acid sources may represent an effective non-invasive resource for studying wildlife viral diversity and emerging viruses pre-emergence. url: https://doi.org/10.1101/2020.03.26.009993 doi: 10.1101/2020.03.26.009993 id: cord-303111-iv4lzpev author: Almazán, Fernando title: Reprint of: Coronavirus reverse genetic systems: Infectious clones and replicons() date: 2014-12-19 words: 7071.0 sentences: 314.0 pages: flesch: 42.0 cache: ./cache/cord-303111-iv4lzpev.txt txt: ./txt/cord-303111-iv4lzpev.txt summary: Until recently, the study of CoV genetics was broadly restricted to the analysis of temperature-sensitive (ts) mutants Baric, 1992, 1994; Lai and Cavanagh, 1997; Schaad and Baric, 1994; Stalcup et al., 1998) , defective RNA templates which depend on replicase proteins provided in trans by a helper virus (Izeta et al., 1999; Narayanan and Makino, 2001; Repass and Makino, 1998; Williams et al., 1999) , and recombinant viruses generated by targeted recombination (Masters, 1999; Masters and Rottier, 2005 reverse genetic system devised for CoVs at a time when it was not clear whether the construction of full-length infectious cDNA clones would ever be technically feasible. These reverse genetic systems have been established using non-traditional approaches, which are based on the use of targeted recombination, BACs, in vitro ligation of CoV cDNA fragments, and vaccinia virus as a vector for the propagation of CoV genomic cDNAs. The availability of CoV full-length infectious clones and recombinant viruses expressing reporter genes constitute important tools for the study of CoV replication and transcription mechanisms, virus-host interaction and pathogenesis, and also for the rapid and rational development and testing of genetically defined vaccines. abstract: Coronaviruses (CoVs) infect humans and many animal species, and are associated with respiratory, enteric, hepatic, and central nervous system diseases. The large size of the CoV genome and the instability of some CoV replicase gene sequences during its propagation in bacteria, represent serious obstacles for the development of reverse genetic systems similar to those used for smaller positive sense RNA viruses. To overcome these limitations, several alternatives to more conventional plasmid-based approaches have been established in the last 13 years. In this report, we briefly review and discuss the different reverse genetic systems developed for CoVs, paying special attention to the severe acute respiratory syndrome CoV (SARS-CoV). url: https://www.sciencedirect.com/science/article/pii/S0168170214003827 doi: 10.1016/j.virusres.2014.09.006 id: cord-303915-14yfs4pa author: Almazán, Fernando title: Engineering a Replication-Competent, Propagation-Defective Middle East Respiratory Syndrome Coronavirus as a Vaccine Candidate date: 2013-09-10 words: 7132.0 sentences: 336.0 pages: flesch: 50.0 cache: ./cache/cord-303915-14yfs4pa.txt txt: ./txt/cord-303915-14yfs4pa.txt summary: The construction of a full-length infectious cDNA clone of the MERS-CoV genome in a bacterial artificial chromosome is reported here, providing a reverse genetics system to study the molecular biology of the virus and to develop attenuated viruses as vaccine candidates. The mutant viruses presented growth kinetics similar to those of the wild-type virus, indicating that accessory genes were not essential for MERS-CoV replication in cell cultures. Using this clone, recombinant MERS-CoV (rMERS-CoV) deletion mutants were constructed lacking genes nonessential for virus replication. An infectious cDNA clone was assembled as a BAC under the control of the cytomegalovirus (CMV) immediate-early pro-moter, based on the genome sequence of the MERS-CoV-EMC12 strain (GenBank accession number JX869059) (15) . Based on published data showing that the deletion of CoV E protein resulted in either replication-competent, propagation-defective viruses (24) or attenuated viruses (25, 26, 31) , a cDNA clone with the E gene deleted (pBAC-MERS-⌬E) was constructed from pBAC-MERS FL . abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging coronavirus infecting humans that is associated with acute pneumonia, occasional renal failure, and a high mortality rate and is considered a threat to public health. The construction of a full-length infectious cDNA clone of the MERS-CoV genome in a bacterial artificial chromosome is reported here, providing a reverse genetics system to study the molecular biology of the virus and to develop attenuated viruses as vaccine candidates. Following transfection with the cDNA clone, infectious virus was rescued in both Vero A66 and Huh-7 cells. Recombinant MERS-CoVs (rMERS-CoVs) lacking the accessory genes 3, 4a, 4b, and 5 were successfully rescued from cDNA clones with these genes deleted. The mutant viruses presented growth kinetics similar to those of the wild-type virus, indicating that accessory genes were not essential for MERS-CoV replication in cell cultures. In contrast, an engineered mutant virus lacking the structural E protein (rMERS-CoV-ΔE) was not successfully rescued, since viral infectivity was lost at early passages. Interestingly, the rMERS-CoV-ΔE genome replicated after cDNA clone was transfected into cells. The infectious virus was rescued and propagated in cells expressing the E protein in trans, indicating that this virus was replication competent and propagation defective. Therefore, the rMERS-CoV-ΔE mutant virus is potentially a safe and promising vaccine candidate to prevent MERS-CoV infection. IMPORTANCE Since the emergence of MERS-CoV in the Arabian Peninsula during the summer of 2012, it has already spread to 10 different countries, infecting around 94 persons and showing a mortality rate higher than 50%. This article describes the development of the first reverse genetics system for MERS-CoV, based on the construction of an infectious cDNA clone inserted into a bacterial artificial chromosome. Using this system, a collection of rMERS-CoV deletion mutants has been generated. Interestingly, one of the mutants with the E gene deleted was a replication-competent, propagation-defective virus that could only be grown in the laboratory by providing E protein in trans, whereas it would only survive a single virus infection cycle in vivo. This virus constitutes a vaccine candidate that may represent a balance between safety and efficacy for the induction of mucosal immunity, which is needed to prevent MERS-CoV infection. url: https://doi.org/10.1128/mbio.00650-13 doi: 10.1128/mbio.00650-13 id: cord-289612-4x5t4c5u author: Alsuliman, Tamim title: COVID-19 paraclinical diagnostic tools: Updates and future trends date: 2020-06-20 words: 7353.0 sentences: 387.0 pages: flesch: 48.0 cache: ./cache/cord-289612-4x5t4c5u.txt txt: ./txt/cord-289612-4x5t4c5u.txt summary: Laboratory-confirmed SARS-CoV-2 infection requires the detection of viral nucleic acid in respiratory tract samples by the use of real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay. In the course of this phase, upper respiratory specimens were tested by RT-PCR for viral RNA and the majority of the patients showed positive results for SARS-CoV-2. These results contrast with another German smaller study by Wolfel et al., conducted on 9 COVID-19 patients, with no discernible difference in viral loads or detection rates when comparing nasal and throat swabs [38] . found that 66.67% of laboratory-confirmed COVID-19 patients were tested positive for SARS-CoV-2 RNA in stool specimens. enrolled a total of 173 confirmed cases of COVID-19 by the use of rRT-PCR on samples from the respiratory track reported that the seroconversion sequentially appeared for the total antibody (Ab), IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases abstract: MOTIVATION: COVID-19 is one of the most widely affecting pandemics. As for many respiratory viruses-caused diseases, diagnosis of COVID-19 relies on two main compartments: clinical and paraclinical diagnostic criteria. Rapid and accurate diagnosis is vital in such a pandemic. On one side, rapidity may enhance management effectiveness, while on the other, coupling efficiency and less costly procedures may permit more effective community-scale management. METHODOLOGY AND MAIN STRUCTURE: In this review, we shed light on the most used and the most validated diagnostic tools. Furthermore, we intend to include few under-development techniques that may be potentially useful in this context. The practical intent of our work is to provide clinicians with a realistic summarized review of the essential elements in the applied paraclinical diagnosis of COVID-19. url: https://doi.org/10.1016/j.retram.2020.06.001 doi: 10.1016/j.retram.2020.06.001 id: cord-276997-hbovh7s9 author: Alsved, Malin title: Aerosolization and recovery of viable murine norovirus in an experimental setup date: 2020-09-29 words: 6031.0 sentences: 297.0 pages: flesch: 46.0 cache: ./cache/cord-276997-hbovh7s9.txt txt: ./txt/cord-276997-hbovh7s9.txt summary: However, the infectivity of airborne human noroviruses has not been possible to assess in real-world environments, nor in laboratory experiments, since there is no well-established cell culturing system for these viruses working at the low concentrations obtained in air samples 6 . SLAG: Sparging liquid aerosol generator; HEPA filter: high efficiency particulate air filter; nsRNA: negative sense RNA; psRNA: positive sense RNA; MNV: murine norovirus; qRT-PCR: quantitative reverse transcriptase polymerase chain reaction. Taken together, as compared to the atomizer, a smaller amount of SLAG aerosol is collected by the BioSampler (i.e., higher physical dilution), but these particles contain more MNV psRNA copies (lower viral dilution relative the physical dilution). The experimental setup described here highlights some difficulties in studies on aerosolized viruses: (1) the lack of standards in how to generate bioaerosol that results in significant differences in aerosol particle size and concentration, (2) the necessity to determine both physical and viral dilution factors, and (3) www.nature.com/scientificreports/ during airborne transport due to the low-solute solution and dilution in the setup. abstract: Noroviruses are the major cause for viral acute gastroenteritis in the world. Despite the existing infection prevention strategies in hospitals, the disease continues to spread and causes extensive and numerous outbreaks. Hence, there is a need to investigate the possibility of airborne transmission of norovirus. In this study, we developed an experimental setup for studies on the infectivity of aerosolized murine norovirus (MNV), a model for the human norovirus. Two aerosol generation principles were evaluated: bubble bursting, a common natural aerosolization mechanism, and nebulization, a common aerosolization technique in laboratory studies. The aerosolization setup was characterized by physical and viral dilution factors, generated aerosol particle size distributions, and the viral infectivity after aerosolization. We found a lower physical dilution factor when using the nebulization generator than with the bubble bursting generator. The viral dilution factor of the system was higher than the physical dilution; however, when comparing the physical and viral dilution factors, bubble bursting generation was more efficient. The infectivity per virus was similar using either generation principle, suggesting that the generation itself had a minor impact on MNV infectivity and that instead, the effect of drying in air could be a major reason for infectivity losses. url: https://doi.org/10.1038/s41598-020-72932-5 doi: 10.1038/s41598-020-72932-5 id: cord-003597-zj3w9ptj author: Altman, Matthew C. title: Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children date: 2019-04-08 words: 13552.0 sentences: 661.0 pages: flesch: 44.0 cache: ./cache/cord-003597-zj3w9ptj.txt txt: ./txt/cord-003597-zj3w9ptj.txt summary: We combined nasal virus PCR, nasal and peripheral blood cell differentials, and nasal and blood RNA-seq for serial sample collections at baseline and longitudinally during episodes when participants reported cold symptoms to determine the key molecular pathways associated with subsequent asthma exacerbations. The primary aim of the study was to identify patterns of gene expression induced during events that progressed to asthma exacerbations (exacerbation, Ex + ), defined by clinical symptoms that resulted in systemic corticosteroid use within 10 d of cold Fig. 1 | Study design and primary and secondary endpoints. From nasal and blood samples, we combined measured cell percentages with RNA-seq data and used cell deconvolution and WGCNA to construct and validate a repertoire of 94 distinct gene expression modules representing a diverse array of biological functions (Supplementary Fig. 1 and Supplementary Table 1 ). abstract: Respiratory infections are common precursors to asthma exacerbations in children, but molecular immune responses that determine whether and how an infection causes an exacerbation are poorly understood. By using systems-scale network analysis, we identify repertoires of cellular transcriptional pathways that lead to and underlie distinct patterns of asthma exacerbation. Specifically, in both virus-associated and nonviral exacerbations, we demonstrate a set of core exacerbation modules, among which epithelial-associated SMAD3 signaling is upregulated and lymphocyte response pathways are downregulated early in exacerbation, followed by later upregulation of effector pathways including epidermal growth factor receptor signaling, extracellular matrix production, mucus hypersecretion, and eosinophil activation. We show an additional set of multiple inflammatory cell pathways involved in virus-associated exacerbations, in contrast to squamous cell pathways associated with nonviral exacerbations. Our work introduces an in vivo molecular platform to investigate, in a clinical setting, both the mechanisms of disease pathogenesis and therapeutic targets to modify exacerbations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472965/ doi: 10.1038/s41590-019-0347-8 id: cord-297323-l3f12hg4 author: Amor, Sandra title: Innate immunity during SARS‐CoV‐2: evasion strategies and activation trigger hypoxia and vascular damage date: 2020-09-26 words: 4982.0 sentences: 304.0 pages: flesch: 43.0 cache: ./cache/cord-297323-l3f12hg4.txt txt: ./txt/cord-297323-l3f12hg4.txt summary: Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. These subsequently induce expression of type I IFNs (IFNα/β) and interferon stimulated genes (ISGs) [figure 2] many of which have potent antiviral activities, as well as other proinflammatory mediators e.g. cytokines, chemokines and antimicrobial peptides that are essential to initiate the host innate and adaptive immune response. Likewise, viral load, obesity, gender, race, blood groups and comorbidities have all been reported to influence the response to SARS-CoV-2 infection, [ Table 4 ; (101) (102) (103) (104) (105) (106) (107) (108) (109) (110) (111) (112) ] although few studies have fully examined the extent to which subversion and activation of innate immune components contribute to susceptibility in these cases. Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune Response to Severe Acute Respiratory Syndrome Coronavirus Infection abstract: Innate immune sensing of viral molecular patterns is essential for development of antiviral responses. Like many viruses, SARS‐CoV‐2 has evolved strategies to circumvent innate immune detection including low CpG levels in the genome, glycosylation to shield essential elements including the receptor binding domain, RNA shielding and generation of viral proteins that actively impede anti‐viral interferon responses. Together these strategies allow widespread infection and increased viral load. Despite the efforts of immune subversion, SARS‐CoV‐2 infection activates innate immune pathways inducing a robust type I/III interferon response, production of proinflammatory cytokines, and recruitment of neutrophils and myeloid cells. This may induce hyperinflammation or alternatively, effectively recruit adaptive immune responses that help clear the infection and prevent reinfection. The dysregulation of the renin‐angiotensin system due to downregulation of angiotensin converting enzyme 2, the receptor for SARS‐CoV‐2, together with the activation of type I/III interferon response, and inflammasome response converge to promote free radical production and oxidative stress. This exacerbates tissue damage in the respiratory system but also leads to widespread activation of coagulation pathways leading to thrombosis. Here, we review the current knowledge of the role of the innate immune response following SARS‐CoV‐2 infection, much of which is based on the knowledge from SARS‐CoV and other coronaviruses. Understanding how the virus subverts the initial immune response and how an aberrant innate immune response contributes to the respiratory and vascular damage in COVID‐19 may help explain factors that contribute to the variety of clinical manifestations and outcome of SARS‐CoV‐2 infection. url: https://doi.org/10.1111/cei.13523 doi: 10.1111/cei.13523 id: cord-309469-2naxn580 author: An, Hongliu title: Identification and formation mechanism of a novel noncoding RNA produced by avian infectious bronchitis virus date: 2019-01-05 words: 3600.0 sentences: 234.0 pages: flesch: 54.0 cache: ./cache/cord-309469-2naxn580.txt txt: ./txt/cord-309469-2naxn580.txt summary: For example, polyadenylated nuclear (PAN) RNA encoded by Kaposi''s sarcoma-associated herpesvirus (Sun et al., 1996; Zhong and Ganem, 1997) , the~2-kb latency-associated transcript (LAT) expressed by Herpes simplex virus (Bloom, 2004 ), a con-served~5-kb intron expressed by Human cytomegalovirus (hCMV) (Kulesza and Shenk, 2004) , and a 7.2-kb RNA expressed by mouse CMV (Kulesza and Shenk, 2006) , U-rich RNAs (HSURs) produced by Herpesvirus saimiri (HVS), (Albrecht and Fleckenstein, 1992; Ensser and Fleckenstein, 2005) ; (3) Subgenomic ncRNAs from single-stranded RNA viruses by incomplete degradation of genomic RNA by the cellular 5-3′ exonuclease XRN1. The results confirmed previous report that IBV can synthesize sgRNA via template switch mediated by a noncanonical core sequence (Bentley et al., 2013) Notably, the mutant virus carrying four mutations (A27100U/A27111U/G27113C/G27114C) was also unable to produce ncRNA (Fig. 4) , suggesting these nucleotides are required for ncRNA production. abstract: Viral noncoding (nc) RNAs have been shown to play important roles in viral life cycle. Many viruses employ different mechanism to produce ncRNAs. Here, we report that coronavirus infectious bronchitis virus (IBV) produces a novel ncRNA in virus-infected cells. This ncRNA consists of 563 nucleotides excluding a poly(A) tail, is mainly derived from the 3′-untranslated region of IBV genome, and contains a 63-nt-long of terminal leader sequence derived from the 5′ end of the viral genome. Using mutagenesis and reverse genetics, we reveal that this ncRNA is a subgenomic RNA generated by discontinuous transcription mechanism. url: https://doi.org/10.1016/j.virol.2018.12.019 doi: 10.1016/j.virol.2018.12.019 id: cord-253501-hkxlq3os author: Anang, Saumya title: Recent Advances Towards the Development of a Potent Antiviral Against the Hepatitis E Virus date: 2018-06-28 words: 4416.0 sentences: 290.0 pages: flesch: 38.0 cache: ./cache/cord-253501-hkxlq3os.txt txt: ./txt/cord-253501-hkxlq3os.txt summary: [29] [30] [31] [32] Ribavirin inhibits host inosine monophosphate dehydrogenase, thereby depleting cellular GTP pools and blocking viral replication during HEV infection. Sofosbuvir, a prodrug of a uridine nucleoside analogue that acts as a direct-acting antiviral against hepatitis C virus (HCV) RNA-dependent RNA polymerase in its active form, was reported by Dao Thi et al. 63, 64 Zinc salts were shown to block the replication of both genotype 1 and genotype 3 HEV by inhibiting the activity of viral RNA-dependent RNA polymerase in cultured human hepatoma cells. Zinc directly inhibits HEV RNA-dependent RNA polymerase activity in vitro and displays moderate cooperativity with ribavirin in inhibiting viral replication in mammalian cell culture models of HEV infection. Ribavirin therapy inhibits viral replication on patients with chronic hepatitis e virus infection Zinc salts block hepatitis E virus replication by inhibiting the activity of viral RNA-dependent RNA polymerase abstract: Hepatitis E virus (HEV) is one of the leading causes of acute viral hepatitis. It also causes acute liver failure and acute-on-chronic liver failure in many patients, such as those suffering from other infections/liver injuries or organ transplant/chemotherapy recipients. Despite widespread sporadic and epidemic incidents, there is no specific treatment against HEV, justifying an urgent need for developing a potent antiviral against it. This review summarizes the known antiviral candidates and provides an overview of the potential targets for the development of specific antivirals against HEV. url: https://doi.org/10.14218/jcth.2018.00005 doi: 10.14218/jcth.2018.00005 id: cord-346544-kk7qyn4w author: Andersson, M. title: SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus date: 2020-05-26 words: 4992.0 sentences: 305.0 pages: flesch: 53.0 cache: ./cache/cord-346544-kk7qyn4w.txt txt: ./txt/cord-346544-kk7qyn4w.txt summary: Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. . https://doi.org/10.1101/2020.05.21.20105486 doi: medRxiv preprint prevalence of vRNA detection in blood, serum or plasma, noting whether this attribute was correlated with clinical or laboratory phenotypes of disease, and recording Ct values when these were reported. We collected 212 serum samples through the microbiology department at Oxford University Hospitals NHS Foundation Trust, OUH NHSFT, comprising adults with a diagnosis of COVID-19, confirmed by SARS-CoV-2 detection by a clinical diagnostic microbiology laboratory using RT-PCR on a respiratory swab, classified in three groups as follows: Based on a systematic review of the literature, together with our own data, we estimate that SARS-CoV-2 RNA may be present at low copy numbers in ~10% of blood samples obtained from individuals with COVID-19 prior to day 28, most of which arise at earlier timepoints and in the setting of more severe disease. abstract: Background: Laboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. Methods: We undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in serum samples from a UK clinical cohort of acute and convalescent COVID-19 cases (n=212), together with convalescent plasma samples collected by NHS Blood and Transplant (NHSBT) (n=212 additional samples). To determine whether PCR-positive blood samples could pose an infection risk, we attempted virus isolation from a subset of RNA-positive samples. Results: We identified 28 relevant studies, reporting SARS-CoV-2 RNA in 0-76% of blood samples; pooled estimate 10% (95%CI 5-18%). Among serum samples from our clinical cohort, 27/212 (12.7%) had SARS-CoV-2 RNA detected by RT-PCR. RNA detection occurred in samples up to day 20 post symptom onset, and was associated with more severe disease (multivariable odds ratio 7.5). Across clinical and convalescent samples collected [≥]28 days post symptom onset, 0/244 (0%, 95%CI 0.0-1.5%) had vRNA detected. Among our PCR-positive samples, cycle threshold (ct) values were high (range 33.5-44.8), suggesting low vRNA copy numbers. PCR-positive sera inoculated into cell culture did not produce any cytopathic effect or yield an increase in detectable SARS-CoV-2 RNA. Conclusions: vRNA was detectable at low viral loads in a minority of serum samples collected in acute infection, but was not associated with infectious SARS-CoV-2 (within the limitations of the assays used). This work helps to inform biosafety precautions for handling blood products from patients with current or previous COVID-19. url: http://medrxiv.org/cgi/content/short/2020.05.21.20105486v1?rss=1 doi: 10.1101/2020.05.21.20105486 id: cord-288962-jgtoehcr author: Andréoletti, Laurent title: Differential detection of rhinoviruses and enteroviruses RNA sequences associated with classical immunofluorescence assay detection of respiratory virus antigens in nasopharyngeal swabs from infants with bronchiolitis date: 2000-06-06 words: 3704.0 sentences: 186.0 pages: flesch: 36.0 cache: ./cache/cord-288962-jgtoehcr.txt txt: ./txt/cord-288962-jgtoehcr.txt summary: To define the role of enteroviruses and human rhinoviruses as etiological agents in childhood bronchiolitis, clinical aspirates from 84 infants admitted to hospital with symptoms of obstructive bronchiolitis were tested by picornavirus RT‐PCR assay, adenovirus PCR assay and classical immunofluorescence antigen detection of common respiratory viral agents. In summary, combination of molecular and classical detection assays of common viruses can be used to demonstrate enterovirus and human rhinovirus respiratory infection in childhood bronchiolitis, and provides an improved approach to obtain new insights into concomitant viral respiratory tract infection in infants. To investigate the role of enteroviruses and human rhinoviruses as etiological agent in bronchiolitis, 84 nasopharyngeal aspirates were tested by picornavirus RT-PCR assay, classical immunofluorescence antigens detection of respiratory syncytial viruses, influenza viruses, parainfluenza viruses, coronaviruses, and adenovirus PCR assay. abstract: To define the role of enteroviruses and human rhinoviruses as etiological agents in childhood bronchiolitis, clinical aspirates from 84 infants admitted to hospital with symptoms of obstructive bronchiolitis were tested by picornavirus RT‐PCR assay, adenovirus PCR assay and classical immunofluorescence antigen detection of common respiratory viral agents. Respiratory syncytial viruses (A&B) were detectable in 45 of 84 (53.6%) nasopharyngeal aspirates from infants with bronchiolitis, whereas coronaviruses, influenza viruses, and parainfluenza viruses were not detectable in the same samples. Adenoviruses were detectable by PCR in 11 of 84 (13.1%) nasopharyngeal swabs. By using a picornavirus RT‐PCR assay followed by a differential molecular hybridisation, rhinovirus and enterovirus RNA sequences were detected in 16 of 84 (19%) and in 10 of 84 (11.9%) of the nasopharyngeal swabs tested. Positive human rhinovirus or enterovirus RT‐PCR assay, however, was the only evidence of respiratory infection in 8 of 84 (9.5%) and in 7 of 84 (8.33%) of the studied patients. Respiratory syncytial viruses, human rhinoviruses, adenoviruses, and enteroviruses occur in dual infections detected in 18 of 84 (21.4%) respiratory samples tested. The median duration of stay in hospital was not significantly different between the patients demonstrating a single viral infection and those with a dual viral infection (6.22 ± 2.07 vs. 5.04 ± 0.95 days; P > 0.05). In summary, combination of molecular and classical detection assays of common viruses can be used to demonstrate enterovirus and human rhinovirus respiratory infection in childhood bronchiolitis, and provides an improved approach to obtain new insights into concomitant viral respiratory tract infection in infants. J. Med. Virol. 61:341–346, 2000. © 2000 Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/10861643/ doi: 10.1002/1096-9071(200007)61:3<341::aid-jmv10>3.0.co;2-0 id: cord-279985-de0b27nq author: Anraku, Itaru title: Kunjin replicon-based simian immunodeficiency virus gag vaccines date: 2008-06-19 words: 6392.0 sentences: 325.0 pages: flesch: 53.0 cache: ./cache/cord-279985-de0b27nq.txt txt: ./txt/cord-279985-de0b27nq.txt summary: Kunjin replicon VLP vaccines encoding HIV-1 gag have also been shown to induce CD8 T cell immunity comparable to that seen after immunisation with recombinant vaccinia [11] . Here we describe the behaviour of four different Kunjin replicon VLP vaccines encoding SIV gag and show that only the Gag-pol vaccine (i) induced good levels of both effector memory and central memory T cell responses 10 weeks post-vaccination, comparable to those induced by the previously described HIV-1 gag Kunjin replicon VLP vaccine [11] , (ii) showed good levels of protection against challenge with A20 cells expressing SIV Gag ≈9 months post-vaccination, and (iii) displayed high levels of insert stability. In summary we describe here a Kunjin replicon SIV Gag-pol VLP vaccine, which showed high insert stability, good induction of effector and central memory responses, and good protection against a model challenge. abstract: An RNA-based, non-cytopathic replicon vector system, based on the flavivirus Kunjin, has shown considerable promise as a new vaccine delivery system. Here we describe the testing in mice of four different SIVmac239 gag vaccines delivered by Kunjin replicon virus-like-particles. The four vaccines encoded the wild type gag gene, an RNA-optimised gag gene, a codon-optimised gag gene and a modified gag-pol gene construct. The vaccines behaved quite differently for induction of effector memory and central memory responses, for mediation of protection, and with respect to insert stability, with the SIV gag-pol vaccine providing the optimal performance. These results illustrate that for an RNA-based vector the RNA sequence of the antigen can have profound and unforeseen consequences on vaccine behaviour. url: https://doi.org/10.1016/j.vaccine.2008.04.001 doi: 10.1016/j.vaccine.2008.04.001 id: cord-283346-0v4b6do2 author: Ansari, Abdul Wahid title: Host chemokine (C-C motif) ligand-2 (CCL2) is differentially regulated in HIV type 1 (HIV-1)-infected individuals date: 2006-08-17 words: 4326.0 sentences: 220.0 pages: flesch: 48.0 cache: ./cache/cord-283346-0v4b6do2.txt txt: ./txt/cord-283346-0v4b6do2.txt summary: CCL2 was the most strongly regulated gene at mRNA level and its serum concentration was significantly elevated in viremic compared with aviremic and HIV-1 seronegative controls, indicating a positive correlation between viremia and CCL2. For example, the C-C chemokines macrophage inflammatory protein (MIP)-1a/CCL3, MIP-1b/CCL4 and regulated upon activation, normal T cell expressed and secreted (RANTES)/ CCL5 inhibit M-tropic HIV-1 infection by competing with the virus for its binding to the co-receptor CCR5 (11) (12) (13) (14) (15) (16) (17) . To investigate the impact of HIV-1 viremia on the host inflammatory cytokine/chemokine network, more specifically on CCL2, we utilized DNA microarray approach on PBMC RNA derived from HIV-1-infected viremic and aviremic individuals. In this study, we report that HIV-1 viremic patients show an altered expression of key inflammatory cytokines and chemokines as compared with aviremic individuals. Furthermore, increased mRNA transcripts were again detected in CCL2, CXCL10 and IFN-c when more RNA samples derived from additional aviremic and viremic patients were analyzed individually. abstract: Several cytokines and chemokines including chemokine (C-C motif) ligand-2 (CCL2) are induced in HIV-1 infection. However, the impact of HIV-1 viremia on CCL2 regulation is largely unknown. We utilized a DNA oligonucleotide microarray covering 110 inflammatory genes. Five genes were induced by at least 2-fold in PBMCs of HIV-1 viremic (>100.000 RNA copies ml(−1)) as compared with aviremic (<50 RNA copies ml(−1)) individuals. These genes were CCL2, CXC chemokine ligand-10, IFN-γ, GTP-cyclohydrolase-1 and C-C chemokine receptor-1. In addition to microarray data verification by real-time PCR, analysis of independent patient samples revealed a similar expression pattern. CCL2 was the most strongly regulated gene at mRNA level and its serum concentration was significantly elevated in viremic compared with aviremic and HIV-1 seronegative controls, indicating a positive correlation between viremia and CCL2. Flow cytometric studies demonstrated a higher percentage of CCL2-expressing CD14+ monocytes in viremic compared with aviremic individuals. These results suggest a highly restricted modulation of host inflammatory gene response by HIV. Genes up-regulated in the viremic state, in particular CCL2, presumably serve as potential enhancing factors in HIV-1 replication, represented by high viral load in HIV-1 viremic patients. Inhibition of increased CCL2 production could provide a new therapeutic intervention in HIV-1 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/16916890/ doi: 10.1093/intimm/dxl078 id: cord-002746-qn34eyul author: Antzin-Anduetza, Irati title: Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication date: 2017-11-09 words: 9118.0 sentences: 491.0 pages: flesch: 56.0 cache: ./cache/cord-002746-qn34eyul.txt txt: ./txt/cord-002746-qn34eyul.txt summary: Codon modification of nucleotides (nt) 22-261 or 22-378 in gag inhibited viral replication by decreasing genomic RNA (gRNA) abundance, gRNA stability, Gag expression, virion production and infectivity. To determine if they are necessary for inhibition of HIV-1 replication, codons introducing CpG dinucleotides were mutated back to the wild type codon, which restored efficient Gag expression and infectious virion production. Gag expression and virion production were similar for wild type HIV-1 and HIV-1 ∆22-261 (Fig. 4c) , indicating that RNA or protein sequences in this region are not necessary for these steps of the viral life cycle. When only 11 CpG dinucleotides are inserted into gag in the context of the codon modified sequence (HIV-1 CM22-165), there is a large decrease in infectivity without a substantial loss of gRNA abundance, Gag expression or virion production (Figs. [100] reported that introducing CpG dinucleotides into env inhibited HIV-1 replication by decreasing the abundance of cytoplasmic gRNA, Gag expression, Env expression and infectious virus production. abstract: BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) structural protein Gag is necessary and sufficient to form viral particles. In addition to encoding the amino acid sequence for Gag, the underlying RNA sequence could encode cis-acting elements or nucleotide biases that are necessary for viral replication. Furthermore, RNA sequences that inhibit viral replication could be suppressed in gag. However, the functional relevance of RNA elements and nucleotide biases that promote or repress HIV-1 replication remain poorly understood. RESULTS: To characterize if the RNA sequence in gag controls HIV-1 replication, the matrix (MA) region was codon modified, allowing the RNA sequence to be altered without affecting the protein sequence. Codon modification of nucleotides (nt) 22-261 or 22-378 in gag inhibited viral replication by decreasing genomic RNA (gRNA) abundance, gRNA stability, Gag expression, virion production and infectivity. Comparing the effect of these point mutations to deletions of the same region revealed that the mutations inhibited infectious virus production while the deletions did not. This demonstrated that codon modification introduced inhibitory sequences. There is a much lower than expected frequency of CpG dinucleotides in HIV-1 and codon modification introduced a substantial increase in CpG abundance. To determine if they are necessary for inhibition of HIV-1 replication, codons introducing CpG dinucleotides were mutated back to the wild type codon, which restored efficient Gag expression and infectious virion production. To determine if they are sufficient to inhibit viral replication, CpG dinucleotides were inserted into gag in the absence of other changes. The increased CpG dinucleotide content decreased HIV-1 infectivity and viral replication. CONCLUSIONS: The HIV-1 RNA sequence contains low abundance of CpG dinucleotides. Increasing the abundance of CpG dinucleotides inhibits multiple steps of the viral life cycle, providing a functional explanation for why CpG dinucleotides are suppressed in HIV-1. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12977-017-0374-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679385/ doi: 10.1186/s12977-017-0374-1 id: cord-287488-h102xn29 author: Araujo, Danielle Bastos title: SARS-CoV-2 isolation from the first reported patients in Brazil and establishment of a coordinated task network date: 2020-10-23 words: 3927.0 sentences: 223.0 pages: flesch: 53.0 cache: ./cache/cord-287488-h102xn29.txt txt: ./txt/cord-287488-h102xn29.txt summary: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. METHODS: After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS: The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks viable (titre 2.11 × 10(6) TCID50/mL, titre 1.5 × 10(6) PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. abstract: BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed in Brazil in February 2020, the first cases were followed by an increase in the number of cases throughout the country, resulting in an important public health crisis that requires fast and coordinated responses. OBJECTIVES: The objective of this work is to describe the isolation and propagation properties of SARS-CoV-2 isolates from the first confirmed cases of coronavirus disease 2019 (COVID-19) in Brazil. METHODS: After diagnosis in patients that returned from Italy to the São Paulo city in late February by RT-PCR, SARS-CoV-2 isolates were obtained in cell cultures and characterised by full genome sequencing, electron microscopy and in vitro replication properties. FINDINGS: The virus isolate was recovered from nasopharyngeal specimen, propagated in Vero cells (E6, CCL-81 and hSLAM), with clear cytopathic effects, and characterised by full genome sequencing, electron microscopy and in vitro replication properties. Virus stocks - viable (titre 2.11 × 10(6) TCID50/mL, titre 1.5 × 10(6) PFUs/mL) and inactivated from isolate SARS.CoV2/SP02.2020.HIAE.Br were prepared and set available to the public health authorities and the scientific community in Brazil and abroad. MAIN CONCLUSION: We believe that the protocols for virus growth and studies here described and the distribution initiative may constitute a viable model for other developing countries, not only to help a rapid effective pandemic response, but also to facilitate and support basic scientific research. url: https://www.ncbi.nlm.nih.gov/pubmed/33111751/ doi: 10.1590/0074-02760200342 id: cord-318751-4v2tl0gi author: Arias, Armando title: Progress towards the prevention and treatment of norovirus infections date: 2013-11-17 words: 6833.0 sentences: 310.0 pages: flesch: 37.0 cache: ./cache/cord-318751-4v2tl0gi.txt txt: ./txt/cord-318751-4v2tl0gi.txt summary: While the efficient culture of human noroviruses (HuNoVs) in immortalized cells has yet to be achieved [5] , the development of a norovirus replicon [6] , which allows the generation of cell lines stably replicating Norwalk virus RNA, has facilitated many small molecule inhibitors to be tested in vitro. The discovery of murine norovirus (MNV) [7] , which replicates efficiently in immortalized macrophage cells and has both reverse genetics systems and small animal models available [8] , has also enabled the examination of the immune responses to noroviruses as well as the efficacy of inhibitors in vitro and in vivo. However, the vast majority of such studies are conducted with norovirus surrogates such as feline calicivirus or MNV, as testing decontamination procedures for HuNoV is difficult owing to the lack of an available cell culture system to detect any remaining infectivity. abstract: Noroviruses are now recognized as the major cause of acute gastroenteritis in the developed world, yet our ability to prevent and control infection is limited. Recent work has highlighted that, while typically an acute infection in the population, immunocompromised patients often experience long-term infections that may last many years. This cohort of patients and those regularly exposed to infectious material, for example, care workers and others, would benefit greatly from the development of a vaccine or antiviral therapy. While a licensed vaccine or antiviral has yet to be developed, work over the past 10 years in this area has intensified and trials with a vaccine candidate have proven promising. Numerous antiviral targets and small molecule inhibitors that have efficacy in cell culture have now been identified; however, further studies in this area are required in order to make these suitable for clinical use. url: https://www.ncbi.nlm.nih.gov/pubmed/24199805/ doi: 10.2217/fmb.13.109 id: cord-350040-e8q7wq0h author: Aronin, N title: Target selectivity in mRNA silencing date: 2006-02-16 words: 6614.0 sentences: 503.0 pages: flesch: 58.0 cache: ./cache/cord-350040-e8q7wq0h.txt txt: ./txt/cord-350040-e8q7wq0h.txt summary: Here is limned a roadmap to explain RISC assemblyhow there are two types of RNAi, one of which is applicable to humans; how thermodynamic properties of siRNA direct strand selection to confer full RNAi activity; how RISC proteins direct siRNA presentation to its target mRNA; and how these principles can be used to design selective and functional siRNAs. Innate mRNA silencing in mammals is currently the province of microRNAs, single stranded, small RNAs that block translation with short-term survival of target mRNA. Not all siRNAs are active, however, even when their guide strands have perfect complementarity to target mRNAs. Designing siRNAs with single nucleotide specificity requires the guide strand to be incorporated into RISC, in preference to the passenger strand. The complexity of siRNA design is that small changes in siRNA:mRNA complementarity can have profound effects on RNAi effectiveness; mismatches might have few consequences or, as shown above, improve silencing by strand selection. abstract: Despite the excitement and promise of RNA interference in treating neurodegenerative disease, disease gene mRNA might resist mRNA silencing. Conventional siRNA design does not uniformly distinguish a mutant from a wild-type allele. CAG expansions in trinucleotide repeat diseases are unselective targets for small siRNAs. This review will consider recent discoveries in mechanisms of RNA interference and siRNA modifications that improve siRNA selectivity, delivery and performance. url: https://www.ncbi.nlm.nih.gov/pubmed/16520821/ doi: 10.1038/sj.gt.3302726 id: cord-329494-cdn52epy author: Artuso, María C. title: Inhibition of Junín virus replication by small interfering RNAs date: 2009-07-08 words: 4725.0 sentences: 244.0 pages: flesch: 51.0 cache: ./cache/cord-329494-cdn52epy.txt txt: ./txt/cord-329494-cdn52epy.txt summary: The efficacy of this Z2-siRNA against JUNV was also demonstrated in virus-infected cells, by testing infectious virus plaque formation (92.8% JUNV yield reduction), viral RNA level or antigen expression, as well as in cells transfected with Z-specific reporter plasmids (91% reduction in expression of Z-EGFP fusion protein). (E) Expression of viral antigens in Vero cells transfected with Z2-siRNA or X-siRNA and infected with JUNV was detected by immunofluorescence assay using a rabbit anti-JUNV polyclonal serum. The efficacy of this agent against JUNV was also demonstrated in virus-infected cells by testing infectious virus plaque formation, viral RNA or antigen expression, as well as in cells transfected with Z-specific reporter plasmids. The present study represents the first report of virus inhibition mediated by RNA interference for a New World arenavirus, a group in the family including four agents of severe viral hemorrhagic fevers in South America (JUNV, Machupo, Sabiá and Guanarito viruses). abstract: Junín virus (JUNV), the etiological agent of the Argentine hemorrhagic fever, has a single-stranded RNA genome with ambisense expression which encodes for five proteins. In previous works we have demonstrated that the Z arenavirus matrix protein represents an attractive target for antiviral therapy. With the aim of studying a new alternative therapeutic mechanism, four Z-specific siRNAs (Z1- to Z4-siRNAs) were tested showing variable efficacy. The most effective inhibitor was Z2-siRNA targeted at the region encompassed by nt 179–197 of Z gene. The efficacy of this Z2-siRNA against JUNV was also demonstrated in virus-infected cells, by testing infectious virus plaque formation (92.8% JUNV yield reduction), viral RNA level or antigen expression, as well as in cells transfected with Z-specific reporter plasmids (91% reduction in expression of Z-EGFP fusion protein). Furthermore, the lack of effect of this Z-siRNA on the expression of other JUNV proteins, such as N and GPC, confirmed the specificity of action exerted by Z2-siRNA on Z transcript. Thus, the present study represents the first report of virus inhibition mediated by RNA interference for a New World arenavirus. url: https://doi.org/10.1016/j.antiviral.2009.07.001 doi: 10.1016/j.antiviral.2009.07.001 id: cord-257456-15bm9psj author: Arumugam, Arunkumar title: A Rapid SARS-CoV-2 RT-PCR Assay for Low Resource Settings date: 2020-09-24 words: 5286.0 sentences: 294.0 pages: flesch: 59.0 cache: ./cache/cord-257456-15bm9psj.txt txt: ./txt/cord-257456-15bm9psj.txt summary: Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. To further improve the speed of a diagnostic assay, we and others tested using untreated or heat-inactivated samples added directly to one-step RT-PCR master mixes without an RNA extraction step [6, [13] [14] [15] [16] [17] [18] [19] . Prior to COVID-19 emerged as a global pandemic, we have tested the feasibility of circumventing the sample preparation steps by adding a few microliters of the unprocessed sample (in VTM) directly into the RT-qPCR assay master mix targeting InfA, InfB, and RSV. abstract: Quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is the gold standard recommended to test for acute SARS-CoV-2 infection. However, it generally requires expensive equipment such as RNA isolation instruments and real-time PCR thermal cyclers. As a pandemic, COVID-19 has spread indiscriminately, and many low resource settings and developing countries do not have the means for fast and accurate COVID-19 detection to control the outbreak. Additionally, long assay times, in part caused by slow sample preparation steps, have created a large backlog when testing patient samples suspected of COVID-19. With many PCR-based molecular assays including an extraction step, this can take a significant amount of time and labor, especially if the extraction is performed manually. Using COVID-19 clinical specimens, we have collected evidence that the RT-qPCR assay can feasibly be performed directly on patient sample material in virus transport medium (VTM) without an RNA extraction step, while still producing sensitive test results. If RNA extraction steps can be omitted without significantly affecting clinical sensitivity, the turn-around time of COVID-19 tests, and the backlog we currently experience can be reduced drastically. Furthermore, our data suggest that rapid RT-PCR can be implemented for sensitive and specific molecular diagnosis of COVID-19 in locations where sophisticated laboratory instruments are not available. Our USD 300 set up achieved rapid RT-PCR using thin-walled PCR tubes and a water bath setup using sous vide immersion heaters, a Raspberry Pi computer, and a single servo motor that can process up to 96 samples at a time. Using COVID-19 positive clinical specimens, we demonstrated that RT-PCR assays can be performed in as little as 12 min using untreated samples, heat-inactivated samples, or extracted RNA templates with our low-cost water bath setup. These findings can help rapid COVID-19 testing to become more accessible and attainable across the globe. url: https://www.ncbi.nlm.nih.gov/pubmed/32987722/ doi: 10.3390/diagnostics10100739 id: cord-258547-47cyyetb author: Asasi, Keramat title: Changes of several acute phase factors in broiler chickens in response to infectious bronchitis virus infection date: 2013-08-01 words: 3588.0 sentences: 217.0 pages: flesch: 54.0 cache: ./cache/cord-258547-47cyyetb.txt txt: ./txt/cord-258547-47cyyetb.txt summary: In the serum the acute phase proteins (haptoglobin and serum amyloid A), pro-inflammatory cytokines (interferon-γ and tumor necrosis factor-α), and serum sialic acid (total, TSA; lipid-bound, LBSA; and protein-bound, PBSA) concentrations were measured using validated standard procedures. Based on this evidence, the present study was undertaken to evaluate alteration in concentrations of the acute phase proteins [haptoglobin (Hp) and serum amyloid A (SAA)], pro-inflammatory cytokines (TNF-α and IFN-γ), and the serum level of total sialic acid (TSA), lipid-bound sialic acid (LBSA), and protein-bound sialic acid (PBSA) in experimentally infected chicks by IBV isolate IRFIBV32 compared with healthy chicks. The serum concentrations of IFN-γ, TNF-α, Hp, SAA, TSA, LBSA, and PBSA were increased significantly 2.50, 1.98, 1.82, 3.33, 2.25, 2.44, and 1.77 times, respectively, during experimental infection with IBV in chickens. abstract: This study was performed to clarify the acute phase response following infectious bronchitis virus inoculation. Ninety clinically healthy 1-d-old Ross chicks were randomly assigned into 2 groups: control (n = 20) and infected group (n = 70). At the age of 20 d, all birds in the infected group were challenged intranasally with allantoic fluid containing 10(5) embryo lethal dose (ELD(50))/0.1 mL of the infectious bronchitis virus. Blood samples were collected from 20 clinically healthy and 70 infected chicks at prior and 1, 2, 3, 5, 7, 11, 13, 15, and 20 d postinoculation. On d 1, 7, and 11 postinoculation 4 chickens from the experimental group and 2 chickens from the control group were randomly selected. Their trachea, lungs, and cecal tonsil were collected for virus detection and quantitation by real-time reverse-transcription PCR assay. In the serum the acute phase proteins (haptoglobin and serum amyloid A), pro-inflammatory cytokines (interferon-γ and tumor necrosis factor-α), and serum sialic acid (total, TSA; lipid-bound, LBSA; and protein-bound, PBSA) concentrations were measured using validated standard procedures. All variables were significantly higher in the infected birds after virus inoculation compared with the healthy group (P < 0.05). There were positive correlations between all variables in the infected group. Correlation coefficients were significantly positive between haptoglobin and interferon-γ, LBSA and TSA, and TSA and LBSA (P < 0.05). There were positive correlations among viral RNA and all studied variables; however, these correlations were not statistically significant (P > 0.05). url: https://www.ncbi.nlm.nih.gov/pubmed/23873545/ doi: 10.3382/ps.2012-02902 id: cord-271648-m2c5bvuj author: Ashour, Hossam M. title: Insights into the Recent 2019 Novel Coronavirus (SARS-CoV-2) in Light of Past Human Coronavirus Outbreaks date: 2020-03-04 words: 7536.0 sentences: 401.0 pages: flesch: 56.0 cache: ./cache/cord-271648-m2c5bvuj.txt txt: ./txt/cord-271648-m2c5bvuj.txt summary: Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. However, unlike SARS-CoV, human-to-human transmission of MERS-CoV is not easy and has not been confirmed except in cases of very close contact with infected patients in health care settings [67] . Similar to the adaptation of SARS-CoV to human host, MERSr-CoVs that are circulating in bats had to undergo several amino acid changes in RBD of S protein to become capable of infecting camels and humans ( Figure 2 ) [74] . S protein of severe acute respiratory syndrome-associated coronavirus mediates entry into hepatoma cell lines and is targeted by neutralizing antibodies in infected patients Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Fully human monoclonal antibody directed to proteolytic cleavage site in severe acute respiratory syndrome (SARS) coronavirus S protein neutralizes the virus in a rhesus macaque SARS model abstract: Coronaviruses (CoVs) are RNA viruses that have become a major public health concern since the Severe Acute Respiratory Syndrome-CoV (SARS-CoV) outbreak in 2002. The continuous evolution of coronaviruses was further highlighted with the emergence of the Middle East Respiratory Syndrome-CoV (MERS-CoV) outbreak in 2012. Currently, the world is concerned about the 2019 novel CoV (SARS-CoV-2) that was initially identified in the city of Wuhan, China in December 2019. Patients presented with severe viral pneumonia and respiratory illness. The number of cases has been mounting since then. As of late February 2020, tens of thousands of cases and several thousand deaths have been reported in China alone, in addition to thousands of cases in other countries. Although the fatality rate of SARS-CoV-2 is currently lower than SARS-CoV, the virus seems to be highly contagious based on the number of infected cases to date. In this review, we discuss structure, genome organization, entry of CoVs into target cells, and provide insights into past and present outbreaks. The future of human CoV outbreaks will not only depend on how the viruses will evolve, but will also depend on how we develop efficient prevention and treatment strategies to deal with this continuous threat. url: https://doi.org/10.3390/pathogens9030186 doi: 10.3390/pathogens9030186 id: cord-255883-mz6nyisw author: Asif, Muhammad title: COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties date: 2020-08-14 words: 5273.0 sentences: 283.0 pages: flesch: 44.0 cache: ./cache/cord-255883-mz6nyisw.txt txt: ./txt/cord-255883-mz6nyisw.txt summary: Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. An in vitro study conducted by Hoffmann and colleagues revealed that SARC-CoV-2 depends on cellular serine protease (TMPRSS2) for S proteins priming which are known to interact with human ACE2 receptors in the lungs and facilitate entry into the cells. The authors opted the following keywords to find relevant studies: "essential oils", "antiviral", "COVID-19", "SARC-CoV-2", "bronchodilation", "immunomodulatory'''', "anti-inflammatory'''', "corona virus''''. Thus, on the basis of these docking and in vitro studies, it is proposed that garlic essential oils and their isolated constituents, especially DAS, have potential to prevent the entry of virus into host cells as well as to activate molecular antioxidant pathways that decrease the secretions of culprit pro-inflammatory cytokines. Essential oils have long been known to have anti-inflammatory, antioxidant, immunomodulatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2. abstract: Coronavirus disease of 2019 (COVID-19) has emerged as a global health threat. Unfortunately, there are very limited approved drugs available with established efficacy against the SARs-CoV-2 virus and its inflammatory complications. Vaccine development is actively being researched, but it may take over a year to become available to general public. Certain medications, for example, dexamethasone, antimalarials (chloroquine/hydroxychloroquine), antiviral (remdesivir), and IL-6 receptor blocking monoclonal antibodies (tocilizumab), are used in various combinations as off-label medications to treat COVID-19. Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. Owing to their lipophilic nature, EOs are advocated to penetrate viral membranes easily leading to membrane disruption. Moreover, EOs contain multiple active phytochemicals that can act synergistically on multiple stages of viral replication and also induce positive effects on host respiratory system including bronchodilation and mucus lysis. At present, only computer-aided docking and few in vitro studies are available which show anti-SARC-CoV-2 activities of EOs. In this review, role of EOs in the prevention and treatment of COVID-19 is discussed. A discussion on possible side effects associated with EOs as well as anti-corona virus claims made by EOs manufacturers are also highlighted. Based on the current knowledge a chemo-herbal (EOs) combination of the drugs could be a more feasible and effective approach to combat this viral pandemic. [Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32803479/ doi: 10.1007/s10787-020-00744-0 id: cord-256508-ce59ovan author: Asselah, Tarik title: COVID-19: discovery, diagnostics and drug development date: 2020-10-08 words: 9214.0 sentences: 556.0 pages: flesch: 46.0 cache: ./cache/cord-256508-ce59ovan.txt txt: ./txt/cord-256508-ce59ovan.txt summary: To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The current diagnostic strategy to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of SARS-CoV-2 specific nucleic acid targets [47] . The neutralization assay is a laboratory-based test that uses live virus and cell culture methods to determine if patient antibodies can prevent viral infection in vitro [72] . A randomized, controlled, openlabel trial involving hospitalized adult patients with confirmed SARS-CoV-2 infection and severe respiratory illness COVID-19 was performed [126] . Viral load dynamics and disease severity in patients infected with SARS-CoV-2 in Zhejiang province, China Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals abstract: An epidemic of acute respiratory syndrome (Covid-19) started in humans in Wuhan in 2019, and became a pandemic. Groups from China Identified and sequenced the virus responsible for COVID-19, named SARS-CoV-2, and determined that it was a novel coronavirus (CoV) that shared high sequence identity with bat- and pangolin-derived SARS-like CoVs, suggesting a zoonotic origin. SARS-CoV-2 is a member of Coronaviridae, a family of enveloped, positive-sense, single-stranded RNA viruses that infect a broad range of vertebrates. The rapid release of the sequence of the virus has allowed the development of diagnostic tools (e.g., RT-PCR). Additionally, serological tests can allow identification of persons who have been infected. In humans, CoVs tend to cause mild to moderate upper respiratory tract infections. The fatality rate is around 1-3% for infected persons. An acute respiratory distress syndrome (ARDS) likely due to an uncontrolled immune activation (“cytokine storm”) occurs in patients with severe disease and poor prognosis. Risk factors for mortality include: advanced age, obesity, diabetes, hypertension and other comorbidities. Drug repurposing has been used to rapidly identify potential treatment for COVID-19, which could move quickly to phase-3. Better knowledge of the virus, its enzymes, will be mandatory to develop more potent and specific direct-acting antiviral agents (DAA). In the long term, a vaccine to prevent infection would be crucial; however even if successful it might not be available before 2021-22. To date, with the exception of intravenous Remdesivir and dexamethasone, which have modest effects in moderate to severe COVID-19, no strong clinical evidence supports the efficacy and safety of any other drugs against SARS-CoV-2. The aim of this review is to provide insights on the discovery of SARS-CoV-2, its virology, the diagnostic tools, and the ongoing drug discovery effort. url: https://www.sciencedirect.com/science/article/pii/S0168827820336758?v=s5 doi: 10.1016/j.jhep.2020.09.031 id: cord-305290-xnjwv0d7 author: Atkins, John F. title: Ribosome gymnastics—Degree of difficulty 9.5, style 10.0 date: 1990-08-10 words: 7996.0 sentences: 417.0 pages: flesch: 62.0 cache: ./cache/cord-305290-xnjwv0d7.txt txt: ./txt/cord-305290-xnjwv0d7.txt summary: A single base change in the mouse mammary tumor virus (MMTV) gag-pro shift site, from the normal A AAA AAC to A AAA AAG, surprisingly leads from ~2% to 50% -1 frameshifting at this sequence (a 25-fold increase); and the lo-fold decrease between A AAA AAG and A AAA AAA affords an interesting glimpse at how the nuances of codon-anticodon interaction can govern the efficiency of this type of shifting. These results should be interpreted with caution, as all the higher eukaryotic frameshifting studies with altered sequences have been done with a reticulocyte lysate cell-free translation system; there are likely to be differences in the number of ribosomes loaded per message, and perhaps in the tRNA balance, from less specialized cells in vivo. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/2199062/ doi: 10.1016/0092-8674(90)90007-2 id: cord-344006-0iq9s94n author: Atzrodt, Cassandra L. title: A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2 date: 2020-05-23 words: 7283.0 sentences: 428.0 pages: flesch: 54.0 cache: ./cache/cord-344006-0iq9s94n.txt txt: ./txt/cord-344006-0iq9s94n.txt summary: All rights reserved Like other coronaviruses, SARS-CoV-2 is a single-stranded, positive-sense RNA virus that uses spike proteins to bind to human lung epithelial cells (Fig. 2) [67] . Upon membrane fusion, the RNA of the coronavirus genome is released into the host cell cytoplasm via an early endosome -unlike SARS-CoV, which employs a late endosome and therefore must cross higher barriers of antiviral host immunity -where it is translated into a replication-translation complex that in turn translates sub-genomic RNA into accessory and structural proteins (Fig. 3) [82-84]. The Vivalytic VRI (viral respiratory tract infections) COVID-19 Test System pioneered by Bosch and Randox Laboratories is similar to the Abbott RealTime SARS-CoV-2 assay in that it reduces hands-on time and can confirm a positive test within 2.5 hours with a reported 95% accuracy [100]. More specific assays have now emerged that are proving very useful in providing a fuller picture of the rates of asymptomatic or mild SARS-Cov2 infection, through detection of anti-viral antibodies that persist for months and even years after the virus has been cleared [107] . abstract: The emergence of the SARS‐CoV‐2 strain of the human coronavirus has thrown the world into the midst of a new pandemic. In the human body, the virus causes COVID‐19, a disease characterized by shortness of breath, fever, and pneumonia, which can be fatal in vulnerable individuals. SARS‐CoV‐2 has characteristics of past human coronaviruses, with close genomic similarities to SARS‐CoV, the virus that causes the disease SARS. Like these related coronaviruses, SARS‐CoV‐2 is transmitted through the inhalation of droplets and interaction with contaminated surfaces. Across the world, laboratories are developing candidate vaccines for the virus – with vaccine trials underway in the US and the United Kingdom ‐ and considering various drugs for possible treatments and prophylaxis. Here, we provide an overview of SARS‐CoV‐2 by analyzing its virology, epidemiology, and modes of transmission while examining the current progress of testing procedures and possible treatments through drugs and vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/32446285/ doi: 10.1111/febs.15375 id: cord-015642-p46abodr author: Backofen, Rolf title: Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures date: 2013 words: 4201.0 sentences: 278.0 pages: flesch: 66.0 cache: ./cache/cord-015642-p46abodr.txt txt: ./txt/cord-015642-p46abodr.txt summary: On a more technical level, the problem to compute the partition function over RNA secondary structures with given end-to-end distance d, usually measured as the number of external bases (plus possibly the number of structural domains) arises for instance when predicting nucleic acid secondary structure in the presence of single-stranded binding proteins [9] or in models of RNA subjected to pulling forces (e.g. in atom force microscopy or export through a small pore) [10, 23, 11] . can be split as follows, This gives the recursion [10] , the investigate of loop entropy dependence [7] , the analysis of FRET signals in the presence of single-stranded binding proteins [9] , as well as in mathematical studies of RNA panhandle-like structures [2, 13] . As the graph-distance for a pair of nucleotides in a given secondary structure can be computed in O(n log n) time, even large samples can be evaluated efficiently 2 . The equilibrium partition function and base pair binding probabilities for RNA secondary structure abstract: Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium therefore provides useful information on the overall shape of the molecule can provide insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between arbitrary nucleotides can be computed in polynomial time by means of dynamic programming. A naive implementation would yield recursions with a very high time complexity of O(n (11)). Although we were able to reduce this to O(n (6)) for many practical applications a further reduction seems difficult. We conclude, therefore, that sampling approaches, which are much easier to implement, are also theoretically favorable for most real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7114971/ doi: 10.1007/978-3-642-40453-5_10 id: cord-284118-z8zwjvbu author: Baczko, Knut title: Measles virus gene expression in subacute sclerosing panencephalitis date: 1984-10-31 words: 3140.0 sentences: 166.0 pages: flesch: 57.0 cache: ./cache/cord-284118-z8zwjvbu.txt txt: ./txt/cord-284118-z8zwjvbu.txt summary: Measles virus-specific mRNAs were present, but the amount of matrix (M) protein mRNA was greatly reduced in comparison to lytically infected cells and phospho-(P) protein mRNA was hardly detectable whereas the level of the corresponding intermediate-sized (is-) RNA was greatly increased. Measles virus-specific mRNAs were present, but the amount of matrix (M) protein mRNA was greatly reduced in comparison to lytically infected cells and phospho-(P) protein mRNA was hardly detectable whereas the level of the corresponding intermediate-sized (is-) RNA was greatly increased. This interpretation is further supported by studies of non-productive cell lines which, although persistently infected with SSPE viruses, do not express measles virus M protein (Lin and Thormar, 1980; Machamer et al., 1981; Carter et al., 1983a) . This failure could result from an alteration of this specific mRNA which would prevent correct function in translation reactions, as studies of non-productive cell lines persistently infected with SSPE virus indicate (Carter et al., 1983a) . abstract: Abstract RNA was extracted from the diseased brain of a case of human subacute sclerosing panencephalitis (SSPE) and analysed for the expression of measles-specific RNA. Measles virus-specific mRNAs were present, but the amount of matrix (M) protein mRNA was greatly reduced in comparison to lytically infected cells and phospho- (P) protein mRNA was hardly detectable whereas the level of the corresponding intermediate-sized (is-) RNA was greatly increased. RNA obtained from the human brain was also translated in vitro and measles virus nucleocapsid and P protein was produced. However, in marked contrast to control reactions M protein was not detected in the products formed by translation in vitro. These results indicate an impaired measles virus M protein mRNA synthesis in infected brain tissue. url: https://www.ncbi.nlm.nih.gov/pubmed/6534032/ doi: 10.1016/0168-1702(84)90015-7 id: cord-270550-if748w2n author: Bailey, Adam L. title: SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis date: 2020-11-05 words: 5808.0 sentences: 440.0 pages: flesch: 49.0 cache: ./cache/cord-270550-if748w2n.txt txt: ./txt/cord-270550-if748w2n.txt summary: To ascertain whether human pluripotent stem cell-derived cardiomyocytes (hPSC-derived 150 CMs) can serve as an appropriate model to study cardiac SARS-CoV-2 infection, we measured 151 ACE2 mRNA expression in hPSC-derived CMs. Quantitative RT-PCR revealed that hPSC-152 derived CMs abundantly expressed ACE2 mRNA. We identified numerous host genes that were differentially 226 regulated upon SARS-CoV-2 infection in each of the examined cell types and two-dimensional 227 tissues (Fig. 3c) . 236 GO pathway analysis revealed that infected hPSC-derived CMs and two-dimensional co-237 culture tissues showed upregulation of genes associated with immune cell activation, stress-238 induced transcription, and responses to pathogens including viruses. Consistent with the 343 possibility that disrupted sarcomere gene expression might contribute to reduced EHT 344 contractility, immunostaining of hPSC-derived CMs infected with SARS-CoV-2 revealed evidence 345 of sarcomere loss 3 days following infection (Fig. 6c) , a time point that preceded cell death. abstract: Epidemiological studies of the COVID-19 pandemic have revealed evidence of cardiac involvement and documented that myocardial injury and myocarditis are predictors of poor outcomes. Nonetheless, little is understood regarding SARS-CoV-2 tropism within the heart and whether cardiac complications result directly from myocardial infection. Here, we develop a human engineered heart tissue model and demonstrate that SARS-CoV-2 selectively infects cardiomyocytes. Viral infection is dependent on expression of angiotensin-I converting enzyme 2 (ACE2) and endosomal cysteine proteases, suggesting an endosomal mechanism of cell entry. After infection with SARS-CoV-2, engineered tissues display typical features of myocarditis, including cardiomyocyte cell death, impaired cardiac contractility, and innate immune cell activation. Consistent with these findings, autopsy tissue obtained from individuals with COVID-19 myocarditis demonstrated cardiomyocyte infection, cell death, and macrophage-predominate immune cell infiltrate. These findings establish human cardiomyocyte tropism for SARS-CoV-2 and provide an experimental platform for interrogating and mitigating cardiac complications of COVID-19. url: https://doi.org/10.1101/2020.11.04.364315 doi: 10.1101/2020.11.04.364315 id: cord-352814-fcl2g5wr author: Balboni, Andrea title: A Real-Time PCR Assay for Bat SARS-Like Coronavirus Detection and Its Application to Italian Greater Horseshoe Bat Faecal Sample Surveys date: 2011-11-22 words: 3998.0 sentences: 177.0 pages: flesch: 49.0 cache: ./cache/cord-352814-fcl2g5wr.txt txt: ./txt/cord-352814-fcl2g5wr.txt summary: In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The aim of this work was to develop a real-time PCR assay for diagnosing infection with SARS-related coronaviruses from bat guano in order to use it as a screening tool in epidemiological surveys for the detection of the viruses. The developed SYBR Green real-time PCR techniques were applied to an SARS-like coronavirus survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) which were sampled in Italy in 2009, resulting in a prevalence of coronavirus infection of 42%. After optimisation of the SYBR Green real-time PCR assay, for each run, duplicates of six 10-fold dilutions of the standard plasmid, triplicates of the viral reverse-transcribed RNA of the bat samples, and a no template control were simultaneously subjected to analysis. abstract: Bats are source of coronaviruses closely related to the severe acute respiratory syndrome (SARS) virus. Numerous studies have been carried out to identify new bat viruses related to SARS-coronavirus (bat-SARS-like CoVs) using a reverse-transcribed-polymerase chain reaction assay. However, a qualitative PCR could underestimate the prevalence of infection, affecting the epidemiological evaluation of bats in viral ecology. In this work an SYBR Green-real time PCR assay was developed for diagnosing infection with SARS-related coronaviruses from bat guano and was applied as screening tool in a survey carried out on 45 greater horseshoe bats (Rhinolophus ferrumequinum) sampled in Italy in 2009. The assay showed high sensitivity and reproducibility. Its application on bats screening resulted in a prevalence of 42%. This method could be suitable as screening tool in epidemiological surveys about the presence of bat-SARS-like CoVs, consequently to obtain a more realistic scenario of the viral prevalence in the population. url: https://www.ncbi.nlm.nih.gov/pubmed/22654650/ doi: 10.1100/2012/989514 id: cord-002413-795wuqz5 author: Balinsky, Corey A. title: IRAV (FLJ11286), an Interferon-Stimulated Gene with Antiviral Activity against Dengue Virus, Interacts with MOV10 date: 2017-02-14 words: 5485.0 sentences: 278.0 pages: flesch: 47.0 cache: ./cache/cord-002413-795wuqz5.txt txt: ./txt/cord-002413-795wuqz5.txt summary: title: IRAV (FLJ11286), an Interferon-Stimulated Gene with Antiviral Activity against Dengue Virus, Interacts with MOV10 IRAV is an RNA binding protein and localizes to cytoplasmic processing bodies (P bodies) in uninfected cells, where it interacts with the MOV10 RISC complex RNA helicase, suggesting a role for IRAV in the processing of viral RNA. FLJ11286, which we refer to here as IRAV (interferon-regulated antiviral gene) (also annotated as C19orf66, UPF0515, or RyDEN), encodes a protein 291 amino acids (aa) in length with a calculated molecular mass of 33.1 kDa. Analysis of published microarray data suggests that IRAV (FLJ11286) is upregulated in response to type I and type II IFNs (6, 20, (24) (25) (26) . IRAV also associates with the host RNA binding proteins UPF1 and HuR (ELAV1) and interacts with MOV10 (a RISC complex RNA helicase), suggesting a role for IRAV in processing or stability of RNA. abstract: Dengue virus (DENV) is a member of the genus Flavivirus and can cause severe febrile illness. Here, we show that FLJ11286, which we refer to as IRAV, is induced by DENV in an interferon-dependent manner, displays antiviral activity against DENV, and localizes to the DENV replication complex. IRAV is an RNA binding protein and localizes to cytoplasmic processing bodies (P bodies) in uninfected cells, where it interacts with the MOV10 RISC complex RNA helicase, suggesting a role for IRAV in the processing of viral RNA. After DENV infection, IRAV, along with MOV10 and Xrn1, localizes to the DENV replication complex and associates with DENV proteins. Depletion of IRAV or MOV10 results in an increase in viral RNA. These data serve to characterize an interferon-stimulated gene with antiviral activity against DENV, as well as to propose a mechanism of activity involving the processing of viral RNA. IMPORTANCE Dengue virus, a member of the family Flaviviridae, can result in a life-threatening illness and has a significant impact on global health. Dengue virus has been shown to be particularly sensitive to the effects of type I interferon; however, little is known about the mechanisms by which interferon-stimulated genes function to inhibit viral replication. A better understanding of the interferon-mediated antiviral response to dengue virus may aid in the development of novel therapeutics. Here, we examine the influence of the interferon-stimulated gene IRAV (FLJ11286) on dengue virus replication. We show that IRAV associates with P bodies in uninfected cells and with the dengue virus replication complex after infection. IRAV also interacts with MOV10, depletion of which is associated with increased viral replication. Our results provide insight into a newly identified antiviral gene, as well as broadening our understanding of the innate immune response to dengue virus infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309953/ doi: 10.1128/jvi.01606-16 id: cord-337199-mbv8kd1k author: Ballarín-González, Borja title: Clinical translation of RNAi-based treatments for respiratory diseases date: 2012-09-07 words: 10541.0 sentences: 571.0 pages: flesch: 41.0 cache: ./cache/cord-337199-mbv8kd1k.txt txt: ./txt/cord-337199-mbv8kd1k.txt summary: This review outlines the essential steps required for the clinical translation of RNAi-based respiratory therapies including disease and RNA target selection, siRNA design, respiratory barriers, and delivery solutions. 1 In vitro screening and selection of siRNA candidates against potential targets such as pathogenic or host factors; 2 optimize siRNA designs with high silencing activity and avoid immune recognition, increase stability, and reduce off-target effects; 3 evaluation of cytokine profile and gene silencing efficiency in preclinical disease models using either naked or a suitable delivery system; and 4 clinical trials to evaluate toxicity and biological activity of lead formulations Considerable efforts have attempted to harness the "exogenous" or "endogenous" branches of the RNAi pathway for therapeutic purposes. The authors suggested that the observed therapeutic effect reported in early studies was most likely due to activation of the innate immune response by the recognition of viral-specific nonmodified siRNA sequences by toll-like receptors (TLRs) instead of an RNAi-mediated effect. abstract: The ability to harness the RNA interference (RNAi) mechanism as a potential potent therapeutic has attracted great interest from academia and industry. Numerous preclinical and recent clinical trials have demonstrated the effectiveness of RNAi triggers such as synthetic small interfering RNA (siRNA). Chemical modification and delivery technologies can be utilized to avoid immune stimulation and improve the bioactivity and pharmacokinetics. Local application to the respiratory epithelia allows direct access to the site of respiratory pathogens that include influenza and respiratory syncytial virus (RSV). This review outlines the essential steps required for the clinical translation of RNAi-based respiratory therapies including disease and RNA target selection, siRNA design, respiratory barriers, and delivery solutions. Attention is given to antiviral therapies and preclinical evaluation with focus on the current status of anti-RSV clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/25787868/ doi: 10.1007/s13346-012-0098-7 id: cord-292983-msuluuuu author: Ballesteros-Briones, María Cristina title: A new generation of vaccines based on alphavirus self-amplifying RNA date: 2020-09-06 words: 4942.0 sentences: 277.0 pages: flesch: 47.0 cache: ./cache/cord-292983-msuluuuu.txt txt: ./txt/cord-292983-msuluuuu.txt summary: In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. This type of LNP-delivered saRNA vaccines, named SAM (for self-amplifying mRNA) platform, have shown great potential to generate immune responses against influenza virus [20] [21] [22] and Toxoplasma gondii [23] . Despite the fact that the ta-RNA system was able to induce good immune responses in vivo against influenza virus HA, it did not outperform vaccination with a single saRNA molecule expressing the same antigen. abstract: DNA or mRNA vaccines have potential advantages over conventional vaccines since they are easier to manufacture and have higher safety profiles. In particular, self-amplifying RNA (saRNA) derived from alphavirus expression vectors has shown to be very efficient to induce humoral and cellular responses against many antigens in preclinical models, being superior to non-replicating mRNA and DNA. This is mainly due to the fact that saRNA can provide very high expression levels and simultaneously induces strong innate responses, potentiating immunity. saRNA can be administered as viral particles or DNA, but direct delivery as RNA represents a safer and more simple approach. Although saRNA can be delivered as naked RNA, in vivo transfection can be enhanced by electroporation or by complexing it with cationic lipids or polymers. Alphavirus saRNA could have broad application to vaccinate against human pathogens, including emerging ones like SARS-CoV-2, for which clinical trials have been recently initiated. url: https://doi.org/10.1016/j.coviro.2020.08.003 doi: 10.1016/j.coviro.2020.08.003 id: cord-342189-ya05m58o author: Banerjee, Abhik K. title: SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses date: 2020-10-08 words: 11469.0 sentences: 647.0 pages: flesch: 55.0 cache: ./cache/cord-342189-ya05m58o.txt txt: ./txt/cord-342189-ya05m58o.txt summary: Here, we comprehensively define the interactions between each SARS-CoV-2 protein and human RNAs. We show that 10 viral proteins form highly specific interactions with mRNAs or ncRNAs, including those involved in progressive steps of host cell protein production. We show J o u r n a l P r e -p r o o f 5 that NSP16 binds to the mRNA recognition domains of the U1 and U2 RNA components of the spliceosome and acts to suppress global mRNA splicing in SARS-CoV-2-infected human cells. We identified several pathogenic functions of SARS-CoV-2 in human cells -including global inhibition of host mRNA splicing, protein translation, and membrane protein trafficking -and described the molecular mechanisms by which the virus acts to disrupt these essential cell processes. abstract: SARS-CoV-2 is a recently identified coronavirus that causes the respiratory disease known as COVID-19. Despite the urgent need, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis. Here, we comprehensively define the interactions between SARS-CoV-2 proteins and human RNAs. NSP16 binds to the mRNA recognition domains of the U1 and U2 splicing RNAs and acts to suppress global mRNA splicing upon SARS-CoV-2 infection. NSP1 binds to 18S ribosomal RNA in the mRNA entry channel of the ribosome and leads to global inhibition of mRNA translation upon infection. Finally, NSP8 and NSP9 bind to the 7SL RNA in the Signal Recognition Particle and interfere with protein trafficking to the cell membrane upon infection. Disruption of each of these essential cellular functions acts to suppress the interferon response to viral infection. Our results uncover a multipronged strategy utilized by SARS-CoV-2 to antagonize essential cellular processes to suppress host defenses. url: https://api.elsevier.com/content/article/pii/S0092867420313106 doi: 10.1016/j.cell.2020.10.004 id: cord-310748-ao29zx1u author: Banner, Lisa R. title: Random nature of coronavirus RNA recombination in the absence of selection pressure date: 1991-11-30 words: 2839.0 sentences: 155.0 pages: flesch: 52.0 cache: ./cache/cord-310748-ao29zx1u.txt txt: ./txt/cord-310748-ao29zx1u.txt summary: Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. To study RNA recombination in the absence of selection pressure, we developed a polymer-ase chain reaction (PCR) assay using two primers specific for the potential recombinant viruses which have a crossover site between the two primers. Only recombinant RNAs which had a crossover between the two primers and contained A59-specific sequences on the 5''-side and JHM-DL-specific sequences on the 3''-side could be detected by this PCR approach. DNA sequence analysis of 35 cloned PCR products showed that the crossover sites were almost randomly distributed throughout the nearly 1-kb region of the peplomer gene studied ( Fig. 2A) . Analysis of 53 recombinant clones revealed that, similar to the intracellular recombinants, the crossover sites in the viral recombinant RNAs were almost randomly distributed over the 1 -kb region of the peplomer gene (Fig. 2B) . abstract: Abstract RNA-RNA recombination is thought to occur preferentially at certain selected sites and in only a few RNA viruses; the mechanism for these restrictions is unknown. In this paper we report the development of a recombination assay for coronavirus, using polymerase chain reaction, in the absence of selection pressure. Our results showed that within a 1-kb region of the peplomer gene, RNA recombination occurred at almost every potential crossover site. Thus, coronavirus RNA recombination appears to be more random than previously realized. However, after serial passages of the recombinant viruses in tissue culture, the recombination sites among the progeny viruses became clustered in the region which contains the previously reported “hot spot” for coronavirus recombination. These results suggest that RNA recombination is common and random in nature, but only certain recombinants can be selected. Thus, the presence of recombinational “hot spots” for coronavirus or other RNA viruses most likely resulted from selection of certain recombinant viruses and not restriction on the occurrence of RNA recombination. The failure to detect recombinants in other RNA viruses may therefore be due to unfavorable properties of recombinant viruses. This approach can be used to detect recombinants in these viruses. url: https://www.sciencedirect.com/science/article/pii/004268229190795D doi: 10.1016/0042-6822(91)90795-d id: cord-340189-jo38hjqa author: Bar-On, Yinon M title: SARS-CoV-2 (COVID-19) by the numbers date: 2020-04-02 words: 7246.0 sentences: 458.0 pages: flesch: 58.0 cache: ./cache/cord-340189-jo38hjqa.txt txt: ./txt/cord-340189-jo38hjqa.txt summary: If you are infectious for 4 days, then you will infect four others on average, which is on the high end of the R 0 values for SARS-CoV-2 in the absence of physical distancing. Assuming entry of the virus to the cells is rapid (we estimate 10 min for SARS-CoV-2), the time it takes to produce progeny can be estimated by quantifying the lag between inoculation and the appearance of new intracellular virions, also known as the ''eclipse period''. While both the time to complete a replication cycle and the burst size may vary significantly in an animal host due to factors including the type of cell infected or the action of the immune system, these numbers provide us with an approximate quantitative view of the viral life-cycle at the cellular level. (Hirano et al., 1976) : "The average per-cell yield of active virus was estimated to be about 6-7 Â 10 2 plaque-forming units." This data is for MHV, so more research is needed to verify these values for SARS-CoV-2. abstract: The COVID-19 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this article we provide a one-stop, curated graphical source for the key numbers (based mostly on the peer-reviewed literature) about the SARS-CoV-2 virus that is responsible for the pandemic. The discussion is framed around two broad themes: i) the biology of the virus itself; ii) the characteristics of the infection of a single human host. url: https://www.ncbi.nlm.nih.gov/pubmed/32228860/ doi: 10.7554/elife.57309 id: cord-328085-7wp18qb6 author: Barage, Sagar title: Identification and characterization of novel RdRp and Nsp15 inhibitors for SARS-COV2 using computational approach date: 2020-11-06 words: 6052.0 sentences: 362.0 pages: flesch: 51.0 cache: ./cache/cord-328085-7wp18qb6.txt txt: ./txt/cord-328085-7wp18qb6.txt summary: This indicates that these compounds have a good binding affinity with RdRp. The resulting top 10 ligand conformations were evaluated for its binding mode and molecular interaction with active site residues of RdRP (Table 1 ). The first compound, namely, Chlorohexidine with binding free energy -10.11 Kcal/mol efficiently accommodated in the active site of RdRp and do molecular mimicry of nucleotides in terms of substructure interactions with RdRp residues (Figure 2(A) ). The second lead molecule, Ergotamine bound conformation, showed slight variation in the side-chain orientation with respect to Naldemedine binding in the active site of Nsp15 (Figure 4) . Thus, based on stability and molecular interaction and binding mode, Alectinib acts as lead molecule to design novel RdRp inhibitor to block the viral replication. The differences in NSP15 residues interaction with Naldemedine in simulated structure and predicted docked pose is due to flipped orientation of Naldemedine (Supporting Information Fig. S4B and Figure 4(B) ). abstract: The World Health Organization has declared COVID-19 as a global health emergency. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and highlights an urgent need for therapeutics. Here, we have employed a series of computer-aided drug repurposing campaign to discover inhibitors of RNA dependent RNA polymerase (RdRp) and Nsp15/EndoU. Subsequently, MD simulation has been performed to observe dynamic behavior of identified leads at the active site of RdRp and Nsp15. We successfully identified novel lead molecule such as Alectinib for RdRp while Naldemedine and Ergotamine for NSP15. These lead molecules were accommodated in the active site of the enzyme and stabilized by the networks of the hydrogen bond, pi type and hydrophobic interaction with key residues of either target. Interestingly, identified compounds show molecular mimicry in terms of molecular interactions with key residues of RdRp and Nsp15 essential for catalysis and substrate interaction. Previously, Alectinib, Naldemedine and Ergotamine were used as drug in different diseases might be repurposed against selected protein targets of COVID19. Finally, we propose that the identified inhibitors represent a novel lead molecule to design a more effective inhibitor to stop the progress of pathogen. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/33155531/ doi: 10.1080/07391102.2020.1841026 id: cord-016313-n4ewq0pt author: Baranyi, Lajos title: Advances in Lentiviral Vector-based Cell Therapy with Mesenchymal Stem Cells date: 2012-09-27 words: 20575.0 sentences: 824.0 pages: flesch: 39.0 cache: ./cache/cord-016313-n4ewq0pt.txt txt: ./txt/cord-016313-n4ewq0pt.txt summary: The field of possible application of mesenchymal stem cells in medicine and research expanded tremendously with the advent of improved Lentiviral-vectors capable of inserting stable copies of genes of interest and expressing proteins or biologically active RNA species ad libitum, performing delicate gene editing or active gene silencing or serving as advanced drug delivery systems utilized in ex vivo cell therapy. Implantation of Lentiviral vector-transduced human bone marrow mesenchymal cells using collagen scaffolds into immunode fi cient mice resulted in ef fi cient engraftment of gene-engineered cells and provided sites for transgene-expression in vivo. Moreover, it did not alter the differentiation potential of either HSCs or MSCs. In addition, the therapeutic potential of CD133+ and MSC progenitor cells transduced ex vivo with Lentiviral vector encoding the mature form of vascular endothelial growth factor D (VEGF-D ) or the enhanced green fl uorescent protein (eGFP) marker gene achieved permanent gene expression. abstract: The field of possible application of mesenchymal stem cells in medicine and research expanded tremendously with the advent of improved Lentiviral-vectors capable of inserting stable copies of genes of interest and expressing proteins or biologically active RNA species ad libitum, performing delicate gene editing or active gene silencing or serving as advanced drug delivery systems utilized in ex vivo cell therapy. The combination of these two fields has created a number of new areas of research in the landscape of modern medicine which are now extensively studied and discussed here. These areas include tissue engineering, tissue repair, wound healing and tissue implants, anticancer therapies, angiogenesis, myocardial infarction and repair as well as understanding and treating acute lung damage and injury. In addition, genetically modified, tagged MSCs are being intensively deployed in research and therapeutic attempts of the various ailments of the central nervous system including Parkinson’s disease, Alzheimer’s disease, various phases of acute ischemia and trauma. The emergence of new and important data for type II diabetes research is being followed with treatment suggestions and studies of senescence to find novel applications for genetically engineered MSCs. We find in ­general that genetically modified MSCs are at the cusp of breaking through from basic research into the next phase of clinical trials. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120558/ doi: 10.1007/978-1-62703-200-1_14 id: cord-265895-ck7eto16 author: Baric, Ralph S. title: Analysis of intracellular small RNAs of mouse hepatitis virus: evidence for discontinuous transcription date: 1987-02-28 words: 4507.0 sentences: 228.0 pages: flesch: 60.0 cache: ./cache/cord-265895-ck7eto16.txt txt: ./txt/cord-265895-ck7eto16.txt summary: These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription. These data, coupled with the presence of discrete large leader-containing RNAs which range from 84 to 1000 nucleotides in length in MHV-infected cells (Baric et a/., 1985) suggest that discontinuous RNA intermediates may be dissociated and reassert between viral RNA templates to generate recombinant viruses by a copy-choice mechanism (Makino eta/., 1986a). The leader-containing RNAs larger than 1 10 nucleotides in length detected by the leader-specific cDNA probe were more heterogeneous (Fig. 2) (Baric et al., 1985) suggesting that multiple RNA species in this size range were present. abstract: Abstract We have previously shown the presence of multiple small leader-containing RNA species in mouse hepatitis virus (MHV)-infected cells. In this paper, we have analyzed the origin, structure, and mechanism of synthesis of these small RNAs. Using cDNA probes specific for leader RNA and genes A, D, and F, we demonstrate that subsets of these small RNAs were derived from the various viral genes. These subsets have discrete and reproducible sizes, varying with the gene from which they are derived. The size of each subset correlates with regions of secondary structure, whose free energy ranges from −1.6 to −77.1 kcal/mol, in each of the mRNAs examined. In addition, identical subsets were detected on the replicative intermediate (RI) RNA, suggesting that they represent functional transcriptional intermediates. The biological significance of these small RNAs is further supported by the detection of leader-containing RNAs of 47, 50, and 57 nucleotides in length, which correspond to the crossover sites in two MHV recombinant viruses. These data, coupled with the high frequency of RNA recombination during MHV infection, suggest that the viral polymerase may pause in or around regions of secondary structure, thereby generating pools of free leader-containing RNA intermediates which can reassociate with the template, acting as primers for the synthesis of full-length or recombinant RNAs. These data suggest that MHV transcription uses a discontinuous and nonprocessive mechanism in which RNA polymerase allows the partial RNA products to be dissociated from the template temporarily during the process of transcription. url: https://api.elsevier.com/content/article/pii/0042682287904144 doi: 10.1016/0042-6822(87)90414-4 id: cord-256561-fnh2do4z author: Barik, Sailen title: Therapy of Respiratory Viral Infections with Intranasal siRNAs date: 2014-09-23 words: 2605.0 sentences: 181.0 pages: flesch: 60.0 cache: ./cache/cord-256561-fnh2do4z.txt txt: ./txt/cord-256561-fnh2do4z.txt summary: Based on these results, we propose the following consensus for designing intranasal antiviral siRNAs: (a) modified 19–27 nt-long double-stranded siRNAs are functional in the lung, (b) excessive 2′-OMe and 2′-F modifications in either or both strands of these siRNAs reduce efficacy, (c) limited modifications in the sense strand are beneficial, although their precise efficacy may be position-dependent, (d) cocktail of multiple siRNAs can be highly effective against multiple viral strains and subtypes. Therefore, enhancement of the intracellular and extracellular stability of synthetic siRNAs while increasing (or without compromising) their RNAi activity is a continuing goal for therapeutic translation of RNAi. A variety of chemical modifi cations, including terminal and internal ones, have been added to the fi rst-generation siRNA sequences to improve stability and delivery, leading to what we call "second-generation" siRNAs. Advantage has been taken of the free 2′-OH group of the ribose moiety of RNA (in contrast to DNA that lacks this OH group), to which various substituents were added. abstract: Chemically synthesized short interfering RNA (siRNA) has ushered a new era in the application of RNA interference (RNAi) against viral genes. We have paid particular attention to respiratory viruses that wreak heavy morbidity and mortality worldwide. The clinically significant ones include respiratory syncytial virus (RSV), parainfluenza virus (PIV) (two Paramyxoviruses), and influenza virus (an Orthomyxovirus). As the infection by these viruses is clinically restricted to the respiratory tissues, mainly the lungs, the logical route for the application of the siRNA was also the same, i.e., via the nasal route. Following the initial success of single intranasal siRNA against RSV, we now offer two new strategies: (1) second-generation siRNAs, used against the paramyxoviral RNA polymerase large subunit (L), (2) siRNA cocktail with a novel transfection reagent, used against influenza virus. Based on these results, we propose the following consensus for designing intranasal antiviral siRNAs: (a) modified 19–27 nt-long double-stranded siRNAs are functional in the lung, (b) excessive 2′-OMe and 2′-F modifications in either or both strands of these siRNAs reduce efficacy, (c) limited modifications in the sense strand are beneficial, although their precise efficacy may be position-dependent, (d) cocktail of multiple siRNAs can be highly effective against multiple viral strains and subtypes. url: https://doi.org/10.1007/978-1-4939-1538-5_14 doi: 10.1007/978-1-4939-1538-5_14 id: cord-286352-uftl1mx5 author: Baril, Martin title: The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot date: 2003-08-15 words: 5666.0 sentences: 254.0 pages: flesch: 57.0 cache: ./cache/cord-286352-uftl1mx5.txt txt: ./txt/cord-286352-uftl1mx5.txt summary: Since the region downstream of the stem-loop increases frameshifting in the presence of this stem-loop, as shown in Figure 3 , these results also support our suggestion that the frameshift stimulatory signal in MVP5180 is more complex than a simple stemloop and could correspond to a pseudoknot structure. The frameshift efficiencies of the constructs containing these mutations were assessed in vitro and in cultured cells and are presented in Figure 4 (b) (see also Table 1 To provide an independent support for the pseudoknot structure in subtype MVP5180 of HIV-1 group O frameshift stimulatory signal, we made a structural probing analysis of an RNA fragment encompassing the gag/pol frameshift region of this subtype. Our results show that the frameshift stimulatory signal of subtype MVP5180 of HIV-1 group O is a pseudoknot, where 8 nt of a 10-nt loop capping an 8-bp stem base-pair with a downstream complementary sequence. abstract: Abstract Human immunodeficiency virus type 1 (HIV-1) requires a programmed −1 ribosomal frameshift to produce Gag–Pol, the precursor of its enzymatic activities. This frameshift occurs at a slippery sequence on the viral messenger RNA and is stimulated by a specific structure, downstream of the shift site. While in group M, the most abundant HIV-1 group, the frameshift stimulatory signal is an extended bulged stem-loop, we show here, using a combination of mutagenesis and probing studies, that it is a pseudoknot in group O. The mutagenesis and probing studies coupled to an in silico analysis show that group O pseudoknot is a hairpin-type pseudoknot with two coaxially stacked stems of eight base-pairs (stem 1 and stem 2), connected by single-stranded loops of 2nt (loop 1) and 20nt (loop 2). Mutations impairing formation of stem 1 or stem 2 of the pseudoknot reduce frameshift efficiency, whereas compensatory changes that allow re-formation of these stems restore the frameshift efficiency to near wild-type level. The difference between the frameshift stimulatory signal of group O and group M supports the hypothesis that these groups originate from a different monkey to human transmission. url: https://www.sciencedirect.com/science/article/pii/S0022283603007848 doi: 10.1016/s0022-2836(03)00784-8 id: cord-258172-p54j4zzo author: Barker, Harlan title: Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2 date: 2020-10-28 words: 8453.0 sentences: 409.0 pages: flesch: 48.0 cache: ./cache/cord-258172-p54j4zzo.txt txt: ./txt/cord-258172-p54j4zzo.txt summary: Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Analysis of ACE2 promoter regions was performed using the TFBSfootprinter tool (https:// github.com/thirtysix/TFBS_footprinting) which uses transcription-relevant data from several major databases to enhance prediction of putative TFBSs, including: all cell types aggregated and merged human ATAC-Seq data from ENCODE [43] , transcription start sites and expression data from FANTOM5 [44] , expression quantitative trail loci from GTEx [39] , TFBS metacluster data from GTRD [45] , TFBS binding profile data from JASPAR [46] , and sequence and conservation data from Ensembl [47] . abstract: The World Health Organization declared the COVID-19 epidemic a public health emergency of international concern on March 11th, 2020, and the pandemic is rapidly spreading worldwide. COVID-19 is caused by a novel coronavirus SARS-CoV-2, which enters human target cells via angiotensin converting enzyme 2 (ACE2). We used a number of bioinformatics tools to computationally characterize ACE2 by determining its cell-specific expression in trachea, lung, and small intestine, derive its putative functions, and predict transcriptional regulation. The small intestine expressed higher levels of ACE2 mRNA than any other organ. By immunohistochemistry, duodenum, kidney and testis showed strong signals, whereas the signal was weak in the respiratory tract. Single cell RNA-Seq data from trachea indicated positive signals along the respiratory tract in key protective cell types including club, goblet, proliferating, and ciliary epithelial cells; while in lung the ratio of ACE2-expressing cells was low in all cell types (<2.6%), but was highest in vascular endothelial and goblet cells. Gene ontology analysis suggested that, besides its classical role in the renin-angiotensin system, ACE2 may be functionally associated with angiogenesis/blood vessel morphogenesis. Using a novel tool for the prediction of transcription factor binding sites we identified several putative binding sites within two tissue-specific promoters of the ACE2 gene as well as a new putative short form of ACE2. These include several interferon-stimulated response elements sites for STAT1, IRF8, and IRF9. Our results also confirmed that age and gender play no significant role in the regulation of ACE2 mRNA expression in the lung. url: https://www.ncbi.nlm.nih.gov/pubmed/33112891/ doi: 10.1371/journal.pone.0240647 id: cord-340423-f8ab7413 author: Barr, J.N. title: Genetic Instability of RNA Viruses date: 2016-09-09 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite having very limited coding capacity, RNA viruses are able to withstand challenge of antiviral drugs, cause epidemics in previously exposed human populations, and, in some cases, infect multiple host species. They are able to achieve this by virtue of their ability to multiply very rapidly, coupled with their extraordinary degree of genetic heterogeneity. RNA viruses exist not as single genotypes, but as a swarm of related variants, and this genomic diversity is an essential feature of their biology. RNA viruses have a variety of mechanisms that act in combination to determine their genetic heterogeneity. These include polymerase fidelity, error-mitigation mechanisms, genomic recombination, and different modes of genome replication. RNA viruses can vary in their ability to tolerate mutations, or “genetic robustness,” and several factors contribute to this. Finally, there is evidence that some RNA viruses exist close to a threshold where polymerase error rate has evolved to maximize the possible sequence space available, while avoiding the accumulation of a lethal load of deleterious mutations. We speculate that different viruses have evolved different error rates to complement the different “life-styles” they possess. url: https://www.sciencedirect.com/science/article/pii/B9780128033098000021 doi: 10.1016/b978-0-12-803309-8.00002-1 id: cord-263433-oldy0gta author: Barriocanal, Marina title: Long Non-Coding RNA BST2/BISPR is Induced by IFN and Regulates the Expression of the Antiviral Factor Tetherin date: 2015-01-09 words: 8773.0 sentences: 497.0 pages: flesch: 50.0 cache: ./cache/cord-263433-oldy0gta.txt txt: ./txt/cord-263433-oldy0gta.txt summary: As the ISGs described to date are coding genes, we sought to determine whether IFN also regulates the expression of long non-coding ISGs. To this aim, we used RNA sequencing to analyze the transcriptome of control and HuH7 cells treated with IFNα2. To address the issue of whether IFN could also regulate expression of lncRNAs, which may play key roles in the antiviral response, we analyzed the transcriptome of cells treated or not with IFNα2 by RNA sequencing (RNASeq). The results showed that at later times post-infection with the influenza virus lacking NS1, there was increased expression of lncISG15, lncBST2/BISPR, and their neighboring coding transcripts (Figure 3A) . To discriminate whether lncISG15 and lncBST2/BISPR are induced directly by the JAK/STAT signaling pathway or by a secondary wave of the IFN response, we evaluated the expression of these lncRNAs and their coding neighboring genes in HuH7 or A549 cells incubated or not with the JAK/STAT inhibitor ruxolitinib. abstract: Many long non-coding RNAs (lncRNAs) are expressed in cells but only a few have been well characterized. In these cases, lncRNAs have been shown to be key regulators of several cellular processes. Therefore, there is a great need to understand the function of more lncRNAs and their regulation in response to stimuli. Interferon (IFN) is a key molecule in the cellular antiviral response. IFN binding to its receptor activates transcription of several IFN-stimulated genes (ISGs) that function as potent antivirals. In addition, several ISGs are positive or negative regulators of the IFN pathway. This is essential to ensure a strong antiviral response and a later return of the cell to homeostasis. As the ISGs described to date are coding genes, we sought to determine whether IFN also regulates the expression of long non-coding ISGs. To this aim, we used RNA sequencing to analyze the transcriptome of control and HuH7 cells treated with IFNα2. The results show that IFN-treatment regulates the expression of several unknown non-coding transcripts. We have validated two lncRNAs upregulated after treatment with different doses of type I IFNα2 in different cells or with type III IFNλ. These lncRNAs were also induced by influenza and vesicular stomatitis virus mutants unable to block the IFN response, but not by several wild-type lytic viruses tested. These lncRNA genes were named lncISG15 and lncBST2 as they are located close to ISGs ISG15 and BST2, respectively. Interestingly, inhibition experiments showed that lncBST2 is a positive regulator of BST2. Therefore lncBST2 has been renamed BISPR, from BST2 IFN-stimulated positive regulator. Our results may have therapeutic implications as lncBST2/BISPR, but also lncISG15 and their coding neighbors, are increased in cells infected with hepatitis C virus and in the liver of infected patients. These results allow us to hypothesize that several lncRNAs could be activated by IFN to control the potency of the antiviral IFN response. url: https://www.ncbi.nlm.nih.gov/pubmed/25620967/ doi: 10.3389/fimmu.2014.00655 id: cord-265410-khwzdi79 author: Bartlett, Stuart title: Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars date: 2020-04-16 words: 9439.0 sentences: 470.0 pages: flesch: 47.0 cache: ./cache/cord-265410-khwzdi79.txt txt: ./txt/cord-265410-khwzdi79.txt summary: Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. Hence, in the search for extraterrestrial life, we must consider that: (1) Life exactly as we know it may be rare in the universe, but a more general class of phenomena with life-like characteristics may be far more common; (2) There may be systems, yet to be discovered or even imagined, that more successfully satisfy the living criteria than even earthly life does; (3) By loosening our constraints on the definition of life, we open ourselves up to exploring the full parameter space of physical and chemical interactions that may create life. Lyfe is any hypothetical phenomenon that maintains a low-entropy state via dissipation and disequilibria conversions, utilizes autocatalytic networks to achieve nonlinear growth and proliferation, employs homeostatic regulatory mechanisms to maintain stability and mitigate external perturbations, and acquires and processes functional information about its environment. abstract: Motivated by the need to paint a more general picture of what life is—and could be—with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research. Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning. Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. This new classification system allows the astrobiological community to more clearly define the questions that propel their research—e.g., whether they are developing a historical narrative to explain the origin of life (on Earth), or a universal narrative for the emergence of lyfe, or whether they are seeking signs of life specifically, or lyfe at large across the universe. While the concept of “life as we don’t know it” is not new, the four pillars of lyfe offer a novel perspective on the living state that is indifferent to the particular components that might produce it. url: https://doi.org/10.3390/life10040042 doi: 10.3390/life10040042 id: cord-307914-lgprrwee author: Bartok, Eva title: Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids date: 2020-07-14 words: 17726.0 sentences: 1100.0 pages: flesch: 51.0 cache: ./cache/cord-307914-lgprrwee.txt txt: ./txt/cord-307914-lgprrwee.txt summary: Indeed, the functionalization of CRISPR/Cas systems as a tool for genomic editing have revealed important differences in human and murine NA sensing, including distinct cell subset expression patterns of NA-sensing Toll-Like Receptors (TLRs) or species differences in the structural requirements for the detection of cyclic dinucleotide cGAMP by STING. As a long dsRNA with a 5 0 diphosphate terminus, polyI:C is known to activate the sensing receptors TLR3, MDA5, and RIG-I (Alexopoulou et al., 2001; Gitlin et al., 2006; Kato et al., 2008; Yoneyama et al., 2005) , accessory proteins such including LGP2 and members of the DDX and DHX families (reviewed in Oshiumi et al., 2016) as well as the restriction factors PKR and the OAS family (Farrell et al., 1978; Hovanessian et al., 1977; Zilberstein et al., 1978) . abstract: All lifeforms have developed highly sophisticated systems equipped to detect altered self and non-self nucleic acids (NA). In vertebrates, NA-sensing receptors safeguard the integrity of the organism by detecting pathogens, dyshomeostasis and damage, and inducing appropriate responses to eliminate pathogens and reconstitute homeostasis. Effector mechanisms include i) immune signaling, ii) restriction of NA functions such as inhibition of mRNA translation, and iii) cell death pathways. An appropriate effector response is necessary for host defense, but dysregulated NA-sensing can lead to devastating autoimmune and autoinflammatory disease. Their inherent biochemical similarity renders the reliable distinction between self NA under homeostatic conditions and altered or exogenous NA particularly challenging. In this review, we provide an overview of recent progress in our understanding of the closely coordinated and regulated network of innate immune receptors, restriction factors, and nucleases to effectively respond to pathogens and maintain host integrity. url: https://doi.org/10.1016/j.immuni.2020.06.014 doi: 10.1016/j.immuni.2020.06.014 id: cord-353640-giznbcpd author: Barza, Ruby title: Use of a Simplified Sample Processing step without RNA Extraction for direct SARS-CoV-2 RT-PCR Detection date: 2020-08-11 words: 1204.0 sentences: 59.0 pages: flesch: 55.0 cache: ./cache/cord-353640-giznbcpd.txt txt: ./txt/cord-353640-giznbcpd.txt summary: RT-PCR results using the ChromaCode HDPCR™ SARS-CoV-2 were compared using the heat-RNA release method and an automated RNA extraction system (EMAG). We compared the diagnostic sensitivity of the heat-RNA release method for detection of SARS-CoV-2 using NP swabs in viral transport media (VTM) to results obtained using an automated RNA extraction system (EMAG ® , bioMerieux, Durham, NC). A total of 174 COVID-19 positive samples were used for the study comprising 87 unique COVID-19 NP including Ct values using the heat-RNA release method were compared to the results obtained using the automated RNA-extraction method with both the LDT and ChromaCode SARS-CoV-2 assays. Comparison of the heat-RNA release method to EMAG ® using the ChromaCode SARS-CoV-2 RUO alone yielded a 94% agreement (81/86 positive samples). We found that the direct detection of SARS-CoV-2 using a 65°C heat inactivation and release step for 20minutes without RNA extraction and purification performed very well compared to the use of an automated RNA extraction instrument. abstract: The severe acute respiratory syndrome coronavirus (SARS-CoV-2) pandemic has resulted in significant shortages of RT-PCR testing supplies including RNA extraction kits. The goal of our study was to determine if a simplified heat-RNA release method would provide comparable detection of SARS-CoV-2 without the need for nucleic acid extraction. RT-PCR results using the ChromaCode HDPCR™ SARS-CoV-2 were compared using the heat-RNA release method and an automated RNA extraction system (EMAG). The heat-RNA release method correctly identified 94% (81/86 nasopharyngeal samples) that were positive for SARS-CoV-2. Five samples that were missed by heat-RNA release method had a mean Ct value: 35 using the automated extraction instrument, indicating a very low viral load. Our findings show that a simple heat-RNA release method is a reasonable alternative for the majority of COVID-19 positive patients and can help overcome the cost and availability issues of RNA extraction reagents. url: https://api.elsevier.com/content/article/pii/S1386653220303292 doi: 10.1016/j.jcv.2020.104587 id: cord-003187-qdbcdn2j author: Bassi, Maria Rosaria title: Extinction of Zika Virus and Usutu Virus by Lethal Mutagenesis Reveals Different Patterns of Sensitivity to Three Mutagenic Drugs date: 2018-08-27 words: 6701.0 sentences: 337.0 pages: flesch: 41.0 cache: ./cache/cord-003187-qdbcdn2j.txt txt: ./txt/cord-003187-qdbcdn2j.txt summary: Although the two viruses are inhibited by the same three drugs, ZIKV is relatively more susceptive to serial passage in the presence of purine analogues (favipiravir and ribavirin), while USUV replication is suppressed more efficiently by 5-fluorouracil. We observe that ribavirin, favipiravir, and 5-fluorouracil are all inhibitors of both ZIKV and USUV, and that consecutive passage of virus in the presence of these drugs can lead to the complete extinction of infectivity. To investigate whether ZIKV replication could be affected by increased mutagenesis, we tested four different compounds known to be mutagenic for diverse viruses, 5-fluorouracil, ribavirin, favipiravir, and decitabine (25, 32, 35, (37) (38) (39) . To investigate whether the antiviral activities observed during treatment with favipiravir, ribavirin, and 5-fluorouracil are connected to their predicted mutagenic activity, we analyzed the mutation frequencies of both ZIKV and USUV rescued after 5 passages in the presence of these compounds. abstract: Flaviviruses constitute an increasing source of public health concern, with growing numbers of pathogens causing disease and geographic spread to temperate climates. Despite a large body of evidence supporting mutagenesis as a conceivable antiviral strategy, there are currently no data on the sensitivity to increased mutagenesis for Zika virus (ZIKV) and Usutu virus (USUV), two emerging flaviviral threats. In this study, we demonstrate that both viruses are sensitive to three ribonucleosides, favipiravir, ribavirin, and 5-fluorouracil, that have shown mutagenic activity against other RNA viruses while remaining unaffected by a mutagenic deoxyribonucleoside. Serial cell culture passages of ZIKV in the presence of these compounds resulted in the rapid extinction of infectivity, suggesting elevated sensitivity to mutagenesis. USUV extinction was achieved when a 10-fold dilution was applied between every passage, but not in experiments involving undiluted virus, indicating an overall lower susceptibility than ZIKV. Although the two viruses are inhibited by the same three drugs, ZIKV is relatively more susceptive to serial passage in the presence of purine analogues (favipiravir and ribavirin), while USUV replication is suppressed more efficiently by 5-fluorouracil. These differences in sensitivity typically correlate with the increases in the mutation frequencies observed in each nucleoside treatment. These results are relevant to the development of efficient therapies based on lethal mutagenesis and support the rational selection of different mutagenic nucleosides for each pathogen. We will discuss the implications of these results to the fidelity of flavivirus replication and the design of antiviral therapies based on lethal mutagenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125542/ doi: 10.1128/aac.00380-18 id: cord-319821-ij34t1ae author: Bauer, Lisa title: Direct-acting antivirals and host-targeting strategies to combat enterovirus infections date: 2017-04-12 words: 4041.0 sentences: 235.0 pages: flesch: 40.0 cache: ./cache/cord-319821-ij34t1ae.txt txt: ./txt/cord-319821-ij34t1ae.txt summary: Here, we will review recent efforts to develop direct-acting antivirals as well as host factor-targeting inhibitors to treat enterovirus infections (Table 1) . 2C ATPase and 3D pol may be more promising targets for direct-acting antiviral drugs as they can be inhibited by small molecules, and several inhibitors of these factors were found to have broad-range anti-enteroviral activity. Since targeted drug discovery depends heavily on basic knowledge of virus replication, fundamental research on the role of viral enzymes as well as essential host factors for enterovirus replication remains needed for the development of broad-range antiviral drugs against these important pathogens. FDA-aroved drug to target fungal infections, is identified as a broad-spectrum enterovirus inhibitor and shown to target the lipid shuttling activity of oxysterol-binding protein that is essential for viral replication organell formation and/or function abstract: Enteroviruses (e.g., poliovirus, enterovirus-A71, coxsackievirus, enterovirus-D68, rhinovirus) include many human pathogens causative of various mild and more severe diseases, especially in young children. Unfortunately, antiviral drugs to treat enterovirus infections have not been approved yet. Over the past decades, several direct-acting inhibitors have been developed, including capsid binders, which block virus entry, and inhibitors of viral enzymes required for genome replication. Capsid binders and protease inhibitors have been clinically evaluated, but failed due to limited efficacy or toxicity issues. As an alternative approach, host-targeting inhibitors with potential broad-spectrum activity have been identified. Furthermore, drug repurposing screens have recently uncovered promising new inhibitors with disparate viral and host targets. Together, these findings raise hope for the development of (broad-range) anti-enteroviral drugs. url: https://api.elsevier.com/content/article/pii/S1879625716301547 doi: 10.1016/j.coviro.2017.03.009 id: cord-275403-g4rohhtt author: Bautista, Elida M. title: Functional Properties of the Predicted Helicase of Porcine Reproductive and Respiratory Syndrome Virus date: 2002-07-05 words: 7432.0 sentences: 401.0 pages: flesch: 48.0 cache: ./cache/cord-275403-g4rohhtt.txt txt: ./txt/cord-275403-g4rohhtt.txt summary: To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. As initial proof of helicase-like activity, experiments were performed to test the ability of purified PRRSV-14 nsp10 protein to hydrolyze radiolabeled ribonucleotides in the presence or absence of polyribonucleotides. To further analyze the predicted helicase activity of the PRRSV nsp10 protein, experiments were performed using duplex substrates prepared with synthetic oligonucleotides containing single-strand regions at the 3Ј or 5Ј ends and short duplex regions (21 and 24 bp). The 5Ј-to-3Ј orientation of the unwinding activity of the PRRSV helicase was further confirmed in experiments using substrates prepared with in vitro transcribed RNA that contained singlestrand regions at the 5Ј end of both strands and duplex regions of 67 bp (5Ј5ЈDuplex #1) and 85 bp (5Ј5ЈDuplex #2), as shown in Fig. 9B . abstract: Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is a member of the positive-strand RNA virus family Arteriviridae. Although considerable research has focused on this important pathogen, little is known about the function of most PRRSV proteins. To examine characteristics of putative nonstructural proteins (nsp) encoded in ORF1b, which have been identified by nucleotide similarity to domains of equine arteritis virus, defined genomic regions were cloned and expressed in the pRSET expression system. One region, nsp10, encoded a protein with a putative helicase domain and was further examined for functional helicase-like activities. PRRSV nsp10 was found to possess a thermolabile and pH-sensitive NTPase activity that was modulated by polynucleotides and to unwind dsRNA in a 5′ to 3′ polarity. These results provide the first evidence of the functional properties of PRRSV helicase and further support the finding that nidovirus helicases possess properties that distinguish them from other viral helicases. url: https://www.ncbi.nlm.nih.gov/pubmed/12127789/ doi: 10.1006/viro.2002.1495 id: cord-348669-mizygp4j author: Beall, Anne title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A date: 2016-01-05 words: 6021.0 sentences: 293.0 pages: flesch: 43.0 cache: ./cache/cord-348669-mizygp4j.txt txt: ./txt/cord-348669-mizygp4j.txt summary: title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. While the recombinant icPEDV replicated the clinical phenotypes of parental PC22A in vivo, icPEDV-⌬ORF3-RFP infection resulted in a partial attenuation in pigs based on lower diarrhea scores. Both the parental PEDV PC22A strain and its derivative recombinant cloned virus were genetically stable and fully pathogenic in neonatal gnotobiotic pigs, demonstrating that icPEDV provides not only a strategy that allows for the systematic evaluation of the role of viral genes in pathogenesis, tropism, and virulence but also a translational platform for the development of rationally attenuated live virus vaccines. abstract: Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic alphacoronavirus. In the United States, highly virulent PEDV strains cause between 80 and 100% mortality in suckling piglets and are rapidly transmitted between animals and farms. To study the genetic factors that regulate pathogenesis and transmission, we developed a molecular clone of PEDV strain PC22A. The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. Using reverse genetics, we removed open reading frame 3 (ORF3) and replaced this region with a red fluorescent protein (RFP) gene to generate icPEDV-ΔORF3-RFP. icPEDV-ΔORF3-RFP replicated efficiently in vitro and in vivo, was efficiently transmitted among pigs, and produced lethal disease outcomes. However, the diarrheic scores in icPEDV-ΔORF3-RFP-infected pigs were lower than those in wild-type-virus- or icPEDV-infected pigs, and the virus formed smaller plaques than those of PC22A. Together, these data describe the development of a robust reverse-genetics platform for identifying genetic factors that regulate pathogenic outcomes and transmission efficiency in vivo, providing key infrastructural developments for developing and evaluating the efficacy of live attenuated vaccines and therapeutics in a clinical setting. url: https://doi.org/10.1128/mbio.01451-15 doi: 10.1128/mbio.01451-15 id: cord-289093-si8btsab author: Beard, Philippa M. title: A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference date: 2014-06-05 words: 6578.0 sentences: 310.0 pages: flesch: 49.0 cache: ./cache/cord-289093-si8btsab.txt txt: ./txt/cord-289093-si8btsab.txt summary: To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. The methodology in the previously published VACV screens varied considerably; Mercer et al [32] measured the growth of a thymidine-kinase-deficient VACV (strain Western Reserve) after only 8 h of infection, thereby identifying cellular proteins involved in the initial stages of virus replication but excluding analysis of viral spread. abstract: Vaccinia virus (VACV) is a large, cytoplasmic, double-stranded DNA virus that requires complex interactions with host proteins in order to replicate. To explore these interactions a functional high throughput small interfering RNA (siRNA) screen targeting 6719 druggable cellular genes was undertaken to identify host factors (HF) influencing the replication and spread of an eGFP-tagged VACV. The experimental design incorporated a low multiplicity of infection, thereby enhancing detection of cellular proteins involved in cell-to-cell spread of VACV. The screen revealed 153 pro- and 149 anti-viral HFs that strongly influenced VACV replication. These HFs were investigated further by comparisons with transcriptional profiling data sets and HFs identified in RNAi screens of other viruses. In addition, functional and pathway analysis of the entire screen was carried out to highlight cellular mechanisms involved in VACV replication. This revealed, as anticipated, that many pro-viral HFs are involved in translation of mRNA and, unexpectedly, suggested that a range of proteins involved in cellular transcriptional processes and several DNA repair pathways possess anti-viral activity. Multiple components of the AMPK complex were found to act as pro-viral HFs, while several septins, a group of highly conserved GTP binding proteins with a role in sequestering intracellular bacteria, were identified as strong anti-viral VACV HFs. This screen has identified novel and previously unexplored roles for cellular factors in poxvirus replication. This advancement in our understanding of the VACV life cycle provides a reliable knowledge base for the improvement of poxvirus-based vaccine vectors and development of anti-viral theraputics. url: https://doi.org/10.1371/journal.pone.0098431 doi: 10.1371/journal.pone.0098431 id: cord-325326-2bbqz4o7 author: Beitzel, Brett F. title: High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing date: 2010-10-14 words: 7781.0 sentences: 388.0 pages: flesch: 51.0 cache: ./cache/cord-325326-2bbqz4o7.txt txt: ./txt/cord-325326-2bbqz4o7.txt summary: We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. Toward this goal, we used transposon mutagenesis, reverse genetics, and fragment analysis by capillary electrophoresis to identify regions of the nsP3 gene that are important for replication and that result in temperature sensitive (ts) mutations. We used transposon mutagenesis to construct a cDNA library with small DNA fragments randomly inserted throughout the VEEV genome and then produced replication-competent virus through reverse genetics. Comparing transposon insertion sites in the resultant viruses to those in the starting library, we were able to produce a functional map of the entire genome of VEEV, and to identify several hundred potential ts mutations, including those we originally identified with the capillary electrophoresis method. abstract: We have developed a high-resolution genomic mapping technique that combines transposon-mediated insertional mutagenesis with either capillary electrophoresis or massively parallel sequencing to identify functionally important regions of the Venezuelan equine encephalitis virus (VEEV) genome. We initially used a capillary electrophoresis method to gain insight into the role of the VEEV nonstructural protein 3 (nsP3) in viral replication. We identified several regions in nsP3 that are intolerant to small (15 bp) insertions, and thus are presumably functionally important. We also identified nine separate regions in nsP3 that will tolerate small insertions at low temperatures (30°C), but not at higher temperatures (37°C, and 40°C). Because we found this method to be extremely effective at identifying temperature sensitive (ts) mutations, but limited by capillary electrophoresis capacity, we replaced the capillary electrophoresis with massively parallel sequencing and used the improved method to generate a functional map of the entire VEEV genome. We identified several hundred potential ts mutations throughout the genome and we validated several of the mutations in nsP2, nsP3, E3, E2, E1 and capsid using single-cycle growth curve experiments with virus generated through reverse genetics. We further demonstrated that two of the nsP3 ts mutants were attenuated for virulence in mice but could elicit protective immunity against challenge with wild-type VEEV. The recombinant ts mutants will be valuable tools for further studies of VEEV replication and virulence. Moreover, the method that we developed is applicable for generating such tools for any virus with a robust reverse genetics system. url: https://doi.org/10.1371/journal.ppat.1001146 doi: 10.1371/journal.ppat.1001146 id: cord-000159-8y8ho2x5 author: Bekaert, Michaël title: Recode-2: new design, new search tools, and many more genes date: 2009-09-25 words: 2625.0 sentences: 138.0 pages: flesch: 42.0 cache: ./cache/cord-000159-8y8ho2x5.txt txt: ./txt/cord-000159-8y8ho2x5.txt summary: ''Recoding'' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. The term ''translational recoding'' describes the utilization of non-standard decoding during protein synthesis and encompasses such processes as ribosomal frameshifting, codon redefinition, translational bypassing and StopGo (1) (2) (3) (4) (5) (6) (7) . To facilitate further development of computational tools for the prediction of recoded genes in the ever faster growing body of sequence data, as well as to provide bench researchers with upto-date information on recoding, an efficient means of Recode database population and annotation are now required. RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression abstract: ‘Recoding’ is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of ‘recoded’ genes lags far behind annotation of ‘standard’ genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression—a factor of approximately three increase over the previous version of the database. Recode-2 is available at http://recode.ucc.ie url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808893/ doi: 10.1093/nar/gkp788 id: cord-000895-z5rdf0mi author: Belalov, Ilya S. title: Causes and Implications of Codon Usage Bias in RNA Viruses date: 2013-02-25 words: 5449.0 sentences: 272.0 pages: flesch: 45.0 cache: ./cache/cord-000895-z5rdf0mi.txt txt: ./txt/cord-000895-z5rdf0mi.txt summary: A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. A general rationale for analyzing impact of (di)nucleotide bias on ENC is randomizing or shuffling synonymous codons in the original genome sequence whilst preserving the factor under study [37] . Unfortunately, common statistical tests were poorly applicable to this approach, because all factors that affect codon preference (e.g. structural RNA elements) could not be accounted for, and therefore even a negligible difference in ENC between the original and generated sequences (e.g. 0.2 SD) passed a formal significance test upon increasing the number of replicates. Overall, dN 23 and dN 231 shuffling produced ENC values that differed from the original sequence by less than one in 25 of 29 viruses, indicating that we explored almost all types of pressure that affect overall codon usage. abstract: Choice of synonymous codons depends on nucleotide/dinucleotide composition of the genome (termed mutational pressure) and relative abundance of tRNAs in a cell (translational pressure). Mutational pressure is commonly simplified to genomic GC content; however mononucleotide and dinucleotide frequencies in different genomes or mRNAs may vary significantly, especially in RNA viruses. A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. Total GC content was a poor descriptor of viral genome composition and causes of codon usage bias. Genomic nucleotide content was the single most important factor of synonymous codon usage. Moreover, the choice between compatible amino acids (e.g., leucine and isoleucine) was strongly affected by genomic nucleotide composition. Dinucleotide composition at codon positions 2-3 had additional effect on codon usage. Together with mononucleotide composition bias, it could explain almost the entire codon usage bias in RNA viruses. On the other hand, strong dinucleotide content bias at codon position 3-1 found in some viruses had very little effect on codon usage. A hypothetical innate immunity sensor for CpG in RNA could partially explain the codon usage bias, but due to dependence of virus translation upon biased host translation machinery, experimental studies are required to further explore the source of dinucleotide bias in RNA viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581513/ doi: 10.1371/journal.pone.0056642 id: cord-281565-v8s2ski3 author: Belmonte-Reche, Efres title: Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2 date: 2020-08-20 words: 4545.0 sentences: 253.0 pages: flesch: 53.0 cache: ./cache/cord-281565-v8s2ski3.txt txt: ./txt/cord-281565-v8s2ski3.txt summary: These PQS and PiMS have been assessed according to their potential to form, uniqueness, frequency of appearance, conservation rates between 3297 different 2019-nCoV clinical cases, confirmed quadruplex-forming sequence presence and localization within the genome. Then, these PQS and PiMS were evaluated by their frequency of appearance in the corresponding genome, the presence of known-to-form quadruplex structures sequences within and their probability of quadruplex-formation score (as the mean of G4Hunter (52) and the adaptation of the PQSfinder algorithm (53) ). A flexible configuration of quadruplex definitions will detect larger amounts of candidates at the expense of requiring more computing power and accepting sequences that are more ambiguous in forming quadruplex structures in vitro (as determined by their score; with longer loops, smaller runs, more bulges and more complementary G/C %, Figure 1 , B). Expanding the search for common candidates to the entire virus realm, we matched one PQS and PiMS from the 2019-nCoV with the potential quadruplexes found in four viruses from abstract: In this paper we report the analysis of the 2019-nCoV genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. The quadruplex definitions of the algorithm were optimized for 2019-nCoV. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, hundreds of potential quadruplex candidates were discovered. These sequences were evaluated by their in vitro formation probability, their position in the viral RNA, their uniqueness and their conservation rates (calculated in over three thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were compared sequentially to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire realm. Sequences found in common with other species were further analyzed and characterized. Sequences with high scores unique to the 2019-nCoV were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates was then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable theranostic targets against the 2019-nCoV. GRAPHICAL ABSTRACT url: https://doi.org/10.1101/2020.08.19.257493 doi: 10.1101/2020.08.19.257493 id: cord-281020-g1muealp author: Belov, George A title: (+)RNA viruses rewire cellular pathways to build replication organelles date: 2012-10-01 words: 3965.0 sentences: 202.0 pages: flesch: 30.0 cache: ./cache/cord-281020-g1muealp.txt txt: ./txt/cord-281020-g1muealp.txt summary: The universal requirement of (+)RNA viruses for cellular membranes for genome replication, and the formation of membranous replication organelles with similar architecture, suggest that they target essential control mechanisms of membrane metabolism conserved among eukaryotes. These viruses universally require cellular membranes for assembly of their replication complexescontaining viral proteins, RNA, and host factorsto amplify their genome. Expression of poliovirus and HCV proteins in the presence of BFA resulted in the appearance of new membrane structures that are indistinguishable from those observed without the drug, indicating that GBF1 is more probably involved in the function of replication organelles than in their formation [41, 45] . For HCV, the absence of PI4KIIIa activity induced a dramatic change in the ultrastructural morphology of the membranous replication complex, suggesting a role of PI4P in recruiting specific membrane-shaping proteins [51 ] . abstract: Positive-strand RNA [(+)RNA] viruses show a significant degree of conservation of their mechanisms of replication. The universal requirement of (+)RNA viruses for cellular membranes for genome replication, and the formation of membranous replication organelles with similar architecture, suggest that they target essential control mechanisms of membrane metabolism conserved among eukaryotes. Recently, significant progress has been made in understanding the role of key host factors and pathways that are hijacked for the development of replication organelles. In addition, electron tomography studies have shed new light on their ultrastructure. Collectively, these studies reveal an unexpected complexity of the spatial organization of the replication membranes and suggest that (+)RNA viruses actively change cellular membrane composition to build their replication organelles. url: https://doi.org/10.1016/j.coviro.2012.09.006 doi: 10.1016/j.coviro.2012.09.006 id: cord-297039-vfuem6bk author: Beltrán-García, Jesús title: Circular RNAs in Sepsis: Biogenesis, Function, and Clinical Significance date: 2020-06-25 words: 7502.0 sentences: 468.0 pages: flesch: 46.0 cache: ./cache/cord-297039-vfuem6bk.txt txt: ./txt/cord-297039-vfuem6bk.txt summary: Recent findings propose that circular RNAs (circRNAs) may play a prominent role in regulating the patients'' immune system against different pathogens, including bacteria and viruses. Due to the role that circRNAs play in the modulation of different cytokines and immune proteins [62, 63] , altered states of alternative splicing in sepsis may alter the expression of circRNAs, which could partially explain the changes in the immune response of septic patients. However, circRNAs may play a key role in sepsis because of their ability to modulate different molecular mechanisms [10] , including inflammation [83] and immune response [62] , and to control multiple biological processes in metabolic organs (i.e., liver, pancreas [84] ) ( Figure 3 and Table 1 ). Interestingly, circRNAs may function as "molecular sponges", by controlling the expression of different types of non-coding RNAs, such as miRNAS, involved in regulating different processes in sepsis [105] [106] [107] [108] . abstract: Sepsis is a life-threatening condition that occurs when the body responds to an infection that damages it is own tissues. The major problem in sepsis is rapid, vital status deterioration in patients, which can progress to septic shock with multiple organ failure if not properly treated. As there are no specific treatments, early diagnosis is mandatory to reduce high mortality. Despite more than 170 different biomarkers being postulated, early sepsis diagnosis and prognosis remain a challenge for clinicians. Recent findings propose that circular RNAs (circRNAs) may play a prominent role in regulating the patients’ immune system against different pathogens, including bacteria and viruses. Mounting evidence also suggests that the misregulation of circRNAs is an early event in a wide range of diseases, including sepsis. Despite circRNA levels being altered in sepsis, the specific mechanisms controlling the dysregulation of these noncoding RNAs are not completely elucidated, although many factors are known to affect circRNA biogenesis. Therefore, there is a need to explore the molecular pathways that lead to this disorder. This review describes the role of this new class of regulatory RNAs in sepsis and the feasibility of using circRNAs as diagnostic biomarkers for sepsis, opening up new avenues for circRNA-based medicine. url: https://doi.org/10.3390/cells9061544 doi: 10.3390/cells9061544 id: cord-325529-pid58g2r author: Ben-Ami, Roni title: Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection date: 2020-06-23 words: 2822.0 sentences: 158.0 pages: flesch: 50.0 cache: ./cache/cord-325529-pid58g2r.txt txt: ./txt/cord-325529-pid58g2r.txt summary: METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. Some key constrains are (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; and (3) favorability of simple algorithms which may minimize human error in a laboratory setting. Specifically, we have demonstrated that pooling lysates from 5 or 8 nasopharyngeal swab samples retains sufficient sensitivity of viral RNA detection, allowing identification of SARS-CoV-2-positive individuals, while increasing throughput 5-fold to 7.5-fold. abstract: OBJECTIVES: Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck, while the need to increase testing throughput only rises. We aim to overcome these challenges by pooling samples together, performing RNA extraction and RT-PCR in pools. METHODS: We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of 8 samples in large-scale clinical tests. RESULTS: We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of 8 samples, showed that test results were not significantly affected. Implementing the 8-sample Dorfman pooling to test 26,576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput. CONCLUSIONS: Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations. url: https://www.sciencedirect.com/science/article/pii/S1198743X20303499?v=s5 doi: 10.1016/j.cmi.2020.06.009 id: cord-351854-5s03f0pp author: Ben-Ami, Roni title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection date: 2020-04-22 words: 3316.0 sentences: 197.0 pages: flesch: 54.0 cache: ./cache/cord-351854-5s03f0pp.txt txt: ./txt/cord-351854-5s03f0pp.txt summary: title: Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. Three such limitations might be: (1) a limit on the number of stages due to the importance of delivering a test result quickly, exemplified by the urgent clinical context of COVID-19 diagnosis; (2) a limit on the ability to dilute samples and still safely identify a single positive sample in a pool; (3) favorability of simple algorithms which may minimize human error in a laboratory setting. . https://doi.org/10.1101/2020.04.17.20069062 doi: medRxiv preprint probability of a sample to be positive by p (prevalence of detectable COVID-19 patients in the relevant population) and the pool size by n. This allows for reliable and efficient screening of large asymptomatic populations for the presence of SARS-CoV-2 infection, even when RNA extraction and RT-PCR reagents are in short supply. abstract: Testing for active SARS-CoV-2 infection is a fundamental tool in public health measures taken to control the COVID-19 pandemic. Due to the overwhelming use of SARS-CoV-2 RT-PCR tests worldwide, availability of test kits has become a major bottleneck. Here we demonstrate the reliability and efficiency of two simple pooling strategies that can increase testing capacity about 5-fold to 7.5-fold, in populations with a low infection rate. We have implemented the method in a routine clinical diagnosis setting, and already tested 2,168 individuals for SARS-CoV-2 using 311 RNA extraction and RT-PCR kits. url: https://doi.org/10.1101/2020.04.17.20069062 doi: 10.1101/2020.04.17.20069062 id: cord-283411-40ojqv1y author: Ben-Shmuel, Amir title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities date: 2020-09-10 words: 1174.0 sentences: 91.0 pages: flesch: 56.0 cache: ./cache/cord-283411-40ojqv1y.txt txt: ./txt/cord-283411-40ojqv1y.txt summary: title: Detection and infectivity potential of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) environmental contamination in isolation units and quarantine facilities This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. Surface Environmental, and 263 Personal Protective Equipment Contamination by Severe Acute Respiratory Syndrome Coronavirus 2 264 (SARS-CoV-2) From a Symptomatic Patient Detection of Severe Acute 268 Respiratory Syndrome Coronavirus 2 RNA on Surfaces in Quarantine Rooms. Severe acute respiratory 294 syndrome coronavirus 2 RNA contamination of inanimate surfaces and virus viability in a health care 295 emergency unit. abstract: OBJECTIVES: Environmental surfaces have been suggested as likely contributors to the transmission of COVID-19. This study assessed the infectivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) contamination on surfaces and objects in hospital isolation units and a quarantine hotel. METHODS: SARS-CoV-2 virus stability and infectivity on non-porous surfaces was tested under controlled laboratory conditions. Surfaces and air sampling was conducted at two COVID-19 isolation units and in a quarantine hotel. Viral RNA detected by RT-PCR and infectivity was assessed by VERO E6 CPE test. RESULTS: In laboratory-controlled conditions, SARS-CoV-2 gradually lost its infectivity completely at day 4 at ambient temperature and the decay rate of viral viability on surfaces directly correlated with increase in temperature. Viral RNA detected in 29/55 (52.7%) and 16/42 (38%) surface samples from the surrounding of symptomatic COVID-19 patients in isolation units of two hospitals and in a quarantine hotel for asymptomatic and very mild COVID-19 patients. None of the surface and air samples from all three sites (0/97) were found to contain infectious titers SARS-Cov-2 in tissue culture assay. CONCLUSIONS: Despite prolonged viability of SARS-CoV-2 in laboratory-controlled conditions, uncultivable viral contamination on inanimate surfaces might suggest low feasibility for indirect fomite transmission. url: https://www.sciencedirect.com/science/article/pii/S1198743X20305322?v=s5 doi: 10.1016/j.cmi.2020.09.004 id: cord-000547-adfigzc1 author: Beniac, Daniel R. title: The Organisation of Ebola Virus Reveals a Capacity for Extensive, Modular Polyploidy date: 2012-01-11 words: 7782.0 sentences: 392.0 pages: flesch: 51.0 cache: ./cache/cord-000547-adfigzc1.txt txt: ./txt/cord-000547-adfigzc1.txt summary: METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. From the same image data set, we combined extracted volumes from tomograms with 2-D single particle processing to determine the structure of the GP spikes ( Figure 5 ) to a resolution of 14 Å as measured by the Fourier Shell Correlation (FSC) 0.5 criterion. Analysis of 2090 distinct intact virions with a nucleocapsid from cryo-electron micrographs shows that the most common class length (53%) of virus particles is 982679 nm ( Figure 1A , Table S1 ). abstract: BACKGROUND: Filoviruses, including Ebola virus, are unusual in being filamentous animal viruses. Structural data on the arrangement, stoichiometry and organisation of the component molecules of filoviruses has until now been lacking, partially due to the need to work under level 4 biological containment. The present study provides unique insights into the structure of this deadly pathogen. METHODOLOGY AND PRINCIPAL FINDINGS: We have investigated the structure of Ebola virus using a combination of cryo-electron microscopy, cryo-electron tomography, sub-tomogram averaging, and single particle image processing. Here we report the three-dimensional structure and architecture of Ebola virus and establish that multiple copies of the RNA genome can be packaged to produce polyploid virus particles, through an extreme degree of length polymorphism. We show that the helical Ebola virus inner nucleocapsid containing RNA and nucleoprotein is stabilized by an outer layer of VP24-VP35 bridges. Elucidation of the structure of the membrane-associated glycoprotein in its native state indicates that the putative receptor-binding site is occluded within the molecule, while a major neutralizing epitope is exposed on its surface proximal to the viral envelope. The matrix protein VP40 forms a regular lattice within the envelope, although its contacts with the nucleocapsid are irregular. CONCLUSIONS: The results of this study demonstrate a modular organization in Ebola virus that accommodates a well-ordered, symmetrical nucleocapsid within a flexible, tubular membrane envelope. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256159/ doi: 10.1371/journal.pone.0029608 id: cord-329361-0mpbau1b author: Bennasser, Yamina title: RNAi Therapy for HIV Infection: Principles and Practicalities date: 2012-08-16 words: 2645.0 sentences: 200.0 pages: flesch: 56.0 cache: ./cache/cord-329361-0mpbau1b.txt txt: ./txt/cord-329361-0mpbau1b.txt summary: Inside eukaryotic cells, small RNA duplexes, called small interfering RNAs (siRNAs), activate a conserved RNA interference (RNAi) pathway which leads to specific degradation of complementary target mRNAs through base-pairing recognition. The practical use of RNAi therapy for HIV infection will depend on overcoming several challenges, including the ability to establish long-term expression of siRNA without off-target effects and the capacity to counteract mutant escape viruses. [4] Hence, in plants and Drosophila, when a cell they have sequence specificity for silencing mRNAs, these small is infected by a virus, an RNAi response is triggered by the foreign RNAs potentially represent a future class of antiviral drugs. [42] silencing of viral RNA and transient suppression of HIV replicaobserved that an siRNA targeted to nef rapidly elicited the emertion over a period of 3 to 4 days in single round infection of gence of siRNA-resistant viruses with point mutations in the nef cultured cells have been achieved. abstract: Inside eukaryotic cells, small RNA duplexes, called small interfering RNAs (siRNAs), activate a conserved RNA interference (RNAi) pathway which leads to specific degradation of complementary target mRNAs through base-pairing recognition. As with other viruses, studies have shown that replication of the HIV-1 in cultured cells can be targeted and inhibited by synthetic siRNAs. The relative ease of siRNA design and the versatility of RNAi to target a broad spectrum of mRNAs have led to the promise that drug discovery in the RNAi pathway could be effective against pathogens. This review discusses the current experimental principles that guide the application of RNAi against HIV and describes challenges and limitations that need to be surmounted in order for siRNAs to become practical antiviral drugs. The practical use of RNAi therapy for HIV infection will depend on overcoming several challenges, including the ability to establish long-term expression of siRNA without off-target effects and the capacity to counteract mutant escape viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17263586/ doi: 10.2165/00063030-200721010-00003 id: cord-022290-p0l1kv6n author: Bergmann, Ernst M. title: Proteolytic Enzymes of the Viruses of the Family Picornaviridae date: 2007-05-09 words: 9450.0 sentences: 480.0 pages: flesch: 56.0 cache: ./cache/cord-022290-p0l1kv6n.txt txt: ./txt/cord-022290-p0l1kv6n.txt summary: The primary function of the picornaviral proteinases is the cotranslational, specific cleavage of the viral polyprotein into the structural and nonstructural proteins. This is true even for some families of + RNA viruses which have developed additional strategies to generate individual gene products from a single RNA genome, e.g., subgenomic RNAs or multiple ORFs. Proteolytic cleavage as a covalent modification of the precursors of viral structural proteins is even more common and occurs even in DNA viruses. The sequence of the residues which form the last turn of this helix is highly conserved throughout the picornaviral 3C genes (K/RR/KNL/I), It is interesting that the structural and functional details of the proteolytic active site of the 3C proteinases are not the most conserved part of the 3C structure (Gorbalenya et al., 1988) . While the details of the specific enzyme substrate interactions gleaned from the crystal structures of 3C proteinases provide valuable information for the design of effective inhibitors, there is little experimental evidence for the mechanism of the chymotrypsin-like cysteine proteinases. abstract: This chapter deals with proteolytic enzymes of the viruses of the family picornaviridae. The picornaviral 3C proteinases constitute an ideal target for the rational design of antiviral drugs. The chapter discusses the chymotrypsin-like cysteine proteinases, which constitute a unique class of enzymes with a distinct substrate specificity, and are so far only found in +RNA viruses. Within these viruses the 3C proteinases perform a central and indispensable role during the viral life cycle and 3C proteinase inhibitors have the potential to limit the spread of viral infections. The chapter concludes that there is a wealth of experimental information available for the best-studied examples of the viruses of the Picornaviridae. This information provides an opportunity to design inhibitors against the viral 3C proteinase. Effective inhibitors of the picornaviral 3C proteinase have the potential to become effective antiviral drugs against human diseases such as the common cold, HAV, enteroviral infections, and diseases caused by related + RNA viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155532/ doi: 10.1016/b978-012420510-9/50032-6 id: cord-000248-zueoyesj author: Berretta, Regina title: Cancer Biomarker Discovery: The Entropic Hallmark date: 2010-08-18 words: 33594.0 sentences: 1678.0 pages: flesch: 43.0 cache: ./cache/cord-000248-zueoyesj.txt txt: ./txt/cord-000248-zueoyesj.txt summary: These authors cite, for example, ''''mitochondrial dysfunction'''' [5, 6] (including, but not limited to ''''glucose avidity'''' [7] and ''''a shift in glucosemetabolism from oxidative phosphorylation to glycolysis'''' [6, 8] , ''''altered glycolysis'''' [9] , ''''altered bioenergetic function of mitochondria'''' [10] ), ''''dysregulation of cell cycle and defective genome-integrity checkpoints'''' [11] , ''''aberrant DNA methylation'''' [12] (''''promoter hypermethylation of hallmark cancer genes'''' [13] and ''''CpG island hypermethylation and global genomic hypomethylation'''' [14] ), ''''shift in cellular metabolism'''' [15, 16, 17] , ''''regional hypoxia'''' [18] , ''''microenviroment acidosis'''' [19] , ''''abnormal microRNA regulation'''' [20, 21] , ''''aneuploidy'''' and ''''chromosome aberrations'''' [22, 23, 24, 25, 26] , ''''disruption of cellular junctions'''' [27] , ''''avoidance of the immune response'''' [28] , ''''pre-existing chronic inflammatory conditions'''' [29, 30] , ''''cancerrelated inflammation'''' [29] , ''''disabled autophagy'''' [28] , ''''impaired cellular senescence'''' [31] , ''''altered NF-kappaB signalling'''' [32] , ''''altered growth patterns, not altered growth per se'''' [33] , ''''disregulated DNA methylation and histone modifications'''' [34] , ''''tissue dedifferentiation'''' [35, 36] , and ''''somatically heritable molecular alterations'''' [37] . abstract: BACKGROUND: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. METHODOLOGY/PRINCIPAL FINDINGS: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. CONCLUSIONS/SIGNIFICANCE: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-througput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923618/ doi: 10.1371/journal.pone.0012262 id: cord-355758-tk7eturq author: Berrio, Alejandro title: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function date: 2020-09-22 words: 2175.0 sentences: 156.0 pages: flesch: 49.0 cache: ./cache/cord-355758-tk7eturq.txt txt: ./txt/cord-355758-tk7eturq.txt summary: Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. In Importantly, we also detected signals of positive selection in two additional regions of the 414 SARS-CoV-2 genome, specifically within the genes encoding Nsp4 and Nsp16 (Fig 1A) . Comparative analysis of coronavirus genomic RNA structure reveals 718 conservation in SARS-like coronaviruses. abstract: Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. Thermodynamic modeling of RNA stability and structure, however, indicates that RNA secondary structure within both genes in the SARS-CoV-2 genome differs from those of RaTG13, the reconstructed common ancestor, and Pan-CoV-GD (Guangdong). These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle. url: https://doi.org/10.1101/2020.09.16.300038 doi: 10.1101/2020.09.16.300038 id: cord-318276-so5jooj0 author: Bertholet, Christine title: Vaccinia virus produces late mRNAs by discontinuous synthesis date: 1987-07-17 words: 6225.0 sentences: 329.0 pages: flesch: 60.0 cache: ./cache/cord-318276-so5jooj0.txt txt: ./txt/cord-318276-so5jooj0.txt summary: RNA was isolated from noninfected or infected cells and then hybridized to 32P-labeled probes isolated from the 5'' end region, upstream of the 11K coding sequences of cDNA clones 3, 8, and 9 (see Figure 2 ). To confirm this, and to identify the regions from which they are transcribed, the cDNA-derived probes used in the previous experiment were hybridized to cloned DNA restriction fragments representing the entire vaccinia virus genome ( Figure 4 ). %P-labeled DNA probes (~3, ~9, p9, pllK) derived from the 5'' region of the corresponding cDNA clones or from genomic DNA (see Figure 2 ) were hybridized lo RNA isolated from uninfected (HeLa) or infected (Early, Late) cells, or to tRNA immobilized on a nitrocellulose membrane. Total late RNA from infected cells protected fragments of 127 and 128 nucleotides of the genomic probe, consistent with the previous experiments, which demonstrated that the sequence complementarity between the genomic DNA and 11K mRNA ends just upstream of the 11K ATG codon. abstract: Abstract We describe the unusual structure of a vaccinia virus late mRNA. In these molecules, the protein-coding sequences of a major late structural polypeptide are preceded by long leader RNAs, which in some cases are thousands of nucleotides long. These sequences map to different regions of the viral genome and in one instance are separated from the late gene by more than 100 kb of DNA. Moreover, the leader sequences map either upstream or downstream of the late gene, are transcribed from either DNA strand, and are fused to the late gene coding sequence via a poly(A) stretch. This demonstrates that vaccinia virus produces late mRNAs by tagging the protein-coding sequences onto the 3′ end of other RNAs. url: https://www.sciencedirect.com/science/article/pii/009286748790211X doi: 10.1016/0092-8674(87)90211-x id: cord-341071-nwrl1qws author: Berzal-Herranz, Alfredo title: Two Examples of RNA Aptamers with Antiviral Activity. Are Aptamers the Wished Antiviral Drugs? date: 2020-07-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The current Covid-19 pandemic has pointed out some major deficiencies of the even most advanced societies to fight against viral RNA infections. Once more, it has been demonstrated that there is a lack of efficient drugs to control RNA viruses. Aptamers are efficient ligands of a great variety of molecules including proteins and nucleic acids. Their specificity and mechanism of action make them very promising molecules for interfering with the function encoded in viral RNA genomes. RNA viruses store essential information in conserved structural genomic RNA elements that promote important steps for the consecution of the infective cycle. This work describes two well documented examples of RNA aptamers with antiviral activity against highly conserved structural domains of the HIV-1 and HCV RNA genome, respectively, performed in our laboratory. They are two good examples that illustrate the potential of the aptamers to fill the therapeutic gaps in the fight against RNA viruses. url: https://doi.org/10.3390/ph13080157 doi: 10.3390/ph13080157 id: cord-102866-40s64455 author: Bhadra, Sanchita title: One enzyme reverse transcription qPCR using Taq DNA polymerase date: 2020-05-30 words: 2863.0 sentences: 161.0 pages: flesch: 58.0 cache: ./cache/cord-102866-40s64455.txt txt: ./txt/cord-102866-40s64455.txt summary: To verify this activity and to determine whether Taq polymerasemediated reverse transcription might be leveraged for single enzyme RNA detection, we carried out the CDC-approved SARS-CoV-2-specific N1 TaqMan RT-qPCR assay using only Taq DNA polymerase and its accompanying commercial reaction buffer, ThermoPol, (New England Biolabs) seeded with different copies of N gene armored RNA (Asuragen), a commercial template preparation that is devoid of DNA. Even though the only polymerase present in these reactions was Taq DNA polymerase (NEB), and no dedicated reverse transcriptase was added, amplification curves were generated in response to 3 x 10 5 , 3 x 10 4 , and 3 x 10 3 copies of the SARS-CoV-2 N gene armored RNA templates (Figure 1 ). Similar to our results with armored N gene RNA, the NEB Taq DNA polymerase was able to perform TaqMan RT-qPCR analysis of SARS-CoV-2 viral genomic RNA with all three CDC assays (Figure 2 ). abstract: Taq DNA polymerase, one of the first thermostable DNA polymerases to be discovered, has been typecast as a DNA-dependent DNA polymerase commonly employed for PCR. However, Taq polymerase belongs to the same DNA polymerase superfamily as the Molony murine leukemia virus reverse transcriptase and has in the past been shown to possess reverse transcriptase activity. We report optimized buffer and salt compositions that promote the reverse transcriptase activity of Taq DNA polymerase, and thereby allow it to be used as the sole enzyme in TaqMan RT-qPCR reactions. We demonstrate the utility of Taq-alone RT-qPCR reactions by executing CDC SARS-CoV-2 N1, N2, and N3 TaqMan RT-qPCR assays that could detect as few as 2 copies/µL of input viral genomic RNA. url: https://doi.org/10.1101/2020.05.27.120238 doi: 10.1101/2020.05.27.120238 id: cord-003045-r707jl16 author: Bhuvaneshwar, Krithika title: viGEN: An Open Source Pipeline for the Detection and Quantification of Viral RNA in Human Tumors date: 2018-06-05 words: 6546.0 sentences: 359.0 pages: flesch: 54.0 cache: ./cache/cord-003045-r707jl16.txt txt: ./txt/cord-003045-r707jl16.txt summary: The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. Available online at: https:// www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts/ licensedproductsblas/blooddonorscreening/infectiousdisease/ucm080466.htm Abbreviations: HBV, Hepatitis B virus; HCV, Hepatitis C Virus; HERV K113, Human Endogenous Retrovirus K113; TCGA, The Cancer Genome Atlas; HCC, Hepatocellular carcinoma; NAFLD, nonalcoholic fatty liver disease; Hep B, Hepatitis B; Hep C, Hepatitis C; HepB + HepC, coinfected with both Hepatitis B and C virus; HBsAg, Hepatitis B surface antigen; HBeAg, Hepatitis B type e antigen; NGS, next-generation sequencing; RNA-seq, whole transcriptome sequencing; BAM, Binary version of Sequence alignment/map format; CDS, coding sequence; Cox PH, Cox Proportional Hazard; HBx, viral gene X; STS, Sequence-tagged sites; NCBI, National Center for Biotechnology Information; GFF, general-feature-format. abstract: An estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples. We present an open source bioinformatics pipeline viGEN, which allows for not only the detection and quantification of viral RNA, but also variants in the viral transcripts. The pipeline includes 4 major modules: The first module aligns and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral-gene level thus allowing for downstream differential expression analysis of viral genes between case and controls groups. The fourth module calls variants in these viruses. To the best of our knowledge, there are no publicly available pipelines or packages that would provide this type of complete analysis in one open source package. In this paper, we applied the viGEN pipeline to two case studies. We first demonstrate the working of our pipeline on a large public dataset, the TCGA cervical cancer cohort. In the second case study, we performed an in-depth analysis on a small focused study of TCGA liver cancer patients. In the latter cohort, we performed viral-gene quantification, viral-variant extraction and survival analysis. This allowed us to find differentially expressed viral-transcripts and viral-variants between the groups of patients, and connect them to clinical outcome. From our analyses, we show that we were able to successfully detect the human papilloma virus among the TCGA cervical cancer patients. We compared the viGEN pipeline with two metagenomics tools and demonstrate similar sensitivity/specificity. We were also able to quantify viral-transcripts and extract viral-variants using the liver cancer dataset. The results presented corresponded with published literature in terms of rate of detection, and impact of several known variants of HBV genome. This pipeline is generalizable, and can be used to provide novel biological insights into microbial infections in complex diseases and tumorigeneses. Our viral pipeline could be used in conjunction with additional type of immuno-oncology analysis based on RNA-seq data of host RNA for cancer immunology applications. The source code, with example data and tutorial is available at: https://github.com/ICBI/viGEN/. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996193/ doi: 10.3389/fmicb.2018.01172 id: cord-331509-p19dg1jw author: Bigault, Lionel title: Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR date: 2020-05-31 words: 4317.0 sentences: 240.0 pages: flesch: 60.0 cache: ./cache/cord-331509-p19dg1jw.txt txt: ./txt/cord-331509-p19dg1jw.txt summary: title: Porcine epidemic diarrhea virus: Viral RNA detection and quantification using a validated one-step real time RT-PCR In this study we described the development and validation of a SYBR™ Green one-step RT-qPCR according to the French norm NF U47-600, for the detection and quantification of PEDV viral RNA. Specificity and sensitivity, limit of detection (LoD), limit of quantification (LQ), linearity, intra and inter assay variability were evaluated using transcribed RNA and fecal and jejunum matrices spiked with virus. For a rapid, accurate and reliable diagnosis of PED in the veterinary laboratory, a method for the detection of PEDV viral RNA has been developed and more importantly validated according to the "Association Francaise de NORmalisation" (AFNOR) French NF U47-600 norm entitled "requirement and recommendation for the implementation, development and validation of PCR in animal health" (AFNOR, 2015a; AFNOR, 2015b) . This method should help harmonize detection and quantification of viral RNA from PEDV belonging to both S-non-INDEL and S-INDEL strains in both field and experimental settings. abstract: Since 2014, porcine epidemic diarrhea virus (PEDV) has reemerged in Europe. RT-PCR methods have been described for the detection of PEDV, but none have been validated according to a norm. In this study we described the development and validation of a SYBR™ Green one-step RT-qPCR according to the French norm NF U47-600, for the detection and quantification of PEDV viral RNA. The method was validated from sample preparation (feces or jejunum) through to nucleic acid extraction and RT-qPCR detection. Specificity and sensitivity, limit of detection (LoD), limit of quantification (LQ), linearity, intra and inter assay variability were evaluated using transcribed RNA and fecal and jejunum matrices spiked with virus. The analytical and diagnostic specificities and sensitivities of this RT-qPCR were 100% in this study. A LoD of 50 genome copies/5 µl of extract from fecal matrices spiked with virus or RNA transcript and 100 genome copies/5 µl of extract from jejunum matrices spiked with virus were obtained. The Lower LQ (LLQ) was 100 genome copies/5 µl and the Upper LQ (ULQ) 10(8) copies/5 µl. This method is the first, validated according a norm for PEDV and may serve as a global reference method to harmonize detection and quantification of PEDV viral RNA in both field and experimental settings. url: https://www.sciencedirect.com/science/article/pii/S0166093420301580?v=s5 doi: 10.1016/j.jviromet.2020.113906 id: cord-011794-ejoufvvj author: Binder, Florian title: Isolation and characterization of new Puumala orthohantavirus strains from Germany date: 2020-04-23 words: 5972.0 sentences: 309.0 pages: flesch: 51.0 cache: ./cache/cord-011794-ejoufvvj.txt txt: ./txt/cord-011794-ejoufvvj.txt summary: Additionally, glycoprotein precursor (GPC)-derived virus-like particles of a German PUUV sequence allowed the generation of monoclonal antibodies that allowed the reliable detection of the isolated PUUV strain in the immunofluorescence assay. Finally, the reactivity of the isolates was determined with novel monoclonal antibodies raised against PUUV GPC VLPs. Bank voles were trapped in spring 2019 in the PUUV endemic region around Osnabrück following a standard snap trapping protocol [25, 26] . Dissection on site and inoculation of VeroE6 and bank vole MGN-2-R cells with homogenized lung samples resulted after three blind passages in four potential isolates that were detected by a novel PUUV RT-qPCR (Table S1 , Fig. 1) . Reactivity of novel PUUV GPC-specific monoclonal antibodies with hantavirus-infected VeroE6 cells in immunofluorescence assay (IFA). In conclusion, the PUUV isolate described here replicates in a bank vole cell line and its N and GPC proteins can be detected by specific monoclonal antibodies. abstract: Orthohantaviruses are re-emerging rodent-borne pathogens distributed all over the world. Here, we report the isolation of a Puumala orthohantavirus (PUUV) strain from bank voles caught in a highly endemic region around the city Osnabrück, north-west Germany. Coding and non-coding sequences of all three segments (S, M, and L) were determined from original lung tissue, after isolation and after additional passaging in VeroE6 cells and a bank vole-derived kidney cell line. Different single amino acid substitutions were observed in the RNA-dependent RNA polymerase (RdRP) of the two stable PUUV isolates. The PUUV strain from VeroE6 cells showed a lower titer when propagated on bank vole cells compared to VeroE6 cells. Additionally, glycoprotein precursor (GPC)-derived virus-like particles of a German PUUV sequence allowed the generation of monoclonal antibodies that allowed the reliable detection of the isolated PUUV strain in the immunofluorescence assay. In conclusion, this is the first isolation of a PUUV strain from Central Europe and the generation of glycoprotein-specific monoclonal antibodies for this PUUV isolate. The obtained virus isolate and GPC-specific antibodies are instrumental tools for future reservoir host studies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s11262-020-01755-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329759/ doi: 10.1007/s11262-020-01755-3 id: cord-310371-pylrg91h author: Bishop, R.F. title: Enteric Viruses date: 2008-07-30 words: 4467.0 sentences: 253.0 pages: flesch: 41.0 cache: ./cache/cord-310371-pylrg91h.txt txt: ./txt/cord-310371-pylrg91h.txt summary: The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. . viruses causing localized inflammation at any level of the intestinal tract, predominantly in small intestinal mucosa, resulting in acute gastroenteritis, for example, rotaviruses, caliciviruses, adenoviruses, astroviruses; . The family Caliciviridae contain small RNA viruses that cause enteric disease in a wide variety of hosts including cattle, pigs, rabbits, and humans. Caliciviruses causing enteric infections (in humans and other animals) are classified as belonging to the family Caliciviridae, which is divided into four genera. The recent demonstration that human noroviruses can infect and replicate in a three-dimensional cell culture model of human intestinal epithelium, should improve our understanding of the pathogenesis, and antigenic diversity of this important group of enteric viruses. abstract: Many viruses use the enteric tract as a route of entry to the human, animal, or avian host. The onset of acute enteritis is associated with infection by viruses that replicate at or near the site of entry into the intestinal mucosa, including caliciviruses, rotaviruses, adenoviruses, astroviruses, and coronaviruses. These ‘enteric’ viruses occur globally and share similar features. Most are RNA viruses that replicate in the cytoplasm of mature absorptive epithelial cells lining the villi of the small intestine, leading to inflammation and villus atrophy. Vomiting and diarrhea can result in dehydration and death if untreated. Despite abundant growth in vivo, they initially proved difficult or impossible to grow in vitro. Most are genetically diverse, species specific, highly infectious within species and transmitted by the fecal–oral route. Severe symptoms are most commonly associated with primary infections of young animals, and are followed by short-lived immunity. Reinfections are common throughout life, but are often only mildly symptomatic. Safe and effective vaccines have been developed to prevent severe rotavirus disease in young children. In addition to these enterotropic viruses, enteric disease can also result from spread to the intestine of HIV or cytomegaloviruses during the later stages of systemic disease in immunocompromised hosts. url: https://www.sciencedirect.com/science/article/pii/B9780123744104003861 doi: 10.1016/b978-012374410-4.00386-1 id: cord-337899-w5zh40gv author: Bissoyi, Akalabya title: Alphavirus Nonstructural Proteases and Their Inhibitors date: 2017-07-14 words: 7294.0 sentences: 399.0 pages: flesch: 48.0 cache: ./cache/cord-337899-w5zh40gv.txt txt: ./txt/cord-337899-w5zh40gv.txt summary: Recently, several protease inhibitors have been developed using computeraided drug design methodologies (Gupta, 2013; Gupta et al., 1983; Wlodawer and Vondrasek, 1998) , synthetic approaches, high-throughput screening method (Mayr and Bojanic, 2009) , and drug reposition-based approaches (Sundberg, 2000) , which could possibly target the NSPs responsible for virus replication. The former ligand is therefore supposed to be a promising inhibitor of NSP2 protease of CHIKV virus, and has been emerged as one of the promising antiviral drug candidates with potential symptomatic and disease-modifying effects. Exploring the polymerase activity of Chikungunya viral non structural protein 4 (nsP4) using molecular modeling, epharmacophore and docking studies. Molecular modeling and docking study to elucidate novel Chikungunya virus nsP2 protease inhibitors Exploring the polymerase activity of Chikungunya viral nonstructural protein 4 (nsP4) using molecular modeling, e-pharmacophore and docking studies abstract: Alphaviruses, such as Chikungunya virus, O’Nyong–Nyong virus, Ross River virus, have been widely known to cause fever, rash, and rheumatic diseases. In addition, several other alphaviruses, for instance Eastern equine encephalitis virus, Venezuelan equine encephalitis virus, and Western equine encephalitis virus, potentially cause fatal encephalitis in humans. These diseases are considered as neglected tropical diseases for which there are no current antiviral therapies or vaccines available. The replication process in alphaviruses depends on four nonstructural proteins, NSP1–NSP4, which are produced as a single polyprotein. Therefore, the Alphavirus-mediated diseases in humans remain challenging among the virologists worldwide. Thus researchers are trying to find out proficient approaches, including the discovery of novel chemotherapeutic agents for the possible management and treatment of infected patients. Attempts were also made to identify an active compound against alphaviruses from natural sources. The genomes of various alphaviruses have already been revealed, and the function of proteins may be predicted by homology modeling, with the known proteins of closely related viruses. With the help of this information of protein modeling and subsequent virtual screening approach, the research teams will be able to identify few potential leads. The drug discovery against various alphaviruses is still in its early stages. Moreover, consolidating the available information and making it available for the scientific community are urgent requirements to expedite the research of potential drug discovery. The current chapter describes the techniques available to prevent Alphavirus infection and to treat Alphavirus-associated malignancies. In addition, we also discuss the recent outcomes in the fields of synthetic and natural medicinal chemistry research that were solely aimed to fight against Alphavirus infection. Thus the present chapter may also help and expedite the drug discovery and development of inhibitors against nonstructural proteins of various alphaviruses. url: https://www.sciencedirect.com/science/article/pii/B9780128097120000046 doi: 10.1016/b978-0-12-809712-0.00004-6 id: cord-005281-wy0zk9p8 author: Blinov, V. M. title: Viral component of the human genome date: 2017-05-09 words: 6583.0 sentences: 306.0 pages: flesch: 44.0 cache: ./cache/cord-005281-wy0zk9p8.txt txt: ./txt/cord-005281-wy0zk9p8.txt summary: In the human genome, this capacity is determined by the portion of chromosomal DNA, which does not contain species-specific protein-encoding sequences and, thus, can basically make a place for novel information that will be modified to reach a new balance. In fact, the scope of the described phenomena is not limited to retroviruses as such, since the ubiquity of retroviral elements in animal genomes, their activity in germline cells [31] , along with the fact that viral replication depends significantly on RNA expression, allow retroviruses to contribute in different ways to the insertion of nonretroviral genes into animal germline cells. Finally, the ability to incorporate parts of the viral genome into the chromosomal DNA of host germline cells can vary strongly among different taxonomic groups of viruses, i.e., orders, families, genera, and even species If insertions of viral sequences remain functionally active in the host cell genome, they can give rise to either proteins that function in a new environment or untranslated RNAs of different sizes. abstract: Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7089383/ doi: 10.1134/s0026893317020066 id: cord-273910-fna7s9te author: Bochud, Pierre-Yves title: Innate immunogenetics: a tool for exploring new frontiers of host defence date: 2007-07-20 words: 7063.0 sentences: 391.0 pages: flesch: 39.0 cache: ./cache/cord-273910-fna7s9te.txt txt: ./txt/cord-273910-fna7s9te.txt summary: Recent immunogenetic studies have associated polymorphisms of the genes encoding TLRs, NLRs, and key signal-transducing molecules, such as interleukin-1 receptor-associated kinase 4 (IRAK4), with increased susceptibility to, or outcome of, infectious diseases. With the availability of high-throughput genotyping techniques, it is becoming increasingly evident that analyses of genetic polymorphisms of innate immune genes will further improve our knowledge of the host antimicrobial defence response and help in identifying individuals who are at increased risk of life-threatening infections. Since the innate immune system senses only a limited number of highly conserved microbial-associated molecular patterns 23 via a limited number of receptors and signalling molecules, as anticipated, several polymorphisms have been found to confer an increased susceptibility to specifi c pathogens (table 2, table 3 , and fi gure 4). [36] [37] [38] Taken together, these data clearly show that mutations in the genes encoding TLRs and downstream signal-transducing molecules infl uence innate immune responses and increase susceptibility to many infectious diseases. abstract: The discovery of innate immune genes, such as those encoding Toll-like receptors (TLRs), nucleotide-binding oligomerisation domain-like receptors (NLRs), and related signal-transducing molecules, has led to a substantial improvement of our understanding of innate immunity. Recent immunogenetic studies have associated polymorphisms of the genes encoding TLRs, NLRs, and key signal-transducing molecules, such as interleukin-1 receptor-associated kinase 4 (IRAK4), with increased susceptibility to, or outcome of, infectious diseases. With the availability of high-throughput genotyping techniques, it is becoming increasingly evident that analyses of genetic polymorphisms of innate immune genes will further improve our knowledge of the host antimicrobial defence response and help in identifying individuals who are at increased risk of life-threatening infections. This is likely to open new perspectives for the development of diagnostic, predictive, and preventive management strategies to combat infectious diseases. url: https://api.elsevier.com/content/article/pii/S1473309907701858 doi: 10.1016/s1473-3099(07)70185-8 id: cord-323029-7hqp8xuq author: Bognár, Zsófia title: Aptamers against Immunoglobulins: Design, Selection and Bioanalytical Applications date: 2020-08-11 words: 19331.0 sentences: 873.0 pages: flesch: 45.0 cache: ./cache/cord-323029-7hqp8xuq.txt txt: ./txt/cord-323029-7hqp8xuq.txt summary: For aptamer selection against rIgG [6] and IgE [7] , homogenous processes were used and the separation of bound and unbound nucleic Several different SELEX methods have been used to generate immunoglobulin aptamers including homogeneous, heterogeneous, bead-based SELEX processes, CE-SELEX (capillary electrophoresis-SELEX), µFFE-SELEX (micro-free flow electrophoresis-SELEX) and fully integrated selection processes selection of aptamers with proper binding properties. Molecular Light Switch Complex 100-800 100 [128] Fluorescence enhancement using a DNA aptamer 92-37,000 57 [130] Amplification through allostery-triggered enzymatic recycling amplification NA 5 [131] Fluorescent oligonucleotide probe based on G-quadruplex scaffold for signal-on ultrasensitive protein assay 4.72-7560 0.095 [132] Fluorescence anisotropy 1000-60,000 350 [133] Fluorescence anisotropy assay NA 20 [134] Fluorescence protection assay 100-50,000 100 [136] Aptamer-barcode-based assay based on instantaneous derivatization chemiluminescence coupled to magnetic beads 4.88-20,000 4.6 [137] Competitive fluorescence quenching assay 350-35,000 170 [138] Rapid fluorescence detection of immunoglobulin E using an aptamer switch based on a binding-induced pyrene excimer NA 1600 [139] 6.1. abstract: Nucleic acid aptamers show clear promise as diagnostic reagents, as highly specific strands were reported against a large variety of biomarkers. They have appealing benefits in terms of reproducible generation by chemical synthesis, controlled modification with labels and functionalities providing versatile means for detection and oriented immobilization, as along with high biochemical and temperature resistance. Aptamers against immunoglobulin targets—IgA, IgM, IgG and IgE—have a clear niche for diagnostic applications, therefore numerous aptamers have been selected and used in combination with a variety of detection techniques. The aim of this review is to overview and evaluate aptamers selected for the recognition of antibodies, in terms of their design, analytical properties and diagnostic applications. Aptamer candidates showed convincing performance among others to identify stress and upper respiratory tract infection through SIgA detection, for cancer cell recognition using membrane bound IgM, to detect and treat hemolytic transfusion reactions, autoimmune diseases with IgG and detection of IgE for allergy diseases. However, in general, their use still lags significantly behind what their claimed benefits and the plethora of application opportunities would forecast. url: https://www.ncbi.nlm.nih.gov/pubmed/32796581/ doi: 10.3390/ijms21165748 id: cord-318551-c1qr27lg author: Boguszewska‐Chachulska, Anna M. title: Rna Viruses Redirect Host Factors to Better Amplify Their Genome date: 2005-12-29 words: 10673.0 sentences: 511.0 pages: flesch: 44.0 cache: ./cache/cord-318551-c1qr27lg.txt txt: ./txt/cord-318551-c1qr27lg.txt summary: (Adapted with permission from Pasternak et al., 2001.) Transcription of segmented (À) strand RNA viruses such as the Orthomyxoviridae, Arenaviridae, Bunyaviridae, and Tenuiviruses requires a primer to initiate synthesis of the mRNAs. This is achieved by cap-snatching in which the replicase complex, or a protein thereof, binds to the 5 0 region of cell mRNAs, cleaves off the cap together with generally 7-15 nucleotides from the 5 0 end of the cell mRNA, and uses this fragment as a primer to initiate synthesis of the viral mRNAs (Bouloy et al., 1978; Nguyen and Haenni, 2003) . (1996) PV, poliovirus; MHV, mouse hepatitis virus; WNV, West Nile virus; BVDV, bovine viral diarrhea virus; HPIV-3, human parainfluenza virus-3; IG (À), intergenic region in (À) RNA; UTR, untranslated region; Leader RNA (À), 3'' end of (À) RNA; Leader RNA (þ), 5'' end of (þ) RNA; HF, host factor; PCBP, poly(C)-binding protein; PABP, poly(A)-binding protein; hnRNP A1, heterogeneous nuclear ribonucleoprotein A1; PTB, polypyrimidine tract-binding protein; TIA-1, T-cell-activated intracellular antigen; TIAR, TIA-1-related; RHA, RNA helicase A; GAPDH, glyceraldehyde-3-phosphate dehydrogenase. abstract: This chapter provides an updated view of the host factors that are, at present, believed to participate in replication/transcription of RNA viruses. One of the major hurdles faced when attempting to identify host factors specifically involved in viral RNA replication/transcription is how to discriminate these factors from those involved in translation. Several of the host factors shown to affect viral RNA synthesis are factors known to be involved in protein synthesis, for example, translation factors. In addition, some of the factors identified to date appear to influence viral RNA amplification as well as viral protein synthesis, and translation and replication are frequently tightly associated. Several specific host factors actively participating in viral RNA transcription/replication have been identified and the regions of host protein/replicase or host protein/viral RNA interaction have been determined. The chapter centers exclusively on those factors that appear functionally important for viral amplification. It presents a list of the viruses for which a specific host factor associates with the polymerase, affecting viral genome amplification. It also indicates the usually accepted cell function of the factor and the viral polymerase or polymerase subunit to which the host factor binds. url: https://www.sciencedirect.com/science/article/pii/S0065352705650026 doi: 10.1016/s0065-3527(05)65002-6 id: cord-329527-0rlotyz3 author: Bohmwald, Karen title: Neurologic Alterations Due to Respiratory Virus Infections date: 2018-10-26 words: 11036.0 sentences: 559.0 pages: flesch: 48.0 cache: ./cache/cord-329527-0rlotyz3.txt txt: ./txt/cord-329527-0rlotyz3.txt summary: In addition to this, a fatal case attributed to the H1N1 pandemic infection was reported, and the clinical finding showed that the cause of death was an intracerebral thrombosis and hemorrhage with presence of the virus in the brain, but not in lungs or CSF (Simon et al., 2013 ; Figure 2) . In another approximation to understand the etiologic agent causing myelopathy post-influenza-like syndrome, CSF obtained from a patient with this disease was inoculated in several cell lines, previously reported to be permissive for the growth FIGURE 2 | Influenza virus (IV) spreads from the lungs to the CNS through the vagus nerve promoting an inflammatory state. As described so far, CoVs are respiratory viruses that exhibit neurotropic capacities that not only allows them to achieve latency and avoid the immune response of the host, but also have neurological implications that can complicate the disease associated to its infection. Although there are extensive case reports that indicate neurological manifestations associated to hMPV-infection in humans, further studies are required in mice models to characterize this disease. abstract: Central Nervous System (CNS) infections are one of the most critical problems in public health, as frequently patients exhibit neurologic sequelae. Usually, CNS pathologies are caused by known neurotropic viruses such as measles virus (MV), herpes virus and human immunodeficiency virus (HIV), among others. However, nowadays respiratory viruses have placed themselves as relevant agents responsible for CNS pathologies. Among these neuropathological viruses are the human respiratory syncytial virus (hRSV), the influenza virus (IV), the coronavirus (CoV) and the human metapneumovirus (hMPV). These viral agents are leading causes of acute respiratory infections every year affecting mainly children under 5 years old and also the elderly. Up to date, several reports have described the association between respiratory viral infections with neurological symptoms. The most frequent clinical manifestations described in these patients are febrile or afebrile seizures, status epilepticus, encephalopathies and encephalitis. All these viruses have been found in cerebrospinal fluid (CSF), which suggests that all these pathogens, once in the lungs, can spread throughout the body and eventually reach the CNS. The current knowledge about the mechanisms and routes used by these neuro-invasive viruses remains scarce. In this review article, we describe the most recent findings associated to neurologic complications, along with data about the possible invasion routes of these viruses in humans and their various effects on the CNS, as studied in animal models. url: https://www.ncbi.nlm.nih.gov/pubmed/30416428/ doi: 10.3389/fncel.2018.00386 id: cord-332003-67e9fchy author: Boisguérin, Prisca title: Delivery of therapeutic oligonucleotides with cell penetrating peptides() date: 2015-06-29 words: 13067.0 sentences: 636.0 pages: flesch: 42.0 cache: ./cache/cord-332003-67e9fchy.txt txt: ./txt/cord-332003-67e9fchy.txt summary: Although challenged later on as detailed in Section 7, this mechanism and the possibility to use such so called cell-penetrating peptides (CPPs) as non-viral delivery vectors for biomolecules, fostered a very large interest. Since the chemical conjugation and purification of negatively charged ONs with the most popular cationic CPPs has turned out to be difficult, most applications have concerned chargeneutral ON analogues such as Peptide Nucleic Acids (PNAs) and PMO (see Section 3). Unexpectedly, in a well-characterized HeLa 705 cell assay with a positive read-out ( Fig. 1) , splicing redirection using PNA or PMO oligomers conjugated to various standard CPPs (Tat, Penetratin or oligo-arginines) was not achieved in our research groups [57] . This led to the development of several arginine-rich peptides as PMO conjugates for use in muscle cells and in vivo mouse models of DMD as outlined in Section 4. abstract: Oligonucleotide-based drugs have received considerable attention for their capacity to modulate gene expression very specifically and as a consequence they have found applications in the treatment of many human acquired or genetic diseases. Clinical translation has been often hampered by poor biodistribution, however. Cell-penetrating peptides (CPPs) appear as a possibility to increase the cellular delivery of non-permeant biomolecules such as nucleic acids. This review focuses on CPP-delivery of several classes of oligonucleotides (ONs), namely antisense oligonucleotides, splice switching oligonucleotides (SSOs) and siRNAs. Two main strategies have been used to transport ONs with CPPs: covalent conjugation (which is more appropriate for charge-neutral ON analogues) and non-covalent complexation (which has been used for siRNA delivery essentially). Chemical synthesis, mechanisms of cellular internalization and various applications will be reviewed. A comprehensive coverage of the enormous amount of published data was not possible. Instead, emphasis has been put on strategies that have proven to be effective in animal models of important human diseases and on examples taken from the authors' own expertise. url: https://api.elsevier.com/content/article/pii/S0169409X15000198 doi: 10.1016/j.addr.2015.02.008 id: cord-297974-sduz0j35 author: Bokelmann, L. title: Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP) date: 2020-08-06 words: 4761.0 sentences: 307.0 pages: flesch: 55.0 cache: ./cache/cord-297974-sduz0j35.txt txt: ./txt/cord-297974-sduz0j35.txt summary: Here we describe a method to detect SARS-CoV-2 RNA of a single infected individual within a bulk sample comprised of up to 26 individual patient samples by combining a hybridizationcapture-based RNA extraction approach with smartphone app-assisted colorimetric detection of RT-LAMP products, a procedure that can be performed in less than one hour ( Figure 1A) . To investigate whether it is possible to detect single infected individuals in pools of gargle lavage samples, we created eleven pools of 25 patient samples each, all of which had been tested negative in RT-qPCR assay and in the Cap-iLAMP assays for the Orf1a and the N gene ( Figure 2D ). All tested gargle lavages from single healthy individuals (n=6) and 11 pools of 25 healthy individuals (n=275) correctly tested negative for both the Orf1a gene and N gene in the Cap-iLAMP assay ( Figure 2C and E), indicating that false positive results which were sometimes observed when samples are added directly into the iLAMP reaction (Supp. abstract: Efforts to contain the spread of SARS-CoV-2 have spurred the need for reliable, rapid, and cost-effective diagnostic methods which can easily be applied to large numbers of people. However, current standard protocols for the detection of viral nucleic acids while sensitive, require a high level of automation, sophisticated laboratory equipment and trained personnel to achieve throughputs that allow whole communities to be tested on a regular basis. Here we present Cap-iLAMP (capture and improved loop-mediated isothermal amplification). This method combines a hybridization capture-based RNA extraction of non-invasive gargle lavage samples to concentrate samples and remove inhibitors with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. In contrast to direct addition of the sample to improved LAMP (iLAMP), Cap-iLAMP does not result in false positives and single infected samples can be detected in a pool among 25 uninfected samples, thus reducing the technical cost per test to ~1 Euro per individual. url: http://medrxiv.org/cgi/content/short/2020.08.04.20168617v1?rss=1 doi: 10.1101/2020.08.04.20168617 id: cord-338083-77re4l0w author: Bolin, Steven R. title: Origination and consequences of bovine viral diarrhea virus diversity date: 2005-03-04 words: 6748.0 sentences: 329.0 pages: flesch: 43.0 cache: ./cache/cord-338083-77re4l0w.txt txt: ./txt/cord-338083-77re4l0w.txt summary: The genetic diversity that occurs among isolates of BVDV is characteristic of RNA viruses that exist in nature as quasispecies (a swarm of viral mutants). However, altered base sequence in this region of the viral genome has been identified after passage of the virus in cell culture, and has been detected in viral RNA that was extracted from tissues of an infected animal [20, 21] . The selection of the antigenic variants likely occurred during the acute infection of the dams of those PI cattle and resulted in transplacental transmission of slightly different BVDV to a group of fetuses. Genetic and antigenic variability in bovine viral diarrhea virus (BVDV) isolates from Belgium Pathogenesis of primary respiratory disease induced by isolates from a new genetic cluster of bovine viral diarrhea virus type I Clinical and immunologic responses of vaccinated and unvaccinated calves to infection with a virulent type-II isolate of bovine viral diarrhea virus abstract: The potential consequences of BVDV genetic and antigenic diversity are far ranging. The complexity of clinical presentations associated with BVDV likely arises from factors encoded by the virus genome. More importantly,prevention and control of BVDV may be complicated by diagnostic and immunization failure resulting from virus diversity. Evolutionary pressures will continue to drive further diversity, making control of BVDV challenging. Current and the potential for future BVDV strain diversity should be considered when designing BVDV control programs both at the individual farm and national herd level. url: https://www.sciencedirect.com/science/article/pii/S0749072003000811 doi: 10.1016/j.cvfa.2003.11.009 id: cord-254070-v9gabn1a author: Bordería, Antonio V. title: Fidelity Variants and RNA Quasispecies date: 2015-10-25 words: 7003.0 sentences: 386.0 pages: flesch: 48.0 cache: ./cache/cord-254070-v9gabn1a.txt txt: ./txt/cord-254070-v9gabn1a.txt summary: For retroviruses, some base analog-resistant HIV strains were reported with reverse transcriptase mutations (e.g., M184V) that altered the fidelity of this RNA-dependent DNA polymerase. Several observations supported this last mechanism: G64S exhibited the same replication as wild-type virus in single-cycle infections; G64S generated fewer escape mutants to antiviral compounds; and G64S was also resistant to base analogs of different structure (Pfeiffer and Kirkegaard 2003; Vignuzzi et al. Finally, a high-fidelity polymerase variant was found for foot-and-mouth disease virus (FMDV, also in the Picornaviridae family), selected by serial passage in the RNA mutagen, 5-fluorouracil (5-FU). As with picornavirus high-fidelity variants, this variant was resistant to multiple RNA mutagens and generated populations with more restricted genetic diversity than wild-type virus. A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity abstract: By now, it is well established that the error rate of the RNA-dependent RNA polymerase (RdRp) that replicates RNA virus genomes is a primary driver of the mutation frequencies observed in RNA virus populations—the basis for the RNA quasispecies. Over the last 10 years, a considerable amount of work has uncovered the molecular determinants of replication fidelity in this enzyme. The isolation of high- and low-fidelity variants for several RNA viruses, in an expanding number of viral families, provides evidence that nature has optimized the fidelity to facilitate genetic diversity and adaptation, while maintaining genetic integrity and infectivity. This chapter will provide an overview of what fidelity variants tell us about RNA virus biology and how they may be used in antiviral approaches. url: https://www.ncbi.nlm.nih.gov/pubmed/26499340/ doi: 10.1007/82_2015_483 id: cord-353274-wozwpvpq author: Borremans, B. title: Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection date: 2020-05-20 words: 6160.0 sentences: 362.0 pages: flesch: 50.0 cache: ./cache/cord-353274-wozwpvpq.txt txt: ./txt/cord-353274-wozwpvpq.txt summary: In this study we quantified IgG and IgM antibody kinetics and RNA shedding probability during SARS-CoV-2 infection (up to 60 days post symptom onset) by drawing on published data. This formal integration approach enabled us to leverage 3,214 data points from 516 individuals with symptoms ranging from asymptomatic to critical, published in 22 studies, resulting in a quantitative synthesis of diverse data on anti-SARS-CoV-2 antibody patterns and RNA shedding during the early phase of infection. One of the goals of this study is to estimate the means and variation of IgG and IgM seroconversion times (time between symptom onset and first antibody detection) for different assays, antigens, and disease severity. . https://doi.org/10.1101/2020.05.15.20103275 doi: medRxiv preprint weighted bootstrapping procedure integrates all types of data that contain useful information about the timing of seroconversion of different antibodies in day(s) post symptom onset (dpo). The probability of detecting SARS-CoV-2 specific IgG or IgM in plasma or serum samples was estimated by integrating data on whether an individual tested positive or negative on a given dpo. abstract: Our ability to understand and mitigate the spread of SARS-CoV-2 depends largely on antibody and viral RNA data that provide information about past exposure and shedding. Five months into the outbreak there is an impressive number of studies reporting antibody kinetics and RNA shedding dynamics, but extensive variation in detection assays, study group demographics, and laboratory protocols has presented a challenge for inferring the true biological patterns. Here, we combine existing data on SARS-CoV-2 IgG, IgM and RNA kinetics using a formal quantitative approach that enables integration of 3,214 data points from 516 individuals, published in 22 studies. This allows us to determine the mean values and distributions of IgG and IgM seroconversion times and titer kinetics, and to characterize how antibody and RNA detection probabilities change during the early phase of infection. We observe extensive variation in antibody response patterns and RNA detection patterns, explained by both individual heterogeneity and protocol differences such as targeted antigen and sample type. These results provide a robust reference for clinical management of individual patients, and a foundation for the mathematical models and serological surveys that underpin public health policies. url: https://doi.org/10.1101/2020.05.15.20103275 doi: 10.1101/2020.05.15.20103275 id: cord-295467-9fnis6ci author: Botella, Leticia title: The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history date: 2014-12-12 words: 5926.0 sentences: 330.0 pages: flesch: 52.0 cache: ./cache/cord-295467-9fnis6ci.txt txt: ./txt/cord-295467-9fnis6ci.txt summary: title: The European race of Gremmeniella abietina hosts a single species of Gammapartitivirus showing a global distribution and possible recombinant events in its history Phylogenetic analysis based on 46 partial coat protein (CP) cDNA sequences divided the GaRV-MS1 population into two closely related clades, while RNA-dependent RNA polymerase (RdRp) sequences revealed only one clade. (2) to analyse their genetic diversity and population structure; and (3) to assess evolutionary processes, such as recombination and selection, to better understand possible host-virus coevolution. The Spanish isolate of Gremmeniella abietina H1-4 was chosen for determination of the full-length sequence of a putative new strain of GaRV-MS1 (GenBank accession numbers for the CP, RdRp, and the unknown protein III: KJ786411eKJ786413). abietina appears to be composed of a single species (GaRV-MS1) with low genetic variability, which is seemingly stable within the different populations of the fungal host. abstract: The population genetics of the family Partitiviridae was studied within the European race of the conifer pathogen Gremmeniella abietina. One hundred sixty-two isolates were collected from different countries, including Canada, the Czech Republic, Finland, Italy, Montenegro, Serbia, Spain, Switzerland, Turkey and the United States. A unique species of G. abietina RNA virus–MS1 (GaRV-MS1) appears to occur indistinctly in G. abietina biotypes A and B, without a particular geographical distribution pattern. Forty-six isolates were shown to host GaRV-MS1 according to direct specific RT-PCR screening, and the virus was more common in biotype A than B. Phylogenetic analysis based on 46 partial coat protein (CP) cDNA sequences divided the GaRV-MS1 population into two closely related clades, while RNA-dependent RNA polymerase (RdRp) sequences revealed only one clade. The evolution of the virus appears to mainly occur through purifying selection but also through recombination. Recombination events were detected within alignments of the three complete CP and RdRp sequences of GaRV-MS1. This is the first time that recombination events have been directly identified in fungal partitiviruses and in G. abietina in particular. The results suggest that the population dynamics of GaRV-MS1 do not have a direct impact on the genetic structure of its host, G. abietina, though they might have had an innocuous ancestral relationship. url: https://www.ncbi.nlm.nih.gov/pubmed/25749364/ doi: 10.1016/j.funbio.2014.12.001 id: cord-336560-m5u6ryy9 author: Boudewijns, Robbert title: STAT2 signaling as double-edged sword restricting viral dissemination but driving severe pneumonia in SARS-CoV-2 infected hamsters date: 2020-07-02 words: 5019.0 sentences: 308.0 pages: flesch: 51.0 cache: ./cache/cord-336560-m5u6ryy9.txt txt: ./txt/cord-336560-m5u6ryy9.txt summary: Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. The lack of readily accessible serum markers or the absence of overt disease symptoms in hamsters prompted us to establish a non-invasive means to score for lung infection and SARS-CoV-2 induced lung disease by computed tomography (CT) as used in standard patient care to aid COVID-19 diagnosis with high sensitivity and monitor progression/recovery 7, 33, 35, 36 . Similar as in humans 37 , semiquantitative lung pathology scores were obtained from high-resolution chest micro-CT scans of freebreathing animals 38 The increase in replication of SARS-CoV-2 seen in IL28R-a -/hamsters, on one hand, combined with a tempered inflammatory response and lung injury as compared to WT hamsters, on the other hand, is in line with the role of type III IFN plays during respiratory virus infections, including SARS-CoV-1 53 . abstract: Since the emergence of SARS-CoV-2 causing COVID-19, the world is being shaken to its core with numerous hospitalizations and hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that productive SARS-CoV-2 infection in the lungs of mice is limited and restricted by early type I interferon responses. In contrast, we show that Syrian hamsters are highly permissive to SARS- CoV-2 and develop bronchopneumonia and a strong inflammatory response in the lungs with neutrophil infiltration and edema. Moreover, we identify an exuberant innate immune response as a key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Finally, we assess SARS-CoV- 2-induced lung pathology in hamsters by micro-CT alike used in clinical practice. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients. url: https://doi.org/10.1101/2020.04.23.056838 doi: 10.1101/2020.04.23.056838 id: cord-265508-t1nfyzf5 author: Boursnell, M.E.G. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B date: 1984-08-31 words: 2130.0 sentences: 125.0 pages: flesch: 61.0 cache: ./cache/cord-265508-t1nfyzf5.txt txt: ./txt/cord-265508-t1nfyzf5.txt summary: authors: Boursnell, M.E.G.; Brown, T.D.K. title: Sequencing of coronavirus IBV genomic RNA: a 195-base open reading frame encoded by mRNA B Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. The organisation of the messenger RNAs and in vitro translation studies have led to the hypothesis that the 5''-most sequences of each mRNA, which are not present in the next smallest mRNA, contain the complete coding sequences for the major protein product produced by that messenger species (Stern and Kennedy, 1980b; Lai et al., 1981) . In this paper we report the nucleotide sequence of a cloned cDNA copy of IBV genomic RNA in the region corresponding to the 5'' end of mRNA B. The region of the IBV sequence presented in this paper contains the 5'' ends, on the viral genome, of mRNAs A and B. abstract: Abstract DNA sequencing of genomic cDNA clones of avian infectious bronchitis virus (IBV) has been carried out. 770 bases have been determined which include genomic sequences spanning the 5' termini of the two smallest mRNAs of the 3'-coterminal “nested” set: mRNA A and mRNA B. This region contains the complete coding sequences for mRNA B which are additional to those present in mRNA A. Two open reading frames are present, predicting proteins of M rs 7500 and 9500. url: https://www.ncbi.nlm.nih.gov/pubmed/6092234/ doi: 10.1016/0378-1119(84)90169-0 id: cord-288093-012ipcdr author: Bouvette, Jonathan title: High-yield production of human Dicer by transfection of human HEK293-EBNA1 cells grown in suspension date: 2018-12-06 words: 7258.0 sentences: 382.0 pages: flesch: 54.0 cache: ./cache/cord-288093-012ipcdr.txt txt: ./txt/cord-288093-012ipcdr.txt summary: Moreover, high-throughput studies have identified additional non-coding RNAs that are likely processed by Dicer [9] as well as several pre-miRNA binding proteins that may regulate its cleavage activity [10] [11] [12] . The structure and activity of the purified Dicer were assessed by size-exclusion chromatography coupled to multi-angle light-scattering and refractive index (SEC-MALS/RI), negative stain transmission electron microscopy (TEM), binding assay and steady-state kinetics. Our kinetic analysis for Dicer cleavage of the pre-let-7a-1 substrate were performed under strict steady state conditions and reveals k cat and K M values that are much higher than previously reported. Moreover, SEC -MALS/RI analysis of a purified Dicer sample stored for 6 months at − 80°C in sucrose/DDM-containing buffer shows that the purified protein remains almost exclusively monomeric ( ≥ 94%), indicating that the protein is intact after long-term storage (Additional file 1: Figure S1 ). abstract: BACKGROUND: Dicer is a 219-kDa protein that plays key roles in gene regulation, particularly as the ribonuclease III enzyme responsible for cleaving precursor miRNA substrates. Its enzymatic activity is highly regulated by protein factors, and this regulation can impact on the levels of miRNAs and modulate the behavior of a cell. To better understand the underlying mechanisms of regulation, detailed enzymatic and structural characterization of Dicer are needed. However, these types of studies generally require several milligrams of recombinant protein, and efficient preparation of such quantities of pure human Dicer remains a challenge. To prepare large quantities of human Dicer, we have optimized transfection in HEK293-6E cells grown in suspension and streamlined a purification procedure. RESULTS: Transfection conditions were first optimized to achieve expression levels between 10 and 18 mg of recombinant Dicer per liter of culture. A three-step purification protocol was then developed that yields 4–9 mg of purified Dicer per liter of culture in a single day. From SEC-MALS/RI analysis and negative stain TEM, we confirmed that the purified protein is monomerically pure ( ≥ 98%) and folds with the characteristic L-shape geometry. Using an electrophoretic mobility shift assay, a dissociation constant (K(d)) of 5 nM was measured for Dicer binding to pre-let-7a-1, in agreement with previous reports. However, when probing the cleavage activity of Dicer for pre-let-7a-1, we measured k(cat) (7.2 ± 0.5 min(− 1)) and K(M) (1.2 ± 0.3 μM) values that are much higher than previously reported due to experimental conditions that better respect the steady-state assumption. CONCLUSIONS: The expression and purification protocols described here provide high yields of monomerically pure and active human Dicer. Cleavage studies of a pre-let-7 substrate with this purified Dicer reveal higher k(cat) and K(M) values than previously reported and support the current view that conformational changes are associated with substrate binding. Large quantities of highly pure Dicer will be valuable for future biochemical, biophysical and structural investigations of this key protein of the miRNA pathway. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12896-018-0485-3) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30522464/ doi: 10.1186/s12896-018-0485-3 id: cord-016796-g4kqqpy1 author: Bramhachari, Pallaval Veera title: Advanced Immunotechnological Methods for Detection and Diagnosis of Viral Infections: Current Applications and Future Challenges date: 2019-11-05 words: 5646.0 sentences: 305.0 pages: flesch: 34.0 cache: ./cache/cord-016796-g4kqqpy1.txt txt: ./txt/cord-016796-g4kqqpy1.txt summary: As a part of modern research on immunotechniques, a diagnostic approach for chronic hepatitis C infection (CHC), detects specific antibody to HCV (anti-HCV) (indirect tests) and assays that can detect, quantify, or characterize components of HCV viral particles, viz. Nonetheless, recent studies on respiratory syncytial virus (RSV) developed Luciferase Immunoprecipitation Systems (LIPS) assay to detect IgG Antibodies against Human RSV G-Glycoprotein. Sensitive and specific detection of Crimean-Congo hemorrhagic fever virus (CCHFV) was developed employing specific IgM and IgG antibodies in human sera using recombinant CCHFV nucleoprotein as antigen in μ-capture and IgG immune complex (IC) ELISA tests (Emmerich et al. A rapid diagnostic platform for colorimetric differential detection of DENV and CHIKV viral infections was recently developed with a possibility to alter clinical diagnosis of acute febrile illnesses in resource-limited settings. This novel antibody demonstrates noteworthy specificity to identify H7N9 virus compared to homemade target-captured ELISA, qRT-PCR, and rapid influenza diagnostic test (RIDT) with high sensitivity (Chang et al. abstract: Diagnosis and identification of viruses is an important component of diagnostic virology laboratory. Although various modes of diagnostic methods are now available at disposal, a vast majority of the diseases across the globe remain undiagnosed. This is largely due to the overlapping undifferentiated set of symptoms across myriad set of RNA and DNA viral diseases. As such, it becomes critical to take into consideration several factors for viral diagnosis ranging from the type and quality of specimen collected, time of specimen collection, mode of transport, accuracy, specificity, sensitivity, and the type of diagnostic method used. This chapter broadly emphasizes various methods on diagnostic virology ranging from the classical methods of diagnosis to the most recently developed molecular methods of detection of virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121190/ doi: 10.1007/978-981-15-1045-8_17 id: cord-002312-jyk7f8hz author: Branton, W. G. title: Brain microbiota disruption within inflammatory demyelinating lesions in multiple sclerosis date: 2016-11-28 words: 4611.0 sentences: 231.0 pages: flesch: 41.0 cache: ./cache/cord-002312-jyk7f8hz.txt txt: ./txt/cord-002312-jyk7f8hz.txt summary: Massively parallel (deep) sequencing (RNAseq) of total RNA permitted analysis of all RNA sequences in MS (n = 6) and nonMS (n = 6) white matter samples, revealing that bacterial RNA (ribosomal and non-ribosomal) sequences were detected in all nonMS and MS brain specimens, including MS patients with relapsing-remitting disease (receiving disease modifying therapy) (RR-MS, n = 3) and progressive (untreated) MS (P-MS; n = 3) ( Fig. 2A) . The current study shows the presence of bacterial RNA and DNA sequences and proteins in human brain which are disrupted in conjunction with inflammatory demyelination in patients with MS. The present studies revealed the ratio of bacterium-encoded 16s rDNA to rRNA in matched brain samples to be ~1:2 in both white matter (and cortex, data not shown) with bacterial numbers of 1200-1400 genomes/cm 3 suggesting both bacterial burden and replication were low compared to active pathogenic infections in other tissues. abstract: Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age- and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients. Both clinical groups displayed 1,200–1,400 bacterial genomes/cm(3) and low bacterial rRNA:rDNA ratios in WM. RNAseq analyses showed a predominance of Proteobacteria in progressive MS patients’ WM, associated with increased inflammatory gene expression, relative to a broader range of bacterial phyla in relapsing-remitting MS patients’ WM. Although bacterial peptidoglycan (PGN) and RNA polymerase beta subunit immunoreactivities were observed in all patients, PGN immunodetection was correlated with demyelination and neuroinflammation in MS brains. Principal component analysis revealed that demyelination, PGN and inflammatory gene expression accounted for 86% of the observed variance. Thus, inflammatory demyelination is linked to an organ-specific dysbiosis in MS that could contribute to underlying disease mechanisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5125007/ doi: 10.1038/srep37344 id: cord-000804-0hlj6r10 author: Brauburger, Kristina title: Forty-Five Years of Marburg Virus Research date: 2012-10-01 words: 14922.0 sentences: 730.0 pages: flesch: 45.0 cache: ./cache/cord-000804-0hlj6r10.txt txt: ./txt/cord-000804-0hlj6r10.txt summary: While the ectodomain, which is mainly formed by GP 1 , mediates binding to entry factors and receptors [87] [88] [89] [90] [91] [92] [93] [94] [95] , the transmembrane subunit GP 2 contains the fusion peptide and is presumed to mediate fusion of the viral and the cellular membrane based on similarity to EBOV GP 2 both at the amino acid and structural level [96, 97] . The IFN-inducible antiviral protein tetherin was shown to block the release of VP40-induced virus-like MARV and EBOV particles, suggesting that tetherin might act as a restriction factor for filovirus release [102, 103] . After the nucleocapsid is released into the cytoplasm of the infected cell, transcription and replication of the viral RNA genome takes place (Figure 7 ). Virus-like particles exhibit potential as a pan-filovirus vaccine for both Ebola and Marburg viral infections abstract: In 1967, the first reported filovirus hemorrhagic fever outbreak took place in Germany and the former Yugoslavia. The causative agent that was identified during this outbreak, Marburg virus, is one of the most deadly human pathogens. This article provides a comprehensive overview of our current knowledge about Marburg virus disease ranging from ecology to pathogenesis and molecular biology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3497034/ doi: 10.3390/v4101878 id: cord-013243-1hj5clsw author: Brewer, Gary title: Editorial for “Methods to characterize virus small RNAs and RNA structures” date: 2020-10-16 words: 576.0 sentences: 41.0 pages: flesch: 48.0 cache: ./cache/cord-013243-1hj5clsw.txt txt: ./txt/cord-013243-1hj5clsw.txt summary: title: Editorial for "Methods to characterize virus small RNAs and RNA structures" One of the advantages of this enzymatic approach is that it minimizes problems that can arise upon annealing two complementary RNA strands, e.g., secondary structure within a ssRNA due to selfannealing; and low yields of long dsRNAs. These RNAs can be subsequently modified (e.g., Here, the small molecule dimethyl sulfate (DMS) preferentially methylates unpaired or dynamic adenosine and cytosine residues within a viral RNA genome. Methods for detection and study of virus derived small RNAs produced from the intramolecular base-pairing region of the picornavirus genome A cytoplasmic RNA virus generates functional viral small RNAs and regulates viral IRES activity in mammalian cells Functional analyses of mammalian virus 5''UTR-derived, small RNAs that regulate virus translation From current knowledge to best practice: A primer on Viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7561520/ doi: 10.1016/j.ymeth.2020.10.007 id: cord-356013-pl3tmky8 author: Brian, D. A. title: Coronavirus Genome Structure and Replication date: 2005 words: 8382.0 sentences: 446.0 pages: flesch: 53.0 cache: ./cache/cord-356013-pl3tmky8.txt txt: ./txt/cord-356013-pl3tmky8.txt summary: In addition to the SARS coronavirus (treated separately elsewhere in this volume), the complete genome sequences of six species in the coronavirus genus of the coronavirus family [avian infectious bronchitis virus-Beaudette strain (IBV-Beaudette), bovine coronavirus-ENT strain (BCoV-ENT), human coronavirus-229E strain (HCoV-229E), murine hepatitis virus-A59 strain (MHV-A59), porcine transmissible gastroenteritis-Purdue 115 strain (TGEV-Purdue 115), and porcine epidemic diarrhea virus-CV777 strain (PEDV-CV777)] have now been reported. With regard to the 5 0 UTR it is known that the 5 0 -terminal sequence is required for DI RNA replication ) and at least two stem-loops (stem-loops III and IV in Fig. 4 ) function as higher-order cis-acting signaling elements (Raman et al. cis-Acting sequences required for coronavirus infectious bronchitis virus defective-RNA replication and packaging abstract: In addition to the SARS coronavirus (treated separately elsewhere in this volume), the complete genome sequences of six species in the coronavirus genus of the coronavirus family [avian infectious bronchitis virus-Beaudette strain (IBV-Beaudette), bovine coronavirus-ENT strain (BCoV-ENT), human coronavirus-229E strain (HCoV-229E), murine hepatitis virus-A59 strain (MHV-A59), porcine transmissible gastroenteritis-Purdue 115 strain (TGEV-Purdue 115), and porcine epidemic diarrhea virus-CV777 strain (PEDV-CV777)] have now been reported. Their lengths range from 27,317 nt for HCoV-229E to 31,357 nt for the murine hepatitis virus-A59, establishing the coronavirus genome as the largest known among RNA viruses. The basic organization of the coronavirus genome is shared with other members of the Nidovirus order (the torovirus genus, also in the family Coronaviridae, and members of the family Arteriviridae) in that the nonstructural proteins involved in proteolytic processing, genome replication, and subgenomic mRNA synthesis (transcription) (an estimated 14–16 end products for coronaviruses) are encoded within the 5′-proximal two-thirds of the genome on gene 1 and the (mostly) structural proteins are encoded within the 3′-proximal one-third of the genome (8–9 genes for coronaviruses). Genes for the major structural proteins in all coronaviruses occur in the 5′ to 3′ order as S, E, M, and N. The precise strategy used by coronaviruses for genome replication is not yet known, but many features have been established. This chapter focuses on some of the known features and presents some current questions regarding genome replication strategy, the cis-acting elements necessary for genome replication [as inferred from defective interfering (DI) RNA molecules], the minimum sequence requirements for autonomous replication of an RNA replicon, and the importance of gene order in genome replication. url: https://www.ncbi.nlm.nih.gov/pubmed/15609507/ doi: 10.1007/3-540-26765-4_1 id: cord-254592-wa5il5go author: Brierley, Liam title: Tissue tropism and transmission ecology predict virulence of human RNA viruses date: 2019-11-26 words: 5887.0 sentences: 269.0 pages: flesch: 37.0 cache: ./cache/cord-254592-wa5il5go.txt txt: ./txt/cord-254592-wa5il5go.txt summary: To quantify the effects of the most informative risk factors, averaged partial dependence was extracted from the random forests, describing the marginal predicted probabilities of severe virulence associated with each virus trait (Fig 4, S2 Table) . Predicted probability of classifying virulence as ''severe'' for each of the most informative risk factors in random forest models applied to all known human RNA viruses and zoonotic viruses only (primary tissue tropism, any known neural tropism, any known renal tropism, level of human-to-human transmissibility, primary transmission route, and any known vector-borne transmission). In both classification tree and random forest models, viruses were more likely to be predicted to cause severe disease if they caused systemic infections, had neural or renal tropism, transmitted via direct contact or respiratory routes, or had limited capability to transmit between humans (0 < R 0 � 1). abstract: Novel infectious diseases continue to emerge within human populations. Predictive studies have begun to identify pathogen traits associated with emergence. However, emerging pathogens vary widely in virulence, a key determinant of their ultimate risk to public health. Here, we use structured literature searches to review the virulence of each of the 214 known human-infective RNA virus species. We then use a machine learning framework to determine whether viral virulence can be predicted by ecological traits, including human-to-human transmissibility, transmission routes, tissue tropisms, and host range. Using severity of clinical disease as a measurement of virulence, we identified potential risk factors using predictive classification tree and random forest ensemble models. The random forest approach predicted literature-assigned disease severity of test data with mean accuracy of 89.4% compared to a null accuracy of 74.2%. In addition to viral taxonomy, the ability to cause systemic infection was the strongest predictor of severe disease. Further notable predictors of severe disease included having neural and/or renal tropism, direct contact or respiratory transmission, and limited (0 < R(0) ≤ 1) human-to-human transmissibility. We present a novel, to our knowledge, comparative perspective on the virulence of all currently known human RNA virus species. The risk factors identified may provide novel perspectives in understanding the evolution of virulence and elucidating molecular virulence mechanisms. These risk factors could also improve planning and preparedness in public health strategies as part of a predictive framework for novel human infections. url: https://doi.org/10.1371/journal.pbio.3000206 doi: 10.1371/journal.pbio.3000206 id: cord-332024-jk983q4p author: Briese, Thomas title: Diagnostic System for Rapid and Sensitive Differential Detection of Pathogens date: 2005-02-17 words: 1738.0 sentences: 84.0 pages: flesch: 36.0 cache: ./cache/cord-332024-jk983q4p.txt txt: ./txt/cord-332024-jk983q4p.txt summary: We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. To address the need for sensitive multiplex assays in diagnostic molecular microbiology, we created a polymerase chain reaction (PCR) platform in which microbial gene targets are coded by a library of 64 distinct Masscode tags (Qiagen Masscode technology, Qiagen, Hilden, Germany). Multiplex primer sets were designed to identify up to 22 respiratory pathogens in a single Mass Tag PCR reaction; sensitivity was established by using synthetic DNA and RNA standards as well as titered viral stocks; the utility of Mass Tag PCR was determined in blinded analysis of previously diagnosed clinical specimens. abstract: Naturally emerging and deliberately released pathogens demand new detection strategies to allow early recognition and containment. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples. url: https://www.ncbi.nlm.nih.gov/pubmed/15752453/ doi: 10.3201/eid1102.040492 id: cord-350836-1enteev7 author: Brisse, Morgan title: Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5 date: 2019-07-17 words: 16347.0 sentences: 859.0 pages: flesch: 47.0 cache: ./cache/cord-350836-1enteev7.txt txt: ./txt/cord-350836-1enteev7.txt summary: RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. For the former, siRNA-mediated knock-down (110, 111) , cellular knockout (112) and inhibition by viral protein (109, (113) (114) (115) (116) conditions for TRIM25 in multiple cell types have been shown to change RIG-I cellular localization (110) and to negatively affect RIG-I K63 ubiquitination, association with MAVS and IFN signaling [when the constitutively active RIG-I CARD domain was overexpressed (109, (112) (113) (114) (115) (116) or during viral infection (109, 111, 114) ]. abstract: RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. While RIG-I and MDA5 share many genetic, structural and functional similarities, there is increasing evidence that they can have significantly different strategies to recognize different pathogens, PAMPs, and in different host species. This review article discusses the similarities and differences between RIG-I and MDA5 from multiple perspectives, including their structures, evolution and functional relationships with other cellular proteins, their differential mechanisms of distinguishing between host and viral dsRNAs and interactions with host and viral protein factors, and their immunogenic signaling. A comprehensive comparative analysis can help inform future studies of RIG-I and MDA5 in order to fully understand their functions in order to optimize potential therapeutic approaches targeting them. url: https://doi.org/10.3389/fimmu.2019.01586 doi: 10.3389/fimmu.2019.01586 id: cord-010045-eqzs01au author: Britton, P. title: Sequence of the nucleoprotein gene from a virulent British field isolate of transmissible gastroenteritis virus and its expression in Saccharomyces cerevisiae date: 2006-10-27 words: 6185.0 sentences: 353.0 pages: flesch: 57.0 cache: ./cache/cord-010045-eqzs01au.txt txt: ./txt/cord-010045-eqzs01au.txt summary: Yeast cells containing recombinant plasmids, with the nucleoprotein gene in the correct orientation, produced a polypeptide of M, 47000, identical to the viral product, that reacted with a specific monoclonal antibody. Three recombinant plasmids, shown to contain cDNA inserts of 1.5 kbp and designated pTS13-2, pTS15-1 and pTSi 5-2, were labelled with p^S]-dATP by nick translation and hybridized to glyoxylated TGEV mRNA species separated on 1 % agarose gels as described in Experimentat procedures. The plasmid also contained the smaller 3'' ORF which initiates, in a different reading frame, 6 bp 3'' from the end of the nucleoprotein gene and terminates 166 bp 5'' to the Drall Sma\ combined site between the TGEV cDNA insert and the pUC9 DNA. A recombinant plasmid, pYNGI, was found to contain the TGEV nucleoprotein gene in the correct orientation for expression under the control of the yeast GAL1 promoter. abstract: Subgenomic mRNA from a virulent isolate of porcine transmissible gastroenteritis virus (TGEV) was used to produce cDNA which was sequenced. Two non‐overlapping open reading frames (ORFs) were identified. The largest, encoding a polypeptide of 382 amino acids (relative molecular mass (M(r)) 43 483), was shown to be the viral nucleoprotein gene. The second ORF, found 3’to the larger ORF, encodes a polypeptide of 78 amino acids (M(r) 9068) which has yet to be assigned to a viral product. The nucleoprotein gene was expressed in yeast cells under the control of two types of yeast promoters: the constitutive PGK promoter, and the inducible GAL1 promoter. Yeast cells containing recombinant plasmids, with the nucleoprotein gene in the correct orientation, produced a polypeptide of M, 47000, identical to the viral product, that reacted with a specific monoclonal antibody. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7168467/ doi: 10.1111/j.1365-2958.1988.tb00010.x id: cord-350342-j4p8235a author: Brocato, Rebecca L. title: Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters date: 2020-10-27 words: 5265.0 sentences: 283.0 pages: flesch: 49.0 cache: ./cache/cord-350342-j4p8235a.txt txt: ./txt/cord-350342-j4p8235a.txt summary: All of the SARS-CoV-2-challenged hamsters had detectable viral RNA in pharyngeal swabs at the first time point assayed, 3 dpi, and remained consistent (10 3 to 10 5 molecules of nucleocapsid using a second primer set [N2] per 100 ng RNA) throughout the duration of CyP treatment (Fig. 1C) . Viral RNA and infectious virus were detected in lung tissue from a subset of hamsters collected 13 dpi, on the day of euthanasia of moribund animals (14 to 34 dpi), or after euthanasia at 35 dpi (end of study) ( Fig. 1E and F). Electron microscopy studies were performed on lung sections of SARS-CoV-2infected, CyP-treated hamsters with various lung viral loads (Fig. 1) . Similarly, lung tissue collected at 13 dpi (end of study) indicate comparable levels of viral RNA detected (Fig. 6D ) but significantly reduced infectious virus in Centi-F1 MAb-treated animals (P ϭ 0.0002; unpaired t test) (Fig. 6E) . abstract: Animal models recapitulating human COVID-19 disease, especially severe disease, are urgently needed to understand pathogenesis and to evaluate candidate vaccines and therapeutics. Here, we develop novel severe-disease animal models for COVID-19 involving disruption of adaptive immunity in Syrian hamsters. Cyclophosphamide (CyP) immunosuppressed or RAG2 knockout (KO) hamsters were exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the respiratory route. Both the CyP-treated and RAG2 KO hamsters developed clinical signs of disease that were more severe than those in immunocompetent hamsters, notably weight loss, viral loads, and fatality (RAG2 KO only). Disease was prolonged in transiently immunosuppressed hamsters and was uniformly lethal in RAG2 KO hamsters. We evaluated the protective efficacy of a neutralizing monoclonal antibody and found that pretreatment, even in immunosuppressed animals, limited infection. Our results suggest that functional B and/or T cells are not only important for the clearance of SARS-CoV-2 but also play an early role in protection from acute disease. IMPORTANCE Syrian hamsters are in use as a model of disease caused by SARS-CoV-2. Pathology is pronounced in the upper and lower respiratory tract, and disease signs and endpoints include weight loss and viral RNA and/or infectious virus in swabs and organs (e.g., lungs). However, a high dose of virus is needed to produce disease, and the disease resolves rapidly. Here, we demonstrate that immunosuppressed hamsters are susceptible to low doses of virus and develop more severe and prolonged disease. We demonstrate the efficacy of a novel neutralizing monoclonal antibody using the cyclophosphamide transient suppression model. Furthermore, we demonstrate that RAG2 knockout hamsters develop severe/fatal disease when exposed to SARS-CoV-2. These immunosuppressed hamster models provide researchers with new tools for evaluating therapies and vaccines and understanding COVID-19 pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/32900822/ doi: 10.1128/jvi.01683-20 id: cord-268139-tgpsu4qz author: Brockway, Sarah M. title: Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication date: 2005-09-30 words: 10127.0 sentences: 558.0 pages: flesch: 54.0 cache: ./cache/cord-268139-tgpsu4qz.txt txt: ./txt/cord-268139-tgpsu4qz.txt summary: title: Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication In the current study, a reverse genetic approach was used to define the role of the 28-kDa amino-terminal product (nsp1) of the gene 1 polyprotein during replication of the coronavirus murine hepatitis virus (MHV) in cell culture. To determine whether nsp1 is required for MHV replication and to identify residues critical for protein function, mutant viruses that contained deletions or point mutations within the nsp1-coding region were generated and assayed for defects in viral replication, viral protein expression, protein localization, and RNA synthesis. Mutagenesis of the murine hepatitis virus nsp1-coding region identifies residues important for protein processing, viral RNA synthesis, and viral replication Experiments were next performed to determine if viral gene expression occurred in cells electroporated with RNA for mutants that did not produce infectious virus (VUSB5, VUSB6, nsp1DFL, and nsp1DMid). abstract: Despite ongoing research investigating mechanisms of coronavirus replication, functions of many viral nonstructural proteins (nsps) remain unknown. In the current study, a reverse genetic approach was used to define the role of the 28-kDa amino-terminal product (nsp1) of the gene 1 polyprotein during replication of the coronavirus murine hepatitis virus (MHV) in cell culture. To determine whether nsp1 is required for MHV replication and to identify residues critical for protein function, mutant viruses that contained deletions or point mutations within the nsp1-coding region were generated and assayed for defects in viral replication, viral protein expression, protein localization, and RNA synthesis. The results demonstrated that the carboxy-terminal half of nsp1 (residues K(124) through L(241)) was dispensable for virus replication in culture but was required for efficient proteolytic cleavage of nsp1 from the gene 1 polyprotein and for optimal viral replication. Furthermore, whereas deletion of nsp1 residues amino-terminal to K(124) failed to produce infectious virus, point mutagenesis of the nsp1 amino-terminus allowed recovery of several mutants with altered replication and RNA synthesis. This study identifies nsp1 residues important for protein processing, viral RNA synthesis, and viral replication. url: https://api.elsevier.com/content/article/pii/S0042682205003776 doi: 10.1016/j.virol.2005.06.035 id: cord-103511-31njndob author: Broggi, Achille title: Type III interferons disrupt the lung epithelial barrier upon viral recognition date: 2020-05-05 words: 3886.0 sentences: 283.0 pages: flesch: 61.0 cache: ./cache/cord-103511-31njndob.txt txt: ./txt/cord-103511-31njndob.txt summary: Accordingly, sorted lung resident dendritic cells express 192 high levels of IFN-λ transcript after 5 days of poly (I:C) treatment, in contrast to epithelial cells, 193 alveolar macrophages and monocytes (Fig. 4A) , which, instead, express inflammatory cytokines (Fig. S8A, B) . Moreover, diphtheria toxin (DT)-mediated depletion of 195 CD11c + cells in CD11c-DT receptor (DTR) mice was sufficient to completely abolish IFN-λ 9 transcript and protein upregulation upon 6 days of poly (I:C) treatment (Fig. 4B, C) , while production remained unaltered (Fig. S8C with the response measured in vivo, TLR7 stimulation did not induce IFN production while it 207 induced upregulation of pro-inflammatory cytokines, and intracellular delivery of poly (I:C) induced 208 high levels of IFN-I but not IFN-λ (Fig.4D, Fig. S9A , B). Dendritic cells sorted from Ticam1 -/mice treated with poly (I:C) for six 222 days did not express appreciable levels of IFN-λ transcripts while still produced type I interferons 223 ( Fig. 4E, F) . abstract: Lower respiratory tract infections are a leading cause of mortality driven by infectious agents. RNA viruses such as influenza virus, respiratory syncytial virus and the new pandemic coronavirus SARS-CoV-2 can be highly pathogenic. Clinical and experimental evidence indicate that most severe and lethal cases do not depend on the viral burden and are, instead, characterized by an aberrant immune response. In this work we assessed how the innate immune response contributes to the pathogenesis of RNA virus infections. We demonstrate that type III interferons produced by dendritic cells in the lung in response to viral recognition cause barrier damage and compromise the host tissue tolerance. In particular, type III interferons inhibit tissue repair and lung epithelial cell proliferation, causing susceptibility to lethal bacterial superinfections. Overall, our data give a strong mandate to rethink the pathophysiological roles of this group of interferons and their possible use in the clinical practice against endemic as well as emerging viral infections. url: https://doi.org/10.1101/2020.05.05.077867 doi: 10.1101/2020.05.05.077867 id: cord-278081-tk7vn1v1 author: Brooks, Wesley H. title: Viral Impact in Autoimmune Diseases: Expanding the “X Chromosome–Nucleolus Nexus” Hypothesis date: 2017-11-28 words: 9823.0 sentences: 457.0 pages: flesch: 42.0 cache: ./cache/cord-278081-tk7vn1v1.txt txt: ./txt/cord-278081-tk7vn1v1.txt summary: Here is presented new details to the hypothesis, explaining how the disrupted chromatin can lead to subsequent disruption of the nucleolus, even nucleolar fragmentation, which results in ineffective nucleolar functioning, misfolded RNAs, misassembled or incompletely assembled ribonucleoprotein (RNP) complexes, and stabilization of nucleolar components in autoantigenic conformations. For now there is no direct connection between viruses and the "X chromosome-nucleolus nexus" hypothesis to the increased risk of cancers among autoimmune disease patients but we can consider the induction by viruses of increased polyamine levels and the possible reactivation of X-linked polyamine genes as means by which competition for the cellular methyl donor, SAM, could reduce DNA methylation and open oncogenes for overexpression in proliferation competent cells. A disrupted Barr body could generate an abundance of polyamines and Alu RNA from X-linked genes and elements that further stress and damage the nucleolus, making it very inefficient in its functions, even fragmenting it and possibly leading to cell death. abstract: Viruses are suspected of significant roles in autoimmune diseases but the mechanisms are unclear. We get some insight by considering demands a virus places on host cells. Viruses not only require production of their own proteins, RNA and/or DNA, but also production of additional cellular machinery, such as ribosomes, to handle the increased demands. Since the nucleolus is a major site of RNA processing and ribonucleoprotein assembly, nucleoli are targeted by viruses, directly when viral RNA and proteins enter the nucleolus and indirectly when viruses induce increased expression of cellular polyamine genes. Polyamines are at high levels in nucleoli to assist in RNA folding. The size and activity of nucleoli increase directly with increases in polyamines. Nucleolar expansion due to abnormal increases in polyamines could disrupt nearby chromatin, such as the inactive X chromosome, leading to expression of previously sequestered DNA. Sudden expression of a large concentration of Alu elements from the disrupted inactive X can compete with RNA transcripts containing intronic Alu sequences that normally maintain nucleolar structural integrity. Such disruption of nucleolar activity can lead to misfolded RNAs, misassembled ribonucleoprotein complexes, and fragmentation of the nucleolus. Many autoantigens in lupus are, at least transiently, components of the nucleolus. Considering these effects of viruses, the “X chromosome–nucleolus nexus” hypothesis, which proposed disruption of the inactive X by the nucleolus during stress, is now expanded here to propose subsequent disruption of the nucleolus by previously sequestered Alu elements, which can fragment the nucleolus, leading to generation of autoantigens. url: https://doi.org/10.3389/fimmu.2017.01657 doi: 10.3389/fimmu.2017.01657 id: cord-329041-coryaz2s author: Brown, Ariane J. title: Broad spectrum antiviral remdesivir inhibits human endemic and zoonotic deltacoronaviruses with a highly divergent RNA dependent RNA polymerase date: 2019-09-30 words: 5934.0 sentences: 325.0 pages: flesch: 54.0 cache: ./cache/cord-329041-coryaz2s.txt txt: ./txt/cord-329041-coryaz2s.txt summary: These data further extend the known breadth and antiviral activity of RDV to include both contemporary human and highly divergent zoonotic CoV and potentially enhance our ability to fight future emerging CoV. We previously reported the antiviral activity of RDV against a genetically diverse panel of human endemic, emerging and zoonotic CoV including HCoV-NL63 (alpha 1b), mouse hepatitis virus (MHV, beta 2a), SARS-CoV and related Bat CoVs WIV1 and SHC014 (beta 2b), as well as MERS-CoV and related Bat CoV HKU5 (beta 2c) (Agostini et al., 2018; Sheahan et al., 2017) . Inhibition of viral protease has also been evaluated with lopinavir, a protease inhibitor designed for human immunodeficiency virus, which like chloroquine exerts a moderate antiviral effect on CoV replication (EC 50 values: MERS-CoV 8 μM, SARS-CoV 17.1 μM, HCoV-229E 6.6 μM) (de Wilde et al., 2014) . abstract: Abstract The genetically diverse Orthocoronavirinae (CoV) family is prone to cross species transmission and disease emergence in both humans and livestock. Viruses similar to known epidemic strains circulating in wild and domestic animals further increase the probability of emergence in the future. Currently, there are no approved therapeutics for any human CoV presenting a clear unmet medical need. Remdesivir (RDV, GS-5734) is a monophosphoramidate prodrug of an adenosine analog with potent activity against an array of RNA virus families including Filoviridae, Paramyxoviridae, Pneumoviridae, and Orthocoronavirinae, through the targeting of the viral RNA dependent RNA polymerase (RdRp). We developed multiple assays to further define the breadth of RDV antiviral activity against the CoV family. Here, we show potent antiviral activity of RDV against endemic human CoVs OC43 (HCoV-OC43) and 229E (HCoV-229E) with submicromolar EC50 values. Of known CoVs, the members of the deltacoronavirus genus have the most divergent RdRp as compared to SARS- and MERS-CoV and both avian and porcine members harbor a native residue in the RdRp that confers resistance in beta-CoVs. Nevertheless, RDV is highly efficacious against porcine deltacoronavirus (PDCoV). These data further extend the known breadth and antiviral activity of RDV to include both contemporary human and highly divergent zoonotic CoV and potentially enhance our ability to fight future emerging CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/31233808/ doi: 10.1016/j.antiviral.2019.104541 id: cord-007714-n3omlvfl author: Brown, J. W. S. title: The Role of the Plant Nucleolus in Pre-mRNA Processing date: 2008 words: 7260.0 sentences: 364.0 pages: flesch: 46.0 cache: ./cache/cord-007714-n3omlvfl.txt txt: ./txt/cord-007714-n3omlvfl.txt summary: In recent years, molecular and proteomic approaches have begun to dissect the pathways of ribosomal subunit assembly and transport from the nucleolus and examine the composition of protein complexes and RNPs involved in these processes (Grandi et al. In plants, the best-characterised nuclear bodies are the nucleolus and CBs. The plant nucleolus differs to some extent in organisation and structure from the animal nucleolus, although its major function in rRNA and ribosomal subunit production remains the same Shaw and Brown 2004) . Finally, the Arabidopsis nucleolus contains exon junction complex proteins, involved in linking transcription and splicing to translation, export and mRNA surveillance (Pendle et al. As with other large RNP complexes such as the spliceosome, correct assembly occurs in a regulated and co-ordinated step-wise pathway involving non-ribosome factors and ribosomal proteins required for correct rRNA folding, protein association and ultimately export of the ribosomal subunits through the nuclear pore complex to the cytoplasm (Venema and Tollervey 1999; Fatica and Tollervey 2002; Grannemann and Baserga 2004) . abstract: The nucleolus is a multifunctional compartment of the eukaryotic nucleus. Besides its well-recognised role in transcription and processing of ribosomal RNA and the assembly of ribosomal subunits, the nucleolus has functions in the processing and assembly of a variety of RNPs and is involved in cell cycle control and senescence and as a sensor of stress. Historically, nucleoli have been tenuously linked to the biogenesis and, in particular, export of mRNAs in yeast and mammalian cells. Recently, data from plants have extended the functions in which the plant nucleolus is involved to include transcriptional gene silencing as well as mRNA surveillance and nonsense-mediated decay, and mRNA export. The nucleolus in plants may therefore have important roles in the biogenesis and quality control of mRNAs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121088/ doi: 10.1007/978-3-540-76776-3_16 id: cord-317455-6qx0v28w author: Brown, Paul A. title: Transmission Kinetics and histopathology induced by European Turkey Coronavirus during experimental infection of specific pathogen free turkeys date: 2018-09-10 words: 3562.0 sentences: 174.0 pages: flesch: 52.0 cache: ./cache/cord-317455-6qx0v28w.txt txt: ./txt/cord-317455-6qx0v28w.txt summary: Turkey coronavirus, originally identified in the USA in the 1970s as one of the agents responsible for an acute enteritis named bluecomb (Panigrahy, Naqi, & Hall, 1973; Ritchie, Deshmukh, Larsen, & Pomeroy, 1973) and since with a multifactorial disease known as poult enteritis complex of turkeys (PEC) , has now been detected in most areas where turkeys are farmed Cavanagh et al., 2001; Dea & Tijssen, 1988; Domańska-Blicharz, Seroka, Lisowska, Tomczyk, & Minta, 2010; Martin, Vinco, Cordioli, & Lavazza, 2002; Maurel et al., 2009; Teixeira et al., 2007) , although TCoVs isolated in Europe have been shown to have a different genetic lineage to those isolated in the USA (Brown et al., 2016; Maurel et al., 2011) . At 1-day post-inoculation (dpi), two SPF turkey contacts were introduced into groups 1-4 as sentinels to demonstrate horizontal transmission of infectious virus. They were housed in a negative pressure room, under the same rearing conditions as in Exp 2, with three 11-day-old SPF turkeys introduced as contact-birds at 1 dpi to demonstrate horizontal transmission. abstract: Numerous viruses, mostly in mixed infections, have been associated worldwide with poult enteritis complex (PEC). In 2008 a coronavirus (Fr‐TCoV 080385d) was isolated in France from turkey poults exhibiting clinical signs compatible with this syndrome. In the present study, the median infectious dose (ID (50))(,) transmission kinetics and pathogenicity of Fr‐TCoV were investigated in 10‐day‐old SPF turkeys. Results revealed a titre of 10(4.88) ID (50)/ml with 1 ID (50)/ml being beyond the limit of genome detection using a well‐characterized qRT‐PCR for avian coronaviruses. Horizontal transmission of the virus via the airborne route was not observed however, via the oro‐faecal route this proved to be extremely rapid (one infectious individual infecting another every 2.5 hr) and infectious virus was excreted for at least 6 weeks in several birds. Histological examination of different zones of the intestinal tract of the Fr‐TCoV‐infected turkeys showed that the virus had a preference for the lower part of the intestinal tract with an abundance of viral antigen being present in epithelial cells of the ileum, caecum and bursa of Fabricius. Viral antigen was also detected in dendritic cells, monocytes and macrophages in these areas, which may indicate a potential for Fr‐TCoV to replicate in antigen‐presenting cells. Together these results highlight the importance of good sanitary practices in turkey farms to avoid introducing minute amounts of virus that could suffice to initiate an outbreak, and the need to consider that infected individuals may still be infectious long after a clinical episode, to avoid virus dissemination through the movements of apparently recovered birds. url: https://doi.org/10.1111/tbed.13006 doi: 10.1111/tbed.13006 id: cord-273366-xd84f8ct author: Brownsword, Matthew J. title: Infectious Bronchitis Virus Regulates Cellular Stress Granule Signaling date: 2020-05-14 words: 8910.0 sentences: 520.0 pages: flesch: 47.0 cache: ./cache/cord-273366-xd84f8ct.txt txt: ./txt/cord-273366-xd84f8ct.txt summary: Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. Vero cells were infected with IBV and at the indicated time points, cells were fixed and labelled with anti-dsRNA to detect virus infection and with anti-G3BP1 to detect SG. Following identification of SG in IBV infected cells, the requirement for active virus replication in induction of granules was assessed. At 24 hpi, cells were fixed and labelled with anti-G3BP1 (red) to detect stress granules (SG) and IBV infected cells were detected with an anti-dsRNA antibody (green). Junin virus infection impairs stress-granule formation in Vero cells treated with arsenite via inhibition of eIF2alpha phosphorylation abstract: Viruses must hijack cellular translation machinery to express viral genes. In many cases, this is impeded by cellular stress responses. These stress responses result in the global inhibition of translation and the storage of stalled mRNAs, into RNA-protein aggregates called stress granules. This results in the translational silencing of the majority of mRNAs excluding those beneficial for the cell to resolve the specific stress. For example, the expression of antiviral factors is maintained during viral infection. Here we investigated stress granule regulation by Gammacoronavirus infectious bronchitis virus (IBV), which causes the economically important poultry disease, infectious bronchitis. Interestingly, we found that IBV is able to inhibit multiple cellular stress granule signaling pathways, whilst at the same time, IBV replication also results in the induction of seemingly canonical stress granules in a proportion of infected cells. Moreover, IBV infection uncouples translational repression and stress granule formation and both processes are independent of eIF2α phosphorylation. These results provide novel insights into how IBV modulates cellular translation and antiviral stress signaling. url: https://www.ncbi.nlm.nih.gov/pubmed/32422883/ doi: 10.3390/v12050536 id: cord-302316-raf5rlkq author: Brüssow, Harald title: COVID‐19: From pathogenesis models to the first drug trials date: 2020-06-23 words: 6944.0 sentences: 350.0 pages: flesch: 44.0 cache: ./cache/cord-302316-raf5rlkq.txt txt: ./txt/cord-302316-raf5rlkq.txt summary: US researchers studied the viral and cellular transcriptional response upon infection of cell cultures and in animal models with different respiratory viruses including influenza A virus and SARS-CoV-2. A French study randomizing 181 COVID-19 patients with pneumonia on hydroxychloroquine or placebo, observed, however, no significant effect of treatment on transfer to ICU, mortality, or in the prevention of development of acute respiratory distress syndrome (Mah evas et al., 2020). A total of 86 COVID-19 cases of patients from China with mild/moderate disease were randomized on the antiviral lopinavir (an inhibitor of HIV protease combined with ritonavir, which prolongs the presence of drugs in the body) or the antiviral arbidol (an influenza virus fusion inhibitor only registered in Russia) or in a control group in a 2:2:1 ratio. Effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection: a randomized clinical trial abstract: The number of people infected with SARS‐CoV‐2, and sadly dying from COVID‐19, has exploded, and so the amount of literature on the novel coronavirus and the disease it causes has increased proportionately. The case numbers in some countries are beyond the epidemic peak, but the uncertainty about a second wave keeps politicians and societies under pressure. Appropriate decision‐making and winning support from the population depends on precise scientific information rather than leaving the field to scaremongers of all proveniences. This mini‐review is an update of earlier reports (Brüssow, Microb Biotechnol 2020a;13:607; Brüssow, Microb Biotechnol 2020b; https://doi.org/10.1111/1751-7915.13592). url: https://doi.org/10.1111/1751-7915.13611 doi: 10.1111/1751-7915.13611 id: cord-255499-31xmue1g author: Bujarski, J.J. title: Recombination date: 2008-07-30 words: 4852.0 sentences: 253.0 pages: flesch: 41.0 cache: ./cache/cord-255499-31xmue1g.txt txt: ./txt/cord-255499-31xmue1g.txt summary: In general, homologous recombination events occur much more often and they are most commonly known as genetic crossing-over that happens in every DNA-based organism during meiosis. The mechanism may involve either homologous crossing-over events or copy-choice processes that rely on template switching by DNA replicase. Aberrant homologous recombination involves crossovers between related RNAs, but the crosses occur at not-corresponding sites leading to sequences insertions or deletions. A double-stranded RNA Pseudomonas phage Phi6 was hypothesized to recombine its RNA based on a copy-choice template switching mechanism, where the crossovers would have occurred inside the virus capsid structures at regions with almost no sequence similarity. In some cases, the base pairing between a partial nascent strand and the acceptor template can lead to the appearance of the rearranged regions in DI RNAs. In addition to rearranged DI RNAs, some RNA viruses accumulate defective RNAs due to a single internal deletion in the genomic RNA of the helper virus. abstract: Genetic recombination of viruses is a commonly found phenomenon in both DNA and RNA viruses. By exchanging of fragments of genetic material viruses gain important means leading to both variability and also to the repair of their genome. Biochemically, the processes of DNA and RNA recombination are different reflecting the specifics of DNA versus RNA replication as well as their use inside the cell. A variety of recombination mechanisms are discussed and illustrated by examples taken from specific viral species. url: https://api.elsevier.com/content/article/pii/B9780123744104005458 doi: 10.1016/b978-012374410-4.00545-8 id: cord-008541-0u2fatbg author: Bujarski, Jozef J. title: Molecular Studies of Genetic RNA–RNA Recombination in Brome Mosaic Virus date: 2008-02-28 words: 6347.0 sentences: 356.0 pages: flesch: 49.0 cache: ./cache/cord-008541-0u2fatbg.txt txt: ./txt/cord-008541-0u2fatbg.txt summary: The idea was to develop an infectious RNA3 molecule stable in infection with a possibility of inserting sequences of interest and studying their recombinational activity. This indicated that progeny recombinants easily accumulated, because they easily outcompeted their parental RNAs. Figure 3 shows that all legitimate crossover events occurred within the long (197-to 220-nt) 3'' region of M4 or DM4 (homologous among three BMV RNA components) and the corresponding part of either wt RNAl or wt RNA2. The recombination activity between pairs of these mutants was determined by coinoculation rearrangements was tested by inserting long palindromic sequences into RNA3 molecules (Section IV,D). The sequence of the inserted region and the presence of a marker mutation a t the 3'' end indicated that B x 4 might have been formed through rearrangements between two mutant B RNA3 molecules. abstract: It is well known that DNA-based organisms rearrange and repair their genomic DNA through recombination processes, and that these rearrangements serve as a powerful source of variability and adaptation for these organisms. In RNA viruses' genetic recombination is defined as any process leading to the exchange of information between viral RNAs. There are two types of recombination events: legitimate and illegitimate. While legitimate (homologous) recombination occurs between closely related sequences at corresponding positions, illegitimate (nonhomologous) recombination could happen at any position among the unrelated RNA molecules. In order to differentiate between the symmetrical and asymmetrical homologous crosses, Lai defined the former as homologous recombination and the latter as aberrant homologous recombination. This chapter uses brome mosaic virus (BMV), a multicomponent plant RNA virus, as an example to discuss the progress in studying the mechanism of genetic recombination in positive-stranded RNA viruses. Studies described in this chapter summarize the molecular approaches used to increase the frequency of recombination among BMV RNA segments and, more importantly, to target the sites of crossovers to specific BMV RNA regions. It demonstrates that the latter can be accomplished by introducing local complementarities to the recombining substrates. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131656/ doi: 10.1016/s0065-3527(08)60051-2 id: cord-337361-salby0fu author: Bujarski, Jozef J. title: Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives date: 2013-03-26 words: 6863.0 sentences: 335.0 pages: flesch: 39.0 cache: ./cache/cord-337361-salby0fu.txt txt: ./txt/cord-337361-salby0fu.txt summary: In some viruses, the frequency of homologous crossing-over is very high and practically every replicated viral RNA molecule can be considered as chimerical in nature, as we have demonstrated for brome mosaic virus (BMV) RNAs (Urbanowicz et al., 2005) . The generally accepted mechanism of RNA recombination is currently explained by a copy-choice model where the viral RNA polymerase (RdRp) complex in mRNA viruses [reverse transcriptase (RT) in retroviruses] changes templates during synthesis of the nascent strand (Galetto et al., 2006) . Among the factors known to promote replicase to switch are sequence homologies between recombination substrates along with secondary structures at the crossover sites, as demonstrated with the BMV and other systems (Figlerowicz and Bujarski, 1998; Nagy et al., 1999b) . Comparison among three plant RNA virus replication systems (TBSV, BMV, and dianthoviruses) reveals general patterns within the stepwise process of viral replicase complex assembly which requires concerted involvement of protein-protein, RNA-protein, and protein-lipid interactions (Mine and Okuno, 2012) . abstract: RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA–RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA–RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented. url: https://www.ncbi.nlm.nih.gov/pubmed/23533000/ doi: 10.3389/fpls.2013.00068 id: cord-016309-6mw8okmt author: Bule, Mohammed title: Antivirals: Past, Present and Future date: 2019-06-06 words: 8200.0 sentences: 405.0 pages: flesch: 36.0 cache: ./cache/cord-016309-6mw8okmt.txt txt: ./txt/cord-016309-6mw8okmt.txt summary: Those included usage restricted to a single virus and specific animal species, problems with high spectrum activity and low cytotoxicity, high costs of development of new chemical compounds and absence of rapid diagnostic techniques allowing prompt use of a specific antiviral agent in the course of an acute infection (Rollinson 1992a, b) . Nevertheless, several licensed human antiviral agents are being used with cascade principle for treatment of animal diseases (e.g. acyclovir, idoxuridine and trifluridine against feline herpesvirus-1 ocular infection in cats) (Thiry et al. The discovery of PAA (Fig. 22.4) as an antiviral drug gave rise to intense research on its biological activities, which demonstrated PAA and its derivatives'' ability to inhibit the replication of a number of viruses such as immunodeficiency, hepatitis and herpes viruses. To conclude with, equine herpesvirus type 1 (EHV-1) infection causes outbreak of respiratory and various neurological diseases in horses, against which acyclovir and valacyclovir are the most common drugs, but also IFN targeting IFNGR complex as a key mediator of virus-specific cellular immunity (Poelaert et al. abstract: The uses of antiviral agents are increasing in the new era along with the development of vaccines for the effective control of viral diseases. The main aims of antiviral agents are to minimize harm to the host system and eradicate deadly viral diseases. However, the replications of viruses in host system represent a massive therapeutic challenge than bacteria and fungi. Antiviral drugs not just penetrate to disrupt the virus’ cellular divisions but also have a negative impact on normal physiological pathways in the host. Due to these issues, antiviral agents have a narrow therapeutic index than antibacterial drugs. Nephrotoxicity is the main adverse reaction of antiviral drugs in human and animals. In this chapter, we summarize the antiviral agents’ past, present and future perspectives with the main focus on the brief history of antiviral in animals, miscellaneous drugs, natural products, herbal and repurposing drugs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120554/ doi: 10.1007/978-981-13-9073-9_22 id: cord-292673-00s3wgem author: Buonaguro, Luigi title: SARS-CoV-2 RNA polymerase as target for antiviral therapy date: 2020-05-05 words: 2062.0 sentences: 120.0 pages: flesch: 50.0 cache: ./cache/cord-292673-00s3wgem.txt txt: ./txt/cord-292673-00s3wgem.txt summary: In the quest of an effective antiviral drug, the most specific target for an RNA virus is the RNA-dependent RNA-polymerase (RdRp) which shows significant differences between positive-sense and negative-sense RNA viruses. Journal of Translational Medicine *Correspondence: l.buonaguro@istitutotumori.na.it 1 Innovative Immunological Models, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale"-IRCCS, Via Mariano Semmola, 52, 80131 Naples, Italy Full list of author information is available at the end of the article SARS-CoV-2 is a positive-sense RNA virus belonging to the Orthocoronavirinae (coronavirus, CoV) family and, in particular, to the genus beta (group 2) together with the other two new human coronaviruses SARS-CoV and MERS-CoV. However, all three of them have been developed for negative-sense RNA viruses which show a significant difference in the RdRp sequence and structure compared to the positive-sense SARS-CoV-2 RNA virus. In conclusion, as for all RNA viruses, the RdRp of the newly identified positive-sense human SARS-CoV-2 RNA virus represents the most optimal target for an antiviral drug. abstract: A new human coronavirus named SARS-CoV-2 was identified in several cases of acute respiratory syndrome in Wuhan, China in December 2019. On March 11 2020, WHO declared the SARS-CoV-2 infection to be a pandemic, based on the involvement of 169 nations. Specific drugs for SARS-CoV-2 are obviously not available. Currently, drugs originally developed for other viruses or parasites are currently in clinical trials based on empiric data. In the quest of an effective antiviral drug, the most specific target for an RNA virus is the RNA-dependent RNA-polymerase (RdRp) which shows significant differences between positive-sense and negative-sense RNA viruses. An accurate evaluation of RdRps from different viruses may guide the development of new drugs or the repositioning of already approved antiviral drugs as treatment of SARS-CoV-2. This can accelerate the containment of the SARS-CoV-2 pandemic and, hopefully, of future pandemics due to other emerging zoonotic RNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32370758/ doi: 10.1186/s12967-020-02355-3 id: cord-327272-fspxett8 author: Buonaguro, Luigi title: Knowledge-based repositioning of the anti-HCV direct antiviral agent Sofosbuvir as SARS-CoV-2 treatment date: 2020-05-12 words: 1432.0 sentences: 83.0 pages: flesch: 46.0 cache: ./cache/cord-327272-fspxett8.txt txt: ./txt/cord-327272-fspxett8.txt summary: The new human coronavirus named SARS-CoV-2 is a positive-sense RNA virus for which no specific drugs are currently available. A knowledge-based analysis strongly suggests a possible repositioning of the anti-HCV direct antiviral agent (DAA) Sofosbuvir as treatment for SARS-CoV-2. The only positive-sense RNA virus, for which a very effective drug targeting specifically the RdRp is available and approved world-wide for clinical use, is hepatitis C virus (HCV). All these sequence and structural modelling evidences strongly support the concept that the SARS-CoV-2 RdRp is much more similar to the one from HCV than the one from negative-sense Influenza and Ebola RNA viruses. Therefore, repositioning of Sofosbuvir (Sovaldi®; Epclusa® by Gilead), the inhibitor of the HCV NS5B RdRp protein, as antiviral in the treatment of the SARS-CoV-2 infection has an extremely high potentiality of success, as recently postulated by others [17] , and is suggested as a potential drug for the treatment of COVID-19 in the very recent EASL-ESCMID position paper [18] . abstract: The new human coronavirus named SARS-CoV-2 is a positive-sense RNA virus for which no specific drugs are currently available. A knowledge-based analysis strongly suggests a possible repositioning of the anti-HCV direct antiviral agent (DAA) Sofosbuvir as treatment for SARS-CoV-2. Indeed, the RNA-dependent RNA-polymerases (RdRp) of the two viruses show high sequence and structural homology, supporting the likelihood of binding the Sofosbuvir molecule with similar efficiency. Such a repositioning would allow the containment of the SARS-CoV-2 pandemic and limit the progression of disease to potentially deadly COVID19. url: https://doi.org/10.1186/s13027-020-00302-x doi: 10.1186/s13027-020-00302-x id: cord-312392-8zxl48af author: Buonavoglia, Canio title: Canine Coronavirus Highly Pathogenic for Dogs date: 2006-03-17 words: 1169.0 sentences: 67.0 pages: flesch: 53.0 cache: ./cache/cord-312392-8zxl48af.txt txt: ./txt/cord-312392-8zxl48af.txt summary: We report an outbreak of fatal disease in puppies caused by a pathogenic variant of CCoV that was isolated from organs with severe lesions. NSP 3b (22 aa) was 49 aa shorter than expected because of a 38-nucleotide deletion and a frame shift mutation in the downstream sequence that introduced To confirm the pathogenic potential of strain CB/05, we experimentally infected two 6-month-old dogs (authorization no. Experimental infection of dogs with the virus isolate resulted in a severe systemic disease that mimicked the clinical symptoms observed in the outbreak. Epidemiologic studies are required to determine whether the pantropic CCoV strain is a new coronavirus variant emerging in canine populations or a widespread infectious agent of dogs that usually goes undetected. Detection of a group 2 coronavirus in dogs with canine infectious respiratory disease Genotype-specific fluorogenic RT-PCR assays for the detection and quantitation of canine coronavirus type I and type II RNA in faecal samples of dogs abstract: Canine coronavirus (CCoV) is usually responsible for mild, self-limiting infections restricted to the enteric tract. We report an outbreak of fatal disease in puppies caused by a pathogenic variant of CCoV that was isolated from organs with severe lesions. url: https://www.ncbi.nlm.nih.gov/pubmed/16704791/ doi: 10.3201/eid1203.050839 id: cord-259710-qrht9tq3 author: Burimuah, Vitus title: Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana date: 2020-10-27 words: 3538.0 sentences: 212.0 pages: flesch: 59.0 cache: ./cache/cord-259710-qrht9tq3.txt txt: ./txt/cord-259710-qrht9tq3.txt summary: title: Molecular-based cross-species evaluation of bovine coronavirus infection in cattle, sheep and goats in Ghana Conclusions: Given that Ghana predominantly practices the extensive and semi-intensive systems of animal rearing, our study highlights the potential for spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species. In this study, we employed a molecular-based detection method to investigate the presence of BCoVs in rectal samples of cattle, sheep and goats from four major regions in Ghana. In a prior study, we reported a high seroprevalence, cross-species infection and serological determinants of BCoV in cattle, sheep and goats in Ghana [19] . In this study, we sought to investigate the presence of BCoVs in rectal samples of cattle, sheep and goats from four major regions in Ghana using molecular-based detection method. abstract: BACKGROUND: Apart from the huge worldwide economic losses often occasioned by bovine coronavirus (BCoV) to the livestock industry, particularly with respect to cattle rearing, continuous surveillance of the virus in cattle and small ruminants is essential in monitoring variations in the virus that could enhance host switching. In this study, we collected rectal swabs from a total of 1,498 cattle, sheep and goats. BCoV detection was based on reverse transcriptase polymerase chain reaction. Sanger sequencing of the partial RNA-dependent RNA polymerase (RdRp) region for postive samples were done and nucleotide sequences were compared with homologous sequences from the GenBank. RESULTS: The study reports a BCoV prevalence of 0.3%, consisting of 4 positive cases; 3 goats and 1 cattle. Less than 10% of all the animals sampled showed clinical signs such as diarrhea and respiratory distress except for high temperature which occurred in > 1000 of the animals. However, none of the 4 BCoV positive animals manifested any clinical signs of the infection at the time of sample collection. Bayesian majority-rule cladogram comparing partial and full length BCoV RdRp genes obtained in the study to data from the GenBank revealed that the sequences obtained from this study formed one large monophyletic group with those from different species and countries. The goat sequences were similar to each other and clustered within the same clade. No major variations were thus observed between our isolates and those from elsewhere. CONCLUSIONS: Given that Ghana predominantly practices the extensive and semi-intensive systems of animal rearing, our study highlights the potential for spillover of BCoV to small ruminants in settings with mixed husbandry and limited separation between species. url: https://doi.org/10.1186/s12917-020-02606-x doi: 10.1186/s12917-020-02606-x id: cord-262776-6k7tcgfs author: Burnouf, Thierry title: Assessment of the viral safety of antivenoms fractionated from equine plasma date: 2004-09-30 words: 8211.0 sentences: 417.0 pages: flesch: 43.0 cache: ./cache/cord-262776-6k7tcgfs.txt txt: ./txt/cord-262776-6k7tcgfs.txt summary: Analysis of production parameters indicate that acid pH treatments and caprylic acid precipitations, which have been validated for the manufacture of some human IgG products, appear to provide the best potential for viral inactivation of antivenoms. Among those, caprylic acid and low pH treatments, both of which are commonly used also for the purification of antivenom IgG, have been shown to contribute to the viral safety of human plasma IgG products as described below. It should be kept in mind that treatment of whole plasma or crude fractions, as is the case for equine antivenoms production, may lead to lower rate and kinetics of viral inactivation, due to the high endogenous lipid content, as found in a study that evaluated the virucidal effect of sodium oleate [85] . However, a comparison with validated manufacturing processes used for human IgG clearly indicates that at least two widely used antivenom production steps, caprylic acid treatment and low-pH incubation, are likely to contribute in a robust manner to viral safety, at least against enveloped viruses. abstract: Abstract Antivenoms are preparations of intact or fragmented (F(ab′)2 or Fab) immunoglobulin G (IgG) used in human medicine to treat the severe envenomings resulting from the bites and stings of various animals, such as snakes, spiders, scorpions, or marine animals, or from the contact with poisonous plants. They are obtained by fractionating plasma collected from immunized horses or, less frequently, sheep. Manufacturing processes usually include pepsin digestion at acid pH, papain digestion, ammonium sulphate precipitation, caprylic acid precipitation, heat coagulation and/or chromatography. Most production processes do not have deliberately introduced viral inactivation or removal treatments, but antivenoms have never been found to transmit viruses to humans. Nevertheless, the recent examples of zoonotic diseases highlight the need to perform a careful assessment of the viral safety of antivenoms. This paper reviews the characteristics of equine viruses of antivenoms and discusses the potential of some manufacturing steps to avoid risks of viral contamination. Analysis of production parameters indicate that acid pH treatments and caprylic acid precipitations, which have been validated for the manufacture of some human IgG products, appear to provide the best potential for viral inactivation of antivenoms. As many manufacturers of antivenoms located in developing countries lack the resources to conduct formal viral validation studies, it is hoped that this review will help in the scientific understanding of the viral safety factors of antivenoms, in the controlled implementation of the manufacturing steps with expected impact on viral safety, and in the overall reinforcement of good manufacturing practices of these essential therapeutic products. url: https://www.sciencedirect.com/science/article/pii/S1045105604000223 doi: 10.1016/j.biologicals.2004.07.001 id: cord-355913-fhvt1ht1 author: Burrell, Christopher J. title: Virus Replication date: 2016-11-11 words: 9861.0 sentences: 405.0 pages: flesch: 42.0 cache: ./cache/cord-355913-fhvt1ht1.txt txt: ./txt/cord-355913-fhvt1ht1.txt summary: Little is known about what determines whether a given picornavirus positive-sense RNA molecule will be directed (1) to a replication complex (a structure bound to smooth endoplasmic reticulum), where it serves as template for transcription by RNA-dependent RNA polymerase into negative-sense RNA, or (2) to a ribosome, where it serves as mRNA for translation into protein, or (3) to a procapsid, with which it associates to form a virion. In the case of positive-sense single-stranded RNA viruses, the incoming RNA genome can bind directly to ribosomes and be translated in full or in part without the need for any prior transcription; all other forms of incoming viral RNA must first be transcribed to produce mRNA, in order to begin the process of expression of the infecting viral genome. abstract: Understanding the molecular events accompanying virus replication is essential for the proper understanding and control of all virus diseases. The virus replication cycle generates new viral genomes and proteins in sufficient quantities to ensure propagation of the viral genome; this requires that the extracellular viral genome is protected from enzymatic degradation and can be introduced into further target cells for further rounds of replication. The initial recognition between virus and host is more complex than originally supposed and may involve more than one cellular receptor. A critical first intracellular step is the generation of viral mRNA by one of a limited number of strategies first described by David Baltimore. Lacking ribosomes, viruses have no means of producing protein and are reliant on the host cell for protein synthesis. Viral proteins are often modified by host cell glycosylation during or after virus assembly. Temporal regulation of intracellular events is critical in all but the very simplest of viruses, and some form of suppression of the host innate immune response is common to nearly all human viruses. Infected cells often produce non-infectious particles with incomplete genomes, and these defective interfering particles may play a role in pathogenesis. Understanding these processes will open up a range of targets for the development of novel therapies. url: https://api.elsevier.com/content/article/pii/B9780123751560000047 doi: 10.1016/b978-0-12-375156-0.00004-7 id: cord-002015-s3tdllby author: Burton, Aaron S. title: The elusive quest for RNA knots date: 2016-02-01 words: 3536.0 sentences: 187.0 pages: flesch: 53.0 cache: ./cache/cord-002015-s3tdllby.txt txt: ./txt/cord-002015-s3tdllby.txt summary: 2, 3 It is therefore a remarkable fact that the statistical incidence of topological entanglement in biomolecules such as proteins and DNA filaments, which are both long and compact, is substantially smaller than expected for general models of equilibrated polymers with equivalent length and packing conditions. It is accordingly plausible, as remarked by Levinthal in more general contexts, 7,8 that protein sequences have evolved to encode not only the thermodynamically-stable native fold, but also the sequence of steps leading to the native structure formation so to minimize the incidence of misfolded states, including knotted ones which would be very challenging to backtrack. It is possible that the sequence of naturally-occurring RNAs, some of which need to be efficiently translocated through biological pores, have evolved to harness folding kinetics and thermodynamics so as to minimize the incidence of various forms of selfentanglement, including knots, in their native structures. abstract: Physical entanglement, and particularly knots arise spontaneously in equilibrated polymers that are sufficiently long and densely packed. Biopolymers are no exceptions: knots have long been known to occur in proteins as well as in encapsidated viral DNA. The rapidly growing number of RNA structures has recently made it possible to investigate the incidence of physical knots in this type of biomolecule, too. Strikingly, no knots have been found to date in the known RNA structures. In this Point of View Article we discuss the absence of knots in currently available RNAs and consider the reasons why knots in RNA have not yet been found, despite the expectation that they should exist in Nature. We conclude by singling out a number of RNA sequences that, based on the properties of their predicted secondary structures, are good candidates for knotted RNAs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829277/ doi: 10.1080/15476286.2015.1132069 id: cord-000981-6vloa2w3 author: Bálint, Zoltán title: Double-Stranded RNA Attenuates the Barrier Function of Human Pulmonary Artery Endothelial Cells date: 2013-06-03 words: 6086.0 sentences: 480.0 pages: flesch: 56.0 cache: ./cache/cord-000981-6vloa2w3.txt txt: ./txt/cord-000981-6vloa2w3.txt summary: The effect of natural and synthetic double-stranded RNA (dsRNA) on hPAECs was investigated using trans-endothelial electric resistance, molecule trafficking, calcium (Ca(2+)) homeostasis, gene expression and proliferation studies. The cells were stimulated with 100 mM histamine or 15 mM 2,5-Di-t-butyl-1,4-benzohydroquinone (BHQ: selective SERCA blocker) in the presence and absence of extracellular Ca 2+ , after incubation for 24 h with 25 mg/mL Poly I:C, 25 mg/mL dsRNA, 2.5 mg/mL L-DNA, 2.5 mg/mL total RNA or control solution. Double-stranded RNA (dsRNA) or its synthetic analogue (Poly I:C) significantly decreased the electric resistance and increased the permeability of the confluent human pulmonary artery endothelial (hPAEC) monolayer as shown on Figure 1 . Altogether, these data suggest that synthetic dsRNA treatment alters the function of SERCA, which inhibits cell proliferation by inducing G1 arrest in the hPAECs and contributing to endothelial dysfunction. abstract: Circulating RNA may result from excessive cell damage or acute viral infection and can interact with vascular endothelial cells. Despite the obvious clinical implications associated with the presence of circulating RNA, its pathological effects on endothelial cells and the governing molecular mechanisms are still not fully elucidated. We analyzed the effects of double stranded RNA on primary human pulmonary artery endothelial cells (hPAECs). The effect of natural and synthetic double-stranded RNA (dsRNA) on hPAECs was investigated using trans-endothelial electric resistance, molecule trafficking, calcium (Ca(2+)) homeostasis, gene expression and proliferation studies. Furthermore, the morphology and mechanical changes of the cells caused by synthetic dsRNA was followed by in-situ atomic force microscopy, by vascular-endothelial cadherin and F-actin staining. Our results indicated that exposure of hPAECs to synthetic dsRNA led to functional deficits. This was reflected by morphological and mechanical changes and an increase in the permeability of the endothelial monolayer. hPAECs treated with synthetic dsRNA accumulated in the G1 phase of the cell cycle. Additionally, the proliferation rate of the cells in the presence of synthetic dsRNA was significantly decreased. Furthermore, we found that natural and synthetic dsRNA modulated Ca(2+) signaling in hPAECs by inhibiting the sarco-endoplasmic Ca(2+)-ATPase (SERCA) which is involved in the regulation of the intracellular Ca(2+) homeostasis and thus cell growth. Even upon synthetic dsRNA stimulation silencing of SERCA3 preserved the endothelial monolayer integrity. Our data identify novel mechanisms by which dsRNA can disrupt endothelial barrier function and these may be relevant in inflammatory processes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670875/ doi: 10.1371/journal.pone.0063776 id: cord-287372-ya5uvoki author: Böszörményi, Kinga P. title: Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques date: 2020-11-05 words: 3973.0 sentences: 249.0 pages: flesch: 58.0 cache: ./cache/cord-287372-ya5uvoki.txt txt: ./txt/cord-287372-ya5uvoki.txt summary: This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. Rhesus macaques have also been applied 116 in COVID-19 pathogenesis studies [22, 24, 32, 33] , and to test the efficacy of remdesivir in the 117 treatment of SARS-CoV-2 infection [34] . we compared SARS-CoV-2 replication in rhesus and cynomolgus macaque species and 129 monitored signs of COVID-19-like disease symptoms for three weeks after infection. The animals from this study were not 342 euthanized to be able to perform re-infection studies or to monitor them for late clinical signs, 343 or co-morbidities related to We conclude that the course of SARS-CoV-2 infection of both macaque species is highly 345 similar, indicating that they are equally suitable models to test vaccines and antivirals in a 346 preclinical setting for safety and efficacy. abstract: SARS-CoV-2 is a coronavirus that sparked the current COVID-19 pandemic. To stop the shattering effect of COVID-19, effective and safe vaccines, and antiviral therapies are urgently needed. To facilitate the preclinical evaluation of intervention approaches, relevant animal models need to be developed and validated. Rhesus macaques (Macaca mulatta) and cynomolgus macaques (Macaca fascicularis) are widely used in biomedical research and serve as models for SARS-CoV-2 infection. However, differences in study design make it difficult to compare and understand potential species-related differences. Here, we directly compared the course of SARS-CoV-2 infection in the two genetically closely-related macaque species. After inoculation with a low passage SARS-CoV-2 isolate, clinical, virological, and immunological characteristics were monitored. Both species showed slightly elevated body temperatures in the first days after exposure while a decrease in physical activity was only observed in the rhesus macaques and not in cynomolgus macaques. The virus was quantified in tracheal, nasal, and anal swabs, and in blood samples by qRT-PCR, and showed high similarity between the two species. Immunoglobulins were detected by various enzyme-linked immunosorbent assays (ELISAs) and showed seroconversion in all animals by day 10 post-infection. The cytokine responses were highly comparable between species and computed tomography (CT) imaging revealed pulmonary lesions in all animals. Consequently, we concluded that both rhesus and cynomolgus macaques represent valid models for evaluation of COVID-19 vaccine and antiviral candidates in a preclinical setting. Author summary SARS-CoV-2 infection can have a wide range of symptoms. It can cause asymptomatic or mild disease, but can also have a severe, potentially deadly outcome. Vaccines and antivirals will therefore be crucial in fighting the current COVID-19 pandemic. For testing these prophylactic and therapeutic treatments, and investigating the progression of infection and disease development, animal models play an essential role. In this study, we compare the course of SARS-CoV-2 infection in rhesus and cynomolgus macaques. Both species showed moderate disease symptoms as shown by pulmonary lesions by CT imaging. Shedding of infectious virus from the respiratory system was also documented. This study provides a detailed description of the pathogenesis of a low-passage SARS-CoV-2 isolate in two macaque models and suggests that both species represent an equally good model in research for both COVID-19 prophylactic and therapeutic treatments. url: https://doi.org/10.1101/2020.11.05.369413 doi: 10.1101/2020.11.05.369413 id: cord-279346-7del8d2p author: Callendret, Benoît title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS date: 2007-07-05 words: 10731.0 sentences: 471.0 pages: flesch: 49.0 cache: ./cache/cord-279346-7del8d2p.txt txt: ./txt/cord-279346-7del8d2p.txt summary: title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. The influence of SS, MPMV-CTE or WPRE on expression of S protein in transfected cells and on induction of a protective SARS-CoV-specific immunity in mice after naked DNA immunization are compared. abstract: The SARS-CoV spike glycoprotein (S) is the main target of the protective immune response in humans and animal models of SARS. Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). The presence of both splice sites and WPRE markedly improved the immunogenicity of S-based DNA vaccines against SARS. Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. Our observations are likely to be useful for the construction of plasmid and viral vectors designed for optimal expression of intronless genes derived from cytoplasmic RNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17331558/ doi: 10.1016/j.virol.2007.01.012 id: cord-293651-96cmduez author: Callison, Scott A. title: Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens date: 2006-08-28 words: 4742.0 sentences: 216.0 pages: flesch: 56.0 cache: ./cache/cord-293651-96cmduez.txt txt: ./txt/cord-293651-96cmduez.txt summary: We also collected a total of 120 tracheal swabs at six different time points from birds experimentally infected with different dosages of IBV and found that, independent of the dose given, the viral load in the trachea plateau at 5 days post-inoculation. Molecular assays use the reverse transcriptase-polymerase chain reaction (RT-PCR) to detect viral RNA directly from a clinical sample or from virus isolated in a laboratory host system. Clinical samples consisting of 229 tracheal swabs from commercial chickens experiencing upper-respiratory disease, submitted as routine diagnostic cases to the Delaware (Georgetown, DE) and Maryland (Salisbury, MD) State Diagnostic Laboratories were tested by the real-time RT-PCR assay, as well as, by virus isolation at those laboratories (Gelb and Jackwood, 1998) . In this report we present the development and evaluation of a real-time Taqman ® -based RT-PCR assay for the detection and quantification of IBV genomic RNA directly from tracheal swabs. abstract: It is important to rapidly differentiate infectious bronchitis virus (IBV) from disease agents like highly pathogenic avian influenza virus and exotic Newcastle disease virus, which can be extremely similar in the early stages of their pathogenesis. In this study, we report the development and testing of a real-time RT-PCR assay using a Taqman(®)-labeled probe for early and rapid detection of IBV. The assay amplifies a 143-bp product in the 5′-UTR of the IBV genome and has a limit of detection and quantification of 100 template copies per reaction. All 15 strains of IBV tested as well as two Turkey coronavirus strains were amplified, whereas none of the other pathogens examined, tested positive. Evaluation of the assay was completed with 1329 tracheal swab samples. A total of 680 samples collected from IBV antibody negative birds were negative for IBV by the real-time RT-PCR assay. We tested 229 tracheal swabs submitted to two different diagnostic laboratories and found 79.04% of the tracheal swabs positive for IBV by real-time RT-PCR, whereas only 27.51% of the samples were positive by virus isolation, which is the reference standard test. We also collected a total of 120 tracheal swabs at six different time points from birds experimentally infected with different dosages of IBV and found that, independent of the dose given, the viral load in the trachea plateau at 5 days post-inoculation. In addition, an inverse relationship between the dose of virus given and the viral load at 14 days post-inoculation was observed. Finally, we tested 300 total tracheal swab samples, from a flock of commercial broilers spray vaccinated for IBV in the field. The percentage of birds infected with the IBV vaccine at 3, 7, and 14 days post-vaccination was 58%, 65%, and 83%, respectively, indicating that only slightly more than half the birds were initially infected then the vaccine was subsequently transmitted to other birds in the flock. This observation is significant because coronaviruses, which have a high mutation rate, can revert to pathogenicity when bird-to-bird transmission occurs. The real-time RT-PCR test described herein can be used to rapidly distinguish IBV from other respiratory pathogens, which is important for control of this highly infectious virus. The test was extremely sensitive and specific, and can be used to quantitate viral genomic RNA in clinical samples. url: https://api.elsevier.com/content/article/pii/S0166093406002734 doi: 10.1016/j.jviromet.2006.07.018 id: cord-354407-zzxjv666 author: Campanacci, Valérie title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein date: 2004-06-07 words: 2338.0 sentences: 137.0 pages: flesch: 60.0 cache: ./cache/cord-354407-zzxjv666.txt txt: ./txt/cord-354407-zzxjv666.txt summary: title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the Nsp9 protein The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive‐stranded RNA virus (SARS‐CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. The crystal structure of the main (or 3CL) protease of transmissible gastroenteritis virus, a related coronavirus, has been determined and was used to construct a model of the SARS-CoV 3CL protease, facilitating future drug design against this important target (Anand et al., 2003) . In the related mouse hepatitis virus, which is a group 2 coronavirus, the SARS-CoV Nsp9 corresponds to a 12 kDa cleavage product (P1a-12) that is found preferentially in the perinuclear region of infected cells, where it co-localizes with other components of the viral replication complex (Bost et al., 2000) . abstract: The aetiologic agent of the recent epidemics of Severe Acute Respiratory Syndrome (SARS) is a positive‐stranded RNA virus (SARS‐CoV) belonging to the Coronaviridae family and its genome differs substantially from those of other known coronaviruses. SARS‐CoV is transmissible mainly by the respiratory route and to date there is no vaccine and no prophylactic or therapeutic treatments against this agent. A SARS‐CoV whole‐genome approach has been developed aimed at determining the crystal structure of all of its proteins or domains. These studies are expected to greatly facilitate drug design. The genomes of coronaviruses are between 27 and 31.5 kbp in length, the largest of the known RNA viruses, and encode 20–30 mature proteins. The functions of many of these polypeptides, including the Nsp9–Nsp10 replicase‐cleavage products, are still unknown. Here, the cloning, Escherichia coli expression, purification and crystallization of the SARS‐CoV Nsp9 protein, the first SARS‐CoV protein to be crystallized, are reported. Nsp9 crystals diffract to 2.8 Å resolution and belong to space group P6(1/5)22, with unit‐cell parameters a = b = 89.7, c = 136.7 Å. With two molecules in the asymmetric unit, the solvent content is 60% (V (M) = 3.1 Å(3) Da(−1)). url: https://www.ncbi.nlm.nih.gov/pubmed/12925794/ doi: 10.1107/s0907444903016779 id: cord-296847-r752bcsu author: Campanini, Giulia title: Human respiratory syncytial virus (hRSV) RNA quantification in nasopharyngeal secretions identifies the hRSV etiologic role in acute respiratory tract infections of hospitalized infants date: 2007-04-23 words: 3045.0 sentences: 163.0 pages: flesch: 55.0 cache: ./cache/cord-296847-r752bcsu.txt txt: ./txt/cord-296847-r752bcsu.txt summary: In the present study, we quantified the hRSV RNA load (both subgroups A and B) in NPAs from hRSV-infected infants by quantitative RT-PCR to investigate the possibility of defining the etiologic role of hRSV in the current ARTI episode from a series of infants admitted to the hospital either with a single hRSV infection or with two or three simultaneous or sequential viral infections including hRSV. NPAs from a series of 253 infants aged less than 1 year and admitted to the hospital in the period November 2005-May 2006 with a diagnosis of ARTI were examined for hRSV as well as other respiratory viruses by DFA, CC, and qualitative RT-PCR, as reported (Rovida et al., 2005) . In addition, 14 infants with multiple simultaneous (coinfections) or sequential (within 30 days) infections in the respiratory tract (including hRSV) were examined prospectively in order to identify the virus responsible for the current ARTI episode. abstract: BACKGROUND: Human respiratory syncytial virus (hRSV) detection in nasopharyngeal aspirates (NPAs) from infants with acute respiratory tract infection (ARTI) does not prove the hRSV etiology of the current ARTI episode. HRSV RNA quantification may help in affording this issue. OBJECTIVES: hRSV was detected by quantitative reverse transcription-PCR in NPAs taken upon admission to hospital and, whenever possible, at discharge and subsequent medical visits. STUDY DESIGN: Prospective study, including 63 infants affected by either hRSV upper or lower ARTI. RESULTS: Based on the kinetics of viral load, hRSV etiology was identified in 25 infants in whom hRSV load dropped from 2.5 × 10(6) upon admission (presence of respiratory symptoms) to 7.5 × 10(2) RNA copies/ml NPA upon discharge (absence of symptoms) after a median time of 5 days, and in 19 infants, in whom hRSV load was determined at admission only, in association with clinical symptoms (2.4 × 10(6) copies/ml). Furthermore, low levels of hRSV RNA (<1 × 10(5) copies/ml NPA) identified 14 patients with non-hRSV ARTI. Finally, in 14 infants with hRSV coinfections or sequential infections, hRSV quantification defined the hRSV role in the current ARTI episode. CONCLUSIONS: hRSV RNA quantification is critical in defining the hRSV role in respiratory infections. url: https://www.ncbi.nlm.nih.gov/pubmed/17452001/ doi: 10.1016/j.jcv.2007.03.009 id: cord-005654-n9u2em10 author: Campbell, David A. title: Apparent discontinuous transcription of Trypanosoma brucei variant surface antigen genes date: 1984 words: 4241.0 sentences: 218.0 pages: flesch: 58.0 cache: ./cache/cord-005654-n9u2em10.txt txt: ./txt/cord-005654-n9u2em10.txt summary: 41 The repeated mini-exon sequence that encodes the first 35 base pairs of all variant surface antigen mRNAs of Trypanosoma brucei directs the synthesis of a discrete I37-nucleotide transcript. 41 The repeated mini-exon sequence that encodes the first 35 base pairs of all variant surface antigen mRNAs of Trypanosoma brucei directs the synthesis of a discrete I37-nucleotide transcript. This result could be interpreted as protection by a short RNA of 137 nucleotides derived from the mini-exon repeats and/or by a longer transcript with a discontinuity at this position in the RNA/DNA duplex. The second method to detect and size transcripts from the mini-exon repeat used Northern blot analysis 31 • For this procedure, total trypanosome RNA was resolved by polyacrylamide gel electrophoresis (PAGE) in denaturing conditions, transferred to GeneScreen membrane 32 and hybridized with a [5/ -32 P]_labelled, synthetic oligonucleotide complementary to positions + 117 to +133. abstract: The repeated mini-exon sequence that encodes the first 35 base pairs of all variant surface antigen mRNAs of Trypanosoma brucei directs the synthesis of a discrete 137-nucleotide transcript. It thus seems that variant surface antigen mRNAs are transcribed discontinuously, and we present two alternative models for how this might occur. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095118/ doi: 10.1038/311350a0 id: cord-023724-5at0rhqk author: Cann, Alan J. title: Infection date: 2015-07-24 words: 14979.0 sentences: 755.0 pages: flesch: 48.0 cache: ./cache/cord-023724-5at0rhqk.txt txt: ./txt/cord-023724-5at0rhqk.txt summary: The problems plant viruses face in initiating infections of host cells have already been described (Chapter 4), as has the fact that no known plant virus employs a specific cellular receptor of the types that animal and bacterial viruses use to attach to cells. There are probably many different mechanisms involved in systemic resistance, but in general terms there is a tendency of these processes to increase local necrosis when substances such as proteases and peroxidases are produced by the plant to destroy the virus and to prevent its spread and subsequent systemic infection. Virus-resistant plants have been created by the production of transgenic plants expressing recombinant virus proteins or nucleic acids which interfere with virus replication without producing the pathogenic consequences of infection, for example: I Virus coat proteins, which have a variety of complex effects, including inhibition of virus uncoating and interference of expression of the virus at the level of RNA ("gene silencing" by "untranslatable" RNAs), I Intact or partial virus replicases which interfere with genome replication, I Antisense RNAs, I Defective virus genomes, I Satellite sequences (see Chapter 8), I Catalytic RNA sequences (ribozymes), I Modified movement proteins. abstract: Virus infection of higher organisms is the cumulative result of all the processes of replication and gene expression described in the previous chapters. Together, these determine the overall course of each infection. Infections range in complexity and duration from a very brief, superficial interaction between the virus and its host to infections that may span the entire life of the host organism, from before birth to its eventual death. A common misconception is that virus infection inevitably results in disease. In reality, the reverse is true—only a small minority of virus infections gives rise to any disease symptoms. This chapter provides an overview of the numerous patterns of virus infection and forms an introduction to the discussion of virus pathogenesis in Chapter 7. Unlike previous and subsequent chapters, this chapter deals primarily with the interaction of viruses with intact organisms rather than with the molecular biologist’s usual concern about the interaction between a virus and the cell. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173531/ doi: 10.1016/b978-0-12-801946-7.00006-7 id: cord-003006-lk2ny1wd author: Cantoni, Diego title: Ebolaviruses: New roles for old proteins date: 2018-05-03 words: 6045.0 sentences: 274.0 pages: flesch: 44.0 cache: ./cache/cord-003006-lk2ny1wd.txt txt: ./txt/cord-003006-lk2ny1wd.txt summary: These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Lastly, VP35 is a suppressor of RNA silencing, functionally equivalent to the human immunodeficiency virus (HIV-1) Trans-activator of transcription (Tat) protein and important for viral evasion of the innate immune response [34] . The authors propose that this mutation is likely a result of EBOV adaptation to the human host, as several viral variants have been seen to increase human cell infectivity while decreasing virus entry in nonhuman primates [83] [84] [85] . In addition, many ebolavirus proteins are seen to interact with immune cells, causing cell activation and/or cell death and facilitating both viral replication and spread (e.g., by recruiting monocytes to infected cells or by increasing vascular leakage) as well as enabling immune evasion (e.g., antibody neutralisation by sGP and by cleaved GP), roles that were previously solely attributed to VP24 and VP35. abstract: In 2014, the world witnessed the largest Ebolavirus outbreak in recorded history. The subsequent humanitarian effort spurred extensive research, significantly enhancing our understanding of ebolavirus replication and pathogenicity. The main functions of each ebolavirus protein have been studied extensively since the discovery of the virus in 1976; however, the recent expansion of ebolavirus research has led to the discovery of new protein functions. These newly discovered roles are revealing new mechanisms of virus replication and pathogenicity, whilst enhancing our understanding of the broad functions of each ebolavirus viral protein (VP). Many of these new functions appear to be unrelated to the protein’s primary function during virus replication. Such new functions range from bystander T-lymphocyte death caused by VP40-secreted exosomes to new roles for VP24 in viral particle formation. This review highlights the newly discovered roles of ebolavirus proteins in order to provide a more encompassing view of ebolavirus replication and pathogenicity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5933699/ doi: 10.1371/journal.pntd.0006349 id: cord-321957-ybtk9cp1 author: Carey, Brian D. title: Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation date: 2020-03-09 words: 6713.0 sentences: 384.0 pages: flesch: 52.0 cache: ./cache/cord-321957-ybtk9cp1.txt txt: ./txt/cord-321957-ybtk9cp1.txt summary: title: Protein Kinase C subtype δ interacts with Venezuelan equine encephalitis virus capsid protein and regulates viral RNA binding through modulation of capsid phosphorylation A virus with capsid phosphorylation sites mutated to alanine (VEEV CPD) displayed a lower genomic copy to pfu ratio than the parental virus; suggesting more efficient viral assembly and more infectious particles being released. These data suggest that cells infected with VEEV CPD output more functional viral particles than VEEV TC-83, potentially due to more efficient viral packaging and this phenotype is due to loss of capsid phosphorylation. Loss of PKCδ through siRNA transfection also resulted in increased capsid viral RNA binding, further solidifying the link between VEEV CPD and PKCδ (Fig 7B) . To determine the impact of VEEV capsid phosphorylation on vRNA binding, we utilized quantitative RNA-IP experiments to probe the interaction between the capsid protein and the vRNA at sites identified as highly enriched, intermediately enriched, and non-enriched by our CLIP-seq studies. abstract: Protein phosphorylation plays an important role during the life cycle of many viruses. Venezuelan equine encephalitis virus (VEEV) capsid protein has recently been shown to be phosphorylated at four residues. Here those studies are extended to determine the kinase responsible for phosphorylation and the importance of capsid phosphorylation during the viral life cycle. Phosphorylation site prediction software suggests that Protein Kinase C (PKC) is responsible for phosphorylation of VEEV capsid. VEEV capsid co-immunoprecipitated with PKCδ, but not other PKC isoforms and siRNA knockdown of PKCδ caused a decrease in viral replication. Furthermore, knockdown of PKCδ by siRNA decreased capsid phosphorylation. A virus with capsid phosphorylation sites mutated to alanine (VEEV CPD) displayed a lower genomic copy to pfu ratio than the parental virus; suggesting more efficient viral assembly and more infectious particles being released. RNA:capsid binding was significantly increased in the mutant virus, confirming these results. Finally, VEEV CPD is attenuated in a mouse model of infection, with mice showing increased survival and decreased clinical signs as compared to mice infected with the parental virus. Collectively our data support a model in which PKCδ mediated capsid phosphorylation regulates viral RNA binding and assembly, significantly impacting viral pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/32150585/ doi: 10.1371/journal.ppat.1008282 id: cord-339782-rybjc58j author: Carmo, Anália title: Clearance and Persistence of SARS‐CoV‐2 RNA in COVID‐19 patients date: 2020-06-02 words: 1844.0 sentences: 106.0 pages: flesch: 52.0 cache: ./cache/cord-339782-rybjc58j.txt txt: ./txt/cord-339782-rybjc58j.txt summary: The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead. In men, the first negative test took 24 ± 9 days (range: 7 -46) and in women it took 25 ± 9 days (range: 9 -44), P>0.05, In an attempt to understand why some patients maintained positive tests for longer, we correlated the detection of SARS-CoV-2 RNA with the host immune response to virus infection. The lack of information regarding persistence of virus RNA and infectivity, disease severity and immune response, supports the current guidance of viral clearance confirmation prior to patient transference out of dedicated COVID-19 wards and of ending isolation in mild illness patients. abstract: COVID‐19 patients may be discharged based on clinical resolution of symptoms, and evidence for viral RNA clearance from the upper respiratory tract. Understanding the SARS‐CoV‐2 viral clearance profile is crucial to establish a re‐testing plan on discharge and ending isolation of patients. We aimed to evaluate the number of days that a patient needed to achieve undetectable levels of SARS‐CoV‐2 in upper respiratory tract specimens (nasopharyngeal swab and/or an oropharyngeal swab). The clearance and persistence of viral RNA was evaluated in two groups of positive patients: those who achieved two negative RT‐PCR tests and those who kept testing positive. Patients were organized thereafter in two subgroups, mild illness patients discharged home and inpatients who had moderate to severe illness. Results from RT‐PCR tests were then correlated with results from the evaluation of the immune response. The study evidenced that most patients tested positive for more than two weeks and that persistence of viral RNA is not necessarily associated with severe disease but may result from a weaker immune response instead. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32484958/ doi: 10.1002/jmv.26103 id: cord-340475-h0q1m3ed author: Carnero, Elena title: Type I Interferon Regulates the Expression of Long Non-Coding RNAs date: 2014-11-06 words: 10164.0 sentences: 544.0 pages: flesch: 55.0 cache: ./cache/cord-340475-h0q1m3ed.txt txt: ./txt/cord-340475-h0q1m3ed.txt summary: Further validation showed that ISR2, 8, and 12 expression mimics that of their neighboring genes GBP1, IRF1, and IL6, respectively, all related to the IFN response.These genes are induced in response to different doses of IFNα2 in different cell lines at early (ISR2 or 8) or later (ISR12) time points. HuH7 cells were treated for 6, 24, 48, or 72 h with increasing doses of IFNα2 up to 10,000 units/ml, and the expression levels of GBP1, IRF1, BST2, OAS, IL6, and ISG15 were evaluated by qRT-PCR (Figure 1) . abstract: Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to limit the strength and duration of IFN response. The ISGs identified so far belong to coding genes. However, only a small proportion of the transcriptome corresponds to coding transcripts and it has been estimated that there could be as many coding as long non-coding RNAs (lncRNAs). To address whether IFN can also regulate the expression of lncRNAs, we analyzed the transcriptome of HuH7 cells treated or not with IFNα2 by expression arrays. Analysis of the arrays showed increased levels of several well-characterized coding genes that respond to IFN both at early or late times. Furthermore, we identified several IFN-stimulated or -downregulated lncRNAs (ISRs and IDRs). Further validation showed that ISR2, 8, and 12 expression mimics that of their neighboring genes GBP1, IRF1, and IL6, respectively, all related to the IFN response. These genes are induced in response to different doses of IFNα2 in different cell lines at early (ISR2 or 8) or later (ISR12) time points. IFNβ also induced the expression of these lncRNAs. ISR2 and 8 were also induced by an influenza virus unable to block the IFN response but not by other wild-type lytic viruses tested. Surprisingly, both ISR2 and 8 were significantly upregulated in cultured cells and livers from patients infected with HCV. Increased levels of ISR2 were also detected in patients chronically infected with HIV. This is relevant as genome-wide guilt-by-association studies predict that ISR2, 8, and 12 may function in viral processes, in the IFN pathway and the antiviral response. Therefore, we propose that these lncRNAs could be induced by IFN to function as positive or negative regulators of the antiviral response. url: https://www.ncbi.nlm.nih.gov/pubmed/25414701/ doi: 10.3389/fimmu.2014.00548 id: cord-252268-o63ep08b author: Carolan, Louise A. title: TaqMan real time RT-PCR assays for detecting ferret innate and adaptive immune responses date: 2014-09-01 words: 6643.0 sentences: 358.0 pages: flesch: 52.0 cache: ./cache/cord-252268-o63ep08b.txt txt: ./txt/cord-252268-o63ep08b.txt summary: As this equation relies on consistency between samples in the RNA quantity assayed, and the optimum reaction efficiency, as well as minimal fluctuation in the expression of housekeeping genes (endogenous controls) (Peters et al., 2007; Mane et al., 2008; Bruder et al., 2010) , these parameters were optimized using RNA extracted from cultured ferret lymph node cells stimulated with mitogens or with influenza virus. To test the ability of ferret leukocytes to produce mRNA cytokines and chemokines, lymph node cells from naïve ferrets were cultured with various mitogens known to activate T and B lymphocyte and macrophage/monocyte responses (Fig. 5) and with live or heat inactivated influenza virus (Fig. 6 ) and the cytokine and chemokine expression profiles were determined (summarized in (ConA) or Phytohaemagglutinin (PHA), which act by cross linking T cell receptors via sugars on the surface of human T lymphocytes (Chilson and Kelly-Chilson, 1989) , induced similar cytokine profiles, increasing expression of IL2, IL4, IL6, IL10, IL17, Granzyme A, TNF␣ and IFN␥, most with high fold changes, consistent with effective stimulation of T lymphocytes (Fig. 5) . abstract: The ferret is an excellent model for many human infectious diseases including influenza, SARS-CoV, henipavirus and pneumococcal infections. The ferret is also used to study cystic fibrosis and various cancers, as well as reproductive biology and physiology. However, the range of reagents available to measure the ferret immune response is very limited. To address this deficiency, high-throughput real time RT-PCR TaqMan assays were developed to measure the expression of fifteen immune mediators associated with the innate and adaptive immune responses (IFNα, IFNβ, IFNγ, IL1α, IL1β, IL2, IL4, IL6, IL8, IL10, IL12p40, IL17, Granzyme A, MCP1, TNFα), as well as four endogenous housekeeping genes (ATF4, HPRT, GAPDH, L32). These assays have been optimized to maximize reaction efficiency, reduce the amount of sample required (down to 1 ng RNA per real time RT-PCR reaction) and to select the most appropriate housekeeping genes. Using these assays, the expression of each of the tested genes could be detected in ferret lymph node cells stimulated with mitogens or infected with influenza virus in vitro. These new tools will allow a more comprehensive analysis of the ferret immune responses following infection or in other disease states. url: https://doi.org/10.1016/j.jviromet.2014.04.014 doi: 10.1016/j.jviromet.2014.04.014 id: cord-279404-u0fs6xcj author: Carrington, Christine V.F. title: Detection and Phylogenetic Analysis of Group 1 Coronaviruses in South American Bats date: 2008-12-17 words: 1761.0 sentences: 126.0 pages: flesch: 66.0 cache: ./cache/cord-279404-u0fs6xcj.txt txt: ./txt/cord-279404-u0fs6xcj.txt summary: The search for the animal reservoir of the severe acute respiratory syndrome coronavirus (SARS-CoV) led to extensive surveys of coronaviruses in wild and domestic animal populations in China, resulting in the detection of a wide variety of novel bat coronaviruses (Bt-CoVs) (2) (3) (4) (5) . Our detection of RNA from group 1 CoVs in Trinidadian bats shows that Bt-CoVs have a wider distribution than previously suspected and is added support for bats as the original host species for these viruses. Despite the geographic proximity of the bats from which the Trinidadian Bt-CoV sequences were derived-Couva and Fyzabad are 28 km (17 miles) apart, and Trinidad has an area of only 4,769 km 2 (1,864 square miles)-they are relatively highly divergent. Trinidadian bat coronavirus (Bt-CoV) sequences are highlighted in red and North American Bt-CoV in blue. Detection of group 1 coronaviruses in bats in North America abstract: Bat coronaviruses (Bt-CoVs) are thought to be the precursors of severe acute respiratory syndrome coronavirus. We detected Bt-CoVs in 2 bat species from Trinidad. Phylogenetic analysis of the RNA-dependent RNA polymerase gene and helicase confirmed them as group 1 coronaviruses. url: https://doi.org/10.3201/eid1412.080642 doi: 10.3201/eid1412.080642 id: cord-292347-d7xq7x5g author: Carter, Linda J. title: Assay Techniques and Test Development for COVID-19 Diagnosis date: 2020-04-30 words: 3426.0 sentences: 227.0 pages: flesch: 51.0 cache: ./cache/cord-292347-d7xq7x5g.txt txt: ./txt/cord-292347-d7xq7x5g.txt summary: 375 While RT-PCR-based viral RNA detection has been widely 376 used in diagnosis of COVID-19, it cannot be used to monitor 377 the progress of the disease stages and cannot be applied to 378 broad identification of past infection and immunity. 46,47 410 The determination of SARS-CoV-2 exposure relies largely 411 on the detection of either IgM or IgG antibodies that are 412 specific for various viral antigens including, but not exclusively, 413 the spike glycoprotein (S1 and S2 subunits, receptor-binding 414 domain) and nucleocapsid protein. While RT-PCR has been 571 the dominant technique for detection of viral RNA, other 572 nucleic acid assays including isothermal amplification assays, 573 hybridization microarray assays, amplicon-based metagenomics 574 sequencing, and the cutting-edge CRISPR-related technologies 575 are also under development or have resulted in approved 576 tests. abstract: nan url: https://doi.org/10.1021/acscentsci.0c00501 doi: 10.1021/acscentsci.0c00501 id: cord-004848-2cfphi88 author: Carter, M. J. title: Transcription of feline calicivirus RNA date: 1990 words: 3361.0 sentences: 190.0 pages: flesch: 60.0 cache: ./cache/cord-004848-2cfphi88.txt txt: ./txt/cord-004848-2cfphi88.txt summary: In this way these workers have identified three intracellular RNAs (4.8, 4.2, and 2.4 kb) as well as the genome (8.2 kb) and shown that these form a nested set of 3'' co-terminal molecules similar to that observed in coronavirus infected cells. We have used this to probe FCV-infected cells for the synthesis of virus specific RNA and confirm and extend the observations of Neill and Mengeling. Subcloning of the virus 3'' end into a single stranded vector has allowed us to examine the occurrence of positive and negative sense RNA separately. Finally this inference was confirmed by subcloning the terminal EcoRI/PstI fragment into M13 and determining its sequence (Fig. 3a) , This showed a poly A stretch preceded by a short run ofpoly C which is exactly that structure expected for cDNA clones derived by this method from an mRNA 3'' end. However, the negative strand-specific probe also showed hybridization to subgenomic messages 2-4, but this was not observed until later in infection than the detection of the positive forms of these molecules. abstract: We report here the cloning and 3′ sequence determination of feline calicivirus strain F9. Subcloning the 3′ terminus enabled the production of strand specific probes for RNA synthesis. We extend the number of virus specific RNAs detected intracellularly to 8, and show that numbers 1–5 are represented as negative strands which may serve as templates in the synthesis of these RNAs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087285/ doi: 10.1007/bf01310744 id: cord-278647-krh63hqp author: Carter, Robert W title: A new look at an old virus: patterns of mutation accumulation in the human H1N1 influenza virus since 1918 date: 2012-10-12 words: 8413.0 sentences: 425.0 pages: flesch: 52.0 cache: ./cache/cord-278647-krh63hqp.txt txt: ./txt/cord-278647-krh63hqp.txt summary: At the time of its disappearance in 2009, the human H1N1 lineage had accumulated over 1400 point mutations (more than 10% of the genome), including approximately 330 non-synonymous changes (7.4% of all codons). This process may play a role in natural pandemic cessation and has apparently contributed to the exponential decline in mortality rates over time, as seen in all major human influenza strains. Given this large body of data, it becomes feasible to test the attenuation model using mutation accumulation rates, non-synonymous amino acid changes, changing dN/dS ratios, changing transition/transversions ratios, and changes in codon specificity over time. Using the amended 1918 Brevig Mission virus as a reference and including all human and porcine viruses in the database, we calculated SNPs, indels, transitions, transversions, non-synonymous amino acid changes, dN/dS ratios, predicted protein lengths (for all 11 proteins), the normalized codon scores (NCS) and relative synonymous codon usage (RSCU) [51] score for each predicted protein of each genome. abstract: BACKGROUND: The H1N1 influenza A virus has been circulating in the human population for over 95 years, first manifesting itself in the pandemic of 1917–1918. Initial mortality was extremely high, but dropped exponentially over time. Influenza viruses have high mutation rates, and H1N1 has undergone significant genetic changes since 1918. The exact nature of H1N1 mutation accumulation over time has not been fully explored. METHODS: We have made a comprehensive historical analysis of mutational changes within H1N1 by examining over 4100 fully-sequenced H1N1 genomes. This has allowed us to examine the genetic changes arising within H1N1 from 1918 to the present. RESULTS: We document multiple extinction events, including the previously known extinction of the human H1N1 lineage in the 1950s, and an apparent second extinction of the human H1N1 lineage in 2009. These extinctions appear to be due to a continuous accumulation of mutations. At the time of its disappearance in 2009, the human H1N1 lineage had accumulated over 1400 point mutations (more than 10% of the genome), including approximately 330 non-synonymous changes (7.4% of all codons). The accumulation of both point mutations and non-synonymous amino acid changes occurred at constant rates (μ = 14.4 and 2.4 new mutations/year, respectively), and mutations accumulated uniformly across the entire influenza genome. We observed a continuous erosion over time of codon-specificity in H1N1, including a shift away from host (human, swine, and bird [duck]) codon preference patterns. CONCLUSIONS: While there have been numerous adaptations within the H1N1 genome, most of the genetic changes we document here appear to be non-adaptive, and much of the change appears to be degenerative. We suggest H1N1 has been undergoing natural genetic attenuation, and that significant attenuation may even occur during a single pandemic. This process may play a role in natural pandemic cessation and has apparently contributed to the exponential decline in mortality rates over time, as seen in all major human influenza strains. These findings may be relevant to the development of strategies for managing influenza pandemics and strain evolution. url: https://www.ncbi.nlm.nih.gov/pubmed/23062055/ doi: 10.1186/1742-4682-9-42 id: cord-355397-y69bk5jc author: Caruso, Ícaro P. title: Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism date: 2020-09-06 words: 5105.0 sentences: 297.0 pages: flesch: 55.0 cache: ./cache/cord-355397-y69bk5jc.txt txt: ./txt/cord-355397-y69bk5jc.txt summary: Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs'' Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. We calculated the structural model of the N-NTD:dsTRS complex based on the experimental data for the N-NTD interaction with a non-specific dsRNA (5''-CACUGAC-3'') (dsNS) (16) using the HADDOCK 2.2 server (20) . In contrast to the decrease in the number of intramolecular hydrogen bonds between the sense and anti-sense strands of dsRNAs (WC base-pairing) due to N-NTD binding, we observed an increase in the average number of intermolecular hydrogen bonds formed between the nitrogenous bases of dsTRS and N-NTD (protein-RNA interaction) along the 100 ns MD simulation, whereas for dsNS, this average value was constant ( Figure 3B top). abstract: The N protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. Its N-terminal domain (NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRS), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs’ Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. N-NTD dsRNA destabilizing activity was more efficient for dsTRS than dsNS. N-NTD dynamics, especially a tweezer-like motion of β2-β3 and 2-β5 loops, played a key role in WC base-pairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event. IMPORTANCE Coronaviruses are among the largest positive-sense RNA viruses. They display a unique discontinous transcription mechanism, involving N protein as a major player. The N-NTD promote the dsRNA melting releasing the nascent sense negative strand via a poorly known mechanism of action. It specifically recognizes the body TRS conserved RNA motif located at the 5’ end of each ORF. N protein has the ability to transfer the nascent RNA strand to the leader TRS. The mechanism is essential and one single mutation at the RNA binding site of the N-NTD impairs the viral replication. Here, we describe a counterintuitive mechanism of action of N-NTD based on molecular dynamics simulation and kinetic modelling of the experimental melting activity of N-NTD. This data impacts directly in the understanding of the way N protein acts in the cell and will guide future experiments. url: https://doi.org/10.1101/2020.08.24.264465 doi: 10.1101/2020.08.24.264465 id: cord-029779-9b6zs1sb author: Casey, Sophie title: Temporally Altered miRNA Expression in a Piglet Model of Hypoxic Ischemic Brain Injury date: 2020-07-27 words: 11367.0 sentences: 662.0 pages: flesch: 52.0 cache: ./cache/cord-029779-9b6zs1sb.txt txt: ./txt/cord-029779-9b6zs1sb.txt summary: miR-181a inhibition increased neurite length in vitro in two different types of cell culture-the SH-SY5Y cell line and primary cultures of E14 rat midbrain-and increased expression of BMPR2 in differentiating SH-SY5Ys. Therefore, this miRNA may be a potential therapeutic target with neuroprotective effects. Analyses of previously performed microarray data showed altered expression levels in 70 miRNAs in umbilical cord whole blood in infants with moderate and severe HIE compared with controls and this data have been previously reported by our group [5] . The predicted downstream targets of the six miRNAs were predicted to exert neuroprotective effects, and functional examination of one of the associated pathways-the BMP signalling pathway (a member of the TGFβ superfamily [31] )-in differentiating SH-SY5Y cells revealed inhibition of miR-181a increases expression of the type II receptor BMPR2. abstract: Hypoxic ischemic encephalopathy (HIE) is the most frequent cause of acquired infant brain injury. Early, clinically relevant biomarkers are required to allow timely application of therapeutic interventions. We previously reported early alterations in several microRNAs (miRNA) in umbilical cord blood at birth in infants with HIE. However, the exact timing of these alterations is unknown. Here, we report serial changes in six circulating, cross-species/bridging biomarkers in a clinically relevant porcine model of neonatal HIE with functional analysis. Six miRNAs—miR-374a, miR-181b, miR-181a, miR-151a, miR-148a and miR-128—were significantly and rapidly upregulated 1-h post-HI. Changes in miR-374a, miR-181b and miR-181a appeared specific to moderate-severe HI. Histopathological injury and five miRNAs displayed positive correlations and were predictive of MRS Lac/Cr ratios. Bioinformatic analysis identified that components of the bone morphogenic protein (BMP) family may be targets of miR-181a. Inhibition of miR-181a increased neurite length in both SH-SY5Y cells at 1 DIV (days in vitro) and in primary cultures of rat neuronal midbrain at 3 DIV. In agreement, inhibition of miR-181a increased expression of BMPR2 in differentiating SH-SY5Y cells. These miRNAs may therefore act as early biomarkers of HIE, thereby allowing for rapid diagnosis and timely therapeutic intervention and may regulate expression of signalling pathways vital to neuronal survival. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12035-020-02018-w) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383124/ doi: 10.1007/s12035-020-02018-w id: cord-000372-wzwpyvll author: Castelló, Alfredo title: The Multifaceted Poliovirus 2A Protease: Regulation of Gene Expression by Picornavirus Proteases date: 2011-04-14 words: 16333.0 sentences: 781.0 pages: flesch: 45.0 cache: ./cache/cord-000372-wzwpyvll.txt txt: ./txt/cord-000372-wzwpyvll.txt summary: These findings are in agreement with the fact that host mRNA transcription takes place in 2A pro -expressing cells when both translation and RNA nuclear export are inhibited, upon cleavage of eIF4G and Nups [17] . In this regard, PV 2A pro has been very useful for examining the requirements for eIF4G to translate different cellular or viral mRNAs. In addition to this, in this paper, we have highlighted the role of PV 2A pro not only in the processing of the poliovirus polyprotein but also in the interaction with the host-cell. In particular, PV 2A pro cleaves cell proteins involved in transcription, pre-mRNA splicing, nucleus/cytoplasm transport and translation, in order to hijack those host functions and to concentrate the cellular resources on the production of the viral progeny. abstract: After entry into animal cells, most viruses hijack essential components involved in gene expression. This is the case of poliovirus, which abrogates cellular translation soon after virus internalization. Abrogation is achieved by cleavage of both eIF4GI and eIF4GII by the viral protease 2A. Apart from the interference of poliovirus with cellular protein synthesis, other gene expression steps such as RNA and protein trafficking between nucleus and cytoplasm are also altered. Poliovirus 2A(pro) is capable of hydrolyzing components of the nuclear pore, thus preventing an efficient antiviral response by the host cell. Here, we compare in detail poliovirus 2A(pro) with other viral proteins (from picornaviruses and unrelated families) as regard to their activity on key host factors that control gene expression. It is possible that future analyses to determine the cellular proteins targeted by 2A(pro) will uncover other cellular functions ablated by poliovirus infection. Further understanding of the cellular proteins hydrolyzed by 2A(pro) will add further insight into the molecular mechanism by which poliovirus and other viruses interact with the host cell. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085340/ doi: 10.1155/2011/369648 id: cord-263468-996kl9jz author: Cattaneo, Roberto title: Biased hypermutation and other genetic changes in defective measles viruses in human brain infections date: 1988-10-21 words: 7642.0 sentences: 306.0 pages: flesch: 50.0 cache: ./cache/cord-263468-996kl9jz.txt txt: ./txt/cord-263468-996kl9jz.txt summary: Abstract We assessed the alterations of viral gene expression occurring during persistent infections by cloning full-length transcripts of measles virus (MV) genes from brain autopsies of two subacute sclerosing panencephalitis patients and one measles inclusion body encephalitis (MIBE) patient. One of these nucleotide substitutions and one deletion resulted in alteration of the reading frames of two fusion genes, as confirmed by in vitro translation of synthetic mRNAs. One cluster of mutations was exceptional; in the matrix gene of the MIBE case, 50% of the U residues were changed to C, which might result from a highly biased copying event exclusively affecting this gene. most likely based on one hand on the low fidelity of RNA To assess the variability in strains of lytic viruses, and replication (Domingo et al., 1978; for review see Steinto estimate the number of mutations introduced during hauer and Holland, 1987) and on the other hand on the persistence, we counted the differences of lytic and perlow selective pressure exerted on viral genomes in nonsistent viruses from a consensus as defined above. abstract: Abstract We assessed the alterations of viral gene expression occurring during persistent infections by cloning full-length transcripts of measles virus (MV) genes from brain autopsies of two subacute sclerosing panencephalitis patients and one measles inclusion body encephalitis (MIBE) patient. The suquence of these MV genes revealed that, most likely, almost 2% of the nucleotides were mutated during persistence, and 35% of these differences resulted in amino acid changes. One of these nucleotide substitutions and one deletion resulted in alteration of the reading frames of two fusion genes, as confirmed by in vitro translation of synthetic mRNAs. One cluster of mutations was exceptional; in the matrix gene of the MIBE case, 50% of the U residues were changed to C, which might result from a highly biased copying event exclusively affecting this gene. We propose that the cluster of mutations in the MIBE case, and other combinations of mutations in other cases, favored propagation of MV infections in brain cells by conferring a selective advantage to the mutated genomes. url: https://api.elsevier.com/content/article/pii/0092867488900487 doi: 10.1016/0092-8674(88)90048-7 id: cord-003044-9uqa39j9 author: Cervera, Héctor title: Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study date: 2018-03-19 words: 10863.0 sentences: 533.0 pages: flesch: 46.0 cache: ./cache/cord-003044-9uqa39j9.txt txt: ./txt/cord-003044-9uqa39j9.txt summary: As viral fitness is reduced, interactions are less optimal and, consequently, the gene expression profile of the plant will be increasingly different from that resulting from the infection with the WT virus. Figure 2A shows the clustering (unweighted average distance method; UPGMA) of average expression data for those genes that significantly changed expression (62-fold) among plants infected with the seven viral genotypes (1-way ANOVAs with false discovery rate (FDR) correction; overall P < 0.05) relative to the mock-inoculated plants. tabacum into a novel, poorly susceptible one, Arabidopsis thaliana, have shown that adaptation of TEV to the novel host (i.e., concomitant to large increases in fitness) was associated with a profound change in the way the ancestral and evolved viruses interacted with the plant''s transcriptome, with genes involved in the response to biotic stresses, including signal transduction and innate immunity pathways, being significantly underexpressed in plants infected with the evolved virus than in plants infected with the ancestral one (Agudelo-Romero et al. abstract: Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995217/ doi: 10.1093/molbev/msy038 id: cord-315054-kji2kfek author: Chakraborty, Nabarun title: Protocol Improvement for RNA Extraction From Compromised Frozen Specimens Generated in Austere Conditions: A Path Forward to Transcriptomics-Pathology Systems Integration date: 2020-07-22 words: 4462.0 sentences: 214.0 pages: flesch: 45.0 cache: ./cache/cord-315054-kji2kfek.txt txt: ./txt/cord-315054-kji2kfek.txt summary: In an effort to be economical with available resources, snap-frozen euthanized mice are the straightforward solution; however, this method increases the risk of temperature abuse during the thawing process at the beginning of the tissue collection. We found that prolonged immersion of snap frozen mouse carcass in 10% neutral buffered formalin at 4°C yielded minimal microscopic signs of ice crystallization and delivered tissues with histomorphology that is optimal for hematoxylin and eosin (H&E) staining and fixation on glass slides. An omics-pathology integration approach could be the most effective for phenometo-genome interpretation if omics assays are conducted using the particular tissue specimen, where injury signatures are informed by histopathology image analysis (Pathak and Dave, 2014; Yu et al., 2017) . These snap-frozen carcasses had to undergo onground freeze-thaw cycles before tissue collection, which is typically expected to compromise overall sample quality and make the histopathologic analysis challenging (Lyons et al., 1979; Pikal-Cleland et al., 2000) . abstract: At the heart of the phenome-to-genome approach is high throughput assays, which are liable to produce false results. This risk can be mitigated by minimizing the sample bias, specifically, recycling the same tissue specimen for both phenotypic and genotypic investigations. Therefore, our aim is to suggest a methodology of obtaining robust results from frozen specimens of compromised quality, particularly if the sample is produced in conditions with limited resources. For example, generating samples at the International Space Station (ISS) is challenging because the time and laboratory footprint allotted to a project can get expensive. In an effort to be economical with available resources, snap-frozen euthanized mice are the straightforward solution; however, this method increases the risk of temperature abuse during the thawing process at the beginning of the tissue collection. We found that prolonged immersion of snap frozen mouse carcass in 10% neutral buffered formalin at 4°C yielded minimal microscopic signs of ice crystallization and delivered tissues with histomorphology that is optimal for hematoxylin and eosin (H&E) staining and fixation on glass slides. We further optimized a method to sequester the tissue specimen from the H&E slides using an incubator shaker. Using this method, we were able to recover an optimal amount of RNA that could be used for downstream transcriptomics assays. Overall, we demonstrated a protocol that enables us to maximize scientific values from tissues collected in austere condition. Furthermore, our protocol can suggest an improvement in the spatial resolution of transcriptomic assays. url: https://doi.org/10.3389/fmolb.2020.00142 doi: 10.3389/fmolb.2020.00142 id: cord-298281-wkje5jyt author: Chan, Vinson Wai-Shun title: A systematic review on COVID-19: urological manifestations, viral RNA detection and special considerations in urological conditions date: 2020-05-27 words: 3492.0 sentences: 271.0 pages: flesch: 54.0 cache: ./cache/cord-298281-wkje5jyt.txt txt: ./txt/cord-298281-wkje5jyt.txt summary: Primary outcomes were the urological manifestations of COVID-19, and SARS-CoV-2 viral RNA detection in urine and stool samples. Primary outcomes of our study included urological manifestations of COVID-19, detection rates of SARS-CoV-2 viral RNA in urine and stool samples, and special considerations in urological conditions. For the urological manifestations and viral RNA detection rates, data were pool analysed using MetaXL and Microsoft Excel when there are two or more studies with at least four patients reporting the same outcome under the same definition. There were a total of 11 studies that reported the number of patients who had their urine tested for SARS-CoV-2 viral RNA. Our meta-analysis included 12 studies that reported the number of patients with stools tested for SARS-CoV-2 viral RNA. Our study showed that 5.74% of the COVID-19 patients had positive viral RNA in urine samples. abstract: PURPOSE AND OBJECTIVE: We performed a systematic review on COVID-19 and its potential urological manifestations. METHODS: A literature search was performed using combination of keywords (MeSH terms and free text words) relating to COVID-19, urology, faeces and stool on multiple databases. Primary outcomes were the urological manifestations of COVID-19, and SARS-CoV-2 viral RNA detection in urine and stool samples. Meta-analyses were performed when there were two or more studies reporting on the same outcome. Special considerations in urological conditions that were relevant in the pandemic of COVID-19 were reported in a narrative manner. RESULTS: There were a total of 21 studies with 3714 COVID-19 patients, and urinary symptoms were absent in all of them. In patients with COVID-19, 7.58% (95% CI 3.30–13.54%) developed acute kidney injury with a mortality rate of 93.27% (95% CI 81.46–100%) amongst them. 5.74% (95% CI 2.88–9.44%) of COVID-19 patients had positive viral RNA in urine samples, but the duration of viral shedding in urine was unknown. 65.82% (95% CI 45.71–83.51%) of COVID-19 patients had positive viral RNA in stool samples, which were detected from 2 to 47 days from symptom onset. 31.6% of renal transplant recipients with COVID-19 required non-invasive ventilation, and the overall mortality rate was 15.4%. CONCLUSIONS: Acute kidney injury leading to mortality is common amongst COVID-19 patients, likely as a result of direct viral toxicity. Viral RNA positivity was detected in both urine and stool samples, so precautions are needed when we perform transurethral or transrectal procedures. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00345-020-03246-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32462305/ doi: 10.1007/s00345-020-03246-4 id: cord-301535-eui41zyg author: Chandler-Brown, Devon title: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing date: 2020-04-10 words: 4143.0 sentences: 228.0 pages: flesch: 52.0 cache: ./cache/cord-301535-eui41zyg.txt txt: ./txt/cord-301535-eui41zyg.txt summary: This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Quantitative analysis of the Sanger sequence chromatogram gives qSanger an extremely high sensitivity and specificity for all positive results with a limit of detection of 10-20 genome copy equivalents (GCE), equivalent to gold-standard qPCR methods. To further evaluate the feasibility of a direct VTM, extraction-free method for Sars-CoV-2 detection, we also examined the ability of qSanger to quantify the amount of viral particles in the Seracare positive control specimens (Fig. 3B ). abstract: There is currently an urgent unmet need to increase coronavirus disease 2019 (COVID-19) testing capability to effectively respond to the COVID-19 pandemic. However, the current shortage in RNA extraction reagents as well as limitations in qPCR protocols have resulted in bottlenecks in testing capacity. Herein, we describe a novel molecular diagnostic for COVID-19 based on Sanger sequencing. This assay uses the addition of a frame-shifted spike-in, a modified PCR master mix, and custom Sanger sequencing data analysis to detect and quantify SARS-CoV-2 RNA at a limit of detection comparable to existing qPCR-based assays, at 10-20 genome copy equivalents. Crucially, our assay was able to detect SARS-CoV-2 RNA from viral particles suspended in transport media that was directly added to the PCR master mix, suggesting that RNA extraction can be skipped entirely without any degradation of test performance. Since Sanger sequencing instruments are widespread in clinical laboratories and commonly have built-in liquid handling automation to support up to 3840 samples per instrument per day, the widespread adoption of qSanger COVID-19 diagnostics can unlock more than 1,000,000 tests per day in the US. url: https://doi.org/10.1101/2020.04.07.029199 doi: 10.1101/2020.04.07.029199 id: cord-282764-d9x1wii6 author: Chang, Chia-Yin title: Influence of intron and exon splicing enhancers on mammalian cell expression of a truncated spike protein of SARS-CoV and its implication for subunit vaccine development date: 2006-02-20 words: 4812.0 sentences: 231.0 pages: flesch: 52.0 cache: ./cache/cord-282764-d9x1wii6.txt txt: ./txt/cord-282764-d9x1wii6.txt summary: title: Influence of intron and exon splicing enhancers on mammalian cell expression of a truncated spike protein of SARS-CoV and its implication for subunit vaccine development A truncated S protein of the TW1 strain, S(TR2) (88 kDa), carrying three S fragments (S74–253, S294–739, and S1129–1255) was investigated to study the influences of intron and exon splicing enhancers to improve S(TR2) protein expression in mammalian cells. Therefore, several different strategies for improving S TR2 protein expression in mammalian cells were investigated in this report, including intron addition and the application of exon splicing enhancers. The intron-dependent enhancement of S TR2 protein expression in CHO/dhFr− cells was further investigated by measuring total RNA level, in vivo RNA stability, and RNA elongation rate in this study. The results indicated that the intron-dependent S TR2 protein expression in mammalian cells correlated with a higher level of total RNA accumulation as determined by quantitative RT-PCR (Fig. 4A) . abstract: The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) is important for vaccine development. A truncated S protein of the TW1 strain, S(TR2) (88 kDa), carrying three S fragments (S74–253, S294–739, and S1129–1255) was investigated to study the influences of intron and exon splicing enhancers to improve S(TR2) protein expression in mammalian cells. Our results showed that S(TR2) protein expression with the use of an 138 base-pair intron addition increased by 1.9-, 2.5-, and 4.1-fold in Vero E6, QBI-293A cells, and CHO/dhFr− cells (dihydrofolate reductase [dhfr] gene deficient CHO cells), respectively. Using the exon splicing enhancers, including a bidirectional splicing enhancer (BSE) or an exon splicing enhancer derived from the EDA alternative exon of the fibronectin gene (EDA ESE), were also found to increase S(TR2) protein expression in CHO/dhFr− cells by 1.7- and 2.6-fold. Nevertheless, combination of the intron and the exon splicing enhancers resulted in suppressing the intron-enhancing e S(TR2) protein expression in in CHO/dhFr− cells. Our studies also demonstrated the S(TR2) protein was mainly as the Endo H-sensitive glycoprotein (115 kDa) expressed in Vero E6, QBI-293A, and CHO/dhFr− cells. However, only a minor form of the Endo H-resistant glycoproteins (∼130 kDa) was detected in CHO/dhFr− cells. Taken together, our results indicated that intron had a better enhancing effect on S(TR2) protein expression than exon splicing enhancers, and the expression of ∼130 kDa S(TR2) glycoprotein was enhanced by the intron addition into the expression vector construct. Results of the present study can provide an optimal strategy to enhance SARS-CoV S protein expression in mammalian cells and may contribute to the development of SARS-CoV subunit vaccine. url: https://www.ncbi.nlm.nih.gov/pubmed/16194584/ doi: 10.1016/j.vaccine.2005.09.011 id: cord-314833-6fue84x6 author: Chang, Chung-ke title: The SARS coronavirus nucleocapsid protein – Forms and functions date: 2014-01-11 words: 9459.0 sentences: 464.0 pages: flesch: 51.0 cache: ./cache/cord-314833-6fue84x6.txt txt: ./txt/cord-314833-6fue84x6.txt summary: The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. proposed a structure-based domain arrangement for SARS-CoV N protein where the NTD and CTD are sandwiched between three IDRs. Sequence alignments suggested that other coronavirus N proteins might share the same structural organization based on intrinsic disorder predictor profiles and secondary structure predictions (Fig. 2) . noticed that effective binding to RNA by MHV N protein in host cells required the presence of both the NTD and CTD (Hurst et al., 2009) , suggesting that the NTD and CTD formed a single bipartite RNA interaction site, a feature to be reiterated in the final SARS-CoV RNP model. Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA abstract: The nucleocapsid phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV N protein) packages the viral genome into a helical ribonucleocapsid (RNP) and plays a fundamental role during viral self-assembly. It is a protein with multifarious activities. In this article we will review our current understanding of the N protein structure and its interaction with nucleic acid. Highlights of the progresses include uncovering the modular organization, determining the structures of the structural domains, realizing the roles of protein disorder in protein–protein and protein–nucleic acid interactions, and visualizing the ribonucleoprotein (RNP) structure inside the virions. It was also demonstrated that N-protein binds to nucleic acid at multiple sites with a coupled-allostery manner. We propose a SARS-CoV RNP model that conforms to existing data and bears resemblance to the existing RNP structures of RNA viruses. The model highlights the critical role of modular organization and intrinsic disorder of the N protein in the formation and functions of the dynamic RNP capsid in RNA viruses. This paper forms part of a symposium in Antiviral Research on “From SARS to MERS: 10 years of research on highly pathogenic human coronaviruses.” url: https://www.ncbi.nlm.nih.gov/pubmed/24418573/ doi: 10.1016/j.antiviral.2013.12.009 id: cord-274663-zyzgk2z3 author: Chang, Stewart T. title: Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line date: 2011-09-20 words: 6991.0 sentences: 358.0 pages: flesch: 48.0 cache: ./cache/cord-274663-zyzgk2z3.txt txt: ./txt/cord-274663-zyzgk2z3.txt summary: Using NGS, we detected small but significant changes in host gene expression affecting T cell function that coincided with the initiation of viral RNA production at 12 h postinfection (hpi). In addition, by using NGS, we observed the dramatic expansion of viral mRNA expression and detected new viral splice events occurring during viral replication and differential expression of noncoding RNA species, including microRNA host genes. In our data set, we observed no change in the expression of the Crm1-encoding gene XPO1, but several members of the Ran signaling pathway were downregulated, suggesting that the overall export of unspliced viral RNA was suppressed (see Fig. S5B in the supplemental material; data not shown for XPO1). The regulation of these and transcription factors specific for other functions (e.g., EGR1, KLF13, and MYC) may explain how HIV initiated replication with minimal disruption to host gene expression at 12 hpi but elicited larger-scale changes later in infection. abstract: Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4(+) T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes. url: https://www.ncbi.nlm.nih.gov/pubmed/21933919/ doi: 10.1128/mbio.00134-11 id: cord-281254-x7ivjvti author: Chang, Zhijie title: Therapeutic and Prophylactic Potential of Small Interfering RNAs against Severe Acute Respiratory Syndrome: Progress to Date date: 2012-08-16 words: 3803.0 sentences: 256.0 pages: flesch: 56.0 cache: ./cache/cord-281254-x7ivjvti.txt txt: ./txt/cord-281254-x7ivjvti.txt summary: The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. Since SARS-CoV rep-To address the issue related to delivery of siRNAs into cells or lication also requires certain host proteins, genes from host cells living organisms, researchers have used several approaches, ininvolved in viral replication can also be selected as targets. Therefore, RNA interference this coronavirus family), siRNAs targeting different genes of can be a tool for down-regulation of gene expression in cultured SARS-CoV were used by various groups to inhibit virus gene cells as well as in living organisms. abstract: Severe acute respiratory syndrome (SARS), caused by the novel coronavirus SARS-CoV, produced a scare when it appeared in 2003 in China and later quickly spread to other countries around the world. Although it has since disappeared, its threat to human health remains. Therefore, studies on the prevention and treatment of SARS are important for dealing with epidemics of this and other infectious diseases. The most promising newly developed technology for intervention in SARS may be RNA interference, an endogenous cellular process for the inhibition of gene expression mediated by sequence-specific double-stranded RNAs. Numerous studies have reported the therapeutic potential of RNA interference for the treatment of various human diseases ranging from cancers to infectious diseases such as HIV and hepatitis. To date, most studies on inhibition of SARS-CoV replication using small interfering RNAs (siRNAs) have been conducted in cell lines in vitro. One study using siRNAs to inhibit SARS-CoV infection in Rhesus macaques demonstrated that siRNAs were effective both prophylactically and therapeutically with no adverse effects in the animals. Challenges remaining for the application of siRNA in vivo for SARS prevention and treatment include the specificity of the siRNAs and the efficiency of delivery. However, with improvements in siRNA design and delivery methods, RNA interference has the potential to become another major weapon for combating dangerous infections due to viruses such as SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/17263585/ doi: 10.2165/00063030-200721010-00002 id: cord-351864-zozrj7w5 author: Chappleboim, A. title: ApharSeq: An Extraction-free Early-Pooling Protocol for Massively Multiplexed SARS-CoV-2 Detection date: 2020-08-13 words: 5782.0 sentences: 321.0 pages: flesch: 57.0 cache: ./cache/cord-351864-zozrj7w5.txt txt: ./txt/cord-351864-zozrj7w5.txt summary: Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Briefly, we show ( Figure 1 ) that we can introduce barcoded and target-specific reverse transcription primers to the samples, allowing them to hybridize to target RNA molecules already in the lysis buffer, or after a brief RNA cleanup step. Observing the target sequence directly allowed us to identify viral sequence variations in some cases ( Figure 2D ).Cross-Sample Contamination is minimal When pooling samples early on in the protocol, the main concern is that RNA molecules will be erroneously tagged due to residual free primers, or due to other artifacts during RT, PCR, or sequencing. abstract: The global SARS-CoV-2 pandemic led to a steep increase in the need for viral detection tests worldwide. Most current tests for SARS-CoV-2 are based on RNA extraction followed by quantitative reverse-transcription PCR assays that involve a separate RNA extraction and qPCR reaction for each sample with a fixed cost and reaction time. While automation and improved logistics can increase the capacity of these tests, they cannot exceed this lower bound dictated by one extraction and reaction per sample. Multiplexed next generation sequencing (NGS) assays provide a dramatic increase in throughput, and hold the promise of richer information on viral strains and host immune response. Here, we establish a significant improvement of existing RNA-seq detection protocols. Our workflow, ApharSeq, includes a fast and cheap RNA capture step, that is coupled to barcoding of individual samples, followed by sample-pooling prior to the reverse transcription, PCR and massively parallel sequencing. Thus, only one step is performed before pooling hundreds of barcoded samples for subsequent steps and further analysis. We characterize the quantitative aspects of the assay, and test ApharSeq on dozens of clinical samples in a robotic workflow. Our proposed workflow is estimated to reduce costs by 10-50 fold, labor by 5-100 fold, automated liquid handling by 5-10 fold, and reagent requirements by 100-1000 fold compared to existing testing methods. url: http://medrxiv.org/cgi/content/short/2020.08.08.20170746v1?rss=1 doi: 10.1101/2020.08.08.20170746 id: cord-008588-4eu9v5d3 author: Chastain, Michael title: Structural Elements in RNA date: 2008-02-29 words: 13667.0 sentences: 617.0 pages: flesch: 54.0 cache: ./cache/cord-008588-4eu9v5d3.txt txt: ./txt/cord-008588-4eu9v5d3.txt summary: The structures of the tRNA anticodon loop and the UUCG loop suggest that the specific loop sequences adopt conformations that are more stable because they contain more hydrogen bonding and stacking interactions-particularly interactions with the sugar-phosphate backbone. Determining the conformation of these loops in RNA is important for understanding how these nucleotides interact with other elements of secondary structure to form tertiary interactions and for understanding how proteins bind to bulge loops. In general, this could occur between any of the secondary structure regions containing unpaired nucleotides (single-stranded regions, hairpin loops, bulge loops, internal loops, and junction loops). There are several examples of RNA molecules containing tertiary contacts between nucleotides that are in loop regions of secondary structure. The high frequency with which known RNA structures contain tertiary pairing between nucleotides that are unpaired in the secondary structure stresses the importance of learning more about such interactions. abstract: This chapter describes the RNA structural characteristics that have emerged so far. Folded RNA molecules are stabilized by a variety of interactions, the most prevalent of which are stacking and hydrogen bonding between bases. Many interactions among backbone atoms also occur in the structure of tRNA, although they are often ignored when considering RNA structure because they are not as well-characterized as interactions among bases. Backbone interactions include hydrogen bonding and the stacking of sugar or phosphate groups with bases or with other sugar and phosphate groups. The interactions found in a three-dimensional RNA structure can be divided into two categories: secondary interactions and tertiary interactions. This division is useful for several reasons. Secondary structures are routinely determined by a combination of techniques discussed in chapter, whereas tertiary interactions are more difficult to determine. Computer algorithms that generate RNA structures can search completely through possible secondary structures, but the inclusion of tertiary interactions makes a complete search of possible structures impractical for RNA molecules even as small as tRNA. The division of RNA structure into building blocks consisting of secondary or tertiary interactions makes it easier to describe RNA structures. In those cases in which RNA studies are incomplete, the studies of DNA are described with the rationalization that RNA structures may be analogous to DNA structures, or that the techniques used to study DNA could be applied to the analogous RNA structures. The chapter focuses on the aspects of RNA structure that affect the three-dimensional shape of RNA and that affect its ability to interact with other molecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133162/ doi: 10.1016/s0079-6603(08)60008-2 id: cord-012909-o6t2srim author: Chaudhari, Jayeshbhai title: Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain date: 2020-07-28 words: 9281.0 sentences: 490.0 pages: flesch: 43.0 cache: ./cache/cord-012909-o6t2srim.txt txt: ./txt/cord-012909-o6t2srim.txt summary: Both virulent and live-attenuated porcine reproductive and respiratory syndrome virus (PRRSV) strains can establish persistent infection in lymphoid tissues of pigs. In this study, expression of several important chemokine ligands (CCL19, CCL21, CCL24, CCL22, CX3CL1, and CCL14) and chemokine receptors (CCR6 and CCR10) which play an essential role in migration and localization of lymphocytes and antigen-presenting cells (APCs) to the lymphoid tissues was down regulated in ILN of CON90-infected pigs (Figure 6a ). In this study, expression of several important chemokine ligands (CCL19, CCL21, CCL24, CCL22, CX3CL1, and CCL14) and chemokine receptors (CCR6 and CCR10) which play an essential role in migration and localization of lymphocytes and antigen-presenting cells (APCs) to the lymphoid tissues was down regulated in ILN of CON90-infected pigs (Figure 6a ). GO terms and KEGG analysis revealed that genes involved in the innate immune (complement and TLR) pathways, apoptosis, cytokine-chemokine signaling, T-cell exhaustion, and humoral responses are highly differentially expressed in PRRSV-infected animals compared to control. abstract: Both virulent and live-attenuated porcine reproductive and respiratory syndrome virus (PRRSV) strains can establish persistent infection in lymphoid tissues of pigs. To investigate the mechanisms of PRRSV persistence, we performed a transcriptional analysis of inguinal lymphoid tissue collected from pigs experimentally infected with an attenuated PRRSV strain at 46 days post infection. A total of 6404 differentially expressed genes (DEGs) were detected of which 3960 DEGs were upregulated and 2444 DEGs were downregulated. Specifically, genes involved in innate immune responses and chemokines and receptors associated with T-cell homing to lymphoid tissues were down regulated. As a result, homing of virus-specific T-cells to lymphoid tissues seems to be ineffective, evidenced by the lower frequencies of virus-specific T-cell in lymphoid tissue than in peripheral blood. Genes associated with T-cell exhaustion were upregulated. Likewise, genes involved in the anti-apoptotic pathway were upregulated. Collectively, the data suggested that the live-attenuated PRRSV strain establishes a pro-survival microenvironment in lymphoid tissue by suppressing innate immune responses, T-cell homing, and preventing cell apoptosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474429/ doi: 10.3390/v12080817 id: cord-331066-ediowz4s author: Chechetkin, Vladimir R. title: Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting date: 2020-09-09 words: 7040.0 sentences: 416.0 pages: flesch: 57.0 cache: ./cache/cord-331066-ediowz4s.txt txt: ./txt/cord-331066-ediowz4s.txt summary: Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Therefore, the putative weakly specific assembly/packaging signals in the genomic RNA of coronaviruses should be coordinated with the parameters of the helical nucleocapsid (such as the helix pitch, inner and outer diameters) which are established by cryoelectron microscopy (cryo-EM) and other structural methods. In this article, we provide methods for the detection and comparative analysis of assembly/packaging signals in the genomic RNA of the coronaviruses SARS-CoV and SARS-CoV-2 and describe main results of our study. The abundance of quasi-periodic patterns in the genomic DNA/RNA sequences can be assessed by the spectral entropy (Balakirev et al., 2003 (Balakirev et al., , 2005 (Balakirev et al., , 2014 Chechetkin, 2011; Chechetkin & Lobzin, 1996; Chechetkin & Turygin, 1994) . abstract: The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Such signals coordinated with the nucleocapsid helical structure were detected and reconstructed in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2. The main period of the signals for both viruses was about 54 nt, that implies 6.75 nt per N protein. The complete coverage of the ssRNA genome of length about 30,000 nt by the nucleocapsid would need 4.4 × 10(3) N proteins, that makes them the most abundant among the structural proteins. The repertoires of motifs for SARS-CoV and SARS-CoV-2 were divergent but nearly coincided for different isolates of SARS-CoV-2. We obtained the distributions of assembly/packaging signals over the genomes with nonoverlapping windows of width 432 nt. Finally, using the spectral entropy, we compared the load from point mutations and indels during virus age for SARS-CoV and SARS-CoV-2. We found the higher mutational load on SARS-CoV. In this sense, SARS-CoV-2 can be treated as a ‘newborn’ virus. These observations may be helpful in practical medical applications and are of basic interest. Communicated by Ramaswamy H. Sarma url: https://arxiv.org/pdf/2007.10274v2.pdf doi: 10.1080/07391102.2020.1815581 id: cord-283590-xvnv17zy author: Chen, Dabiao title: Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report date: 2020-03-05 words: 1499.0 sentences: 96.0 pages: flesch: 48.0 cache: ./cache/cord-283590-xvnv17zy.txt txt: ./txt/cord-283590-xvnv17zy.txt summary: Since December 2019, SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2; previously known as 2019-nCoV) has generated over 70000 cases of COVID-19 (Corona Virus Disease 2019, formerly known as Novel Coronavirus Pneumonia, NCP) in China, including 1870 deaths, as of 17 February 2020 (National Health Commission of the People''s Republic of China, 2020). Currently, COVID-19 patients remain the primary source of infection (Chan et al., 2020 ; General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020; Special Expert Group for Control of the Epidemic of Novel Coronavirus Pneumonia of the Chinese Preventive Medicine Association, 2020). According to the guideline in China, patients should be isolated until two consecutive SARS-CoV-2 RNA tests of respiratory tract specimens are both negative, with an interval of at least 24 h (General Office of National Health Commission and General Office of National Administration of Traditional Chinese Medicine, 2020). abstract: The ongoing outbreak of COVID-19 that began in Wuhan, China, has constituted a Public Health Emergency of International Concern, with cases confirmed in multiple countries. Currently, patients are the primary source of infection. We report a confirmed case of COVID-19 whose oropharyngeal swab test of SARS-CoV-2 RNA turned positive in convalescence. This case highlights the importance of active surveillance of SARS-CoV-2 RNA for infectivity assessment. url: https://www.ncbi.nlm.nih.gov/pubmed/32147538/ doi: 10.1016/j.ijid.2020.03.003 id: cord-261532-q923xxn2 author: Chen, Huihui title: The essential adaptors of innate immune signaling date: 2012-09-21 words: 7414.0 sentences: 401.0 pages: flesch: 45.0 cache: ./cache/cord-261532-q923xxn2.txt txt: ./txt/cord-261532-q923xxn2.txt summary: Microbial components and the endogenous molecules released from damaged cells can stimulate germ-line-encoded pattern recognition receptors (PRRs) to transduce signals to the hub of the innate immune signaling network-the adaptor proteins MyD88/TRIF/MAVS/STING/Caspase-1, where integrated signals relay to the relevant transcription factors IRF3/IRF7/NF-κB/ AP-1 and the signal transducer and activator of transcription 6 (STAT6) to trigger the expression of type I interferons and inflammatory cytokines or the assembly of inflammasomes. These receptors can recruit specific adaptor proteins, like myeloid differentiation primary response gene 88 (MyD88) or Toll/interleukin-1 receptor (TIR) domain-containing adaptor inducing IFN-β (TRIF) in the TLR pathway, mitochondrial antiviral signaling protein (MAVS) downstream of RLRs, stimulator of interferon genes (STING) in the cytosolic DNA response pathway and, cysteine aspartic protease 1 (Caspase-1) as part of the inflammasome, all of which orchestrate the host innate responses, through activation of transcriptional factors such as nuclear factor κB (NF-κB), activator protein 1 (AP-1) and interferon regulatory factors (IRFs), to trigger the production of type І interferons (IFNs), inflammatory cytokines and chemokines. abstract: Microbial components and the endogenous molecules released from damaged cells can stimulate germ-line-encoded pattern recognition receptors (PRRs) to transduce signals to the hub of the innate immune signaling network-the adaptor proteins MyD88/TRIF/MAVS/STING/Caspase-1, where integrated signals relay to the relevant transcription factors IRF3/IRF7/NF-κB/ AP-1 and the signal transducer and activator of transcription 6 (STAT6) to trigger the expression of type I interferons and inflammatory cytokines or the assembly of inflammasomes. Most pleiotropic cytokines are secreted and bind to specific receptors, activating the signaling pathways including JAK-STAT for the proliferation, differentiation and functional capacity of immune cells. This review focuses on several critical adaptors in innate immune signaling cascades and recent progress in their molecular mechanisms. url: https://www.ncbi.nlm.nih.gov/pubmed/22996173/ doi: 10.1007/s13238-012-2063-0 id: cord-346514-vyo8l14p author: Chen, I-Hsuan title: Characterization of the polyadenylation activity in a replicase complex from Bamboo mosaic virus-infected Nicotiana benthamiana plants date: 2013-06-13 words: 5141.0 sentences: 304.0 pages: flesch: 60.0 cache: ./cache/cord-346514-vyo8l14p.txt txt: ./txt/cord-346514-vyo8l14p.txt summary: The polyadenylation signal in the 3′ UTR of BaMV was shown to be involved in the synthesis of minus-strand viral RNA and regulating the length of the poly(A) tail (Chen et al., 2005) . To test whether the replicase preparation could polyadenylate exogenous plus-strand RNA templates, 5′ end-labeled radioactive BaMV plus-strand RNA substrate containing the entire 3′-UTR and 7, 15, or 40 adenylates (r138/7A, r138/15A, or r138/40A, respectively), were subjected to the polyadenylation activity assay. BaMV minigenomes were demonstrated to be suitable templates for an in vitro replication assays (Huang et al., 2009) ; therefore, the exogenous plus-strand or minus-strand BaMV minigenome was added to the reaction to help determine whether the poly(A) tail could be added to the 3′ end of preformed or newly transcribed plus-strand RNA, respectively. abstract: Bamboo mosaic virus (BaMV) has a positive-sense single-stranded RNA genome with a 5′ cap and a 3′ poly(A) tail. To characterize polyadenylation activity in the BaMV replicase complex, we performed the in vitro polyadenylation with various BaMV templates. We conducted a polyadenylation activity assay for BaMV RNA by using a partially purified BaMV replicase complex. The results showed that approximately 200 adenylates at the 3′ end of the RNA were generated on the endogenous RNA templates. Specific fractions derived from uninfected Nicotiana benthamiana plants enhanced the polyadenylation activity, implying that host factors are involved in polyadenylation. Furthermore, polyadenylation can be detected in newly synthesized plus-strand RNA in vitro when using the exogenous BaMV minus-strand minigenome. For polyadenylation on the exogenous plus-strand minigenome, the 3′ end requires at least 4A to reach 22% polyadenylation activity. The results indicate that the BaMV replicase complex recognizes the 3′ end of BaMV for polyadenylation. url: https://www.sciencedirect.com/science/article/pii/S0042682213003139 doi: 10.1016/j.virol.2013.05.032 id: cord-287349-1zcq7kzx author: Chen, James title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex date: 2020-07-28 words: 2959.0 sentences: 215.0 pages: flesch: 53.0 cache: ./cache/cord-287349-1zcq7kzx.txt txt: ./txt/cord-287349-1zcq7kzx.txt summary: title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. The analogous structural 234 arrangement leads us to propose that the SARS-CoV-2 RdRp may backtrack, generating a single-235 stranded RNA segment at the 3''-end that would extrude out the RdRp secondary channel 236 Table S1 ; Video S1). This aspect of helicase function could provide the NTP-296 dependent motor activity necessary to backtrack the RdRp. In cellular organisms, DdRp 297 backtracking plays important roles in many processes, including the control of pausing during 298 transcription elongation, termination, DNA repair, and fidelity (Nudler, 2012) . Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase abstract: Summary SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development. url: https://www.ncbi.nlm.nih.gov/pubmed/32783916/ doi: 10.1016/j.cell.2020.07.033 id: cord-006452-mmdk2xom author: Chen, Jing title: Nucleic Acid-Based Therapeutics for Pulmonary Diseases date: 2018-10-18 words: 6605.0 sentences: 361.0 pages: flesch: 38.0 cache: ./cache/cord-006452-mmdk2xom.txt txt: ./txt/cord-006452-mmdk2xom.txt summary: Nucleic acid-based therapeutics present huge potential in the treatment of pulmonary diseases ranging from lung cancer to asthma and chronic pulmonary diseases, which are often fatal and widely prevalent. In this review, we provide a comprehensive overview of the nucleic acid application for pulmonary diseases, covering action mechanism of the nucleic acid drugs, the novel delivery systems, and the current formulation for the administration to lungs. To overcome these biological barriers, strategies like chemical modification, conjugation, vector encapsulation, and selection of administration route have been utilized to improve the delivery of nucleic acids to lungs. One direction for developing new drugs to treat asthma is to target central pathways to the pathogenesis of the disease, and nucleic acid-mediated therapies silencing the specific effector or the upstream regulator can be a potential approach. Nucleic acid drugs hold great promises as new classes of therapeutic agents for pulmonary diseases, and some candidates have entered into clinical trials (Table III) . abstract: Nucleic acid-based therapeutics present huge potential in the treatment of pulmonary diseases ranging from lung cancer to asthma and chronic pulmonary diseases, which are often fatal and widely prevalent. The susceptibility of nucleic acids to degradation and the complex structure of lungs retard the effective pulmonary delivery of nucleic acid drug. To overcome these barriers, different strategies have been exploited to increase the delivery efficiency using chemically synthesized nucleic acids, vector encapsulation, proper formulation, and administration route. However, several limitations regarding off-target effects and immune stimulation of nucleic acid drugs hamper their translation into the clinical practice. Therefore, their successful clinical application will ultimately rely on well-developed carriers and methods to ensure safety and efficacy. In this review, we provide a comprehensive overview of the nucleic acid application for pulmonary diseases, covering action mechanism of the nucleic acid drugs, the novel delivery systems, and the current formulation for the administration to lungs. The latest advances of nucleic acid drugs under clinical evaluation to treat pulmonary disorders will also be detailed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101845/ doi: 10.1208/s12249-018-1183-0 id: cord-312892-p72zwmtb author: Chen, Nanhua title: RNA sensors of the innate immune system and their detection of pathogens date: 2017-04-04 words: 4237.0 sentences: 237.0 pages: flesch: 44.0 cache: ./cache/cord-312892-p72zwmtb.txt txt: ./txt/cord-312892-p72zwmtb.txt summary: It in turn causes the multimerization of cytoplasmic TIR domains, which will recruit downstream adaptors TRIF or MyD88 through homotypic interaction, further forming signaling complex called signalosome and activating downstream transcription factors: one is NF-jB that induces proinflammtory cytokines, another is interferon regulatory factor (IRF) that induces anti-viral type I Interferon (IFN) (6) . The summary of cellular localizations and distributions, ligand recognitions, activation mechanisms, cell signaling, recognition of pathogens, and cross-talks for RNA PRRs (2) TLR3 (2) RIG-I (2) The understanding of RNA PRR immune biology including the ligand recognitions, cellular localizations, cell signaling pathways, mechanisms of activation, recognized pathogens and the interactions between different RNA PRRs will definitely be helpful to improve the anti-viral immune response. Third, TLR3, 7, 8 are primarily expressed by macrophages and DCs and recognize viral RNA within the endosomal compartment, whereas RLRs (RIG-I, MDA5) and NLRs (NLRP3, NOD2) are ubiquitously expressed and sense viral RNA within the cytoplasm of infected cells (Table 1 ). abstract: The innate immune system plays a critical role in pathogen recognition and initiation of protective immune response through the recognition of pathogen associated molecular patterns (PAMPs) by its pattern recognition receptors (PRRs). Nucleic acids including RNA and DNA have been recognized as very important PAMPs of pathogens especially for viruses. RNA are the major PAMPs of RNA viruses, to which most severe disease causing viruses belong thus posing a tougher challenge to human and animal health. Therefore, the understanding of the immune biology of RNA PRRs is critical for control of pathogen infections especially for RNA virus infections. RNA PRRs are comprised of TLR3, TLR7, TLR8, RIG‐I, MDA5, NLRP3, NOD2, and some other minorities. This review introduces these RNA PRRs by describing the cellular localizations, ligand recognitions, activation mechanisms, cell signaling pathways, and recognition of pathogens; the cross‐talks between various RNA PRRs are also reviewed. The deep insights of these RNA PRRs can be utilized to improve anti‐viral immune response. © 2017 IUBMB Life, 69(5):297–304, 2017 url: https://doi.org/10.1002/iub.1625 doi: 10.1002/iub.1625 id: cord-276914-44ji0g78 author: Chen, Weilie title: Detectable 2019-nCoV viral RNA in blood is a strong indicator for the further clinical severity date: 2020-02-26 words: 2479.0 sentences: 126.0 pages: flesch: 58.0 cache: ./cache/cord-276914-44ji0g78.txt txt: ./txt/cord-276914-44ji0g78.txt summary: However, the concentration of viral RNA in the anal swab (Ct value = 24 + 39) was higher than in the blood (Ct value = 34 + 39) from patient 2, suggesting that the virus might replicate in the digestive tract. Patient 3 (Figure 3(A) ) was transferred to the ICU directly on illness day 11 because of his severe condition, the 2019-nCoV virus was laboratory detected both in pharyngeal (Ct = 30 + 30) and blood samples (Ct = 37 + 39) on day 12, And his infection was confirmed by CDC on day 13. His disease advanced pretty fast and became severe on day 7 and he was transferred to ICU after his blood sample was detected to be virus-positive (Ct = 32 + 37). For patient 1, a high concentration of viral RNA (Ct = 23 + 27, on day 13) was detected in anal swab but not in pharyngeal (the same day) and blood (1 d ahead). abstract: The novel coronavirus (2019-nCoV) infection caused pneumonia. we retrospectively analyzed the virus presence in the pharyngeal swab, blood, and the anal swab detected by real-time PCR in the clinical lab. Unexpectedly, the 2109-nCoV RNA was readily detected in the blood (6 of 57 patients) and the anal swabs (11 of 28 patients). Importantly, all of the 6 patients with detectable viral RNA in the blood cohort progressed to severe symptom stage, indicating a strong correlation of serum viral RNA with the disease severity (p-value = 0.0001). Meanwhile, 8 of the 11 patients with annal swab virus-positive was in severe clinical stage. However, the concentration of viral RNA in the anal swab (Ct value = 24 + 39) was higher than in the blood (Ct value = 34 + 39) from patient 2, suggesting that the virus might replicate in the digestive tract. Altogether, our results confirmed the presence of virus RNA in extra-pulmonary sites. url: https://www.ncbi.nlm.nih.gov/pubmed/32102625/ doi: 10.1080/22221751.2020.1732837 id: cord-285785-29ohzeug author: Chen, Xiaolan title: Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System date: 2020-08-12 words: 9666.0 sentences: 600.0 pages: flesch: 46.0 cache: ./cache/cord-285785-29ohzeug.txt txt: ./txt/cord-285785-29ohzeug.txt summary: Expression analysis and bioinformatical functional annotation through RNA sequence by using line 6 3 and line 7 2 showed that lncRNAs were aberrantly expressed and were involved in immune-related pathways that indicate that lncRNAs participate in regulating MDV infection [70] . Although the underlying functional mechanism of ncRNAs has been revealed in many species, it is still beginning to emerge in response to avian disease, except for miRNAs. Researches on circRNAs and lncRNAs are basically performed on the analysis of their expression profile and associated pathways. For lncRNAs and circRNAs, they mainly exhibit their function through lncRNA/circRNA-miRNA-mRNA axis, however, in some cases they could also regulate the immune process by directly interacting with RNA binding proteins or virus gene sequence. Gene expression profile and long non-coding RNA analysis, using RNA-Seq, in chicken embryonic fibroblast cells infected by avian leukosis virus abstract: The identified non-coding RNAs (ncRNAs) include circular RNAs, long non-coding RNAs, microRNAs, ribosomal RNAs, small interfering RNAs, small nuclear RNAs, piwi-interacting RNAs, and transfer RNAs, etc. Among them, long non-coding RNAs, circular RNAs, and microRNAs are regulatory RNAs that have different functional mechanisms and were extensively participated in various biological processes. Numerous research studies have found that circular RNAs, long non-coding RNAs, and microRNAs played their important roles in avian immune system during the infection of parasites, virus, or bacterium. Here, we specifically review and expand this knowledge with current advances of circular RNAs, long non-coding RNAs, and microRNAs in the regulation of different avian diseases and discuss their functional mechanisms in response to avian diseases. url: https://doi.org/10.3390/life10080148 doi: 10.3390/life10080148 id: cord-294890-93ldjyi5 author: Chen, Yan title: Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour date: 2018-11-06 words: 8668.0 sentences: 451.0 pages: flesch: 54.0 cache: ./cache/cord-294890-93ldjyi5.txt txt: ./txt/cord-294890-93ldjyi5.txt summary: KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. CONCLUSION: Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE. Additionally, 11 potential target genes (mRNAs) and five lncRNAs related to auxin response factors were verified by qPCR in the three stages of early longan SE. Based on the functions of miRNAs and mRNAs in longan and other plants, we speculate that some lncRNAs are involved in regulation of gene expression by acting as miRNA precursors during early longan SE. abstract: BACKGROUND: Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development. RESULTS: In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the “plant-pathogen interaction” and “plant hormone signaling” pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a). CONCLUSION: Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-5158-z) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12864-018-5158-z doi: 10.1186/s12864-018-5158-z id: cord-016179-4i1n9j4x author: Chen, Yi-Ning title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues date: 2015-09-10 words: 2078.0 sentences: 133.0 pages: flesch: 62.0 cache: ./cache/cord-016179-4i1n9j4x.txt txt: ./txt/cord-016179-4i1n9j4x.txt summary: title: Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues A specific one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay using TCoV-specific primers and dual-labeled fluorescent probe for detection and quantitation of TCoV in feces and intestine tissues is described in this chapter. In this chapter, the protocol for one-step real-time RT-PCR to detect, differentiate, and quantitative TCoV RNA in the feces and intestinal tissue is presented. In step 3, the extracted RNA was subjected to one-step real-time RT-PCR for detection and quantitation of TCoV in feces or intestine tissues. Specific real time reverse transcription polymerase chain reaction for detection and quantitation of turkey coronavirus RNA in tissues and feces from turkeys infected with turkey coronavirus The protocol "Real-time reverse transcription-polymerase chain reaction for detection and quantitation of turkey coronavirus RNA in feces and intestine tissues" outlined in this chapter had been successfully carried out in the authors'' studies on molecular diagnostics, molecular virology, immunology, and/or vaccinology of turkey coronaviral enteritis. abstract: Turkey coronavirus (TCoV) infection causes acute atrophic enteritis in turkey poults, leading to significant economic loss in the turkey industry. Rapid detection, differentiation, and quantitation of TCoV are critical to the diagnosis and control of the disease. A specific one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay using TCoV-specific primers and dual-labeled fluorescent probe for detection and quantitation of TCoV in feces and intestine tissues is described in this chapter. The fluorogenic probe labeled with a reporter dye (FAM, 6-carboxytetramethylrhodamine) and a quencher dye (Absolute Quencher™) was designed to bind to a 186 base-pair fragment flanked by the two PCR primers targeting the 3′ end of spike gene (S2) of TCoV. The assay is highly specific and sensitive and can quantitate between 10(2) and 10(10) copies/mL of viral genome. It is useful in monitoring the progression of TCoV-induced atrophic enteritis in the turkey flocks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120390/ doi: 10.1007/978-1-4939-3414-0_13 id: cord-302355-3se1wp8o author: Chen, Yi-Shiuan title: The conserved stem-loop II structure at the 3'' untranslated region of Japanese encephalitis virus genome is required for the formation of subgenomic flaviviral RNA date: 2018-07-26 words: 6004.0 sentences: 292.0 pages: flesch: 53.0 cache: ./cache/cord-302355-3se1wp8o.txt txt: ./txt/cord-302355-3se1wp8o.txt summary: Although XRN1 digestion of a 3''-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Furthermore, the minus-strand templates covering the putative promoter region used for an in vitro RdRp assay gave rise to synthetic products, suggesting that the JEV sfRNA could be initially transcribed from the antigenome and may be further trimmed by XRN1 or other unidentified exoribonucleases. Although efficient RNA replication is required for the detection of any flaviviral RNAs despite which mechanism used for the sfRNA formation, our results were clearly different from the observations from WNV that BHK-21 cells transfected with replicon constructs containing various deletions had no effect on the accumulation of sfRNA when compared to the WT [8] . abstract: Flaviviruses accumulate abundant subgenomic RNA (sfRNA) in infected cells. It has been reported that sfRNA results from stalling of host 5’-to-3’ exoribonuclease XRN1 at the highly structured RNA of the 3’ untranslated region (UTR). Although XRN1 digestion of a 3’-terminal 800-nt RNA could stall at a position to generate the sfRNA in vitro, we found that knocking out XRN1 had no effect on the accumulation of sfRNA in Japanese encephalitis virus (JEV) infected cells. Mutagenesis studies revealed that the stemloop II (SLII) at the 3’ UTR is required for the accumulation of sfRNA. According to the results of an in vitro RNA-dependent RNA polymerase (RdRp) assay, the (-)10431-10566 RNA fragment, containing the putative promoter on the antigenome for the sfRNA transcription, binds to RdRp protein and exhibits a strong promoter activity. Taken together, our results indicate that the JEV sfRNA could be transcribed initially and then be trimmed by XRN1 or other unidentified exoribonucleases. url: https://doi.org/10.1371/journal.pone.0201250 doi: 10.1371/journal.pone.0201250 id: cord-321773-5fw9abzl author: Cheng, Wenyu title: DDX5 RNA Helicases: Emerging Roles in Viral Infection date: 2018-04-09 words: 6739.0 sentences: 370.0 pages: flesch: 48.0 cache: ./cache/cord-321773-5fw9abzl.txt txt: ./txt/cord-321773-5fw9abzl.txt summary: Given the crucial roles of DDX5 in RNA biology, several RNA viruses were found to interact with the protein to promote viral replication (Table 1) , including severe acute respiratory syndrome (SARS) coronavirus (CoV) [16] , human immunodeficiency virus 1 (HIV-1) [17] , hepatitis C virus (HCV) [18] , Japanese encephalitis virus (JEV) [19] , porcine reproductive and respiratory syndrome virus (PRRSV) [20] , and influenza virus [21] . There are several studies that focus on specific inhibitors or drugs of the host DEAD-box helicase to inhibit virus replication or treat cancers [65] [66] [67] , but it remains to be determined whether small molecular inhibitors of the interaction between DDX5 and Rev can be found. The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3 UTR The DEAD-box RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro abstract: Asp-Glu-Ala-Asp (DEAD)-box polypeptide 5 (DDX5), also called p68, is a prototypical member of the large ATP-dependent RNA helicases family and is known to participate in all aspects of RNA metabolism ranging from transcription to translation, RNA decay, and miRNA processing. The roles of DDX5 in cell cycle regulation, tumorigenesis, apoptosis, cancer development, adipogenesis, Wnt-β-catenin signaling, and viral infection have been established. Several RNA viruses have been reported to hijack DDX5 to facilitate various steps of their replication cycles. Furthermore, DDX5 can be bounded by the viral proteins of some viruses with unknown functions. Interestingly, an antiviral function of DDX5 has been reported during hepatitis B virus and myxoma virus infection. Thus, the precise roles of this apparently multifaceted protein remain largely obscure. Here, we provide a rapid and critical overview of the structure and functions of DDX5 with a particular emphasis on its role during virus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/29642538/ doi: 10.3390/ijms19041122 id: cord-269771-hffxb7bm author: Cheung, Ka Shing title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis date: 2020-04-03 words: 4797.0 sentences: 263.0 pages: flesch: 51.0 cache: ./cache/cord-269771-hffxb7bm.txt txt: ./txt/cord-269771-hffxb7bm.txt summary: title: Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool, and also summarized data from a cohort of patients with COVID-19 in Hong Kong. The proportion of patients with detectable stool viral RNA was higher among those with diarrhea than those without diarrhea Table 2 including the hospital admission period, places in which the patients were recruited, sample size, age, sex, disease severity, non-gastrointestinal symptoms (fever and respiratory symptoms) on presentation, and gastrointestinal symptoms (anorexia, nausea/vomiting, diarrhea and abdominal pain/discomfort). In this meta-analysis of 4,243 COVID-19 patients from six countries, the pooled prevalence of all gastrointestinal symptoms (including anorexia, nausea/vomiting, diarrhea or abdominal pain) was 17.6%. Clinical findings in a group of patients infected with the 2019 novel coronavirus (SARS-Cov-2) outside of Wuhan, China: retrospective case series abstract: Abstract Background & Aims Infection with SARS-CoV-2 causes COVID-19, which has been characterized by fever, respiratory, and gastrointestinal symptoms as well as shedding of virus RNA into feces. We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool, and also summarized data from a cohort of patients with COVID-19 in Hong Kong. Methods We collected data from the cohort of patients with COVID-19 in Hong Kong (n=59; diagnosis from February 2 through Feb 29, 2020), and searched PubMed, Embase, Cochrane and three Chinese databases through March 11, 2020 according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We analyzed pooled data on the prevalence of overall and individual gastrointestinal symptoms (anorexia, nausea, vomiting, diarrhea, and abdominal pain or discomfort) using a random effects model. Results Among the 59 patients with COVID-19 in Hong Kong, 15 patients (25.4%) had gastrointestinal symptoms and 9 patients (15.3%) had stool that tested positive for virus RNA. Stool viral RNA was detected in 38.5% and 8.7% among those with and without diarrhea, respectively (P=.02). The median fecal viral load was 5.1 log10cpm in patients with diarrhea vs 3.9 log10cpm in patients without diarrhea (P=.06). In a meta-analysis of 60 studies, comprising 4243 patients, the pooled prevalence of all gastrointestinal symptoms was 17.6% (95% CI, 12.3%–24.5%); 11.8% of patients with non-severe COVID-19 had gastrointestinal symptoms (95% CI, 4.1%–29.1%) and 17.1% of patients with severe COVID-19 had gastrointestinal symptoms (95% CI, 6.9%–36.7%). In the meta-analysis, the pooled prevalence of stool samples that were positive for virus RNA was 48.1% (95% CI, 38.3%–57.9%); of these samples, 70.3% of those collected after loss of virus from respiratory specimens tested positive for the virus (95% CI, 49.6%–85.1%). Conclusions In an analysis of data from the Hong Kong cohort of patients with COVID-19 and a meta-analysis of findings from publications, we found that 17.6% of patients with COVID-19 had gastrointestinal symptoms. Virus RNA was detected in stool samples from 48.1% patients—even in stool collected after respiratory samples tested negative. Healthcare workers should therefore exercise caution in collecting fecal samples or performing endoscopic procedures in patients with COVID-19—even during patient recovery. url: https://www.ncbi.nlm.nih.gov/pubmed/32251668/ doi: 10.1053/j.gastro.2020.03.065 id: cord-267867-q52nvn0n author: Chevalier, Christophe title: Inhibition of Hepatitis C Virus Infection in Cell Culture by Small Interfering RNAs date: 2016-12-14 words: 8001.0 sentences: 395.0 pages: flesch: 48.0 cache: ./cache/cord-267867-q52nvn0n.txt txt: ./txt/cord-267867-q52nvn0n.txt summary: Several siRNAs dramatically reduced or even abrogated the replication of selectable subgenomic HCV replicons upon cotransfection of human hepatoma cells with viral target and siRNAs, or upon transfection of cells supporting autonomous replication of HCV replicon with siRNAs. Importantly, three siRNAs also proved capable of strongly inhibiting virus production in cell culture. Several siRNAs dramatically reduced or even abrogated the replication of selectable subgenomic HCV replicons upon cotransfection of human hepatoma cells with viral target and siRNAs, or upon transfection of cells supporting autonomous replication of HCV replicon with siRNAs. Importantly, three siRNAs also proved capable of strongly inhibiting virus production in cell culture. We sought to determine whether the siRNAs si240-1a, si244, and si313, shown to be the most efficient in inhibiting the replication of HCV subgenomic replicons both transiently and under selective pressure, are also capable of efficiently blocking virus infection in cell culture. abstract: Hepatitis C virus (HCV) infection is a major cause of chronic liver disease and hepatocellular carcinoma, yet fully efficacious treatments are missing. In this study, we investigated RNA interference (RNAi), a specific gene silencing process mediated by small interfering RNA (siRNA) duplexes, as an antiviral strategy against HCV. Synthetic siRNAs were designed to target conserved sequences of the HCV 5′ nontranslated region (NTR) located in a functional, stem–loop structured domain of the HCV internal ribosome entry site (IRES), which is crucial for initiation of polyprotein translation. Several siRNAs dramatically reduced or even abrogated the replication of selectable subgenomic HCV replicons upon cotransfection of human hepatoma cells with viral target and siRNAs, or upon transfection of cells supporting autonomous replication of HCV replicon with siRNAs. Importantly, three siRNAs also proved capable of strongly inhibiting virus production in cell culture. One siRNA, targeting a sequence that is highly conserved across all genotypes and forms a critical pseudoknot structure involved in translation, was identified as the most promising therapeutic candidate. These results indicate that the HCV life cycle can be efficiently blocked by using properly-designed siRNAs that target functionally important, highly conserved sequences of the HCV IRES. This finding offers a novel approach towards developing IRES-based antiviral treatment for chronic HCV infections. url: https://www.sciencedirect.com/science/article/pii/S152500161632439X doi: 10.1038/sj.mt.6300186 id: cord-319635-kh99n7q2 author: Chiang, Wei-Wei title: Cell Type-Dependent RNA Recombination Frequency in the Japanese Encephalitis Virus date: 2014-07-22 words: 5101.0 sentences: 281.0 pages: flesch: 55.0 cache: ./cache/cord-319635-kh99n7q2.txt txt: ./txt/cord-319635-kh99n7q2.txt summary: Such cleaved small RNA fragments may be further degraded through an RNA interference pathway triggered by viral double-stranded RNA during replication in mosquito cells, resulting in a lower frequency of RNA recombination in mosquito cells compared to that which occurs in mammalian cells. Yates'' chi-square test was used to assess the frequency of RNA recombination in cells coinfected by two virus strains or transfected by viral RNA fragments. Two and one recombinant form(s) were, respectively, identified in selected samples from BHK-21 and C6/36 cells, when they were coinfected with the T1P1-S1 and CJN-S1 strains of the Japanese encephalitis virus. As in our previous report, different strains of the JEV can coinfect host cells derived from mosquitoes or mammals [25] , which actually generates recombinant forms of the virus [30] . In this study, we infected host cells with Nakayama strains of the JEV, followed by transfection of the (+)5 3 -UTR-I RNA fragment. abstract: Japanese encephalitis virus (JEV) is one of approximately 70 flaviviruses, frequently causing symptoms involving the central nervous system. Mutations of its genomic RNA frequently occur during viral replication, which is believed to be a force contributing to viral evolution. Nevertheless, accumulating evidences show that some JEV strains may have actually arisen from RNA recombination between genetically different populations of the virus. We have demonstrated that RNA recombination in JEV occurs unequally in different cell types. In the present study, viral RNA fragments transfected into as well as viral RNAs synthesized in mosquito cells were shown not to be stable, especially in the early phase of infection possibly via cleavage by exoribonuclease. Such cleaved small RNA fragments may be further degraded through an RNA interference pathway triggered by viral double-stranded RNA during replication in mosquito cells, resulting in a lower frequency of RNA recombination in mosquito cells compared to that which occurs in mammalian cells. In fact, adjustment of viral RNA to an appropriately lower level in mosquito cells prevents overgrowth of the virus and is beneficial for cells to survive the infection. Our findings may also account for the slower evolution of arboviruses as reported previously. url: https://doi.org/10.1155/2014/471323 doi: 10.1155/2014/471323 id: cord-324638-gwd8qin6 author: Chiu, Rossa WK title: Automated extraction protocol for quantification of SARS-Coronavirus RNA in serum: an evaluation study date: 2006-02-09 words: 3360.0 sentences: 152.0 pages: flesch: 49.0 cache: ./cache/cord-324638-gwd8qin6.txt txt: ./txt/cord-324638-gwd8qin6.txt summary: We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The main objective of this study was to compare the resultant analytical sensitivity and quantitative performance of the serum SARS-CoV RNA test when either the manual or automated extraction protocol was used. The modified large volume protocol with the external lysis step was further compared with the external lysis protocol of the total nucleic acid isolation kit using a transport medium mixture containing 10 6 copies/mL of inactivated SARS-CoV. Serially diluted inactivated SARS-CoV isolate in transport medium was extracted by both the column-based manual method and the MagNA Pure LC instrument using the modified large volume protocol with external lysis. abstract: BACKGROUND: We have previously developed a test for the diagnosis and prognostic assessment of the severe acute respiratory syndrome (SARS) based on the detection of the SARS-coronavirus RNA in serum by real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR). In this study, we evaluated the feasibility of automating the serum RNA extraction procedure in order to increase the throughput of the assay. METHODS: An automated nucleic acid extraction platform using the MagNA Pure LC instrument (Roche Diagnostics) was evaluated. We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The modified protocol was compared with a column-based extraction kit (QIAamp viral RNA mini kit, Qiagen) for quantitative performance, analytical sensitivity and precision. RESULTS: The newly developed automated protocol was shown to be free from carry-over contamination and have comparable performance with other standard protocols and kits designed for the MagNA Pure LC instrument. However, the automated method was found to be less sensitive, less precise and led to consistently lower serum SARS-coronavirus concentrations when compared with the column-based extraction method. CONCLUSION: As the diagnostic efficiency and prognostic value of the serum SARS-CoV RNA RT-PCR test is critically associated with the analytical sensitivity and quantitative performance contributed both by the RNA extraction and RT-PCR components of the test, we recommend the use of the column-based manual RNA extraction method. url: https://www.ncbi.nlm.nih.gov/pubmed/16466582/ doi: 10.1186/1471-2334-6-20 id: cord-314877-db7tze8j author: Chkuaseli, Tamari title: Activation of viral transcription by stepwise largescale folding of an RNA virus genome date: 2020-08-12 words: 8535.0 sentences: 421.0 pages: flesch: 48.0 cache: ./cache/cord-314877-db7tze8j.txt txt: ./txt/cord-314877-db7tze8j.txt summary: When viewed in the context of the RNA secondary structure model for the TBSV genome (48) , the DE/CE interaction corresponds to the closing stem of a sizable RNA domain, termed large domain 3 (LD3), which, along with formation of the adjacent LD2, acts to unite the AS2 and RS2 sequences ( Figure 1B) . Translational readthrough for the CIRV genome requires a long-distance RNA-RNA interaction (LDRI) between RTSL and the 3 UTR, involving the PRTE and DRTE partner sequences, respectively ( Figure 1A , B) (39) . The binding of RTSL-TL to SL59-5 was investigated functionally by introducing compensatory nucleotide substitutions into the candidate partner sequences and assessing the effects on sg mRNA1 accumulation following transfection of mutant viral RNA genomes into protoplasts pairing potential in mutants TC-6 and TC-7 diminished sg mRNA1 plus-and minus-strand levels below ∼10% of wt, while regenerating pairing capacity with alternate nucleotides in mutant TC-8 restored levels up to ∼50-62% of wt ( Figure 3B, C) . abstract: The genomes of RNA viruses contain regulatory elements of varying complexity. Many plus-strand RNA viruses employ largescale intra-genomic RNA-RNA interactions as a means to control viral processes. Here, we describe an elaborate RNA structure formed by multiple distant regions in a tombusvirus genome that activates transcription of a viral subgenomic mRNA. The initial step in assembly of this intramolecular RNA complex involves the folding of a large viral RNA domain, which generates a discontinuous binding pocket. Next, a distally-located protracted stem-loop RNA structure docks, via base-pairing, into the binding site and acts as a linchpin that stabilizes the RNA complex and activates transcription. A multi-step RNA folding pathway is proposed in which rate-limiting steps contribute to a delay in transcription of the capsid protein-encoding viral subgenomic mRNA. This study provides an exceptional example of the complexity of genome-scale viral regulation and offers new insights into the assembly schemes utilized by large intra-genomic RNA structures. url: https://www.ncbi.nlm.nih.gov/pubmed/32785642/ doi: 10.1093/nar/gkaa675 id: cord-305811-987dhnf7 author: Cho, Che-Pei title: Regulation of Programmed Ribosomal Frameshifting by Co-Translational Refolding RNA Hairpins date: 2013-04-29 words: 5837.0 sentences: 301.0 pages: flesch: 49.0 cache: ./cache/cord-305811-987dhnf7.txt txt: ./txt/cord-305811-987dhnf7.txt summary: Because both 59CC-WT and 13363-13520 constructs share 27 identical nucleotides upstream of their slippery sites, the attenuation activity difference is not likely to be caused by an E-site flanking sequences effect [12, 13] but rather by the disruption of the two potential AU base pairs. We noticed a potential to form four extra base pairs between 59and 39-flanking sequences (GACG and CGUU, respectively) of the 6BPGC hairpin stem (and other deletion mutants) due to the existence of a 59 SalI cloning site (Fig. S1A ). The results (Fig. S1C ) indicate that the two potential base pairs involving E-site sequences are not the main cause of observed attenuation activity in 293T cell cultures. Furthermore, mutating two nucleotides (27 nucleotides upstream of the E site) to disrupt Watson-Crick base pairs in the lower hairpin stem dramatically impairs attenuation activity (Fig. 2) , indicating that attenuation is not caused by primary sequencemediated flanking-sequences effects [12, 13] . abstract: RNA structures are unwound for decoding. In the process, they can pause the elongating ribosome for regulation. An example is the stimulation of -1 programmed ribosomal frameshifting, leading to 3′ direction slippage of the reading-frame during elongation, by specific pseudoknot stimulators downstream of the frameshifting site. By investigating a recently identified regulatory element upstream of the SARS coronavirus (SARS-CoV) −1 frameshifting site, it is shown that a minimal functional element with hairpin forming potential is sufficient to down-regulate−1 frameshifting activity. Mutagenesis to disrupt or restore base pairs in the potential hairpin stem reveals that base-pair formation is required for−1 frameshifting attenuation in vitro and in 293T cells. The attenuation efficiency of a hairpin is determined by its stability and proximity to the frameshifting site; however, it is insensitive to E site sequence variation. Additionally, using a dual luciferase assay, it can be shown that a hairpin stimulated +1 frameshifting when placed upstream of a +1 shifty site in yeast. The investigations indicate that the hairpin is indeed a cis-acting programmed reading-frame switch modulator. This result provides insight into mechanisms governing−1 frameshifting stimulation and attenuation. Since the upstream hairpin is unwound (by a marching ribosome) before the downstream stimulator, this study’s findings suggest a new mode of translational regulation that is mediated by the reformed stem of a ribosomal unwound RNA hairpin during elongation. url: https://doi.org/10.1371/journal.pone.0062283 doi: 10.1371/journal.pone.0062283 id: cord-275720-kf9m4zho author: Cho, Won Kyong title: Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection date: 2012-05-06 words: 7132.0 sentences: 390.0 pages: flesch: 47.0 cache: ./cache/cord-275720-kf9m4zho.txt txt: ./txt/cord-275720-kf9m4zho.txt summary: At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. This is the first report of a genome-wide fungal gene expression analysis during mycovirus infection using a 3′ tiling microarray, and our findings show global differences in host cellular pathways in F. For example, according to the qRT-PCR and microarray results, the transcript levels for three genes, including FGSG_01379, FGSG_03143, and FGSG_03911, were highly reduced at both 36 h and 120 h, whereas FGSG_03788, FGSG_00023, FGSG_07804, FGSG_07801, and FGSG_13222 were strongly induced regardless of the time point ( Figure 3A -C). graminearum harboring FgV1-DK21 in detail, samples were harvested at two different time points, thus providing lists of differentially expressed genes early and late in the host containing FgV1-DK21 as compared to an uninfected strain. abstract: BACKGROUND: Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB) disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessary for preventing damage caused by F. graminearum. Therefore, we investigated important cellular regulatory processes in a host containing FgV1-DK21 as compared to an uninfected parent using a transcriptional approach. RESULTS: Using a 3′-tiling microarray covering all known F. graminearum genes, we carried out genome-wide expression analyses of F. graminearum at two different time points. At the early point of growth of an infected strain as compared to an uninfected strain, genes associated with protein synthesis, including ribosome assembly, nucleolus, and ribosomal RNA processing, were significantly up-regulated. In addition, genes required for transcription and signal transduction, including fungal-specific transcription factors and cAMP signaling, respectively, were actively up-regulated. In contrast, genes involved in various metabolic pathways, particularly in producing carboxylic acids, aromatic amino acids, nitrogen compounds, and polyamines, showed dramatic down-regulation at the early time point. Moreover, genes associated with transport systems localizing to transmembranes were down-regulated at both time points. CONCLUSION: This is the first report of global change in the prominent cellular pathways in the Fusarium host containing FgV1-DK21. The significant increase in transcripts for transcription and translation machinery in fungal host cells seems to be related to virus replication. In addition, significant down-regulation of genes required for metabolism and transporting systems in a fungal host containing the virus appears to be related to the host defense mechanism and fungal virulence. Taken together, our data aid in the understanding of how FgV1-DK21 regulates the transcriptional reprogramming of F. graminearum. url: https://www.ncbi.nlm.nih.gov/pubmed/22559730/ doi: 10.1186/1471-2164-13-173 id: cord-270243-moxleyjg author: Cholleti, Harindranath title: Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique date: 2018-05-28 words: 3245.0 sentences: 190.0 pages: flesch: 50.0 cache: ./cache/cord-270243-moxleyjg.txt txt: ./txt/cord-270243-moxleyjg.txt summary: Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Different studies have shown that viral pathogens, such as Thogoto viruses, Wad Medani virus, Nairobi sheep disease virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus and Tick-borne encephalitis virus [1, [6] [7] [8] , can be found in Rhipicephalus ticks. Numerous studies have used metagenomics to explore viral communities in different arthropod species and have in these identified viruses associated with a broad range of animals, plants and insects. However, the identified ORFs exhibit high genetic diversity to known quaranjavirus genomes, with an amino acid identity of only 32-55%, indicating that these represent novel viral sequences belonging to the Quaranjavirus genus. The parvovirus sequences identified in the current study had closest similarity to non-structural protein 1 of different densoviruses, which were shown previously to integrate into tick genomes such as in Ixodes, Amblyomma and Rhipicephalus genera [28, 29] . abstract: Background: Ticks are primary vectors for many well-known disease-causing agents that affect human and animal populations globally such as tick-borne encephalitis, Crimean-Congo hemorrhagic fever and African swine fever. In this study, viral metagenomics was used to identify what viruses are present in Rhipicephalus spp. ticks collected in the Zambezi Valley of Mozambique. Methods: The RNA was amplified with sequence-independent single primer amplification (SISPA) and high-throughput sequencing was performed on the Ion Torrent platform. The generated sequences were subjected to quality check and classfied by BLAST. CodonCode aligner and SeqMan were used to assemble the sequences. Results: The majority of viral sequences showed closest sequence identity to the Orthomyxoviridae family, although viruses similar to the Parvoviridae and Coronaviridae were also identified. Nearly complete sequences of five orthomyxoviral segments (HA, NP, PB1, PB2, and PA) were obtained and these showed an amino acid identity of 32–52% to known quaranjaviruses. The sequences were most closely related to the Wellfleet Bay virus, detected and isolated from common eider during a mortality event in the USA. Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Further genetic and biological studies are needed in order to investigate potential pathogenesis of the identified orthomyxovirus. url: https://www.ncbi.nlm.nih.gov/pubmed/29868166/ doi: 10.1080/20008686.2018.1478585 id: cord-311625-d7iycdyh author: Choong, Oi Kuan title: In Vitro Antiviral Activity of Circular Triple Helix Forming Oligonucleotide RNA towards Feline Infectious Peritonitis Virus Replication date: 2014-02-20 words: 4014.0 sentences: 231.0 pages: flesch: 52.0 cache: ./cache/cord-311625-d7iycdyh.txt txt: ./txt/cord-311625-d7iycdyh.txt summary: The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log(10) from 10(14) in the virus-inoculated cells to 10(9) in the circular TFO RNAs-transfected cells. The data analyzed by one-way ANOVA, Tukey post hoc test showed significant high viral RNA genome copy number of 4.03 × 10 14 for virus inoculated cells as compared to circular TFO1, TFO3, TFO4, and TFO5 treatments ( ≤ 0.05). In this study, circular Triple Helix Forming Oligonucleotide (TFO) RNAs, specifically targeting the short regions of viral genome for triplex formation, were designed and evaluated. abstract: Feline Infectious Peritonitis (FIP) is a severe fatal immune-augmented disease in cat population. It is caused by FIP virus (FIPV), a virulent mutant strain of Feline Enteric Coronavirus (FECV). Current treatments and prophylactics are not effective. The in vitro antiviral properties of five circular Triple-Helix Forming Oligonucleotide (TFO) RNAs (TFO1 to TFO5), which target the different regions of virulent feline coronavirus (FCoV) strain FIPV WSU 79-1146 genome, were tested in FIPV-infected Crandell-Rees Feline Kidney (CRFK) cells. RT-qPCR results showed that the circular TFO RNAs, except TFO2, inhibit FIPV replication, where the viral genome copy numbers decreased significantly by 5-fold log(10) from 10(14) in the virus-inoculated cells to 10(9) in the circular TFO RNAs-transfected cells. Furthermore, the binding of the circular TFO RNA with the targeted viral genome segment was also confirmed using electrophoretic mobility shift assay. The strength of binding kinetics between the TFO RNAs and their target regions was demonstrated by NanoITC assay. In conclusion, the circular TFOs have the potential to be further developed as antiviral agents against FIPV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/24707494/ doi: 10.1155/2014/654712 id: cord-292831-oihcay6w author: Choudhary, Manohar L. title: Development of a multiplex one step RT-PCR that detects eighteen respiratory viruses in clinical specimens and comparison with real time RT-PCR date: 2013-01-08 words: 3725.0 sentences: 210.0 pages: flesch: 53.0 cache: ./cache/cord-292831-oihcay6w.txt txt: ./txt/cord-292831-oihcay6w.txt summary: The purpose of this study was to develop a one step mRT-PCR that could detect respiratory viruses including influenza A viruses, H1N1pdm09, seasonal H1N1, H3N2, influenza B viruses, respiratory syncytial virus (RSV) A and B, human metapneumovirus (HMPV), parainfluenza viruses (PIV) 1, 2, 3, 4, rhinovirus, enterovirus, corona viruses OC43, 229E, NL63 and HKU1 in three sets in human clinical samples and to compare it with rRT-PCR. The specificity of the multiplex PCR assay was evaluated by cross reaction tests with known viral isolates and different panels of sequence confirmed known clinical respiratory samples as reference material. Specificity of the mRT-PCR assay was evaluated by cross reaction tests against known respiratory virus isolates/positive samples and a WHO QA/QC panel for influenza viruses showed no cross reactivity amongst different viruses. For validation of set 1 of the multiplex assay, 114 respiratory clinical specimens previously positive for influenza viruses by rRT-PCR were used and results were 100% concordant. abstract: Rapid and accurate diagnosis of viral respiratory infections is crucial for patient management. Multiplex reverse transcriptase polymerase chain reaction (mRT-PCR) is used increasingly to diagnose respiratory infections and has shown to be more sensitive than viral culture and antigen detection. Objective of the present study was to develop a one-step mRT-PCR that could detect 18 respiratory viruses in three sets. The method was compared with real time RT-PCR (rRT-PCR) for its sensitivity and specificity. Clinical specimens from 843 pediatric patients with respiratory symptoms were used in the study. 503 (59.7%) samples were detected positive by mRT-PCR. Of these 462 (54.8%) exhibited presence of a single pathogen and 41 (4.9%) had multiple pathogens. rRT-PCR detected 439 (52.1%) positive samples, where 419 (49.7%) exhibited one virus and 20 (2.4%) showed co-infections. Concordance between mRT-PCR and rRT-PCR was 91.9% and kappa correlation 0.837. Sensitivity and specificity of mRT-PCR were 99.5% and 83.7% while that of rRT-PCR was 86.9% and 99.4% respectively. Rhinovirus (17.2%) was the most frequently detected virus followed by respiratory syncytial virus B (15.4%), H1N1pdm09 (8.54%), parainfluenza virus-3 (5.8%) and metapneumovirus (5.2%). In conclusion, mRT-PCR is a rapid, cost effective, specific and highly sensitive method for detection of respiratory viruses. url: https://api.elsevier.com/content/article/pii/S0166093413000049 doi: 10.1016/j.jviromet.2012.12.017 id: cord-294483-mozabpcs author: Choudhary, Manohar Lal title: Development of in vitro transcribed RNA as positive control for laboratory diagnosis of SARS-CoV-2 in India date: 2020-04-28 words: 637.0 sentences: 50.0 pages: flesch: 66.0 cache: ./cache/cord-294483-mozabpcs.txt txt: ./txt/cord-294483-mozabpcs.txt summary: Ten-fold serial dilutions of each transcribed RNA products were tested with respective gene primer probe sets for specific detection and limit of detection. Further, the IVT RNA of each gene was serially diluted 10-fold (10 1 to 10 10 ), and the performance was tested with genespecific primer probe by real-time RT-PCR. When the assay was first set up at the National Influenza Centre of ICMR-NIV, Pune, the IVT RNA for E and SARS coronavirus Frankfurt 1 strain were received from EVAg. The real-time PCR screening assay (E gene) was also established at the 13 VRDLs as part of ICMR''s efforts to expand testing to VRDLs closer to major airports 3 . This necessitated the development of an indigenous IVT RNA for E and RdRp. In addition, majority of the WHO screening protocols (5 of 6) are based on N gene targeting different nucleotide positions and require multiple specific positive controls 4 . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32242876/ doi: 10.4103/ijmr.ijmr_671_20 id: cord-334891-4jgtxg07 author: Choudhury, Abhigyan title: In silico analyses on the comparative sensing of SARS-CoV-2 mRNA by intracellular TLRs of human date: 2020-11-11 words: 2926.0 sentences: 169.0 pages: flesch: 54.0 cache: ./cache/cord-334891-4jgtxg07.txt txt: ./txt/cord-334891-4jgtxg07.txt summary: This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. The binding of Spike protein with the human ACE2 receptor triggers the pathogenesis 3 of the SARS-CoV-2, leading to the activation of TLRs to activate the proliferation and 4 production of pro-inflammatory cytokines causing cytokine storm, those results in 5 inflammations. abstract: The worldwide outbreak of COVID-19 pandemic caused by SARS-CoV-2 leads to loss of mankind and global economic stability. The continuous spreading of the disease and its pathogenesis takes millions of lives of peoples and the unavailability of appropriate therapeutic strategy makes it much more severe. Toll-like receptors (TLRs) are the crucial mediators and regulators of host immunity. The role of several TLRs in immunomodulation of host by SARS-CoV-2 is recently demonstrated. However, the functionality of human intracellular TLRs including TLR3,7,8 and 9 is still being untested for sensing of viral RNA. This study is hoped to rationalize the comparative binding and sensing of SARS-CoV-2 mRNA towards the intracellular TLRs, considering the solvent-based force-fields operational in the cytosolic aqueous microenvironment that predominantly drive these reactions. Our in-silico study on the binding of all mRNAs with the intracellular TLRs shown that the mRNA of NSP10, S2, and E proteins of SARS-CoV-2 are potent enough to bind with TLR3, TLR9, and TLR7 and trigger downstream cascade reactions, and may be used as an option for validation of therapeutic option and immunomodulation against COVID-19. url: https://doi.org/10.1101/2020.11.11.377713 doi: 10.1101/2020.11.11.377713 id: cord-289038-15yp9uqy author: Chow, Jonathan Tak-Sum title: Prediction and Analysis of SARS-CoV-2-Targeting MicroRNA in Human Lung Epithelium date: 2020-08-26 words: 5312.0 sentences: 445.0 pages: flesch: 62.0 cache: ./cache/cord-289038-15yp9uqy.txt txt: ./txt/cord-289038-15yp9uqy.txt summary: The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection. Another recent study used a high-throughput reporter screen of miRNA from human and mouse respiratory epithelial cells to identify hsa-miR-127-3p, hsa-miR-486-5p, and hsa-miR-593-5p as contributors to the antiviral defence against influenza A virus by targeting the genomes of the H3N2 and attenuated PR8 (H1N1) viral strains [16] . Given the wealth of evidence supporting a role for miRNA in host cell antiviral defence mechanisms, we sought to identify human miRNA that have the potential to target the SARS-CoV-2 genome. DEA of Calu3 cells infected with SARS-CoV revealed that only hsa-miR-155-3p (upregulated) and hsa-let-7a-3p (downregulated) out of the 128 miRNA we identified in this study, were differentially expressed ( Figure 4B ). abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an RNA virus, is responsible for the coronavirus disease 2019 (COVID-19) pandemic of 2020. Experimental evidence suggests that microRNA can mediate an intracellular defence mechanism against some RNA viruses. The purpose of this study was to identify microRNA with predicted binding sites in the SARS-CoV-2 genome, compare these to their microRNA expression profiles in lung epithelial tissue and make inference towards possible roles for microRNA in mitigating coronavirus infection. We hypothesize that high expression of specific coronavirus-targeting microRNA in lung epithelia may protect against infection and viral propagation, conversely, low expression may confer susceptibility to infection. We have identified 128 human microRNA with potential to target the SARS-CoV-2 genome, most of which have very low expression in lung epithelia. Six of these 128 microRNA are differentially expressed upon in vitro infection of SARS-CoV-2. Additionally, 28 microRNA also target the SARS-CoV genome while 23 microRNA target the MERS-CoV genome. We also found that a number of microRNA are commonly identified in two other studies. Further research into identifying bona fide coronavirus targeting microRNA will be useful in understanding the importance of microRNA as a cellular defence mechanism against pathogenic coronavirus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32858958/ doi: 10.3390/genes11091002 id: cord-322756-ouvn71r9 author: Chow, Michael Y.T. title: Inhaled RNA Therapy: From Promise to Reality date: 2020-09-04 words: 7283.0 sentences: 454.0 pages: flesch: 44.0 cache: ./cache/cord-322756-ouvn71r9.txt txt: ./txt/cord-322756-ouvn71r9.txt summary: Studies investigating RNA therapeutics in pulmonary diseases have rapidly expanded and drug administration by inhalation allows the direct delivery of RNA therapeutics to the target site of action while minimizing systemic exposure. Interestingly, it has been known for over a decade that naked RNA, including both siRNA and mRNA, can be transfected in the lung following pulmonary delivery, as shown in many in vivo studies [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] . Both studies demonstrated a gene-silencing effect of the powder formulations in lung tissues following intratracheal administration in mouse models of lung cancer, taking these delivery systems one step closer to clinical application. To take advantage of this phenomenon, pulmonary surfactant and surfactant protein B-coated dextran-based nanoparticles were developed for siRNA delivery, with successful gene-silencing effects observed in healthy mice and in a model of acute lung injury (ALI), respectively, following pulmonary administration [29, 69] (Table 1) . abstract: RNA-based medicine is receiving growing attention for its diverse roles and potential therapeutic capacity. The largest obstacle in its clinical translation remains identifying a safe and effective delivery system. Studies investigating RNA therapeutics in pulmonary diseases have rapidly expanded and drug administration by inhalation allows the direct delivery of RNA therapeutics to the target site of action while minimizing systemic exposure. In this review, we highlight recent developments in pulmonary RNA delivery systems with the use of nonviral vectors. We also discuss the major knowledge gaps that require thorough investigation and provide insights that will help advance this exciting field towards the bedside. url: https://www.sciencedirect.com/science/article/pii/S0165614720301802 doi: 10.1016/j.tips.2020.08.002 id: cord-304553-gbwb7fqi author: Christopher, Mary E. title: Broad-Spectrum Drugs Against Viral Agents date: 2008-09-01 words: 11323.0 sentences: 550.0 pages: flesch: 40.0 cache: ./cache/cord-304553-gbwb7fqi.txt txt: ./txt/cord-304553-gbwb7fqi.txt summary: Nonspecific, broad-spectrum immune responses can be induced by double-stranded (ds)RNAs such as poly (ICLC), or oligonucleotides (ODNs) containing unmethylated deocycytidyl-deoxyguanosinyl (CpG) motifs. Poly (ICLC), a dsRNA, and CpG ODNs, molecular mimics for TLR3 and TLR9, respectively, have been reported to non-specifically stimulate the innate immune system and to provide protection against various bacterial and viral pathogens, including influenza. Mice treated with two doses of poly (ICLC), 48 h apart, up to 12 d prior to viral challenge were completely protected from infection, whereas survival rates decreased to 80, 40 and 0%, when pre-treatment was given 14, 16 or 20 d prior to virus challenge, respectively [32] . CpG ODN treatment of splenocytes from senescence-accelerated SAM-P1 strain of mice increased IFN-γ and administration in vivo generated virus-specific cytotoxic T lymphocyte responses, NK cell activation, virus-specific Ig isotype switch from IgG1 to IgG2a, increased viral clearance and survival following influenza viral challenge. Viral infection and Toll-like receptor agonists induce a differential expression of type I and lambda interferons in human plasmacytoid and monocyte-derived dendritic cells abstract: Development of antivirals has focused primarily on vaccines and on treatments for specific viral agents. Although effective, these approaches may be limited in situations where the etiologic agent is unknown or when the target virus has undergone mutation, recombination or reassortment. Augmentation of the innate immune response may be an effective alternative for disease amelioration. Nonspecific, broad-spectrum immune responses can be induced by double-stranded (ds)RNAs such as poly (ICLC), or oligonucleotides (ODNs) containing unmethylated deocycytidyl-deoxyguanosinyl (CpG) motifs. These may offer protection against various bacterial and viral pathogens regardless of their genetic makeup, zoonotic origin or drug resistance. url: https://doi.org/10.3390/ijms9091561 doi: 10.3390/ijms9091561 id: cord-261279-6mef38eo author: Chu, Daniel K W title: Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia date: 2020-01-31 words: 2971.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-261279-6mef38eo.txt txt: ./txt/cord-261279-6mef38eo.txt summary: RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). In this study, we report the development of RT-PCR assays to detect this novel virus in human clinical specimens. Two monoplex real-time RT-PCR assays targeting the ORF1b and N gene regions of 2019-nCoV were designed based on the first publicly available sequence in Genbank (Accession number: MN908947). Viral RNA from cells infected by SARS coronavirus or DNA plasmids containing the target sequences were positive in the assays as expected. In addition, the N gene RT-PCR assay was found to be more sensitive in detecting 2019-nCoV RNA in the studied clinical samples. abstract: BACKGROUND: A novel coronavirus of zoonotic origin (2019-nCoV) has recently been identified in patients with acute respiratory disease. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. The outbreak was initially detected in Wuhan, a major city of China, but has subsequently been detected in other provinces of China. Travel-associated cases have also been reported in a few other countries. Outbreaks in health care workers indicate human-to-human transmission. Molecular tests for rapid detection of this virus are urgently needed for early identification of infected patients. METHODS: We developed two 1-step quantitative real-time reverse-transcription PCR assays to detect two different regions (ORF1b and N) of the viral genome. The primer and probe sets were designed to react with this novel coronavirus and its closely related viruses, such as SARS coronavirus. These assays were evaluated using a panel of positive and negative controls. In addition, respiratory specimens from two 2019-nCoV-infected patients were tested. RESULTS: Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10(−4)-2000 TCID(50)/reaction). Using DNA plasmids as positive standards, the detection limits of these assays were found to be below 10 copies per reaction. All negative control samples were negative in the assays. Samples from two 2019-nCoV-infected patients were positive in the tests. CONCLUSIONS: The established assays can achieve a rapid detection of 2019n-CoV in human samples, thereby allowing early identification of patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32031583/ doi: 10.1093/clinchem/hvaa029 id: cord-299848-fft1brwz author: Claridge, Jolyon K. title: A picornaviral loop-to-loop replication complex date: 2009-03-04 words: 8818.0 sentences: 459.0 pages: flesch: 60.0 cache: ./cache/cord-299848-fft1brwz.txt txt: ./txt/cord-299848-fft1brwz.txt summary: Using human rhinovirus as a model system, we have combined NMR contact information, small-angle X-ray scattering (SAXS) data, and previous mutagenesis results to determine the shape, position and relative orientation of the 3C(pro) and SLD components. Binding between SLD and 3C(pro) induces structural changes in the proteolytic active site that is positioned on the opposite side of the protease relative to the RNA/protein interface, suggesting that subtle conformational changes affecting catalytic activity are relayed through the protein. NMR and small-angle X-ray scattering data were combined with results from previous mutational analysis (Andino et al., 1993; Leong et al., 1993) (Fig. 1) to construct a structural model of the HRV-14 3C pro -SLD complex. The largest SLD-induced chemical shift perturbations on the 3C pro surface cluster primarily to a patch (dark red in Fig. 5A ) that includes D32 from the loop connecting b-strands 2-3, N80, F83 and F89 from the inter-domain linker and V179 from the C-terminal region. abstract: Picornaviruses replicate their RNA genomes through a highly conserved mechanism that involves an interaction between the principal viral protease (3C(pro)) and the 5′-UTR region of the viral genome. The 3C(pro) catalytic site is the target of numerous replication inhibitors. This paper describes the first structural model of a complex between a picornaviral 3C(pro) and a region of the 5′-UTR, stem-loop D (SLD). Using human rhinovirus as a model system, we have combined NMR contact information, small-angle X-ray scattering (SAXS) data, and previous mutagenesis results to determine the shape, position and relative orientation of the 3C(pro) and SLD components. The results clearly identify a 1:1 binding stoichiometry, with pronounced loops from each molecule providing the key binding determinants for the interaction. Binding between SLD and 3C(pro) induces structural changes in the proteolytic active site that is positioned on the opposite side of the protease relative to the RNA/protein interface, suggesting that subtle conformational changes affecting catalytic activity are relayed through the protein. url: https://www.ncbi.nlm.nih.gov/pubmed/19268541/ doi: 10.1016/j.jsb.2009.02.010 id: cord-268565-2sg1tlrg author: Clarke, David K. title: Recombinant vesicular stomatitis virus as an HIV-1 vaccine vector date: 2006-09-15 words: 8286.0 sentences: 338.0 pages: flesch: 34.0 cache: ./cache/cord-268565-2sg1tlrg.txt txt: ./txt/cord-268565-2sg1tlrg.txt summary: However, because durable neutralizing antibodies are usually elicited against the VSV surface glycoprotein after a single vaccination with replication-competent rVSV vectors, glycoprotein exchange vectors were designed to allow more effective boosting of immune responses to target antigens. In these pioneering studies, rhesus macaques were immunized with a combination of two prototypic rVSV vectors expressing a HIV-1 89.6 Env gp160/VSV-G fusion polypeptide and simian immunodeficiency virus (SIV) Gag p55 protein. Vaccine vector administration by a combination of intramuscular and intranasal routes clearly demonstrated the ability of rVSV vectors to elicit potent antigen-specific cellmediated immune responses in NHPs. In addition, this study also clearly demonstrated for the first time the ability of rVSV vectors expressing Env and Gag proteins to provide highly significant protection from AIDS after an intravenous heterologous SIV/HIV (SHIV) 89 .6P challenge [89] . Immunogenicity of attenuated vesicular stomatitis virus vectors expressing HIV type 1 Env and SIV Gag proteins: comparison of intranasal and intramuscular vaccination routes abstract: Recombinant vesicular stomatitis virus (rVSV) is currently under evaluation as a human immunodeficiency virus (HIV)-1 vaccine vector. The most compelling reasons to develop rVSV as a vaccine vector include a very low seroprevalence in humans, the ability to infect and robustly express foreign antigens in a broad range of cells, and vigorous growth in continuous cell lines used for vaccine manufacture. Numerous preclinical studies with rVSV vectors expressing antigens from a variety of human pathogens have demonstrated the versatility, flexibility, and potential efficacy of the rVSV vaccine platform. When administered to nonhuman primates (NHPs), rVSV vectors expressing HIV-1 Gag and Env elicited robust HIV-1-specific cellular and humoral immune responses, and animals immunized with rVSV vectors expressing simian immunodeficiency virus (SIV) Gag and HIV Env were protected from AIDS after challenge with a pathogenic SIV/HIV recombinant. However, results from an exploratory neurovirulence study in NHPs indicated that these prototypic rVSV vectors might not be adequately attenuated for widespread use in human populations. To address this safety concern, a variety of different attenuation strategies, designed to produce a range of further attenuated rVSV vectors, are currently under investigation. Additional modifications of further attenuated rVSV vectors to upregulate expression of HIV-1 antigens and coexpress molecular adjuvants are also being developed in an effort to balance immunogenicity and attenuation. url: https://www.ncbi.nlm.nih.gov/pubmed/16977404/ doi: 10.1007/s00281-006-0042-3 id: cord-000830-jiy4cp4n author: Cobo, Fernando title: Application of Molecular Diagnostic Techniques for Viral Testing date: 2012-11-30 words: 7969.0 sentences: 385.0 pages: flesch: 39.0 cache: ./cache/cord-000830-jiy4cp4n.txt txt: ./txt/cord-000830-jiy4cp4n.txt summary: The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. The use of amplification techniques such as polymerase chain reaction (PCR), real-time PCR or nucleic acid sequence-based amplification (NASBA) [3] for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range [4, 5] . NASBA assays could identify active infection by detecting viral messenger RNA (mRNA) but the most widely used tests in clinical virus diagnosis are quantitative real-time PCR techniques [8] . Some real-time PCR assays such as LightCycler parvovirus B19 quantitative assay (Roche Diagnostics, Indianapolis, IN) and ABI TaqMan (Applied Biosystems) have been developed for detecting B19 nucleic acids in association with infection during pregnancy or assessing the prevalence of the virus DNA in blood products [62, 63] . abstract: Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522074/ doi: 10.2174/1874357901206010104 id: cord-303189-ktl4jw8v author: Coccia, Eliana M. title: Early IFN type I response: Learning from microbial evasion strategies date: 2015-03-31 words: 15202.0 sentences: 738.0 pages: flesch: 40.0 cache: ./cache/cord-303189-ktl4jw8v.txt txt: ./txt/cord-303189-ktl4jw8v.txt summary: Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. In these cells, the HCV-induced miR-21 has been recently reported to be involved in evasion of IFN-I production and stimulation of HCV replication, upon suppression of MyD88 and IRAK1 expression, that is required for the TLR7-mediated sensing of the virus [100] . Amongst RNA viruses that, as HCV, can establish a persistent infection, HIV-1, a lentivirus from the Retroviridae family, represents a paradigm for its ability to prevent or circumvent the innate immune response mediated by IFN-I. Overall, viruses as HCV and HIV-1 have evolved nifty strategies to dampen the host innate response in cells where a productive infection may take place, while they induce infection-independent mechanisms in non-permissive cells to facilitate the viral life cycle and promote a chronic inflammation. abstract: Abstract Type I interferon (IFN) comprises a class of cytokines first discovered more than 50 years ago and initially characterized for their ability to interfere with viral replication and restrict locally viral propagation. As such, their induction downstream of germ-line encoded pattern recognition receptors (PRRs) upon recognition of pathogen-associated molecular patterns (PAMPs) is a hallmark of the host antiviral response. The acknowledgment that several PAMPs, not just of viral origin, may induce IFN, pinpoints at these molecules as a first line of host defense against a number of invading pathogens. Acting in both autocrine and paracrine manner, IFN interferes with viral replication by inducing hundreds of different IFN-stimulated genes with both direct anti-pathogenic as well as immunomodulatory activities, therefore functioning as a bridge between innate and adaptive immunity. On the other hand an inverse interference to escape the IFN system is largely exploited by pathogens through a number of tactics and tricks aimed at evading, inhibiting or manipulating the IFN pathway, that result in progression of infection or establishment of chronic disease. In this review we discuss the interplay between the IFN system and some selected clinically important and challenging viruses and bacteria, highlighting the wide array of pathogen-triggered molecular mechanisms involved in evasion strategies. url: https://doi.org/10.1016/j.smim.2015.03.005 doi: 10.1016/j.smim.2015.03.005 id: cord-004280-c470nlie author: Coleman, Kristen K. title: Airborne Influenza A Virus Exposure in an Elementary School date: 2020-02-05 words: 4118.0 sentences: 212.0 pages: flesch: 46.0 cache: ./cache/cord-004280-c470nlie.txt txt: ./txt/cord-004280-c470nlie.txt summary: In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Significantly different (p = 0.049) airborne IAV densities were detected between all three indoor locations (i.e., gymnasium, classroom, and corridor) and all positive samples were collected during the last two weeks of 66 , and a 20-30% relative humidity level; Descriptive of an average elementary school student in the USA weighing ~23-32 kg with an assumed tidal volume (V T ) of 7 mL per kg of body mass. Given the high airborne IAV densities detected in the school corridor, along with elevated student contact rates, it is plausible to conclude that the school corridor is a "hotspot" for influenza virus transmission. abstract: Influenza contributes significantly to childhood morbidity and mortality. Given the magnitude of the school-aged child population, a sizeable proportion of influenza virus transmission events are expected to occur within school settings. However, influenza virus activity in schools is not well-understood, likely due to our limited ability to accurately monitor for respiratory viruses without disrupting the school environment. In this study, we evaluated the use of a bioaerosol sampling method to noninvasively detect and quantify airborne influenza A virus (IAV) densities in a public elementary school. Air samples were collected from multiple locations in the school, two days per week, throughout an eight-week sampling period during influenza season. Real-time RT-PCR targeting the IAV M gene revealed detectable IAV on five occasions in densities ranging from 2.0 × 10(−1) to 1.9 × 10(4). No significant differences in IAV densities were related to student presence/absence. The majority of IAV-associated particles were ≤4 μm in diameter, and theoretical calculations indicate infectious thresholds after minutes of exposure. Our study represents the first identification and quantification of airborne influenza virus in an elementary school, and the results suggest that airborne IAV has the potential to circulate in schools during influenza season, in large enough doses known to cause infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7002614/ doi: 10.1038/s41598-020-58588-1 id: cord-300470-vgd1ol2z author: Conradie, Andelé M. title: Establishment of different plasmid only-based reverse genetics systems for the recovery of African horse sickness virus date: 2016-09-19 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: In an effort to simplify and expand the utility of African horse sickness virus (AHSV) reverse genetics, different plasmid-based reverse genetics systems were developed. Plasmids containing cDNAs corresponding to each of the full-length double-stranded RNA genome segments of AHSV-4 under control of a T7 RNA polymerase promoter were co-transfected in cells expressing T7 RNA polymerase, and infectious AHSV-4 was recovered. This reverse genetics system was improved by reducing the required plasmids from 10 to five and resulted in enhanced virus recovery. Subsequently, a T7 RNA polymerase expression cassette was incorporated into one of the AHSV-4 rescue plasmids. This modified 5-plasmid set enabled virus recovery in BSR or L929 cells, thus offering the possibility to generate AHSV-4 in any cell line. Moreover, mutant and cross-serotype reassortant viruses were recovered. These plasmid DNA-based reverse genetics systems thus offer new possibilities for investigating AHSV biology and development of designer AHSV vaccine strains. url: https://doi.org/10.1016/j.virol.2016.07.010 doi: 10.1016/j.virol.2016.07.010 id: cord-103430-x6zzuu7v author: Contu, Lara title: Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay date: 2020-10-12 words: 8272.0 sentences: 461.0 pages: flesch: 56.0 cache: ./cache/cord-103430-x6zzuu7v.txt txt: ./txt/cord-103430-x6zzuu7v.txt summary: Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus'' hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. Gene ontology (GO) enrichment analyses of protein complexes that could 10 form between the identified host interactors revealed highly significant GO terms related to 11 translation and Nonsense-mediated mRNA Decay (NMD). In addition to ribosomal proteins, many other RNA binding proteins were also 37 identified as having a potential role in SFV replication (Figure 3a (nsP1, nsP2, nsP3-Z, nsP4, capsid and Env) as well as for the merged list (All baits) was also applied. abstract: The positive-sense, single-stranded RNA alphaviruses pose a potential epidemic threat. Understanding the complex interactions between the viral and the host cell proteins is crucial for elucidating the mechanisms underlying successful virus replication strategies and for developing specific antiviral interventions. Here we present the first comprehensive protein-protein interaction map between the proteins of Semliki Forest Virus (SFV), a mosquito-borne member of the alphaviruses, and host cell proteins. Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus’ hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. In addition to observing a general inhibition of NMD about 4 hours post infection, we also demonstrate that transient expression of the SFV capsid protein is sufficient to inhibit NMD in cells, suggesting that the massive production of capsid protein during the SFV reproduction cycle is responsible for NMD inhibition. url: https://doi.org/10.1101/2020.10.12.335497 doi: 10.1101/2020.10.12.335497 id: cord-353342-2n6kqyeo author: Corman, Victor M. title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection date: 2016-02-15 words: 4046.0 sentences: 223.0 pages: flesch: 52.0 cache: ./cache/cord-353342-2n6kqyeo.txt txt: ./txt/cord-353342-2n6kqyeo.txt summary: title: Viral Shedding and Antibody Response in 37 Patients With Middle East Respiratory Syndrome Coronavirus Infection The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Quantitative data, such as viral loads and antibody titers, could enable comparisons with related diseases, in particular, severe acute respiratory syndrome (SARS), for which studies of natural history were conducted in the aftermath of the 2002-2003 epidemic [7] . DISCUSSION We studied quantitative viral excretion and serum antibody kinetics of a substantial group of hospitalized patients infected with MERS-CoV. Detection of SARS coronavirus in patients with severe acute respiratory syndrome by conventional and real-time quantitative reverse transcription-PCR assays abstract: Background. The Middle East respiratory syndrome (MERS) coronavirus causes isolated cases and outbreaks of severe respiratory disease. Essential features of the natural history of disease are poorly understood. Methods. We studied 37 adult patients infected with MERS coronavirus for viral load in the lower and upper respiratory tracts (LRT and URT, respectively), blood, stool, and urine. Antibodies and serum neutralizing activities were determined over the course of disease. Results. One hundred ninety-nine LRT samples collected during the 3 weeks following diagnosis yielded virus RNA in 93% of tests. Average (maximum) viral loads were 5 × 10(6) (6 × 10(10)) copies/mL. Viral loads (positive detection frequencies) in 84 URT samples were 1.9 × 10(4) copies/mL (47.6%). Thirty-three percent of all 108 serum samples tested yielded viral RNA. Only 14.6% of stool and 2.4% of urine samples yielded viral RNA. All seroconversions occurred during the first 2 weeks after diagnosis, which corresponds to the second and third week after symptom onset. Immunoglobulin M detection provided no advantage in sensitivity over immunoglobulin G (IgG) detection. All surviving patients, but only slightly more than half of all fatal cases, produced IgG and neutralizing antibodies. The levels of IgG and neutralizing antibodies were weakly and inversely correlated with LRT viral loads. Presence of antibodies did not lead to the elimination of virus from LRT. Conclusions. The timing and intensity of respiratory viral shedding in patients with MERS closely matches that of those with severe acute respiratory syndrome. Blood viral RNA does not seem to be infectious. Extrapulmonary loci of virus replication seem possible. Neutralizing antibodies do not suffice to clear the infection. url: https://www.ncbi.nlm.nih.gov/pubmed/26565003/ doi: 10.1093/cid/civ951 id: cord-327259-7o7fs4yb author: Correa, I. A. title: Boosting SARS-CoV-2 qRT-PCR detection combining pool sample strategy and mathematical modeling date: 2020-08-19 words: 4584.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-327259-7o7fs4yb.txt txt: ./txt/cord-327259-7o7fs4yb.txt summary: We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. To assess the advantages of the pooling approach, we used previous qRT-PCR results obtained in the diagnostic analyses performed with industrial workers of Rio de Janeiro state as a base to calculate the prevalence rates (%) of positive cases and to build the statistical modeling methodology. Our study adopted the statistical modeling approach and validated the data with pooling biological samples for COVID-19 diagnostic, confirming that the pool size must be selected according to the prevalence rate of positive cases in the population (Figure 2) . abstract: qRT-PCR is the gold standard technique available for SARS-CoV-2 detection. However, the long test run time and costs associated with this type of molecular testing are a challenge in the actual pandemic scenario. Due to high testing demand, pooling sample strategy is an interesting approach to allow cost savings. We aim to evaluate pooling tests in experimental procedures, as well as perform in silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). Although the sensitivity reduction in samples pooled with 32 individuals was observed, the high-test sensitivity is maintained even when 16 and 8 samples were pooled. The in silico analysis showed high-cost savings in populations with positive rates lower than 15.0% according to the pool size. This data was validated with the results obtained in our mass testing program: statistical modeling predicted a cost saving of 48.0%, which in practice, was 51.5%, already considering the expenditures with pool sampling that were analyzed individually. Our data confirmed that mathematical modeling is a powerful strategy to improve the pooling approach for SARS-CoV-2 mass testing around the world while maintaining high sensitivity and robustness. url: http://medrxiv.org/cgi/content/short/2020.08.16.20167536v1?rss=1 doi: 10.1101/2020.08.16.20167536 id: cord-302425-aaxvlktp author: Cortey, Martí title: High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea date: 2019-12-05 words: 4998.0 sentences: 248.0 pages: flesch: 52.0 cache: ./cache/cord-302425-aaxvlktp.txt txt: ./txt/cord-302425-aaxvlktp.txt summary: In contrast, other RNA viruses including Kobuvirus, Astrovirus, Sapovirus, Sapelovirus, Teschovirus, and Torovirus, have been detected in pig faeces but its role as causative agents of neonatal diarrhoea has not so far been fully elucidated [10] [11] [12] [13] [14] . The results reported among the 47 diarrhoeic samples analysed include representatives of 12 virus species corresponding to 8 genera of RNA viruses (Additional file 1): Kobuvirus, Rotavirus (RVA, RVB and RVC), Sapovirus (SAV), Mamastrovirus (Porcine Astrovirus types 3 -AstV3 -, 4 -AstV4 -and 5 -AstV5 -), Alphacoronavirus (PEDV), Enterovirus (Enterovirus G, EntVG), Pasivirus (PasiV) and Posavirus (PosaV). Regarding KobuV, our results also agree with an increased prevalence of this agent observed in cases of diarrhoea in suckling piglets worldwide: Brazil [22] , Korea [29] and Vietnam [30] ; despite several (See figure on previous page.) Fig. 5 Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus B. abstract: BACKGROUND: Diarrhoea is a major cause of death in neonate pigs and most of the viruses that cause it are RNA viruses. Next Generation Sequencing (NGS) deeply characterize the genetic diversity among rapidly mutating virus populations at the interspecific as well as the intraspecific level. The diversity of RNA viruses present in faeces of neonatal piglets suffering from diarrhoea in 47 farms, plus 4 samples from non-diarrhoeic piglets has been evaluated by NGS. Samples were selected among the cases submitted to the Veterinary Diagnostic Laboratories of Infectious Diseases of the Universitat Autònoma de Barcelona (Barcelona, Spain) and Universidad de León (León, Spain). RESULTS: The analyses identified the presence of 12 virus species corresponding to 8 genera of RNA viruses. Most samples were co-infected by several viruses. Kobuvirus and Rotavirus were more commonly reported, with Sapovirus, Astrovirus 3, 4 and 5, Enterovirus G, Porcine epidemic diarrhoea virus, Pasivirus and Posavirus being less frequently detected. Most sequences showed a low identity with the sequences deposited in GenBank, allowing us to propose several new VP4 and VP7 genotypes for Rotavirus B and Rotavirus C. CONCLUSIONS: Among the cases analysed, Rotaviruses were the main aetiological agents of diarrhoea in neonate pigs. Besides, in a small number of cases Kobuvirus and Sapovirus may also have an aetiological role. Even most animals were co-infected in early life, the association with enteric disease among the other examined viruses was unclear. The NGS method applied successfully characterized the RNA virome present in faeces and detected a high level of unreported intraspecific diversity. url: https://www.ncbi.nlm.nih.gov/pubmed/31805938/ doi: 10.1186/s12917-019-2204-2 id: cord-260647-7bjhobg7 author: Coudray-Meunier, Coralie title: A Novel High-Throughput Method for Molecular Detection of Human Pathogenic Viruses Using a Nanofluidic Real-Time PCR System date: 2016-01-29 words: 5581.0 sentences: 278.0 pages: flesch: 48.0 cache: ./cache/cord-260647-7bjhobg7.txt txt: ./txt/cord-260647-7bjhobg7.txt summary: A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The aim of this study was to develop real time RT-PCR assays for detection of a total of 19 human enteric viruses (including 3 genogroupes of norovirus and 4 coronaviruses) and two control process viruses (mengovirus and murine norovirus) generally used for monitoring the recovery of viral foodstuff extraction methods. The sensitivity of conventional qPCR assays targeting 21 viral genomes was compared to the quantitative digital RT-PCR array and to the qualitative nanofluidic real-time PCR array performed on Fluidigm''s BioMark System. Similarly, by testing genomes from viruses in stools and RNA from virus production in cells, the limit of detection (LOD) as determined by RT-dPCR was respectively 1.5 to 3.4 log 10 and 1.6 to 2.1 log 10 lower than the expected copy numbers calculated via the standard curve by RT-qPCR. abstract: Human enteric viruses are recognized as the main causes of food- and waterborne diseases worldwide. Sensitive and quantitative detection of human enteric viruses is typically achieved through quantitative RT-PCR (RT-qPCR). A nanofluidic real-time PCR system was used to develop novel high-throughput methods for qualitative molecular detection (RT-qPCR array) and quantification of human pathogenic viruses by digital RT-PCR (RT-dPCR). The performance of high-throughput PCR methods was investigated for detecting 19 human pathogenic viruses and two main process controls used in food virology. The conventional real-time PCR system was compared to the RT-dPCR and RT-qPCR array. Based on the number of genome copies calculated by spectrophotometry, sensitivity was found to be slightly better with RT-qPCR than with RT-dPCR for 14 viruses by a factor range of from 0.3 to 1.6 log(10). Conversely, sensitivity was better with RT-dPCR than with RT-qPCR for seven viruses by a factor range of from 0.10 to 1.40 log(10). Interestingly, the number of genome copies determined by RT-dPCR was always from 1 to 2 log(10) lower than the expected copy number calculated by RT-qPCR standard curve. The sensitivity of the RT-qPCR and RT-qPCR array assays was found to be similar for two viruses, and better with RT-qPCR than with RT-qPCR array for eighteen viruses by a factor range of from 0.7 to 3.0 log(10). Conversely, sensitivity was only 0.30 log(10) better with the RT-qPCR array than with conventional RT-qPCR assays for norovirus GIV detection. Finally, the RT-qPCR array and RT-dPCR assays were successfully used together to screen clinical samples and quantify pathogenic viruses. Additionally, this method made it possible to identify co-infection in clinical samples. In conclusion, given the rapidity and potential for large numbers of viral targets, this nanofluidic RT-qPCR assay should have a major impact on human pathogenic virus surveillance and outbreak investigations and is likely to be of benefit to public health. url: https://www.ncbi.nlm.nih.gov/pubmed/26824897/ doi: 10.1371/journal.pone.0147832 id: cord-344464-if6js43s author: Cowley, J. A. title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report date: 2002 words: 3523.0 sentences: 183.0 pages: flesch: 54.0 cache: ./cache/cord-344464-if6js43s.txt txt: ./txt/cord-344464-if6js43s.txt summary: title: The complete genome sequence of gill-associated virus of Penaeus monodon prawns indicates a gene organisation unique among nidoviruses(*): Brief Report We report here a 5596 nt sequence comprising the 3′-end of the (+) ssRNA genome of gill-associated virus (GAV), an invertebrate nidovirus of Penaeus monodon prawns. The sequence extends from a subgenomic RNA start site 35 nt upstream of the 4923 nt ORF3 gene to a 3′-poly(A) tail of the 26235 nt genome of GAV. Completion of the genome sequence of GAV has revealed a gene organisation unique among nidoviruses in there is no discrete membrane protein gene and that the putative ORF3 spike glycoprotein gene resides downstream of a gene (ORF2) encoding a structural protein associated with nucleocapsids. A contig of a 5596 nt sequence from the GAV genomic 3 -poly(A) tail to an intergenic 5 -sgRNA start site 35 nt upstream of the ORF3 start codon [10] was deduced from overlapping cDNA clones (Figs. abstract: We report here a 5596 nt sequence comprising the 3′-end of the (+) ssRNA genome of gill-associated virus (GAV), an invertebrate nidovirus of Penaeus monodon prawns. The sequence extends from a subgenomic RNA start site 35 nt upstream of the 4923 nt ORF3 gene to a 3′-poly(A) tail of the 26235 nt genome of GAV. The putative 1640 amino acid (aa) ORF3 protein (MW = 182049 Da, pI = 6.62) contains 15 potential N-linked glycosylation sites, 15 potential O-linked glycosylation sites and six highly hydrophobic regions predicted to represent transmembrane (TM) domains. Three of the predicted TM domains occur in the amino-terminal 228 aa, two in the central portion, and one near the carboxy-terminus of ORF3. Only one short (83 aa) open reading frame (ORF4) was identified between ORF3 and the 3′-poly(A) tail. Completion of the genome sequence of GAV has revealed a gene organisation unique among nidoviruses in there is no discrete membrane protein gene and that the putative ORF3 spike glycoprotein gene resides downstream of a gene (ORF2) encoding a structural protein associated with nucleocapsids. url: https://www.ncbi.nlm.nih.gov/pubmed/12376758/ doi: 10.1007/s00705-002-0847-x id: cord-287466-ag5y781z author: Cowley, J.A. title: Nidoviruses of Fish and Crustaceans date: 2016-09-09 words: 17715.0 sentences: 760.0 pages: flesch: 47.0 cache: ./cache/cord-287466-ag5y781z.txt txt: ./txt/cord-287466-ag5y781z.txt summary: As evidenced by the presence of genomic-length and sgmRNA-length replicativeintermediate double-stranded (ds)RNAs in shrimp cells infected with gill-associated virus (GAV) (Cowley et al., 2002a) , the type species okavirus (Cowley et al., 2012) , it is speculated that transcription termination of the antisense RNAs might occur at precise positions, resulting in common 3′-termini, and that these then act directly as promoters for transcription initiation of the genomic and sgmRNAs. In all other nidoviruses, however, and for the longest of the sgmRNAs transcribed by toroviruses, the (−) and (+) strand sgmRNAs are transcribed using a far more complex discontinuous process involving the splicing of a common "anti-leader" sequence derived from the genome 5′-terminus to each (−) strand sgmRNA that then acts as a universal promoter for transcribing each (+) strand sgmRNA (Pasternak et al., 2006; Sawicki et al., 2007; Smits et al., 2005; van Vliet et al., 2002) . Nidoviruses of aquatic species include the rod-shaped okaviruses GAV and yellow head virus (YHV) that primarily infect Penaeid shrimp (Longyant et al., 2005; Flegel, 2012; Flegel et al., 1997a; Cowley et al., 2000a Cowley et al., , 2002a Cowley and Walker, 2002; Sittidilokratna et al., 2008) and a morphologically similar virus with a ~22 kb ssRNA genome detected in diseased Chinese mitten crabs (Zhang and Bonami, 2007) . abstract: Viruses with diverse virion architectures demarcated into four families in the order Nidovirales have been discovered in vertebrate mammalian and fish species, as well as in invertebrate crustacean and mosquito species. The order is unified by nidoviruses sharing intermediate (12.7 kb) to very long (31.7 kb) (+) ssRNA genomes, each possessing a long 5′-terminal gene encoding overlapping ORF1a and ORF1b reading frames that contain a diversity of functionally related enzymes and that are translated in toto using a −1 ribosomal frameshift mechanism, as well as by semiconserved strategies for transcribing a nested set of 3′-coterminal subgenomic mRNAs that translate the viral proteins. The nidovirus that is most important to an aquaculture species is yellow head virus (YHV), which causes disease in shrimp farmed throughout the Eastern Hemisphere and is classified in the genus Okavirus, family Roniviridae. Fathead minnow nidovirus, genus Bafinivirus, subfamily Torovirinae, family Coronaviridae, also causes disease in minnows grown for the baitfish industry in the United States. Virions similar in morphology to okaviruses and bafiniviruses have also been detected in several crab species. Of these, however, only Eriocheir sinensis ronivirus, which causes disease in the Chinese mitten crab, an important freshwater aquaculture species in China, has been shown to possess a ~22 kb ssRNA genome that supports its being a nidovirus, but its taxonomic classification awaits genome sequence analysis. This chapter provides an overview of the structure, replication and biology of these viruses with a particular focus on YHV disease characteristics, diagnostic methods and disease prevention strategies. url: https://www.sciencedirect.com/science/article/pii/B9780128015735000322 doi: 10.1016/b978-0-12-801573-5.00032-2 id: cord-325197-j1uo8qmf author: Crimi, Ettore title: Epigenetic susceptibility to severe respiratory viral infections: pathogenic and therapeutic implications: a narrative review date: 2020-08-20 words: 6066.0 sentences: 342.0 pages: flesch: 34.0 cache: ./cache/cord-325197-j1uo8qmf.txt txt: ./txt/cord-325197-j1uo8qmf.txt summary: Viruses causing severe pulmonary illness can use epigenetic-regulated mechanisms during host–pathogen interaction to interfere with innate and adaptive immunity, adequacy of inflammatory response, and overall outcome of viral infections. In this article, we provide an update on epigenetic-sensitive mechanisms and repurposed drugs interfering with epigenetic pathways which may be clinically suitable for risk stratification and beneficial for treatment of patients affected by severe viral respiratory infections. The goal of the review was to provide an appropriate pathogenic scenario in which epigenetic-sensitive mechanisms and epidrugs may be clinically useful to stratify risk and treatment of patients in ICU affected by severe viral respiratory infections. Here, we give an update on clinical evidence about the usefulness of novel and FDA-approved drugs interfering with epigenetic pathways, which were applied to ICU patients affected by highly pathogenic strains of influenza virus and CoV, with a particular interest about the novel SARS-CoV-2 (Table 4 ). abstract: The emergence of highly pathogenic strains of influenza virus and coronavirus (CoV) has been responsible for large epidemic and pandemic outbreaks characterised by severe pulmonary illness associated with high morbidity and mortality. One major challenge for critical care is to stratify and minimise the risk of multi-organ failure during the stay in the intensive care unit (ICU). Epigenetic-sensitive mechanisms, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) methylation, histone modifications, and non-coding RNAs may lead to perturbations of the host immune-related transcriptional programmes by regulating chromatin structure and gene expression patterns. Viruses causing severe pulmonary illness can use epigenetic-regulated mechanisms during host–pathogen interaction to interfere with innate and adaptive immunity, adequacy of inflammatory response, and overall outcome of viral infections. For example, Middle East respiratory syndrome-CoV and H5N1 can affect host antigen presentation through DNA methylation and histone modifications. The same mechanisms would presumably occur in patients with coronavirus disease 2019, in which tocilizumab may epigenetically reduce microvascular damage. Targeting epigenetic pathways by immune modulators (e.g. tocilizumab) or repurposed drugs (e.g. statins) may provide novel therapeutic opportunities to control viral–host interaction during critical illness. In this article, we provide an update on epigenetic-sensitive mechanisms and repurposed drugs interfering with epigenetic pathways which may be clinically suitable for risk stratification and beneficial for treatment of patients affected by severe viral respiratory infections. url: https://api.elsevier.com/content/article/pii/S0007091220305638 doi: 10.1016/j.bja.2020.06.060 id: cord-329504-91te3nu8 author: Croll, Tristan title: Making the invisible enemy visible date: 2020-10-07 words: 4826.0 sentences: 219.0 pages: flesch: 52.0 cache: ./cache/cord-329504-91te3nu8.txt txt: ./txt/cord-329504-91te3nu8.txt summary: A general indication of how well the atomic model fits the measurement data can be obtained by comparing the deposited R-factors to results from PDB-REDO (10) (including Whatcheck (11)) to determine the overall density fit as well as many other diagnostics. Our remodelled structure is offering a valuable structural basis for future studies, such as in-silico docking and drug design targeting at SARS-CoV-2 RdRp (34), as well as for computational modelling or simulations to investigate the molecular mechanism of viral replication (31, 35, 36) . This has included a number of posts on our homepage aimed at non-scientists and live streaming the reprocessing of data on Twitch, as well as the design, production, and public release of an accurate 3D printed model of SARS-CoV-2 based on deposited structures for use as a prop for outreach activities. abstract: During the COVID-19 pandemic, structural biologists have rushed to solve the structures of the 28 proteins encoded by the SARS-CoV-2 genome in order to understand the viral life cycle and enable structure-based drug design. In addition to the 200 structures from SARS-CoV previously solved, 367 structures covering 16 of the viral proteins have been released in the span of only 6 months. These structural models serve as basis for research worldwide to understand how the virus hijacks human cells, for structure-based drug design and to aid in the development of vaccines. However, errors often occur in even the most careful structure determination - and are even more common among these structures, which were solved under immense pressure. From the beginning of the pandemic, the Coronavirus Structural Taskforce has categorized, evaluated and reviewed all of these experimental protein structures in order to help downstream users and original authors. Our website also offers improved models for many key structures, which have been used by Folding@Home, OpenPandemics, the EU JEDI COVID-19 challenge, and others. Here, we describe our work for the first time, give an overview of common problems, and describe a few of these structures that have since acquired better versions in the worldwide Protein Data Bank, either from new data or as depositor re-versions using our suggested changes. url: https://doi.org/10.1101/2020.10.07.307546 doi: 10.1101/2020.10.07.307546 id: cord-302980-2jlz4c58 author: Crucière, C. title: Sequence and analysis of bovine enteritic coronavirus (F15) genome I.—Sequence of the gene coding for the nucleocapsid protein; analysis of the predicted protein date: 1988-03-31 words: 3914.0 sentences: 386.0 pages: flesch: 70.0 cache: ./cache/cord-302980-2jlz4c58.txt txt: ./txt/cord-302980-2jlz4c58.txt summary: Summary Sequences encoding the N protein of the bovine enteritic coronavirus-F15 strain (BECV-F15) have been cloned in PBR322 plasmid using cDNA produced by priming with oligo-dT on purified viral genomic RNA. The 3′-non-coding end of the gene has an 8-nucleotide sequence in common with the homologous genome areas of MHV, TGE and IBV viruses. The location of the insert along the viral genome was determined by Northern blot analysis: full length or purified products of insert restriction cleavage were hybridized with poly(A) § RNA extracted from infected or non-infected cells. We have determined, by cDNA cloning of BECV-F15 genomic RNA using an oligo-dT primer, a sequence of 1,710 nucleotides. For every coronavirus so far studied, the gene coding for the N protein is located at the 3''-end of the viral genome. Recently [11] it was described for the US Mebus strain of the related bovine corona virus (BCV), that the N protein gene was at the 3''-end of the viral genome. abstract: Summary Sequences encoding the N protein of the bovine enteritic coronavirus-F15 strain (BECV-F15) have been cloned in PBR322 plasmid using cDNA produced by priming with oligo-dT on purified viral genomic RNA. Some 265 insert-containing clones were studied. Hybridization of these inserts with poly(A)+ RNA extracted from infected cells led to the conclusion that they were located at the 3′-end of the genome. After subcloning in M13 phage DNA, clones were sequenced by the Sanger technique. A 1,710-nucleotide sequence corresponding to the gene coding for the viral N-protein was established. It shows 2 overlapping open reading frames (ORF). The 3′-non-coding end of the gene has an 8-nucleotide sequence in common with the homologous genome areas of MHV, TGE and IBV viruses. This sequence may represent the polymerase RNA binding site. An upstream sequence surrounding the first AUG of the smaller ORF corresponds to a potentially functional initiation codon. The sequence of the primary translation product deduced from the DNA sequence predicts a polypeptide of 207 amino acids (22.9 Kd) with a high leucine (19.8%) content, possessing a hydrophobic N-terminal end. The larger ORF has a coding capacity of 448 amino acids (49.4 Kd), corresponding to the N-protein molecular weight. The deduced protein possesses 43 serine residues (9.6% of the total amino acid content) which may be phosporylated and involved in N-protein/RNA binding. N-protein also has 5 regions with a high basic amino acid content. One of them is also serine-rich and has a strong homology site with MHV, TGE and IBV viruses. In the first part of the N-terminal, a 12-amino-acid sequence (PRWYFYYLGTGP) is highly conserved for BECV-F15, JHM, TGE and IBV viruses. BCV Mebus strain and BECV-F15 have only minor differences in their N-protein sequence. url: https://www.ncbi.nlm.nih.gov/pubmed/3207501/ doi: 10.1016/s0769-2617(88)80012-1 id: cord-262592-0rdiosxd author: Cuevas, José M. title: Human norovirus hyper-mutation revealed by ultra-deep sequencing date: 2016-04-17 words: 5828.0 sentences: 276.0 pages: flesch: 54.0 cache: ./cache/cord-262592-0rdiosxd.txt txt: ./txt/cord-262592-0rdiosxd.txt summary: This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. Based on the sequence context of the observed changes, we propose that NoV hypermutation might be driven by ADAR-mediated editing of the viral genomic RNA of either polarity during replication. We used 16 stool samples from patients acutely infected with NoV GII.4 to amplify by RT-PCR a 386-base region encompassing nucleotides 1 to 386 of the VP1 gene (reference sequence: GenBank JX459908; Fig. 1A ). After 48 h incubation, total RNA was extracted from cells, residual DNA was removed with DNAse I, a specific primer annealing to the minus-strand of the VP1 capsid gene was used for reverse transcription, and high-fidelity PCR amplification of a region encompassing positions 19 to 323 of the VP1 gene (305 bases, although only the 266 bases excluding primer regions Fig. 1 . abstract: Human noroviruses (NoVs) are a major cause of gastroenteritis worldwide. It is thought that, similar to other RNA viruses, high mutation rates allow NoVs to evolve fast and to undergo rapid immune escape at the population level. However, the rate and spectrum of spontaneous mutations of human NoVs have not been quantified previously. Here, we analyzed the intra-patient diversity of the NoV capsid by carrying out RT-PCR and ultra-deep sequencing with 100,000-fold coverage of 16 stool samples from symptomatic patients. This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. To more directly test for hyper-mutation, we performed transfection assays in which the production of mutations was restricted to a single cell infection cycle. This confirmed the presence of sequences with multiple U-to-C/A-to-G transitions, and suggested that hyper-mutation contributed a large fraction of the total NoV spontaneous mutation rate. The type of changes produced and their sequence context are compatible with ADAR-mediated editing of the viral RNA. url: https://api.elsevier.com/content/article/pii/S1567134816301435 doi: 10.1016/j.meegid.2016.04.017 id: cord-104186-fyw1xfgi author: Cui, Y title: Mof4-1 is an allele of the UPF1/IFS2 gene which affects both mRNA turnover and -1 ribosomal frameshifting efficiency. date: 1996-10-15 words: 7815.0 sentences: 361.0 pages: flesch: 58.0 cache: ./cache/cord-104186-fyw1xfgi.txt txt: ./txt/cord-104186-fyw1xfgi.txt summary: Cells harboring the above hybrid UPFJ gene had the same three phenotypes as the mof4-1 strain, including: (i) elevated abundance of CYH2 precursor and frameshift reporter LacZ mRNA (Figures 2B and IC); (ii) inability to propagate the M1 killer virus (Table IV, Table IV , #5). A upflA strain (YGC106) containing the lacZ frameshift reporter construct in the zero or -1 frame relative to the translation start site (p315-JD86-ter or p315-JD85-ter) was transformed with a single copy plasmid harboring either the wild-type UPFJ gene, the mof4-1 allele or the vector alone. Thus, the higher expression level of the lacZ gene product in the -1 reading frame in mof4-1 cells as compared Hybrid genes between the wild-type UPFI and the mof4-1 alleles schematically represented in (A) were constructed, transformed into a upflA strain (Y52-) and CYH2 precursor abundance was determined by RNA blotting analysis as described in Figure 1 . abstract: The mof4-1 (maintenance of frame) allele in the yeast Saccharomyces cerevisiae was isolated as a chromosomal mutation that increased the efficiency of -1 ribosomal frameshifting at the L-A virus frameshift site and caused loss of M1, the satellite virus of L-A. Here, we demonstrate that strains harboring the mof4-1 allele inactivated the nonsense-mediated mRNA decay pathway. The MOF4 gene was shown to be allelic to UPF1, a gene whose product is involved in the nonsense-mediated mRNA decay pathway. Although cells harboring the mof4-1 allele of the UPF1 gene lose the M1 virus, mutations in other UPF genes involved in nonsense-mediated mRNA decay maintain the M1 virus. The mof4-1 strain is more sensitive to the aminoglycoside antibiotic paromomycin than a upf1 delta strain, and frameshifting efficiency increases in a mof4-1 strain grown in the presence of this drug. Further, the ifs1 and ifs2 alleles previously identified as mutations that enhance frameshifting were shown to be allelic to the UPF2 and UPF1 genes, respectively, and both ifs strains maintained M1. These results indicate that mof4-1 is a unique allele of the UPF1 gene and that the gene product of the mof4-1 allele affects both -1 ribosomal frameshifting and mRNA turnover. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC452316/ doi: nan id: cord-252433-0e9lonq4 author: Cullen, Bryan R. title: Viral RNAs: Lessons from the Enemy date: 2009-02-20 words: 3564.0 sentences: 172.0 pages: flesch: 52.0 cache: ./cache/cord-252433-0e9lonq4.txt txt: ./txt/cord-252433-0e9lonq4.txt summary: As a result, HIV-1 mutants lacking a functional rev gene are able to express the proteins encoded by fully spliced viral mRNAs, that is, Tat, Nef, and the defective Rev protein itself, but cannot express any of the proteins encoded by incompletely spliced viral mRNAs, including Gag, Pol, and Env. The transcripts encoding these viral structural proteins, however, can be detected in the nucleus of cells infected by Rev-deficient viruses, where they are either degraded or eventually fully spliced and then exported (Cullen, 2003) . MPMV has a simpler genomic organization than HIV-1 and only encodes the three structural proteins Picornaviruses and some flaviviruses Recruits cellular translation factors and ribosomal subunits to viral translation initiation codons in the absence of an mRNA cap Gag, Pol, and Env. Nevertheless, MPMV expresses both a genome-length Gag/ Pol mRNA and a spliced Env mRNA. abstract: Viruses are adept at evolving or co-opting genomic elements that allow them to maximize their replication potential in the infected host. This evolutionary plasticity makes viruses an invaluable system to identify new mechanisms used not only by viruses but also by vertebrate cells to modulate gene expression. Here, I discuss the identification and characterization of viral mRNA structures and noncoding RNAs that have led to important insights into the molecular mechanisms of eukaryotic cells. url: https://doi.org/10.1016/j.cell.2009.01.048 doi: 10.1016/j.cell.2009.01.048 id: cord-270604-u62437dh author: Cuthill, Jennifer Hoyal title: A SIMPLE MODEL EXPLAINS THE DYNAMICS OF PREFERENTIAL HOST SWITCHING AMONG MAMMAL RNA VIRUSES date: 2013-02-19 words: 7441.0 sentences: 322.0 pages: flesch: 42.0 cache: ./cache/cord-270604-u62437dh.txt txt: ./txt/cord-270604-u62437dh.txt summary: We present an empirical test of two theoretical models of preferential host switching, using observed phylogenetic distributions of host species for RNA viruses of three mammal orders (primates, carnivores, and ungulates). To overcome the above complications, this study takes an alternative approach, and reconstructs the dynamics of preferential host switching among 38 recorded "multihost" RNA viruses of mammals, on phylogenies of their primate, carnivore, and ungulate hosts. To achieve this, approximate Bayesian computation (ABC) is used to test the fit of the two models of preferential host switching to the observed distributions of multihost RNA viruses on the phylogenies of their mammal hosts (primates, carnivores, and terrestrial ungulates). This indicates that ABC model selection was effective with each of the three sample sizes used for calculation of the HSD summary statistics (which corresponded to the number of observed host-virus associations, of 22 for primates, 12 for carnivores, and 4 for ungulates). abstract: A growing number of studies support a tendency toward preferential host switching, by parasites and pathogens, over relatively short phylogenetic distances. This suggests that a host switch is more probable if a potential host is closely related to the original host than if it is a more distant relative. However, despite its importance for the health of humans, livestock, and wildlife, the detailed dynamics of preferential host switching have, so far, been little studied. We present an empirical test of two theoretical models of preferential host switching, using observed phylogenetic distributions of host species for RNA viruses of three mammal orders (primates, carnivores, and ungulates). The analysis focuses on multihost RNA virus species, because their presence on multiple hosts and their estimated ages of origin indicate recent host switching. Approximate Bayesian computation was used to compare observed phylogenetic distances between hosts with those simulated under the theoretical models. The results support a decreasing sigmoidal model of preferential host switching, with a strong effect from increasing phylogenetic distance, on all three studied host phylogenies. This suggests that the dynamics of host switching are fundamentally similar for RNA viruses of different mammal orders and, potentially, a wider range of coevolutionary systems. url: https://www.ncbi.nlm.nih.gov/pubmed/23550750/ doi: 10.1111/evo.12064 id: cord-286877-0h5vgi5c author: Dahiya, Shyam S. title: Immunogenicity of a DNA-launched replicon-based canine parvovirus DNA vaccine expressing VP2 antigen in dogs date: 2012-10-31 words: 5260.0 sentences: 261.0 pages: flesch: 43.0 cache: ./cache/cord-286877-0h5vgi5c.txt txt: ./txt/cord-286877-0h5vgi5c.txt summary: When the pAlpha-CPV-VP2 was injected intradermal as DNA-launched replicon-based DNA vaccine in dogs, it induced CPV-specific humoral and cell mediated immune responses. To increase antigen production and immunogenicity with DNA vaccines, a new strategy has been developed to express the target heterologous antigen under the control of replicon from positive-strand RNA viruses with the promise of using the ability of these viruses to produce large amounts of viral proteins in infected cells. The replicon-based CPV DNA vaccine plasmid (pAlpha-CPV-VP2) encoding CPV-VP2 was constructed and evaluated to express CPV-VP2 protein in transfected cells in SDS-PAGE and Western blot (data not shown). To assess the protective efficacy of different CPV vaccines, sera collected from all immunized and control dogs were analyzed for presence of virus neutralizing (VN) antibody. CD8 + lymphocytes in dogs immunized with replicon-based CPV DNA vaccine compared to controls (Fig. 7) . There were over 24 thousand times more CPV-VP2 mRNA transcripts in pAlpha-CPV-VP2-transfected BHK-21 cells compared to respective non-replicating control indicating the self-replicating ability of replicon-based CPV-VP2 DNA vaccine. abstract: Abstract A replicon-based DNA vaccine encoding VP2 gene of canine parvovirus (CPV) was developed by cloning CPV-VP2 gene into a replicon-based DNA vaccine vector (pAlpha). The characteristics of a replicon-based DNA vaccine like, self-amplification of transcripts and induction of apoptosis were analyzed in transfected mammalian cells. When the pAlpha-CPV-VP2 was injected intradermal as DNA-launched replicon-based DNA vaccine in dogs, it induced CPV-specific humoral and cell mediated immune responses. The virus neutralization antibody and lymphocyte proliferative responses were higher than conventional CPV DNA vaccine and commercial CPV vaccine. These results indicated that DNA-launched replicon-based CPV DNA vaccine was effective in inducing both CPV-specific humoral and cellular immune responses and can be considered as effective alternative to conventional CPV DNA vaccine and commercial CPV vaccine. url: https://api.elsevier.com/content/article/pii/S0034528812000616 doi: 10.1016/j.rvsc.2012.01.017 id: cord-338582-o976nab9 author: Dahlhausen, Bob title: Future Veterinary Diagnostics date: 2010-09-19 words: 9199.0 sentences: 511.0 pages: flesch: 35.0 cache: ./cache/cord-338582-o976nab9.txt txt: ./txt/cord-338582-o976nab9.txt summary: Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. PCR uses the highly specific molecular recognition ability of Watson-Crick base pairing to provide the selectivity needed for a nucleic acid probe to bind to a targeted DNA sequence and allow for its exponential amplification. It has been used to develop rapid diagnostic tests for several pathogenic viruses with singlestranded RNA genomes, including influenza A, 13 footand-mouth disease virus, 14 and severe acute respiratory syndrome (SARS)-associated coronavirus. DNA microarrays also permit relatively rapid interrogation of a clinical sample against thousands of genetic targets, allowing for simultaneous detection and discrimination among hundreds of pathogenic agents of veterinary interest. Unlike PCR technology where the target agent must be known to use specific test primers, microarrays can allow for the rapid diagnosis of multiple pathogenic agents in disease outbreaks and epidemics of unknown etiology. abstract: The development of rapid, accurate, and sensitive diagnostic methods for detecting pathogens is the basis for treating, controlling, and eradicating infectious diseases of veterinary importance. Scientific and technological advancements have revolutionized the field of veterinary diagnostics. Genome sequencing has allowed efficient, sensitive, and specific diagnostic assays to be developed based on the detection of nucleic acids. The integration of advances in biochemistry, proteomics, engineering, and medicine offers enormous potential for the rapid and accurate diagnosis of viral, microbial, genetic, and metabolic disease. In the future, polymerase chain reaction assays, microarray testing, genomic analysis, and metabolic profiling will be accomplished in a rapid, portable, sensitive, and cost-efficient manner. url: https://doi.org/10.1053/j.jepm.2010.05.006 doi: 10.1053/j.jepm.2010.05.006 id: cord-330131-yfhrmbvx author: Danchin, Antoine title: Cytosine drives evolution of SARS‐CoV‐2 date: 2020-04-27 words: 5318.0 sentences: 244.0 pages: flesch: 42.0 cache: ./cache/cord-330131-yfhrmbvx.txt txt: ./txt/cord-330131-yfhrmbvx.txt summary: In this article, we show, in the specific case of SARS-CoV-2, that the role of cytosine-based metabolites used as cell growth coordinators is central to understanding both innate antiviral immunity and the evolution of the virus. Here we (i) highlight the deviation of SARS-CoV-2 RNA chemical composition compared with that of its human host; (ii) formulate a hypothesis grounded on the canonical organization of cytosine metabolism as a way to coordinate non-homothetic growth of cells-i.e., the simultaneous growth of the cytoplasm (three dimensions), the membrane (two dimensions) and the genome (one dimension)-, and point out the emergence of the endogenous antinucleotide viperin as a cognate adaptive antiviral metabolite and (iii) predict evolutionary trends of CoV-2 for maximizing compositional fitness-which seem to show up in ongoing mutation survey of radiative evolution. abstract: nan url: https://doi.org/10.1111/1462-2920.15025 doi: 10.1111/1462-2920.15025 id: cord-342145-cq6xe5r7 author: Dao Thi, Viet Loan title: A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples date: 2020-08-12 words: 9311.0 sentences: 507.0 pages: flesch: 58.0 cache: ./cache/cord-342145-cq6xe5r7.txt txt: ./txt/cord-342145-cq6xe5r7.txt summary: The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR. During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital''s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. For samples with a CT ≤ 30 as measured by RT-qPCR with E-Sarbeco primers, we found overall satisfactory sensitivity and specificity values for SARS-CoV-2 RNA detection by the RT-LAMP assay using RNA samples isolated from pharyngeal swab specimens ( Fig. 3 and Table 1 ). abstract: The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)–based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab–to–RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions. url: https://www.ncbi.nlm.nih.gov/pubmed/32719001/ doi: 10.1126/scitranslmed.abc7075 id: cord-349672-2kt7xw8i author: Dasgupta, Tumpa title: Mechanism of Type IA Topoisomerases date: 2020-10-17 words: 8538.0 sentences: 463.0 pages: flesch: 53.0 cache: ./cache/cord-349672-2kt7xw8i.txt txt: ./txt/cord-349672-2kt7xw8i.txt summary: Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. In type IA topoisomerases, the hydroxyl group in the side chain of the active site tyrosine residue is responsible for the first nucleophilic attack on the scissile phosphate of a single-stranded DNA resulting in the cleavage of the G-strand and the formation of the transient 5 -phospho-tyrosyl covalent linkage [66] . Though the type IA topoisomerase core domain that forms the characteristic torus structure contains all the highly conserved motifs responsible for G-strand binding and cleavage religation, the C-terminal domains of bacterial topoisomerase I have been shown to be required for removing negative supercoils from DNA rapidly in a processive mechanism [61, 72, [84] [85] [86] [87] . abstract: Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5′-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 3′-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates. url: https://doi.org/10.3390/molecules25204769 doi: 10.3390/molecules25204769 id: cord-002180-gsdk5x3e author: Davies, Colin title: Expression of the NS5 (VPg) Protein of Murine Norovirus Induces a G1/S Phase Arrest date: 2016-08-24 words: 4491.0 sentences: 223.0 pages: flesch: 52.0 cache: ./cache/cord-002180-gsdk5x3e.txt txt: ./txt/cord-002180-gsdk5x3e.txt summary: Amino acid substitutions of NS5(Y26A) and NS5(F123A) that inhibit the ability for NS5 to attach to RNA and recruit host eukaryotic translation initiation factors, respectively, retained the ability to induce an accumulation of cells in the G(0)/G(1) phase as identified for wild-type NS5. Several RNA viruses, including murine norovirus 1 (MNV-1) have been characterized to manipulate cell cycle progression at the G 1 /S restriction point, often creating favorable conditions for viral replication [14] [15] [16] [17] [18] [19] [20] [21] . The effect of NS5 on the host cell cycle was therefore determined by transfection of RAW-Blue cells with RNA transcripts, encoding individual viral genes, NS1-2 from MNV-1 was included as a negative control (Fig 1A) . Furthermore, the NS5(F123A) variant decreased cyclin A protein expression by 67% when compared to the mocktransfected population in a synonymous manner to NS5, strongly implying that the host eukaryotic initiation factor binding domain of NS5 does not play a role in its cell cycle manipulation (Fig 3D) . abstract: Murine norovirus-1 (MNV-1) is known to subvert host cell division inducing an accumulation of cells in the G(0)/G(1) phase, creating conditions where viral replication is favored. This study identified that NS5 (VPg), is capable of inducing cell cycle arrest in the absence of viral replication or other viral proteins in an analogous manner to MNV-1 infection. NS5 expression induced an accumulation of cells in the G(0)/G(1) phase in an asynchronous population by inhibiting progression at the G(1)/S restriction point. Furthermore, NS5 expression resulted in a down-regulation of cyclin A expression in asynchronous cells and inhibited cyclin A expression in cells progressing from G(1) to S phase. The activity of NS5 on the host cell cycle occurs through an uncharacterized function. Amino acid substitutions of NS5(Y26A) and NS5(F123A) that inhibit the ability for NS5 to attach to RNA and recruit host eukaryotic translation initiation factors, respectively, retained the ability to induce an accumulation of cells in the G(0)/G(1) phase as identified for wild-type NS5. To the best of our knowledge, this is the first report of a VPg protein manipulating the host cell cycle. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996510/ doi: 10.1371/journal.pone.0161582 id: cord-005010-xg2bv9gy author: Dayer, Mohammad Reza title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus date: 2015-01-30 words: 4251.0 sentences: 213.0 pages: flesch: 46.0 cache: ./cache/cord-005010-xg2bv9gy.txt txt: ./txt/cord-005010-xg2bv9gy.txt summary: title: Mechanism of Preferential Packaging of Negative Sense Genomic RNA by Viral Nucleoproteins in Crimean-Congo Hemorrhagic Fever Virus In the present work, by analyzing genomic sequences of RNA viruses either with negative or positive sense, performing different docking experiments and carrying out molecular dynamic (MD) simulations, we undertook to study the mechanism conferring different affinities to CCHFV nucleoprotein for negative and positive sense RNAs''. Figure 1 , also, shows that irrespective of their senses, long RNAs have comparatively higher affinities to nucleoprotein than short RNAs. Based on the results of aforementioned docking experiments, we then selected CCHFV nucleoproteins-RNA complexes of maximum binding energies for positive and negative sense RNAs (both short and long) to carry out MD simulations. abstract: The Crimean-Congo Hemorrhagic Fever (CCHF) is an infectious disease of high virulence and mortality caused by a negative sense RNA nairovirus. The genomic RNA of CCHFV is enwrapped by its nucleoprotein. Positively charged residues on CCHFV nucleoprotein provide multiple binding sites to facilitate genomic RNA encapsidation. In the present work, we investigated the mechanism underlying preferential packaging of the negative sense genomic RNA by CCHFV nucleoprotein in the presence of host cell RNAs during viral assembly. The work included genome sequence analyses for different families of negative and positive sense RNA viruses, using serial docking experiments and molecular dynamic simulations. Our results indicated that the main determinant parameter of the nucleoprotein binding affinity for negative sense RNA is the ratio of purine/pyrimidine in the RNA molecule. A negative sense RNA with a purine/pyrimidine ratio (>1) higher than that of a positive sense RNA (<1) exhibits higher affinity for the nucleoprotein. Our calculations revealed that a negative sense RNA expresses about 0.5 kJ/mol higher binding energy per nucleotide compared to a positive sense RNA. This energy difference produces a binding energy high enough to make the negative sense RNA, the preferred substrate for packaging by CCHFV nucleoprotein in the presence of cellular or complementary positive sense RNAs. The outcome of this study may contribute to ongoing researches on other viral diseases caused by negative sense RNA viruses such as Ebola virus which poses a security threat to all humanity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087998/ doi: 10.1007/s10930-015-9601-6 id: cord-336986-rmxin1da author: De Clercq, Erik title: New Nucleoside Analogues for the Treatment of Hemorrhagic Fever Virus Infections date: 2019-08-07 words: 2711.0 sentences: 221.0 pages: flesch: 57.0 cache: ./cache/cord-336986-rmxin1da.txt txt: ./txt/cord-336986-rmxin1da.txt summary: Eight different compounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/or other hemorrhagic fever virus (HFV) infections. Abstract: Eight differentc ompounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/oro ther hemorrhagic fever virus (HFV) infections.T hey can be considered as either (i)adenine analogues (3-deazaneplanocin A, galidesivir,G S-6620 andr emdesivir) or (ii)guanine analogues containing the carboxamide entity (ribavirin, EICAR, pyrazofurin and favipiravir). [26] It wasa lso found active against other emerging viruses such as respiratory syncytial virus (RSV) and hepatitis Cv irus (HCV),a nd the presence of the 1''-cyano group in remdesivir wasf ound to be critical in providing selectivity toward the viral (RNA) polymerases. abstract: Eight different compounds, all nucleoside analogues, could presently be considered as potential drug candidates for the treatment of Ebola virus (EBOV) and/or other hemorrhagic fever virus (HFV) infections. They can be considered as either (i) adenine analogues (3‐deazaneplanocin A, galidesivir, GS‐6620 and remdesivir) or (ii) guanine analogues containing the carboxamide entity (ribavirin, EICAR, pyrazofurin and favipiravir). All eight owe their mechanism of action to hydrogen bonded base pairing with either (i) uracil or (ii) cytosine. Four out of the eight compounds (galidesivir, GS‐6620, remdesivir and pyrazofurin) are C‐nucleosides, and two of them (GS‐6620, remdesivir) also contain a phosphoramidate part. The C‐nucleoside and phosphoramidate (and for the adenine analogues the 1′‐cyano group as well) may be considered as essential attributes for their antiviral activity. url: https://doi.org/10.1002/asia.201900841 doi: 10.1002/asia.201900841 id: cord-102336-ex3zlq38 author: De Wijngaert, Brent title: Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase date: 2020-04-14 words: 2266.0 sentences: 127.0 pages: flesch: 60.0 cache: ./cache/cord-102336-ex3zlq38.txt txt: ./txt/cord-102336-ex3zlq38.txt summary: Cryo-EM structures of transcription pre-initiation complex (PIC) and initiation complex (IC) of yeast mitochondrial RNA polymerase show fully resolved transcription bubbles and explain promoter melting, template alignment, DNA scrunching, transition into elongation, and abortive synthesis. Hence, the structural basis for promoter melting, DNA scrunching, and transcription initiation remains largely unknown for the mtRNAPs. RPO41 (∆N100) and MTF1 were assembled on a pre-melted promoter (-21 to +12, 15S yeast mtDNA promoter; Fig. 1A ) to generate the yeast mitochondrial transcription preinitiation complex (y-mtPIC) (Fig. S1 ). The 3.7 Å density map of IC locates many previously uncharacterized structural elements, including the C-tail of MTF1 and the scrunched DNA ( Fig. 2B-C) , and reveals the mechanism of template alignment and RNA synthesis during initiation. During the transition, the upstream DNA from position -1 onward is locked in the MTF1 NT-groove while the template strand undergoes a large conformational switching to align with the 2-mer RNA and the incoming UTPaS at the active site ( Fig. 2C; Movie S2). abstract: Cryo-EM structures of transcription pre-initiation complex (PIC) and initiation complex (IC) of yeast mitochondrial RNA polymerase show fully resolved transcription bubbles and explain promoter melting, template alignment, DNA scrunching, transition into elongation, and abortive synthesis. Promoter melting initiates in PIC with MTF1 trapping the −4 to −2 non-template (NT) bases in its NT-groove. Transition to IC is marked by a large-scale movement that aligns the template with RNA at the active site. RNA synthesis scrunches the NT strand into an NT-loop, which interacts with centrally positioned MTF1 C-tail. Steric clashes of the C-tail with RNA:DNA and NT-loop, and dynamic scrunching-unscrunching of DNA explain abortive synthesis and transition into elongation. Capturing the catalytically active IC-state with UTPαS poised for incorporation enables modeling toxicity of antiviral nucleosides/nucleotides. url: https://doi.org/10.1101/2020.04.13.038620 doi: 10.1101/2020.04.13.038620 id: cord-258035-2tk7maqk author: DeFilippis, Victor title: Functional genomics in virology and antiviral drug discovery date: 2003-10-31 words: 4769.0 sentences: 255.0 pages: flesch: 39.0 cache: ./cache/cord-258035-2tk7maqk.txt txt: ./txt/cord-258035-2tk7maqk.txt summary: Given that virus replication involves use and manipulation of multiple host proteins and molecular processes, cellular pathways related to transcription and translation, signal transduction, metabolism, host defense and cell cycle control are Review commonly altered in response to, or as a result of, infection with diverse virus types. A special case of virus modulation of host cell gene expression in which functional genomics will reveal novel targets and treatments is viral oncogenesis. The most recent method for analyzing gene inhibition studies has been RNAi or siRNA, where small 21 -23-nucleotide (nt) RNA duplexes interfere with the transcription program by directing degradation of homologous mRNA [34] [35] [36] [37] . Both new-generation antisense oligomers and siRNA can be used to knockdown expression of genes that were found by DNA microarrays to be upregulated in virally infected cells or organisms. RNA interference directed against viral and cellular targets inhibits human immunodeficiency virus type 1 replication abstract: Abstract Virology research and antiviral drug discovery are poised to benefit from the post-genomic revolution for three main reasons. First, viruses need the host to replicate and are therefore vulnerable to inhibition of cellular pathways. Knowledge of complete genomic sequences of both virus and host now permits the study of this interplay on a global scale. Combining transcriptomics and proteomics with large-scale gene knockdown experiments will enable the identification of novel antiviral targets. Second, massive parallel assay systems, such as DNA microarrays, which define the post-genomic era, will facilitate viral diagnostics. Third, the combination of genetics with genomics will enable the analysis of viral mutants and strains on an unprecedented scale. The dramatic effects of viral infection on host cell transcriptional patterns have been well-documented and will be briefly highlighted. In addition, we discuss recent trends that apply functional genomics methods to the discovery of new targets and therapies for viral disease. url: https://www.ncbi.nlm.nih.gov/pubmed/14512232/ doi: 10.1016/s0167-7799(03)00207-5 id: cord-261110-cnj0e0s9 author: Debarnot, Claire title: Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex date: 2011-02-25 words: 2656.0 sentences: 169.0 pages: flesch: 64.0 cache: ./cache/cord-261110-cnj0e0s9.txt txt: ./txt/cord-261110-cnj0e0s9.txt summary: This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. We present X-ray diffraction data from these SARS-CoV nsp10-nsp16 crystals. The purified SARS-CoV nsp10-nsp16 complex was analyzed by 12% SDS-PAGE and stained using Coomassie Blue. Lane MK, molecular-weight markers; lane 1, 2 mg nsp10-nsp16 protein complex eluted from the Strep-Tactin column. The nsp10-nsp16 complex eluted from the Strep-Tactin column was analyzed on a 16/60 S200 gel-filtration column and the elution of protein and nucleic acid was followed by measuring the absorption at 280 nm (blue) and 260 nm (orange), respectively. The purified SARS-CoV nsp10-nsp16 complex was loaded onto a 4-12% NuPAGE gel and stained using Coomassie Blue. We have crystallized a complex of the SARS-CoV nsp10 and nsp16 proteins. abstract: To date, the SARS coronavirus is the only known highly pathogenic human coronavirus. In 2003, it was responsible for a large outbreak associated with a 10% fatality rate. This positive RNA virus encodes a large replicase polyprotein made up of 16 gene products (nsp1–16), amongst which two methyltransferases, nsp14 and nsp16, are involved in viral mRNA cap formation. The crystal structure of nsp16 is unknown. Nsp16 is an RNA-cap AdoMet-dependent (nucleoside-2′-O-)-methyltransferase that is only active in the presence of nsp10. In this paper, the expression, purification and crystallization of nsp10 in complex with nsp16 are reported. The crystals diffracted to a resolution of 1.9 Å resolution and crystal structure determination is in progress. url: http://journals.iucr.org/f/issues/2011/03/00/nj5077/nj5077.pdf doi: 10.1107/s1744309111002867 id: cord-258696-01wj76es author: Decaro, Nicola title: Experimental infection of dogs with a novel strain of canine coronavirus causing systemic disease and lymphopenia date: 2008-04-30 words: 3428.0 sentences: 177.0 pages: flesch: 61.0 cache: ./cache/cord-258696-01wj76es.txt txt: ./txt/cord-258696-01wj76es.txt summary: The dogs, three 2.5-month-old and two 6-month-old pups, were successfully infected, shedding viral RNA with their faeces for the entire observation period (21 days) and displaying systemic clinical signs resembling those observed during the course of natural infection. At postmortem examination, remarkable lesions were observed in the internal organs of the euthanized pups, that tested positive for CCoV by real-time RT-PCR and virus isolation on cell cultures. Unexpectedly, CCoV type II RNA was detected at very high titres in the internal organs of the dead pups and the virus (strain CB/05) was isolated on canine cell cultures. (last day of observation) reaching the maximal mean value of 6.79 Â 10 5 RNA copy numbers/ml of template at day 10 p.i. Surprisingly, CCoV RNA was never detected in the blood of the 6-month-old pups, as well as in the euthanized animals, in whose organs remarkable viral RNA titres were found. abstract: A pantropic canine coronavirus (CCoV) strain (CB/05) has been recently associated to a fatal outbreak of systemic disease in young dogs. We report the clinical, virological and serological findings in dogs experimentally infected with strain CB/05. The dogs, three 2.5-month-old and two 6-month-old pups, were successfully infected, shedding viral RNA with their faeces for the entire observation period (21 days) and displaying systemic clinical signs resembling those observed during the course of natural infection. Leucopenia (acute lymphopenia) occurred in all infected dogs, with values dropping below 60% of the initial counts. Considering the severity of the CB/05-induced disease, two of the youngest pups were euthanized for ethical reasons at days 8–9 postinfection, whereas the other pups underwent a slow but progressive improvement of their clinical status with complete recovery. At postmortem examination, remarkable lesions were observed in the internal organs of the euthanized pups, that tested positive for CCoV by real-time RT-PCR and virus isolation on cell cultures. All pups seroconverted for CCoV, as shown by the high optical density values and antibody titres detected by ELISA and virusneutralisation tests, respectively. The present study confirms that strain CB/05 is highly pathogenic for dogs, being able to induce a severe disease (and in some cases the death) even in experimental conditions. url: https://www.sciencedirect.com/science/article/pii/S0378113507005172 doi: 10.1016/j.vetmic.2007.10.008 id: cord-260250-t48y27wg author: Decaro, Nicola title: Quantitation of canine coronavirus RNA in the faeces of dogs by TaqMan RT-PCR date: 2004-05-07 words: 3322.0 sentences: 157.0 pages: flesch: 51.0 cache: ./cache/cord-260250-t48y27wg.txt txt: ./txt/cord-260250-t48y27wg.txt summary: A TaqMan(®) fluorogenic reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed for the detection and quantitation of canine coronavirus (CCoV) RNA in the faeces of naturally or experimentally infected dogs. The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. As shown in Table 2 , the detec-tion limit of the TaqMan RT-PCR was 1-2 log higher than that of conventional RT-PCR, ranging around 10 1 copies/l and 10 −1.50 TCID 50 /50 l for standard RNA and CCoV strain, respectively, with a detection rate of 100% for each positive dilution. The results of the conventional amplification and real-time analysis carried out on the faecal samples of the CCoV experimentally infected dog are summarized in Fig. 3 . abstract: A TaqMan(®) fluorogenic reverse transcriptase-polymerase chain reaction (RT-PCR) assay was developed for the detection and quantitation of canine coronavirus (CCoV) RNA in the faeces of naturally or experimentally infected dogs. The CCoV fluorogenic RT-PCR assay, which targeted the ORF5 (M gene), was more sensitive than a conventional RT-PCR assay targeting the same gene, showing a detection limit of 10 copies of CCoV standard RNA, and was linear from 10 to 10(8) copies, allowing quantitation of samples with a wide range of CCoV RNA loads. A total of 78 faecal samples of diarrhoeic dogs were tested simultaneously by conventional and fluorogenic RT-PCR: 29 were negative by both techniques, whereas 27 tested positive by conventional RT-PCR and 48 by the established CCoV fluorogenic assay. One sample, which was positive by conventional RT-PCR, gave no signal in the fluorogenic assay. In addition, by the fluorogenic assay CCoV shedding in the faecal samples of an experimentally infected dog was monitored for 28 days. The high sensitivity, simplicity and reproducibility of the CCoV fluorogenic RT-PCR assay, combined with its wide dynamic range and high throughput, make this method especially suitable for efficacy trials on CCoV vaccines. url: https://api.elsevier.com/content/article/pii/S0166093404001028 doi: 10.1016/j.jviromet.2004.03.012 id: cord-324324-8ybfiz8f author: Decaro, Nicola title: Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses date: 2020-04-14 words: 14927.0 sentences: 720.0 pages: flesch: 49.0 cache: ./cache/cord-324324-8ybfiz8f.txt txt: ./txt/cord-324324-8ybfiz8f.txt summary: In addition, the close contact between human beings and different animal species sold at the wet markets of East Asia represents the optimal situation for the host species jump and adaptation to humans of potentially zoonotic agents like CoVs. It is not a coincidence that two of the most severe zoonoses of the last two decades (highly pathogenic H5N1 avian influenza and SARS) have emerged in the same Chinese province of Guangdong where the contact between humans and animals is closer (Lorusso et al., 2020) . All these viruses as well as analogous IBV-like CoVs detected in other birds including penguins, pigeons, peafowl, parrots, waterfowl, teal, quail, duck and whooper swan (Cavanagh et al., 2002; Circella et al., 2007; Domanska-Blicharz et al., 2014; Torres et al., 2013; Hughes et al., 2009; Liu et al., 2005; Wille et al., 2016; Jordan et al., 2015; Bande et al., 2016; Suryaman et al., 2019) have been assigned to the same viral species known as Avian coronavirus (ACoV) within the subgenus Igacovirus of genus Gammacoronavirus. abstract: The recent pandemic caused by the novel human coronavirus, referrred to as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), not only is having a great impact on the health care systems and economies in all continents but it is also causing radical changes of common habits and life styles. The novel coronavirus (CoV) recognises, with high probability, a zoonotic origin but the role of animals in the SARS-CoV-2 epidemiology is still largely unknown. However, CoVs have been known in animals since several decades, so that veterinary coronavirologists have a great expertise on how to face CoV infections in animals, which could represent a model for SARS-CoV-2 infection in humans. In the present paper, we provide an up-to-date review of the literature currently available on animal CoVs, focusing on the molecular mechanisms that are responsible for the emergence of novel CoV strains with different antigenic, biologic and/or pathogenetic features. A full comprehension of the mechanisms driving the evolution of animal CoVs will help better understand the emergence, spreading, and evolution of SARS-CoV-2. url: https://www.sciencedirect.com/science/article/pii/S0378113520302935 doi: 10.1016/j.vetmic.2020.108693 id: cord-265461-hj2b1wc4 author: Decroly, Etienne title: Biochemical principles and inhibitors to interfere with viral capping pathways date: 2017-05-18 words: 5089.0 sentences: 262.0 pages: flesch: 46.0 cache: ./cache/cord-265461-hj2b1wc4.txt txt: ./txt/cord-265461-hj2b1wc4.txt summary: Some virus families code for two different MTase domains carrying a cap-binding site (e.g., poxviruses [11] , coronaviruses [ Structure of inhibitors targeting enzymes involved in viral RNA capping pathways. Cap analogues exemplified here with m7 GTP, and several inhibitors of cap-binding protein have been identified through X-ray structure analysis of the influenza virus PB2-CBD in complex with the corresponding ligands. The X-ray structure of influenza A or B virus PB2 in complex with m7 GTP [49, 50] reveals a conserved cap-recognition mechanism in which the methylated guanosine is stacked between two aromatic residues similar to its binding mode with the eukaryotic initiation factor (eIF4E). However, the past research decade has a contrario unveiled that RNA capping is essential for virus replication, and is in fact a most interesting target for the design of potent antivirals due to two main reasons: (i) incomplete/inhibited RNA capping triggers a potent host immune response adding up to direct inhibition of viral gene expression, and (ii) structural and functional studies of viral capping enzymes have revealed a profound uniqueness of the viral enzymes involved, which shows promises to achieve high drug selectivity. abstract: Messenger RNAs are decorated by a cap structure, which is essential for their translation into proteins. Many viruses have developed strategies in order to cap their mRNAs. The cap is either synthetized by a subset of viral or cellular enzymes, or stolen from capped cellular mRNAs by viral endonucleases (‘cap-snatching’). Reverse genetic studies provide evidence that inhibition of viral enzymes belonging to the capping pathway leads to inhibition of virus replication. The replication defect results from reduced protein synthesis as well as from detection of incompletely capped RNAs by cellular innate immunity sensors. Thus, it is now admitted that capping enzymes are validated antiviral targets, as their inhibition will support an antiviral response in addition to the attenuation of viral mRNA translation. In this review, we describe the different viral enzymes involved in mRNA capping together with relevant inhibitors, and their biochemical features useful in inhibitor discovery. url: https://doi.org/10.1016/j.coviro.2017.04.003 doi: 10.1016/j.coviro.2017.04.003 id: cord-301362-f3lp10lm author: Delgui, Laura R. title: A Novel Mechanism Underlying the Innate Immune Response Induction upon Viral-Dependent Replication of Host Cell mRNA: A Mistake of +sRNA Viruses'' Replicases date: 2017-01-20 words: 7007.0 sentences: 343.0 pages: flesch: 42.0 cache: ./cache/cord-301362-f3lp10lm.txt txt: ./txt/cord-301362-f3lp10lm.txt summary: Recognition of viral double-strand RNA (dsRNA) molecules by intracellular Toll-like receptors (TLRs) or retinoic acid inducible gene I-like receptors (RLRs) is a central event which entails the early steps of the immune response elicited during viral infections. Despite several differences among host range, viral structure, genome organization or membrane-donor organelles from the cell, these analyses revealed that +sRNA viruses are able to induce two types of membranous modifications as replicative niches: invaginated vesicles or spherules or a double membrane vesicle type. Endogenous RNAs forming secondary double-stranded structures that are released after necrosis and tissue damage after viral infection represent another source of dsRNA molecules reaching the endosomes, inducing host-derived dsRNA-mediated inflammatory responses through TLR-3 recognition (Kawai and Akira, 2010) . Other +sRNA viruses such as the enterovirus Coxsackievirus (Kemball et al., 2010) , Hepatitis C virus (Flaviviridae family) (Sir et al., 2012) , or Coronavirus such as MVH (Reggiori et al., 2010) also usurp the autophagy pathway and induce remarkably alterations in intracellular membranous components to harbor the sites for viral RNA replication. abstract: Viruses are lifeless particles designed for setting virus-host interactome assuring a new generation of virions for dissemination. This interactome generates a pressure on host organisms evolving mechanisms to neutralize viral infection, which places the pressure back onto virus, a process known as virus-host cell co-evolution. Positive-single stranded RNA (+sRNA) viruses are an important group of viral agents illustrating this interesting phenomenon. During replication, their genomic +sRNA is employed as template for translation of viral proteins; among them the RNA-dependent RNA polymerase (RdRp) is responsible of viral genome replication originating double-strand RNA molecules (dsRNA) as intermediates, which accumulate representing a potent threat for cellular dsRNA receptors to initiate an antiviral response. A common feature shared by these viruses is their ability to rearrange cellular membranes to serve as platforms for genome replication and assembly of new virions, supporting replication efficiency increase by concentrating critical factors and protecting the viral genome from host anti-viral systems. This review summarizes current knowledge regarding cellular dsRNA receptors and describes prototype viruses developing replication niches inside rearranged membranes. However, for several viral agents it's been observed both, a complex rearrangement of cellular membranes and a strong innate immune antiviral response induction. So, we have included recent data explaining the mechanism by, even though viruses have evolved elegant hideouts, host cells are still able to develop dsRNA receptors-dependent antiviral response. url: https://www.ncbi.nlm.nih.gov/pubmed/28164038/ doi: 10.3389/fcimb.2017.00005 id: cord-343662-scn7b4c6 author: Delli Ponti, Riccardo title: A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs date: 2018-12-03 words: 6568.0 sentences: 336.0 pages: flesch: 51.0 cache: ./cache/cord-343662-scn7b4c6.txt txt: ./txt/cord-343662-scn7b4c6.txt summary: CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. CROSSalign, available at our webpages http://service.tartaglialab.com//new_submission/ crossalign, is based on the combination of two methods: (1) Computational Recognition Of Secondary Structure (CROSS), which is an algorithm trained on experimental data to predict RNA secondary structure profiles without sequence length restrictions and at single-nucleotide resolution (Delli Ponti et al., 2017) ; (2) the Dynamic Time Warping (DTW) algorithm to assess the similarity of two profiles of different lengths (Giorgino, 2009) . We developed the CROSSalign method based on the combination of the CROSS algorithm to predict the RNA secondary structure at single-nucleotide resolution (Delli Ponti et al., 2017) and the DTW algorithm to align profiles of different lengths (Giorgino, 2009 ). abstract: To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. CROSSalign performs pair-wise comparisons and is able to find homologs between thousands of matches identifying the exact regions of similarity between profiles of different lengths. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modeling. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/crossalign. url: https://doi.org/10.3389/fmolb.2018.00111 doi: 10.3389/fmolb.2018.00111 id: cord-254747-vox5xsgd author: Deng, Xufang title: An “Old” Protein with A New Story: Coronavirus Endoribonuclease Is Important for Evading Host Antiviral Defenses date: 2018-04-01 words: 5730.0 sentences: 323.0 pages: flesch: 53.0 cache: ./cache/cord-254747-vox5xsgd.txt txt: ./txt/cord-254747-vox5xsgd.txt summary: Overall, current evidence indicates that the EndoU activity of CoV nsp15 is dispensable for viral RNA synthesis and virus replication in cell culture. It was first discovered that the EndoU activity of nsp15 mediates the evasion of host recognition of viral dsRNA by infecting primary macrophages with EndoU-deficient CoVs (Deng et al., 2017; Kindler et al., 2017) . Moreover, treatment with the PKR inhibitor did not affect IFN induction or RNase L-mediated ribosomal RNA degradation in the EndoU-deficient CoV infected-macrophages (Deng et al., unpublished data) . Macrophages infected by the EndoU-deficient CoVs exhibited an early, RNase L-mediated degradation of ribosomal RNA, demonstrating that the OAS-RNase L system was activated (Deng et al., 2017; Kindler et al., 2017) . Lack of MDA5 expression or treatment with the PKR inhibitor did not affect virus-induced RNA degradation (Deng et al., 2017; Kindler et al., 2017) , suggesting that the nsp15-mediated blockage of OAS-RNase L activation is independent of the MDA5-IFN and PKR pathways. abstract: Here we review the evolving story of the coronavirus endoribonuclease (EndoU). Coronavirus EndoU is encoded within the sequence of nonstructural protein (nsp) 15, which was initially identified as a component of the viral replication complex. Biochemical and structural studies revealed the enzymatic nature of nsp15/EndoU, which was postulated to be essential for the unique replication cycle of viruses in the order Nidovirales. However, the role of nsp15 in coronavirus replication was enigmatic as EndoU-deficient coronaviruses were viable and replicated to near wild-type virus levels in fibroblast cells. A breakthrough in our understanding of the role of EndoU was revealed in recent studies, which showed that EndoU mediates the evasion of viral double-stranded RNA recognition by host sensors in macrophages. This new discovery of nsp15/EndoU function leads to new opportunities for investigating how a viral EndoU contributes to pathogenesis and exploiting this enzyme for therapeutics and vaccine design against pathogenic coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29307596/ doi: 10.1016/j.virol.2017.12.024 id: cord-302895-471zei5o author: Deng, Zengqin title: Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase date: 2013-12-24 words: 8471.0 sentences: 369.0 pages: flesch: 50.0 cache: ./cache/cord-302895-471zei5o.txt txt: ./txt/cord-302895-471zei5o.txt summary: Biochemical studies using recombinant arterivirus and coronavirus helicases revealed similar enzymatic properties, including nucleic acid-stimulated ATPase and 5 0 -3 0 duplex unwinding activities on both RNA and DNA substrates containing 5 0 single-stranded regions (34, 35) . Amino acid substitutions in ZBD or the adjacent ''spacer'' that connects it to the downstream domain can profoundly affect EAV helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replicationnegative virus phenotypes (36, 37) . Thus, our study not only highlights how nidovirus helicase activity depends on the extensive relay of interactions between the ZBD, accessory and HEL1 domains but also provides a framework to propose and explore a role for the enzyme in the posttranscriptional quality control of nidovirus RNAs. Nsp10 of the EAV-Bucyrus isolate (NCBI Reference Sequence NC_002532) is composed of amino acids 2371-2837 of replicase pp1ab, which will throughout this study be referred to as nsp10 residues 1-467. abstract: All positive-stranded RNA viruses with genomes >∼7 kb encode helicases, which generally are poorly characterized. The core of the nidovirus superfamily 1 helicase (HEL1) is associated with a unique N-terminal zinc-binding domain (ZBD) that was previously implicated in helicase regulation, genome replication and subgenomic mRNA synthesis. The high-resolution structure of the arterivirus helicase (nsp10), alone and in complex with a polynucleotide substrate, now provides first insights into the structural basis for nidovirus helicase function. A previously uncharacterized domain 1B connects HEL1 domains 1A and 2A to a long linker of ZBD, which further consists of a novel RING-like module and treble-clef zinc finger, together coordinating three Zn atoms. On substrate binding, major conformational changes were evident outside the HEL1 domains, notably in domain 1B. Structural characterization, mutagenesis and biochemistry revealed that helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. url: https://www.ncbi.nlm.nih.gov/pubmed/24369429/ doi: 10.1093/nar/gkt1310 id: cord-319179-gqaxf7mz author: Denison, M. title: Identification of putative polymerase gene product in cells infected with murine coronavirus A59 date: 1987-04-30 words: 1638.0 sentences: 88.0 pages: flesch: 59.0 cache: ./cache/cord-319179-gqaxf7mz.txt txt: ./txt/cord-319179-gqaxf7mz.txt summary: When infected cells and isolated virions were assayed for this protein by two-dimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. When infected cells and isolated virions were assayed for this protein by twodimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. To determine if p28 was a minor protein actually present in virions, infected 17CL-1 cells were labeled with [35S] methionine and virus was purified as described in Fig. 4 . A portion of the labeled virus preparation was analyzed directly by two-dimensional gel electrophoresis whereas a second part was mixed with the [35S] methionine-labeled cell-free products prior to analysis (Fig. 4) . abstract: Abstract The virion RNA of mouse hepatitis virus, strain A59 (MHV-A59) is believed to be the mRNA for the viral RNA-dependent RNA polymerase. The cell-free translation of virion RNA results in the synthesis of two predominant products p220 and p28 (M. R. Denison and S. Perlman, 1986, J. Virol. 60, 12–18). p28 is a basic protein and is readily detected by two-dimensional gel electrophoresis. When infected cells and isolated virions were assayed for this protein by two-dimensional gel electrophoresis, p28 could be detected in infected cells labeled at late times after infection, but not at early times or in purified virions. p28 represents the first protein product of the putative coronavirus polymerase gene to be identified in infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/3029990/ doi: 10.1016/0042-6822(87)90303-5 id: cord-304498-ty41xob0 author: Denison, Mark R title: Coronaviruses: An RNA proofreading machine regulates replication fidelity and diversity date: 2011-03-01 words: 7332.0 sentences: 345.0 pages: flesch: 38.0 cache: ./cache/cord-304498-ty41xob0.txt txt: ./txt/cord-304498-ty41xob0.txt summary: Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. Genetic inactivation of exoN activity in engineered SArS-Cov and MHv genomes by alanine substitution at conserved De-D-D active site residues results in viable mutants that demonstrate 15-to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other rNA viruses. The high mutation rates of RNA viruses also render them particularly susceptible to repeated genetic bottleneck events during replication, transmission between hosts or spread within a host, resulting in progressive deviation from the consensus sequence associated with decreased viral fitness and sometimes extinction. abstract: In order to survive and propagate, RNA viruses must achieve a balance between the capacity for adaptation to new environmental conditions or host cells with the need to maintain an intact and replication competent genome. Several virus families in the order Nidovirales, such as the coronaviruses (CoVs) must achieve these objectives with the largest and most complex replicating RNA genomes known, up to 32 kb of positive-sense RNA. The CoVs encode sixteen nonstructural proteins (nsp 1–16) with known or predicted RNA synthesis and modification activities, and it has been proposed that they are also responsible for the evolution of large genomes. The CoVs, including murine hepatitis virus (MHV) and SARS-CoV, encode a 3′-to-5′ exoribonuclease activity (ExoN) in nsp14. Genetic inactivation of ExoN activity in engineered SARS-CoV and MHV genomes by alanine substitution at conserved DE-D-D active site residues results in viable mutants that demonstrate 15- to 20-fold increases in mutation rates, up to 18 times greater than those tolerated for fidelity mutants of other RNA viruses. Thus nsp14-ExoN is essential for replication fidelity, and likely serves either as a direct mediator or regulator of a more complex RNA proofreading machine, a process previously unprecedented in RNA virus biology. Elucidation of the mechanisms of nsp14-mediated proofreading will have major implications for our understanding of the evolution of RNA viruses, and also will provide a robust model to investigate the balance between fidelity, diversity and pathogenesis. The discovery of a protein distinct from a viral RdRp that regulates replication fidelity also raises the possibility that RNA genome replication fidelity may be adaptable to differing replication environments and selective pressures, rather than being a fixed determinant. url: https://www.ncbi.nlm.nih.gov/pubmed/21593585/ doi: 10.4161/rna.8.2.15013 id: cord-345654-vyz6f3he author: Dennehy, John J. title: Evolutionary ecology of virus emergence date: 2016-12-30 words: 11475.0 sentences: 701.0 pages: flesch: 43.0 cache: ./cache/cord-345654-vyz6f3he.txt txt: ./txt/cord-345654-vyz6f3he.txt summary: Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between‐host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between‐host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead‐end spillover infections. Virus quasispecies may facilitate host range expansion Viruses are among the smallest nucleic acid-based replicating entities and possess characteristics associated with exceptionally fast evolutionary change: small genomes, short generation times, high mutation rates, large population sizes, high levels of genetic diversity, and strong selection pressures. abstract: The cross‐species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between‐host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between‐host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead‐end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/28036113/ doi: 10.1111/nyas.13304 id: cord-008407-jbp8bxjz author: Derdeyn, Cynthia A. title: Characterization of defective-interfering RNAs of rubella virusgenerated during serial undiluted passage date: 1995-01-10 words: 6710.0 sentences: 298.0 pages: flesch: 56.0 cache: ./cache/cord-008407-jbp8bxjz.txt txt: ./txt/cord-008407-jbp8bxjz.txt summary: During serial undiluted passage of rubella virus (RUB) in Vero cells, two species of defective-interfering (DI) RNAs of approximately 7000 and 800 nucleotides (nts) in length were generated (Frey, T. Finally, to determine whether the majority of DI RNAs present in P12 RNA contained a deletion in the SP-ORF, an oligonucleotide probe which is complementary to a sequence located within the E1 protein coding region (nts 8472 to 8488, eligonucleotide 83, Fig. 3E ) that was deleted in all three cDNA clones was hybridized to P12 RNA. Analysis of the 5'' terminus of DI RNA generated during serial passage As shown in Figure 3A , oligonucleotide probes complementary to the exact 5'' terminal sequences of the RUB genome hybridized to the large DI RNAs. To confirm that these DI RNAs contained the authentic 5'' end of the genome, primer extension was performed on intraceilular RNA from standard RUB-infected cells and P12 RNA. abstract: During serial undiluted passage of rubella virus (RUB) in Vero cells, two species of defective-interfering (DI) RNAs of approximately 7000 and 800 nucleotides (nts) in length were generated (Frey, T. K., and Hemphill, M. L., Virology 164, 22–29, 1988). In this study, these DI RNAs were characterized by molecular cloning, hybridization with probes of defined sequence, and primer extension. The 7000-nt DI RNA species were found to be authentic DI RNAs which contain a single 2500- to 2700-nt deletion in the structural protein open reading frame (ORF) region of the genome. The 800-nt RNAs were found to be subgenomic DI RNAs synthesized from the large DI RNA templates. Analysis of the extent of the deletions using a reverse-transcription-PCR protocol revealed that the 3′ end of the deletions did not extend beyond the 3′ terminal 244 nts of the genome. The 5′ end of the deletions did not extend into the nonstructural protein ORF; however, DI RNAs in which the subgenomic start site was deleted were present. Following serial undiluted passage of seven independent stocks of RUB, this was the only pattern of DI RNAs generated. DI RNAs of 2000 to 3000 nt in length were the majority DI RNA species in a persistently infected line of Vero cells, showing that other types of RUB DI RNAs can be generated and selected. However, when supernatant from the persistently infected cells was passaged, the only DI RNAs present after two passages were 7000 nts in length, indicating that this species has a selective advantage over other types of DI RNAs during serial passage. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130850/ doi: 10.1016/s0042-6822(95)80036-0 id: cord-102968-mhawyect author: Desirò, Daniel title: SilentMutations (SIM): a tool for analyzing long-range RNA-RNA interactions in viral genomes and structural RNAs date: 2018-09-23 words: 4044.0 sentences: 233.0 pages: flesch: 58.0 cache: ./cache/cord-102968-mhawyect.txt txt: ./txt/cord-102968-mhawyect.txt summary: Results Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate destructive and compensatory mutants of two interacting single-stranded RNAs. This will facilitate a fast and accurate assessment of key regions, possibly involved in functional long-range RNA-RNA interactions and finally help virologists to design appropriate experiments. In this study, we present a tool called SilentMutations (SIM) that effectively simulates synonymous (silent) compensatory mutations in two single-stranded viral RNAs and is therefore appropriate for the in vitro assessment of predicted LRIs. Here, we present a command-line tool, called SilentMutations (SIM), that can simulate synonymous structure-destroying and structurepreserving mutation pairs within coding regions for long-range RNA-RNA interaction experiments. Figure 1 : Overall workflow of the SilentMutations tool, exemplary shown for two sequences from a negative single-stranded RNA virus genome (ssRNA-) (a) The first step will extract the defined range in each sequence and possibly increase the range to preserve codons in the given reading frame. abstract: Background A single nucleotide change or mutation in the coding region can alter the amino acid sequence of a protein. In consequence, natural or artificial sequence changes in viral RNAs may have various effects not only on protein stability, function and structure but also on viral replication. In the last decade, several tools have been developed to predict the effect of mutations in structural RNA genomes. Some tools employ multiple point mutations and are also taking coding regions into account. However, none of these tools was designed to specifically simulate the effect of mutations on viral long-range interactions. Results Here, we developed SilentMutations (SIM), an easy-to-use tool to analyze the effect of multiple point mutations on the secondary structures of two interacting viral RNAs. The tool can simulate destructive and compensatory mutants of two interacting single-stranded RNAs. This will facilitate a fast and accurate assessment of key regions, possibly involved in functional long-range RNA-RNA interactions and finally help virologists to design appropriate experiments. SIM only needs two interacting single-stranded RNA regions as input. The output is a plain text file containing the most promising mutants and a graphical representation of all interactions. Conclusion We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments. Availability The source code and documentation of SIM are freely available at github.com/desiro/SilentMutations url: https://doi.org/10.1101/424002 doi: 10.1101/424002 id: cord-004827-bnf3mvaf author: Desselberger, U. title: Report on an ICTV-sponsored symposium on Virus Evolution date: 2005-01-13 words: 2766.0 sentences: 164.0 pages: flesch: 48.0 cache: ./cache/cord-004827-bnf3mvaf.txt txt: ./txt/cord-004827-bnf3mvaf.txt summary: Phylogenetic relationships have been found useful for virus identification, work on origin, speed and mechanisms of evolution, taxonomy, and the elucidation of transmission pathways (e.g. the transmission of HIV from a source to a victim [16] ). In vitro, a single round of replication of HIV-1 in T lymphocytes generated on average 9 recombination events per virus [14] . Approximately 50% of sequence changes are consistent with evolution by point mutations; other changes are due to multiple recombination events. After an introduction in which basic genetic terms were defined (mutation and mutation rate, hypermutation, recombination, reassortment, segmentation etc), the quasispecies concept was presented according to which any sample of an RNA virus represents a ''swarm'' of closely related mutants. ''To maintain RNA structure, evolution selects against better alternatives elsewhere in the genome''. The aim of the talk was to show the significance of RNA structural considerations for the evolution of viruses. Plant RNA virus evolution abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087184/ doi: 10.1007/s00705-004-0466-9 id: cord-294764-v28wbrqp author: Deval, Jerome title: Structure(s), function(s), and inhibition of the RNA-dependent RNA polymerase of noroviruses date: 2017-04-15 words: 8316.0 sentences: 433.0 pages: flesch: 46.0 cache: ./cache/cord-294764-v28wbrqp.txt txt: ./txt/cord-294764-v28wbrqp.txt summary: The in vitro assays and in vivo animal models that have been developed to identify and characterize inhibitors of norovirus RdRp are also summarized, followed by an update on the current antiviral research targeting different regions of norovirus RdRp. In the future, structure-based drug design and rational optimization of known nucleoside and non-nucleoside inhibitors of norovirus RdRp may pave the way towards the next generation of direct-acting antivirals. Despite this limitation, the in vitro effect of small molecules on HuNoV replication has been studied using a stable human hepatoma cell line expressing the part of the Norwalk virus RNA genome encoding the non-structural proteins and carrying the neomycin resistance gene (Chang et al., 2006) . Finally, since norovirus RdRp shares functional and structural features with proteins from other RNA viruses such as HCV, it may be possible to identify nucleo(s/t)ide analogs, like 2CM-C, which inhibits a range of viral polymerases. abstract: Noroviruses belong to the Caliciviridae family of single-stranded positive-sense RNA viruses. The genus Norovirus includes seven genogroups (designated GI-GVII), of which GI, GII and GIV infect humans. Human noroviruses are responsible for widespread outbreaks of acute gastroenteritis and represent one of the most common causes of foodborne illness. No vaccine or antiviral treatment options are available for norovirus infection. The RNA-dependent RNA polymerase (RdRp) of noroviruses is a key enzyme responsible for transcription and replication of the viral genome. Here, we review the progress made in understanding the structures and functions of norovirus RdRp and its use as a target for small molecule inhibitors. Crystal structures of the RdRp at different stages of substrate interaction have been determined, which shed light on its multi-step catalytic cycle. The in vitro assays and in vivo animal models that have been developed to identify and characterize inhibitors of norovirus RdRp are also summarized, followed by an update on the current antiviral research targeting different regions of norovirus RdRp. In the future, structure-based drug design and rational optimization of known nucleoside and non-nucleoside inhibitors of norovirus RdRp may pave the way towards the next generation of direct-acting antivirals. url: https://doi.org/10.1016/j.virusres.2016.12.018 doi: 10.1016/j.virusres.2016.12.018 id: cord-299747-qovrstak author: Deval, Jerome title: Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus date: 2014-09-17 words: 4336.0 sentences: 247.0 pages: flesch: 45.0 cache: ./cache/cord-299747-qovrstak.txt txt: ./txt/cord-299747-qovrstak.txt summary: title: Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus Inhibition of viral RNA polymerases by nucleoside and nucleotide analogs: therapeutic applications against positive-strand RNA viruses beyond hepatitis C virus Jerome Deval, Julian A Symons and Leo Beigelman A number of important human infections are caused by positive-strand RNA viruses, yet almost none can be treated with small molecule antiviral therapeutics. The initial major class of nucleoside analogs of therapeutic potential to demonstrate potent inhibition of HCV RNA polymerase activity were 2 0 C-methyl-ribonucleosides, The first 2 0 C-methyl ribonucleosides were originally synthesized in the 1960s [18] . 0 -azidocytidine) is a potent inhibitor of NS5B-dependent RNA synthesis and hepatitis C virus replication in cell culture abstract: A number of important human infections are caused by positive-strand RNA viruses, yet almost none can be treated with small molecule antiviral therapeutics. One exception is the chronic infection caused by hepatitis C virus (HCV), against which new generations of potent inhibitors are being developed. One of the main molecular targets for anti-HCV drugs is the viral RNA-dependent RNA polymerase, NS5B. This review summarizes the search for nucleoside and nucleotide analogs that inhibit HCV NS5B, which led to the FDA approval of sofosbuvir in 2013. Advances in anti-HCV therapeutics have also stimulated efforts to develop nucleoside analogs against other positive-strand RNA viruses. Although it remains to be validated in the clinic, the prospect of using nucleoside analogs to treat acute infections caused by RNA viruses represents an important paradigm shift and a new frontier for future antiviral therapies. url: https://api.elsevier.com/content/article/pii/S1879625714001692 doi: 10.1016/j.coviro.2014.08.004 id: cord-345302-wbkfjz8r author: Devaney, Ryan title: A metagenomic comparison of endemic viruses from broiler chickens with runting-stunting syndrome and from normal birds date: 2016-10-04 words: 7869.0 sentences: 352.0 pages: flesch: 41.0 cache: ./cache/cord-345302-wbkfjz8r.txt txt: ./txt/cord-345302-wbkfjz8r.txt summary: This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Of specific interest is the enteric viral population associated with RSS of which many RNA and DNA viruses have been implicated and co-infections of multiple viruses such as rotavirus, chicken astrovirus (CAstV), avian nephritis virus (ANV), and reoviruses have been detected in birds affected with RSS or with poor performance (Reynolds et al., 1986; Guy, 1998; Kang et al., 2012) . Other enteric pathogens associated with avian malabsorption diseases include reoviruses, parvoviruses, and members of the family Caliciviridae; many of which have also been observed in broiler chickens Smyth et al., 2007; Pantin-Jackwood et al., 2008 , Wolf et al., 2011 . abstract: Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterize to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterize the viral pathogens associated with 2–3-week-old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA and RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study. url: https://www.ncbi.nlm.nih.gov/pubmed/27215546/ doi: 10.1080/03079457.2016.1193123 id: cord-007920-mh3tesdc author: Dhar, Arun K. title: Genomic Organization, Biology, and Diagnosis of Taura Syndrome Virus and Yellowhead Virus of Penaeid Shrimp date: 2004-11-11 words: 19308.0 sentences: 1000.0 pages: flesch: 52.0 cache: ./cache/cord-007920-mh3tesdc.txt txt: ./txt/cord-007920-mh3tesdc.txt summary: The three most detrimental shrimp viruses are white spot syndrome virus (WSSV), yellowhead virus (YHV), and Taura syndrome virus (TSV), all of which have caused serious epizootics in various regions of Asia and are considered notifiable by the Office International de Epizooties (OIE, 2002) . The RNA helicase consensus sequence, Gx 4 GK, is present at ORF1 amino acid positions 752 to 758, and the TSV helicase domain shows significant similarity with the cognate domain of insect picorna-like viruses (Drosophila C virus, DCV; Rhophalosiphum padi virus, RhPV; Plautia stali intestinal virus, PSIV; black queen cell virus, BQCV; Triatoma virus of the fungus Triatoma infestans, TrV; and Himetobi P virus, HiPV). In addition to helicase, protease, and RdRp motifs, the TSV genome contains a short aa sequence at the N-terminal end of ORF1 (positions 166 to 230) that shows significant similarity with the inhibition of apoptosis (IAP) proteins found in mammals, yeast, insects, and some DNA viruses (Mari et al., 2002) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7127055/ doi: 10.1016/s0065-3527(04)63006-5 id: cord-312332-rwmuucsp author: Dicker, Kate title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity date: 2020-09-10 words: 9235.0 sentences: 480.0 pages: flesch: 45.0 cache: ./cache/cord-312332-rwmuucsp.txt txt: ./txt/cord-312332-rwmuucsp.txt summary: title: The importance of virion-incorporated cellular RNA-Binding Proteins in viral particle assembly and infectivity Different proteomic studies have identified hundreds of cellular factors within the particles of several RNA viruses [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] , many of which are RBPs. Here, we discuss the ''knowns'' and ''unknowns'' of the roles that virion-incorporated cellular RBPs could play in the assembly of viral particles and the early steps of infection in the new host cell. Many ivRBPs such as annexins, heat shock family proteins (HSP), peptidylprolyl isomerase A (PPIA -also cyclophilin A), eukaryotic translation elongation factors (EEF), heterogeneous nuclear ribonucleoproteins (HNRNP) or poly(rC) binding protein 1 (PCBP1), have been linked to infection in multiple ways (Fig. S2) , and here we show that they are incorporated in the particles of several viruses (Table S1B) . abstract: RNA is a central molecule in RNA virus biology due to its dual function as messenger and genome. However, the small number of proteins encoded by viral genomes is insufficient to enable virus infection. Hence, viruses hijack cellular RNA-binding proteins (RBPs) to aid replication and spread. In this review we discuss the ‘knowns’ and ‘unknowns’ regarding the contribution of host RBPs to the formation of viral particles and the initial steps of infection in the newly infected cell. Through comparison of the virion proteomes of ten different human RNA viruses, we confirm that a pool of cellular RBPs are typically incorporated into viral particles. We describe here illustrative examples supporting the important functions of these RBPs in viral particle formation and infectivity and we propose that the role of host RBPs in these steps can be broader than previously anticipated. Understanding how cellular RBPs regulate virus infection can lead to the discovery of novel therapeutic targets against viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32921578/ doi: 10.1016/j.semcdb.2020.08.002 id: cord-281717-kzd9vvci author: Digard, Paul title: Intra-genome variability in the dinucleotide composition of SARS-CoV-2 date: 2020-05-08 words: 4473.0 sentences: 266.0 pages: flesch: 53.0 cache: ./cache/cord-281717-kzd9vvci.txt txt: ./txt/cord-281717-kzd9vvci.txt summary: CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. 79 SARS-CoV-2 was recently reported to have a CpG composition lower than other members of the 80 betacoronavirus genus, comparable to certain canine alphacoronaviruses; an observation used to draw 81 inferences over its origin and/or epizootic potential (Xia 2020 in GC content (from ~ 0.32 -0.47) was seen across the Coronaviridae, and as expected, all viruses 97 exhibited some degree of CpG suppression, with CpG O:E ratios ranging from 0.37 to 0.74 (Fig 2A) . abstract: CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development, and if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the newly emerged SARS-CoV-2 genome was characterised in the context of other coronaviruses. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. Although SARS-CoV-2 exhibits overall strong CpG suppression, this varies considerably across the genome, and the Envelope (E) open reading frame (ORF) and ORF10 demonstrate an absence of CpG suppression. While ORF10 is only present in the genomes of a subset of coronaviruses, E is essential for virus replication. Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. Phylogeny indicates that this is an ancestrally-derived trait reflecting their origin in bats, rather than something selected for after zoonotic transfer. Conservation of CpG motifs in these regions suggests that they have a functionality which over-rides the need to suppress CpG; an observation relevant to future strategies towards a rationally attenuated SARS-CoV-2 vaccine. url: https://doi.org/10.1101/2020.05.08.083816 doi: 10.1101/2020.05.08.083816 id: cord-303377-lkewcf8a author: Dimke, H. title: Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems date: 2020-05-27 words: 4112.0 sentences: 205.0 pages: flesch: 52.0 cache: ./cache/cord-303377-lkewcf8a.txt txt: ./txt/cord-303377-lkewcf8a.txt summary: Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. A total of 87 clinical sample specimens were chosen based on SARS-CoV-2 status from the Cobas ® 6800 system and used to evaluate the analytical sensitivity, specificity and accuracy of our in-house SARS-CoV-2 RT-qPCR assay after RNA purification using the Maxwell ® RSC 48 and AGPC methods. The AGPC method delivers high analytical sensitivity, specificity and accuracy for SARS-CoV-2 testing To evaluate whether conventional AGPC based extraction of RNA could serve as a viable alternative to automated systems with respect to reliability and accuracy, we isolated RNA using the AGPC method from 87 clinical specimens (oropharyngeal or nasopharyngeal swabs) with known SARS-CoV-2 status (57 positive and 30 negative), and performed a side-by-side comparison with the identical samples extracted on a Maxwell ® RSC 48 instrument. abstract: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly reached pandemic levels. Sufficient testing for SARS-CoV-2 remains essential for tracking and containing the rapid spread of the virus. However, due to increased global demand, kits and proprietary reagents for RNA extraction are limited, which markedly reduce SARS-CoV-2 testing capabilities in many countries. Here, we explore the use of conventional acid guanidinium thiocyanate-phenol-chloroform (AGPC)-based RNA purification as an alternative to commercial automated systems for detection of SARS-CoV-2 by RT-qPCR. 87 clinical oropharyngeal or nasopharyngeal swab specimens were extracted by AGPC and compared to the commercial platforms, the Maxwell(R) RSC 48 instrument for automated RNA extraction and the fully integrated diagnostic system, the Cobas(R)6800 apparatus. Our results show that RNA extracted using the AGPC method is fully comparable to modern automated systems regarding analytical sensitivity, specificity and accuracy with respect to detection of SARS-CoV-2 as evaluated by RT-qPCR. Moreover, we find that the AGPC method is easily scalable and implemented in conventional laboratories. Taken together, these data identify conventional AGPC-based RNA extraction as a low cost and suitable alternative to automated systems for the detection of SARS-CoV-2, when automated systems, kits and reagents are not readily available. url: http://medrxiv.org/cgi/content/short/2020.05.26.20099440v1?rss=1 doi: 10.1101/2020.05.26.20099440 id: cord-348777-pk9y6vfp author: Ding, Cheng title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study date: 2020-09-28 words: 3609.0 sentences: 190.0 pages: flesch: 46.0 cache: ./cache/cord-348777-pk9y6vfp.txt txt: ./txt/cord-348777-pk9y6vfp.txt summary: title: Effect of Corticosteroid Therapy on the Duration of SARS-CoV-2 Clearance in Patients with Mild COVID-19: A Retrospective Cohort Study This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. Our observational results revealed that corticosteroid therapy had no positive effect on the durations of SARS-CoV-2 RNA clearance among patients with mild COVID-19. Results from this study suggested that patients with mild COVID-19 may not benefit from corticosteroid therapy in terms of the duration of SARS-CoV-2 clearance. abstract: INTRODUCTION: In December, 2019, an outbreak of the coronavirus disease 2019 (COVID-19), which was caused by a novel coronavirus, started in Wuhan, China. So far, there is limited clinical evidence on the effect of corticosteroid therapy for this disease. This study aims to investigate the association between corticosteroid therapy and the duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clearance among patients with mild COVID-19. METHODS: Patients with mild COVID-19 were enrolled from two medical centers in China between January 13, 2020 and February 29, 2020. Baseline characteristics and durations of RNA clearance were compared between the corticosteroid and non-corticosteroid therapy groups. The independent effects of corticosteroid therapy on the duration of RNA clearance were estimated by generalized linear models. RESULTS: Of 82 patients with a mild infection, 40 patients were male (48.8%), with a median age of 49 years (interquartile range, IQR 36–61). Among those patients, 36 patients (43.9%) received corticosteroid therapy. The adjusted multivariate models showed that the effects of corticosteroids were non-significant on the durations of onset to first RNA clearance [β 2.48, 95% CI (95% confidence interval) − 0.42 to 5.38, P = 0.0926] and to persistent RNA clearance (β 1.54, 95% CI − 1.41 to 4.48, P = 0.3016), and durations of therapy to first RNA clearance (β 2.16, 95% CI − 0.56 to 4.89, P = 0.1184) and to persistent RNA clearance (β 1.22, 95% CI − 1.52 to 3.95, P = 0.3787). CONCLUSIONS: Corticosteroid therapy in patients with mild COVID-19 was not associated with the duration of SARS-CoV-2 clearance, suggesting that the use of corticosteroids may not be beneficial for patients with mild COVID-19 and should be prudently recommended in clinical practice. However, further studies are needed to verify the findings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40121-020-00337-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32986226/ doi: 10.1007/s40121-020-00337-y id: cord-010120-mqvm9zn4 author: Dinman, Jonathan D. title: Ribosomal frameshifting in yeast viruses date: 2004-01-29 words: 6721.0 sentences: 406.0 pages: flesch: 64.0 cache: ./cache/cord-010120-mqvm9zn4.txt txt: ./txt/cord-010120-mqvm9zn4.txt summary: Ribosomal frameshifting is different from frameshift suppression in that these events are directed by specific mRNA sequences and structures, rather than being a consequence of mutations in host gene products, e.g. tRNAs containing four base anticodon loops. In eukaryotes, frameshifting in the +1, or 3'' direction has been observed in the Ty retrotransposable elements in yeast (for review, see reference 25), and in the ornithine decarboxylase antizyme gene in mammalian ~e l l s .~~,~~ In Tyl and Ty3, +1 they splice their RNA.4 I: s6 All of these classes ribosomal frameshifting between the T Y A and T Y B genes in Tyl and the GAG3 and POL3 genes in Ty3 also results in the production of Gag-Pol fusion proteins. A longer ribosomal pause over the slippery site would follow, yielding increased efficiencies of -1 ribosomal frame~hifting.~.''~ A weak point of this model is that, in some mRNA pseudoknots, stem 1 is only five or six base pairs in slippery site, eliminating frameshifting. abstract: Proper maintenance of translational reading frame by ribosomes is essential for cell growth and viability. In the last 10 years it has been shown that a number of viruses induce ribosomes to shift reading frame in order to regulate the expression of gene products having enzymatic functions. Studies on ribosomal frameshifting in viruses of yeast have been particularly enlightening. The roles of viral mRNA sequences and secondary structures have been elucidated and a picture of how these interact with host chromosomal gene products is beginning to emerge. The efficiency of ribosomal frameshifting is important for viral particle assembly, and has identified ribosomal frameshifting as a potential target for antiviral agents. The availability of mutants of host chromosomal gene products involved in maintaining the efficiency of ribosomal frameshifting bodes well for the use of yeast in future studies of ribosomal frameshifting. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169727/ doi: 10.1002/yea.320111202 id: cord-282742-eyukbot7 author: Diosa-Toro, Mayra title: Arthropod-Borne Flaviviruses and RNA Interference: Seeking New Approaches for Antiviral Therapy date: 2013-02-20 words: 6493.0 sentences: 364.0 pages: flesch: 48.0 cache: ./cache/cord-282742-eyukbot7.txt txt: ./txt/cord-282742-eyukbot7.txt summary: Geiss, Pierson, and Diamond (2005) observed that siRNAs targeting the C gene had no effect on virus replication when transfected into cells 10 h after WNV infection using lipid-based reagents. In addition, no significant reduction in viral protein or RNA levels was seen in WNV replicon-expressing cells transfected with siRNAs targeting the NS3 gene using lipid-based reagents. Also, a recent report showed that siRNA toward the TNF-a gene reduced cytokine response in DENV-infected DCs, highlighting the potential of targeted RNAi-based approaches to simultaneously decrease viral replication and the detrimental host immune response (Subramanya et al., 2010) . In addition, it has been shown that WNV (Chotkowski et al., 2008) and DENV (Mukherjee & Hanley, 2010) infection (Mukherjee & Hanley, 2010) of Drosophila cell lines induce functional virus-specific siRNAs that promote a protective RNAi response. So far we have described the antiviral effect of the RNAi mechanism induced by exogenous delivery of siRNA or precursors, and how cellular miRNA can target sequences artificially introduced within the genome of flaviviruses. abstract: Flaviviruses are the most prevalent arthropod-borne viruses worldwide, and nearly half of the 70 Flavivirus members identified are human pathogens. Despite the huge clinical impact of flaviviruses, there is no specific human antiviral therapy available to treat infection with any of the flaviviruses. Therefore, there is a continued search for novel therapies, and this review describes the current knowledge on the usage of RNA interference (RNAi) in combating flavivirus infections. RNAi is a process of sequence-specific gene silencing triggered by double-stranded RNA. Antiviral RNAi strategies against arthropod-borne flaviviruses have been reported and although several hurdles must be overcome to employ this technology in clinical applications, they potentially represent a new therapeutic tool. url: https://www.sciencedirect.com/science/article/pii/B9780124081161000045 doi: 10.1016/b978-0-12-408116-1.00004-5 id: cord-102934-7e2mqooe author: Dogra, N. title: exRNA Signatures in Extracellular Vesicles and their Tumor-Lineage from Prostate Cancer date: 2020-09-30 words: 5830.0 sentences: 385.0 pages: flesch: 51.0 cache: ./cache/cord-102934-7e2mqooe.txt txt: ./txt/cord-102934-7e2mqooe.txt summary: Here, we established 60 total small RNA-sequencing profiles from 17 aggressive prostate cancer (PCa) patients tumor and adjacent normal tissue, and EVs isolated from urine, serum, and cancer cell culture media. We interrogated the key satellite alteration in tumor-derived EVs and found that resection of tumor prostate tissue leads to differential expression of reactive oxygen species (ROS), P53 pathways, inflammatory/cytokines, oncogenes, and tumor suppressor genes in the EV nanosatellites. We have conducted the total small RNA sequencing (n = 60) of aggressive prostate cancer patients (n = 17) tumor and adjacent normal tissue and EVs from urine, serum, and 22RV1 PCa cell line. We interrogated the key satellite alteration in tumor-derived EVs and found that resection of tumor prostate cancer tissue leads to differential expression of novel RNA biomarkers, ROS, P53 pathways, inflammatory/cytokines, major oncogenes, and tumor suppressors in the EV nanosatellites. abstract: Circulating extracellular vesicles (EVs) present in the bodily fluids of patients with cancer may provide non-invasive access to the tumor tissue. Yet, the transcriptomic lineage of tumor-derived EVs before and after tumor-resection remains poorly understood. Here, we established 60 total small RNA-sequencing profiles from 17 aggressive prostate cancer (PCa) patients tumor and adjacent normal tissue, and EVs isolated from urine, serum, and cancer cell culture media. We interrogated the key satellite alteration in tumor-derived EVs and found that resection of tumor prostate tissue leads to differential expression of reactive oxygen species (ROS), P53 pathways, inflammatory/cytokines, oncogenes, and tumor suppressor genes in the EV nanosatellites. Furthermore, we provide a set of novel EV-specific RNA signature, which are present in cancer but are nonexistent in post-resection patients with undetectable cancer. Finally, using a de novo RNAseq assembly followed by characterization of the small RNA landscape, we found novel small RNA clusters (smRCs) in the EVs, which reside in the unannotated regions. Novel smRCs were orthogonally validated for their differential expression in the biomarker discovery cohort using RT-qPCR. We demonstrate that circulating tumor EVs provide a glimpse of the tumor tissue biology, resolving a major bottleneck in the current liquid biopsy efforts. Secretory vesicles appear to be playing a key role in non-canonical Wnt signaling and miRNA pathways, similar to the circulating tumor cells (CTCs), hence, we propose that such vesicles be called circulating tumor extracellular vesicles (CTEVs). url: http://medrxiv.org/cgi/content/short/2020.09.28.20190009v1?rss=1 doi: 10.1101/2020.09.28.20190009 id: cord-016538-4og05fuo author: Dolja, V. V. title: Biotechnology Applications of Grapevine Viruses date: 2017-03-30 words: 6266.0 sentences: 292.0 pages: flesch: 44.0 cache: ./cache/cord-016538-4og05fuo.txt txt: ./txt/cord-016538-4og05fuo.txt summary: Although in theory any of the grapevine-infecting viruses can be engineered into transient gene expression or VIGS vector, in practice, only one of them, the filamentous Grapevine leafroll-associated virus-2 (GLRaV-2) from the genus Closterovirus (family Closteroviridae), was demonstrated to fulfill these roles (Dolja and Koonin 2013; Kurth et al. Among these viruses, only GLRaV-2, a closterovirus, has been so far engineered into a vector capable of systemic infection of grapevine that either produces recombinant protein or elicits VIGS response (Kurth et al. The more recently developed CTV-based gene expression vectors were shown to be not only capable of systemic infection in the natural citrus hosts but also exhibited remark-able genetic stability in regard to retention of the inserted recombinant gene, as well as VIGS capability (Dawson et al. Another candidate to be developed as a vector for protein expression and VIGS is GRSPaV, which is the only grapevine-infecting member of the genus Foveavirus that was recently characterized (Meng et al. abstract: Plant virus genomes are engineered as vectors for functional genomics and production of foreign proteins. The application of plant virus vectors is of potential interest to the worldwide, multibillion dollar, grape and wine industries. These applications include grapevine functional genomics, pathogen control, and production of beneficial proteins such as vaccines and enzymes. However, grapevine virus biology exerts certain limitations on the utility of the virus-derived gene expression and RNA interference vectors. As is typical for viruses infecting woody plants, several grapevine viruses exhibit prolonged infection cycles and relatively low overall accumulation levels, mainly because of their phloem-specific pattern of systemic infection. Here we consider the biotechnology potential of grapevine virus vectors with a special emphasis on members of the families Closteroviridae and Betaflexiviridae. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120854/ doi: 10.1007/978-3-319-57706-7_31 id: cord-290481-i2ppvsh5 author: Dolja, Valerian V. title: Comparative and functional genomics of closteroviruses date: 2006-03-09 words: 9298.0 sentences: 455.0 pages: flesch: 47.0 cache: ./cache/cord-290481-i2ppvsh5.txt txt: ./txt/cord-290481-i2ppvsh5.txt summary: It was concluded that, at least in part, viral pathogenicity is due to interference of silencing suppressors with developmental function of plant small RNAs. Despite their mechanistic similarity, p21 and p19 appear to be structurally and evolutionarily unrelated and neither has detectable homologues outside the respective virus genera (Vargason et al., 2003; Ye and Patel, 2005) . Although Citrus tristeza virus (CTV) encodes p20, a p21like suppressor of RNA silencing, screening of the CTV genome revealed an additional suppressor, p23, that has no homologues in other closteroviruses (Fig. 2) (Lu et al., 2004) . A comparison of TMV and BYV, which both evolved from the alphavirus-like ancestors, shows that the large part of the ∼9 kb genomic surplus of BYV is dedicated to facilitating the synthesis of the virion RNA and multiple sgRNAs. The rest of the surplus was invested in the formation of the complex virion tail that empowers virus transport within and transmission between the host plants and in suppression of RNA silencing (Fig. 1) . abstract: The largest extant RNA genomes are found in two diverse families of positive-strand RNA viruses, the animal Coronaviridae and the plant Closteroviridae. Comparative analysis of the viruses from the latter family reveals three levels of gene conservation. The most conserved gene module defines RNA replication and is shared with plant and animal viruses in the alphavirus-like superfamily. A module of five genes that function in particle assembly and transport is a hallmark of the family Closteroviridae and was likely present in the ancestor of all three closterovirus genera. This module includes a homologue of Hsp70 molecular chaperones and three diverged copies of the capsid protein gene. The remaining genes show dramatic variation in their numbers, functions, and origins among closteroviruses within and between the genera. Proteins encoded by these genes include suppressors of RNA silencing, RNAse III, papain-like proteases, the AlkB domain implicated in RNA repair, Zn-ribbon-containing protein, and a variety of proteins with no detectable homologues in the current databases. The evolutionary processes that have shaped the complex and fluid genomes of the large RNA viruses might be similar to those that have been involved in evolution of genomic complexity in other divisions of life. url: https://www.ncbi.nlm.nih.gov/pubmed/16529837/ doi: 10.1016/j.virusres.2006.02.002 id: cord-270670-cubh9jxc author: Domingo, E. title: Viruses as Quasispecies: Biological Implications date: 2006 words: 10489.0 sentences: 453.0 pages: flesch: 39.0 cache: ./cache/cord-270670-cubh9jxc.txt txt: ./txt/cord-270670-cubh9jxc.txt summary: a Upon infection with an RNA virus (even with a single particle, as depicted here, enlarged about 10 6 times), viral replication leads to a mutant spectrum of related genomes, termed viral quasispecies. As further discussed in the text, in real infections multiple mutant spectra that can amount to a large number of replicating (or potentially replicating) genomes (up to 10 9 or even 10 12 per infected individual) provide highly dynamic mutant repertoire viral yields in cell culture, have been immensely powerful in characterizing the population dynamics of RNA viruses (see references in the reviews by Domingo and Holland 1997; Quiñones-Mateu and Arts 2002; Novella 2003; and the chapters by Quiñones-Mateu and Arts and Escarmís et al., this volume) . Despite these limitations, determination of nucleotide sequence heterogeneities in virus populations using correct reagents and adequate controls has consistently documented that most RNA viruses (and also some DNA viruses) consist of complex mutant spectra, with an average number of 1-100 mutations per genome (Sect. abstract: During viral infections, the complex and dynamic distributions of variants, termed viral quasispecies, play a key role in the adaptability of viruses to changing environments and the fate of the population as a whole. Mutant spectra are continuously and avoidably generated during RNA genome replication, and they are not just a by-product of error-prone replication, devoid of biological relevance. On the contrary, current evidence indicates that mutant spectra contribute to viral pathogenesis, can modulate the expression of phenotypic traits by subpopulations of viruses, can include memory genomes that reflect the past evolutionary history of the viral lineage, and, furthermore, can participate in viral extinction through lethal mutagenesis. Also, mutant spectra are the target on which selection and random drift act to shape the long-term evolution of viruses. The biological relevance of mutant spectra is the central topic of this chapter. url: https://www.ncbi.nlm.nih.gov/pubmed/16568896/ doi: 10.1007/3-540-26397-7_3 id: cord-022128-r8el8nqm author: Domingo, Esteban title: Molecular basis of genetic variation of viruses: error-prone replication date: 2019-11-08 words: 17663.0 sentences: 798.0 pages: flesch: 39.0 cache: ./cache/cord-022128-r8el8nqm.txt txt: ./txt/cord-022128-r8el8nqm.txt summary: In the case of viral genomes, mutations can result from different mechanisms: (i) template miscopying (direct incorporation of an incorrect nucleotide); (ii) primer-template misalignments that include miscoding followed by realignment, and misalignment of the template relative to the growing chain (polymerase "slippage" or "stuttering"); (iii) activity of cellular enzymes (i.e., deaminases), or (iv) chemical damage to the viral nucleic acids (deamination, depurination, depyrimidination, reactions with oxygen radicals, direct and indirect effects of ionizing radiation, photochemical reactions, etc.) (Naegeli, 1997; Bloomfield et al., 2000; Friedberg et al., 2006) . In addition to the general environmental and sequence context consequences for templatecopying fidelity that may affect any genome type, mutation rates for DNA viruses will also be influenced by: (i) whether the DNA polymerase that catalyzes viral DNA synthesis includes or lacks a functional proofreading-repair activity. abstract: Genetic variation is a necessity of all biological systems. Viruses use all known mechanisms of variation; mutation, several forms of recombination, and segment reassortment in the case of viruses with a segmented genome. These processes are intimately connected with the replicative machineries of viruses, as well as with fundamental physical-chemical properties of nucleotides when acting as template or substrate residues. Recombination has been viewed as a means to rescue viable genomes from unfit parents or to produce large modifications for the exploration of phenotypic novelty. All types of genetic variation can act conjointly as blind processes to provide the raw materials for adaptation to the changing environments in which viruses must replicate. A distinction is made between mechanistically unavoidable and evolutionarily relevant mutation and recombination. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153327/ doi: 10.1016/b978-0-12-816331-3.00002-7 id: cord-256918-mauzesor author: Domingo, Esteban title: Quasispecies and the implications for virus persistence and escape date: 1998-07-15 words: 2093.0 sentences: 112.0 pages: flesch: 38.0 cache: ./cache/cord-256918-mauzesor.txt txt: ./txt/cord-256918-mauzesor.txt summary: Objectives: To discuss indeterminations inherent to a quasispecies structure and to the analytical procedures to define it, biological implications of quasispecies, and the need to take into account this type of population structure, in order to design effective strategies to prevent and control diseases caused by highly variable viruses. Results: Quasispecies have many biological implications, extending from viral pathogenesis to the emergence of new pathogens, rapid antigenic variation, and alterations in cell tropism, virulence, host range and viral gene expression. Since adaptability of RNA viruses is key to viral pathogenesis and strategies for disease control, it would seem obvious that quasispecies should have been regarded as highly relevant to these questions (Domingo, 1989 (Domingo, , 1996 Domingo and Holland, 1992; Duarte et al., 1994; Novella et al., 1995) . The evolution of an RNA virus may be rapid or slow, but mutant swarms are always hidden in their replicating genome populations. abstract: Abstract Background: In the 1970s Manfred Eigen and colleagues proposed a new model of molecular evolution to explain adaptability and rapid evolution of simple replicons, as those that probably populated the earth at the onset of life. This model of evolution placed emphasis on mutant generation, to the point of invalidating the concept of wild-type genomes as a defined sequence of nucleotides. In striking similarity with the proposals for such early replicons, present-day RNA viruses consist of complex distributions of nonidentical but closely related genomes termed quasispecies. Objectives: To discuss indeterminations inherent to a quasispecies structure and to the analytical procedures to define it, biological implications of quasispecies, and the need to take into account this type of population structure, in order to design effective strategies to prevent and control diseases caused by highly variable viruses. Results: Quasispecies have many biological implications, extending from viral pathogenesis to the emergence of new pathogens, rapid antigenic variation, and alterations in cell tropism, virulence, host range and viral gene expression. Conclusions: Diseases caused by highly variable RNA viruses prove very difficult to control and vaccine development against such viruses are largely unsuccessful. It is important to understand quasispecies composition and dynamics, as quasispecies are an important step in the natural history of RNA viruses. url: https://api.elsevier.com/content/article/pii/S0928019798000324 doi: 10.1016/s0928-0197(98)00032-4 id: cord-280048-b4dz1lnn author: Domingo, Esteban title: Viral quasispecies date: 2019-10-17 words: 7955.0 sentences: 411.0 pages: flesch: 36.0 cache: ./cache/cord-280048-b4dz1lnn.txt txt: ./txt/cord-280048-b4dz1lnn.txt summary: Research on quasispecies has proceeded through several theoretical and experimental avenues that include continuing studies on evolutionary optimization and the origin of life, RNA-RNA interactions and replicator networks, the error threshold in variable fitness landscapes, consideration of chemical mutagenesis and proofreading mechanisms, evolution of tumor cells, bacterial populations or stem cells, chromosomal instability, drug resistance, and conformation distributions in prions (a class of proteins with conformation-dependent pathogenic potential; in this case the quasispecies is defined by a distribution of conformations) [16, 20] . Adaptability of RNA viruses is linked to parameters that facilitate exploration of sequence space: genome size (1.8 to 33 Kb), population size (variable but that can attain an impressive 10 12 individual genomes in an infected host at a given time), replication rate, mutation rate, fecundity (yield of viral particles per cell), and number of mutations required for a phenotypic change (surprisingly low for several relevant traits) (see [49] ). abstract: Viral quasispecies refers to a population structure that consists of extremely large numbers of variant genomes, termed mutant spectra, mutant swarms or mutant clouds. Fueled by high mutation rates, mutants arise continually, and they change in relative frequency as viral replication proceeds. The term quasispecies was adopted from a theory of the origin of life in which primitive replicons) consisted of mutant distributions, as found experimentally with present day RNA viruses. The theory provided a new definition of wild type, and a conceptual framework for the interpretation of the adaptive potential of RNA viruses that contrasted with classical studies based on consensus sequences. Standard clonal analyses and deep sequencing methodologies have confirmed the presence of myriads of mutant genomes in viral populations, and their participation in adaptive processes. The quasispecies concept applies to any biological entity, but its impact is more evident when the genome size is limited and the mutation rate is high. This is the case of the RNA viruses, ubiquitous in our biosphere, and that comprise many important pathogens. In virology, quasispecies are defined as complex distributions of closely related variant genomes subjected to genetic variation, competition and selection, and that may act as a unit of selection. Despite being an integral part of their replication, high mutation rates have an upper limit compatible with inheritable information. Crossing such a limit leads to RNA virus extinction, a transition that is the basis of an antiviral design termed lethal mutagenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/31622336/ doi: 10.1371/journal.pgen.1008271 id: cord-303265-v6ci69n0 author: Domingo, Esteban title: Introduction to virus origins and their role in biological evolution date: 2019-11-08 words: 15685.0 sentences: 764.0 pages: flesch: 42.0 cache: ./cache/cord-303265-v6ci69n0.txt txt: ./txt/cord-303265-v6ci69n0.txt summary: Topics covered include molecular mechanisms of genetic variation, with emphasis on high mutation rates, Darwinian principles acting on viruses, quasispecies dynamics and its implications, consequences for virus-host interactions, fitness as a relevant parameter, experimental model systems in cell culture, ex-vivo and in vivo, long-term virus evolution, the current situation of antiviral strategies to confront quasispecies swarms, and conceptual extensions of quasispecies to nonviral systems. With regard to the concepts of genome stability versus variation addressed in this book, it is helpful to divide viruses into four groups, depending on whether it is DNA or RNA the type of genetic material, which acts as a replicative intermediate in the infected cell (bottom gray shaded boxes in Fig. 1.1 ). They were selected for replicability, stability, and evolvability with trade-offs 1.4 Origin of life: a brief historical account and current views (acquisition of benefits for one of the three traits at some cost for another trait) likely play a role at this stage (see Chapter 4 for trade-offs in virus evolution). abstract: Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms. url: https://www.sciencedirect.com/science/article/pii/B9780128163313000015 doi: 10.1016/b978-0-12-816331-3.00001-5 id: cord-318749-k91oku7h author: Dong, Hui-Jun title: Selective regulation in ribosome biogenesis and protein production for efficient viral translation date: 2020-10-29 words: 7265.0 sentences: 384.0 pages: flesch: 38.0 cache: ./cache/cord-318749-k91oku7h.txt txt: ./txt/cord-318749-k91oku7h.txt summary: Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Similarly, ribosomes are required for the protein synthesis of host cells and viruses, but the biogenesis factor RBFs can also impact the proliferation of virus and cell-intrinsic immune responses. The multifunctional nucleolar phosphoprotein nucleophosmin (NPM) plays a lead role in ribosome biogenesis to stimulate RNA Pol I-dependent transcription (Li and Hann 2013) and regulates SARS-CoV, IBV, HIV-1, HCV Recruited by viral proteins to facilitate viral replication Chen et al. RPS25 deletion in yeast or mammalian cells has minimal effects on cellular protein synthesis, which implies that this ribosomal protein may be selectively required for viral IRES-mediated translation (Jack et al. Conservation of multifunctional ribosomal protein metallopanstimulin-1 (RPS27) through complex evolution demonstrates its key role in growth regulation in Archaea, eukaryotic cells, DNA repair, translation and viral replication abstract: As intracellular parasites, viruses depend heavily on host cell structures and their functions to complete their life cycle and produce new viral particles. Viruses utilize or modulate cellular translational machinery to achieve efficient replication; the role of ribosome biogenesis and protein synthesis in viral replication particularly highlights the importance of the ribosome quantity and/or quality in controlling viral protein synthesis. Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Here we summarize the recent literature on RBFs and RPs and their association with subcellular redistribution, post-translational modification, enzyme catalysis, and direct interaction with viral proteins. The advances described in this literature establish a rationale for targeting ribosome production and function in the design of the next generation of antiviral agents. url: https://www.ncbi.nlm.nih.gov/pubmed/33124672/ doi: 10.1007/s00203-020-02094-5 id: cord-263239-andje0wu author: Dorobantu, Cristina M. title: Modulation of the Host Lipid Landscape to Promote RNA Virus Replication: The Picornavirus Encephalomyocarditis Virus Converges on the Pathway Used by Hepatitis C Virus date: 2015-09-25 words: 8997.0 sentences: 455.0 pages: flesch: 45.0 cache: ./cache/cord-263239-andje0wu.txt txt: ./txt/cord-263239-andje0wu.txt summary: Here we show that cardioviruses manipulate another PI4K, namely the ER-localized phosphatidylinositol 4-kinase III alpha (PI4KA), to generate PI4P-enriched ROs. By siRNA-mediated knockdown and pharmacological inhibition, we demonstrate that PI4KA is an essential host factor for EMCV genome replication. To corroborate that PI4KA activity is required for the step of viral genome replication, we performed a time-of-addition experiment in which AL-9 was added to the cells at different time points after infection with RLuc-EMCV. The Picornavirus EMCV Converges on the Host Lipid Pathway Used by HCV localized throughout the cytoplasm and at the Golgi, OSBP was mainly found at ROs in infected cells, where it largely colocalized with 3AB ( Fig 6D, Pearson''s correlation coefficient = 0.71). Finally, data are presented suggesting that the OSBP-mediated exchange of PI4P and cholesterol at RO-MCSs is critical for EMCV genome replication and the global organization of ROs. Membrane alterations in the cytoplasm of cardiovirus-infected cells were already observed decades ago by electron microscopy [37, 38, 63] . abstract: Cardioviruses, including encephalomyocarditis virus (EMCV) and the human Saffold virus, are small non-enveloped viruses belonging to the Picornaviridae, a large family of positive-sense RNA [(+)RNA] viruses. All (+)RNA viruses remodel intracellular membranes into unique structures for viral genome replication. Accumulating evidence suggests that picornaviruses from different genera use different strategies to generate viral replication organelles (ROs). For instance, enteroviruses (e.g. poliovirus, coxsackievirus, rhinovirus) rely on the Golgi-localized phosphatidylinositol 4-kinase III beta (PI4KB), while cardioviruses replicate independently of the kinase. By which mechanisms cardioviruses develop their ROs is currently unknown. Here we show that cardioviruses manipulate another PI4K, namely the ER-localized phosphatidylinositol 4-kinase III alpha (PI4KA), to generate PI4P-enriched ROs. By siRNA-mediated knockdown and pharmacological inhibition, we demonstrate that PI4KA is an essential host factor for EMCV genome replication. We reveal that the EMCV nonstructural protein 3A interacts with and is responsible for PI4KA recruitment to viral ROs. The ensuing phosphatidylinositol 4-phosphate (PI4P) proved important for the recruitment of oxysterol-binding protein (OSBP), which delivers cholesterol to EMCV ROs in a PI4P-dependent manner. PI4P lipids and cholesterol are shown to be required for the global organization of the ROs and for viral genome replication. Consistently, inhibition of OSBP expression or function efficiently blocked EMCV RNA replication. In conclusion, we describe for the first time a cellular pathway involved in the biogenesis of cardiovirus ROs. Remarkably, the same pathway was reported to promote formation of the replication sites of hepatitis C virus, a member of the Flaviviridae family, but not other picornaviruses or flaviviruses. Thus, our results highlight the convergent recruitment by distantly related (+)RNA viruses of a host lipid-modifying pathway underlying formation of viral replication sites. url: https://doi.org/10.1371/journal.ppat.1005185 doi: 10.1371/journal.ppat.1005185 id: cord-310605-r63sg73c author: Dorward, D. A. title: Tissue-specific tolerance in fatal Covid-19 date: 2020-07-04 words: 4482.0 sentences: 256.0 pages: flesch: 39.0 cache: ./cache/cord-310605-r63sg73c.txt txt: ./txt/cord-310605-r63sg73c.txt summary: Here we report an aberrant immune response in fatal Covid-19, principally involving the lung and reticuloendothelial system, that is not clearly topologically associated with the virus, indicating tissue-specific tolerance of SARS-CoV-2. This supports prioritising pathogen tolerance as a therapeutic strategy in Covid-19, by better understanding non-injurious organ-specific viral tolerance mechanisms and targeting aberrant macrophage and plasma cell responses. As analysis of SARS-CoV-2 RNA confirmed presence in numerous organs, detailed histological analysis of multiple tissues was undertaken on every patient to determine the associated pathological consequences and inflammatory responses. The present study shows that fatal Covid-19 is associated with variable but widespread distribution of viral RNA and protein but with a discordant inflammatory response to local viral presence, both between and within tissues, demonstrating tissue-specific tolerance of SARS-CoV-2. abstract: Successful host defence against a pathogen can involve resistance or tolerance, with implications for prioritising either antimicrobial or immunomodulatory therapeutic approaches. Hyper-inflammation occurs in Covid-19 and is associated with worse outcomes. The efficacy of dexamethasone in preventing mortality in critical Covid-19 suggests that inflammation has a causal role in death. Whether this deleterious inflammation is primarily a direct response to the presence of SARS-CoV-2 requiring enhanced resistance, or an independent immunopathologic process necessitating enhanced tolerance, is unknown. Here we report an aberrant immune response in fatal Covid-19, principally involving the lung and reticuloendothelial system, that is not clearly topologically associated with the virus, indicating tissue-specific tolerance of SARS-CoV-2. We found that inflammation and organ dysfunction in fatal Covid-19 did not map to the widespread tissue and cellular distribution of SARS-CoV-2 RNA and protein, both between and within tissues. A monocyte/myeloid-rich vasculitis was identified in the lung, along with an influx of macrophages/monocytes into the parenchyma. In addition, stereotyped abnormal reticulo-endothelial responses (reactive plasmacytosis and iron-laden macrophages) were present and dissociated from the presence of virus in lymphoid tissues. Our results support virus-independent immunopathology being one of the primary mechanisms underlying fatal Covid-19. This supports prioritising pathogen tolerance as a therapeutic strategy in Covid-19, by better understanding non-injurious organ-specific viral tolerance mechanisms and targeting aberrant macrophage and plasma cell responses. url: https://doi.org/10.1101/2020.07.02.20145003 doi: 10.1101/2020.07.02.20145003 id: cord-003122-a3f4l6iu author: Dou, Dan title: Influenza A Virus Cell Entry, Replication, Virion Assembly and Movement date: 2018-07-20 words: 10272.0 sentences: 565.0 pages: flesch: 43.0 cache: ./cache/cord-003122-a3f4l6iu.txt txt: ./txt/cord-003122-a3f4l6iu.txt summary: The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. Influenza A viruses (IAVs) and type B viruses (IBVs) contain 8, negative-sense, single-stranded viral RNA (vRNA) gene segments ( Figure 1A ) (3, 4) , which encode transcripts for 10 essential viral proteins, as well as several strain-dependent accessory proteins ( Figure 1B) . In contrast to the early steps in IAV entry, vRNP trafficking to the nucleus following the fusion event is highly dependent on the host cell machinery and transport pathways [reviewed in Ref. abstract: Influenza viruses replicate within the nucleus of the host cell. This uncommon RNA virus trait provides influenza with the advantage of access to the nuclear machinery during replication. However, it also increases the complexity of the intracellular trafficking that is required for the viral components to establish a productive infection. The segmentation of the influenza genome makes these additional trafficking requirements especially challenging, as each viral RNA (vRNA) gene segment must navigate the network of cellular membrane barriers during the processes of entry and assembly. To accomplish this goal, influenza A viruses (IAVs) utilize a combination of viral and cellular mechanisms to coordinate the transport of their proteins and the eight vRNA gene segments in and out of the cell. The aim of this review is to present the current mechanistic understanding for how IAVs facilitate cell entry, replication, virion assembly, and intercellular movement, in an effort to highlight some of the unanswered questions regarding the coordination of the IAV infection process. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6062596/ doi: 10.3389/fimmu.2018.01581 id: cord-272666-3uidpr79 author: Doyle, Nicole title: Infectious Bronchitis Virus Nonstructural Protein 4 Alone Induces Membrane Pairing date: 2018-09-06 words: 7472.0 sentences: 358.0 pages: flesch: 52.0 cache: ./cache/cord-272666-3uidpr79.txt txt: ./txt/cord-272666-3uidpr79.txt summary: In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. In a subsequent study by others, it was shown that expression of only nsp3 and 4 from either MERS-CoV or SARS-CoV was able to induce DMV formation, and furthermore, addition of nsp6 made no difference to their shape or size, and did not induce the spherule-like structures seen following infection with whole virus [26] . abstract: Positive-strand RNA viruses, such as coronaviruses, induce cellular membrane rearrangements during replication to form replication organelles allowing for efficient viral RNA synthesis. Infectious bronchitis virus (IBV), a pathogenic avian Gammacoronavirus of significant importance to the global poultry industry, has been shown to induce the formation of double membrane vesicles (DMVs), zippered endoplasmic reticulum (zER) and tethered vesicles, known as spherules. These membrane rearrangements are virally induced; however, it remains unclear which viral proteins are responsible. In this study, membrane rearrangements induced when expressing viral non-structural proteins (nsps) from two different strains of IBV were compared. Three non-structural transmembrane proteins, nsp3, nsp4, and nsp6, were expressed in cells singularly or in combination and the effects on cellular membranes investigated using electron microscopy and electron tomography. In contrast to previously studied coronaviruses, IBV nsp4 alone is necessary and sufficient to induce membrane pairing; however, expression of the transmembrane proteins together was not sufficient to fully recapitulate DMVs. This indicates that although nsp4 is able to singularly induce membrane pairing, further viral or host factors are required in order to fully assemble IBV replicative structures. This study highlights further differences in the mechanism of membrane rearrangements between members of the coronavirus family. url: https://doi.org/10.3390/v10090477 doi: 10.3390/v10090477 id: cord-286719-1xjmlwqr author: Draz, Mohamed Shehata title: Applications of gold nanoparticles in virus detection date: 2018-02-15 words: 18990.0 sentences: 901.0 pages: flesch: 37.0 cache: ./cache/cord-286719-1xjmlwqr.txt txt: ./txt/cord-286719-1xjmlwqr.txt summary: The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. These techniques represent the majority of molecular techniques applied in virus detection and include various types of target amplification techniques (e.g., PCR, loop-mediated isothermal amplification (LAMP), transcription-mediated amplification, and nucleic acid sequence-based amplification), signal amplification techniques (e.g., branched DNA and hybrid capture), and probe amplification techniques (e.g., ligase chain reaction and strand-displacement amplification). [70] developed an impedimetric electrochemical assay for the detection of AIV M gene sequences based on measuring changes in the impedimetric behavior of the electrode when the target DNA hybridizes with the capture DNA probes immobilized onto its surface and is subsequently labeled by AuNPs via streptavidin/ biotin interaction (Fig. 12C) . abstract: Viruses are the smallest known microbes, yet they cause the most significant losses in human health. Most of the time, the best-known cure for viruses is the innate immunological defense system of the host; otherwise, the initial prevention of viral infection is the only alternative. Therefore, diagnosis is the primary strategy toward the overarching goal of virus control and elimination. The introduction of a new class of nanoscale materials with multiple unique properties and functions has sparked a series of breakthrough applications. Gold nanoparticles (AuNPs) are widely reported to guide an impressive resurgence in biomedical and diagnostic applications. Here, we review the applications of AuNPs in virus testing and detection. The developed AuNP-based detection techniques are reported for various groups of clinically relevant viruses with a special focus on the applied types of bio-AuNP hybrid structures, virus detection targets, and assay modalities and formats. We pay particular attention to highlighting the functional role and activity of each core Au nanostructure and the resultant detection improvements in terms of sensitivity, detection range, and time. In addition, we provide a general summary of the contributions of AuNPs to the mainstream methods of virus detection, technical measures, and recommendations required in guidance toward commercial in-field applications. url: https://doi.org/10.7150/thno.23856 doi: 10.7150/thno.23856 id: cord-345863-j01l71dh author: Drechsler, Yvonne title: Host Gene Expression of Macrophages in Response to Feline Coronavirus Infection date: 2020-06-09 words: 5530.0 sentences: 259.0 pages: flesch: 43.0 cache: ./cache/cord-345863-j01l71dh.txt txt: ./txt/cord-345863-j01l71dh.txt summary: Considering the importance of genetics and host immune responses in viral infections, the goal of this study was to elucidate host gene expression in macrophages using RNA sequencing. Our results highlight individual host responses playing an important role, consistent with the fact that few cats develop feline infectious peritonitis despite a common presence of enteric FCoV. Cultured macrophages were infected with the FIPV 79-1146 for 2 and 17 h before RNA was collected for the expression analysis of host genes and viral reads. Viral RNA load per sample in both raw read count summation and normalized fragments per kilobase million (FPKM) average from all virus'' genes combined, obtained in cellular extracts of either macrophages or CRFK cells infected with FIPV, at 2 and 17 h post-infection. In contrast to the macrophages exposed to the virus, RNA sequencing showed several log-fold increases of viral isolates in the CRFK cells used as replication controls from 2 to 17 h (Table 1 ). abstract: Feline coronavirus is a highly contagious virus potentially resulting in feline infectious peritonitis (FIP), while the pathogenesis of FIP remains not well understood, particularly in the events leading to the disease. A predominant theory is that the pathogenic FIPV arises from a mutation, so that it could replicate not only in enterocytes of the intestines but also in monocytes, subsequently systemically transporting the virus. The immune status and genetics of affected cats certainly play an important role in the pathogenesis. Considering the importance of genetics and host immune responses in viral infections, the goal of this study was to elucidate host gene expression in macrophages using RNA sequencing. Macrophages from healthy male cats infected with FIPV 79-1146 ex vivo displayed a differential host gene expression. Despite the virus uptake, aligned viral reads did not increase from 2 to 17 h. The overlap of host gene expression among macrophages from different cats was limited, even though viral transcripts were detected in the cells. Interestingly, some of the downregulated genes in all macrophages were involved in immune signaling, while some upregulated genes common for all cats were found to be inhibiting immune activation. Our results highlight individual host responses playing an important role, consistent with the fact that few cats develop feline infectious peritonitis despite a common presence of enteric FCoV. url: https://doi.org/10.3390/cells9061431 doi: 10.3390/cells9061431 id: cord-308216-s6rd8p41 author: Duan, Fang title: Small interfering RNA targeting for infected‐cell polypeptide 4 inhibits herpes simplex virus type 1 replication in retinal pigment epithelial cells date: 2011-10-20 words: 5037.0 sentences: 317.0 pages: flesch: 54.0 cache: ./cache/cord-308216-s6rd8p41.txt txt: ./txt/cord-308216-s6rd8p41.txt summary: title: Small interfering RNA targeting for infected‐cell polypeptide 4 inhibits herpes simplex virus type 1 replication in retinal pigment epithelial cells Background: This study sought to inhibit herpes simplex virus type 1 replication using small interfering RNA which targeting infected‐cell polypeptide 4 genes to mediate transcription of early and late viral genes in herpes simplex virus type 1 lytic (productive) infection in retina epithelial cells. Compared with herpes simplex virus type 1 infection alone or transfection with negative control small interfering RNA, the viral titre and the retina epithelial cell cytopathic effect were significantly decreased in retina epithelial cells transfected with infected‐cell polypeptide 4‐targeting small interfering RNA (50 and 100 nM) (P < 0.05). The inhibition of infected‐cell polypeptide 4‐targeting small interfering RNA on infected‐cell polypeptide 4 protein expression was also verified by Western blot in herpes simplex virus type 1 infected human cornea epithelial cell, human trabecular meshwork cells and Vero cells. abstract: Background: This study sought to inhibit herpes simplex virus type 1 replication using small interfering RNA which targeting infected‐cell polypeptide 4 genes to mediate transcription of early and late viral genes in herpes simplex virus type 1 lytic (productive) infection in retina epithelial cells. Methods: After pre‐ or post‐infecting with herpes simplex virus type 1, small interfering RNAs were transfected into retina epithelial cells. The antiviral effects of small interfering RNA were evaluated by Western blot, plaque assays, indirect immunofluorescence and reverse transcription polymerase chain reaction. The viral titre was detected by the 50% tissue culture infective dose method. Results: Small interfering RNA decreased infected‐cell polypeptide 4 expression in retina epithelial cells that were infected with herpes simplex virus type 1 before or after small interfering RNA transfection. Compared with herpes simplex virus type 1 infection alone or transfection with negative control small interfering RNA, the viral titre and the retina epithelial cell cytopathic effect were significantly decreased in retina epithelial cells transfected with infected‐cell polypeptide 4‐targeting small interfering RNA (50 and 100 nM) (P < 0.05). The small interfering RNA effectively silenced herpes simplex virus type 1 infected‐cell polypeptide 4 expression on both mRNA and the protein levels (P < 0.05). The inhibition of infected‐cell polypeptide 4‐targeting small interfering RNA on infected‐cell polypeptide 4 protein expression was also verified by Western blot in herpes simplex virus type 1 infected human cornea epithelial cell, human trabecular meshwork cells and Vero cells. Conclusions: Infected‐cell polypeptide 4‐targeting small interfering RNA can inhibit herpes simplex virus type 1 replication in retina epithelial cells, providing a foundation for development of RNA interference as an antiviral therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/21883773/ doi: 10.1111/j.1442-9071.2011.02668.x id: cord-286603-4p3t0vre author: Duan, Zhiqiang title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein date: 2020-06-27 words: 10674.0 sentences: 464.0 pages: flesch: 40.0 cache: ./cache/cord-286603-4p3t0vre.txt txt: ./txt/cord-286603-4p3t0vre.txt summary: title: TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein Therefore, the reduced viral RNA synthesis and transcription caused by M/NLS mutation might be one of the reasons responsible for the attenuated replication of rSS1GFP-M/NLSm. Virus-host protein interactions based on quantitative proteomics analysis have become important methods in understanding cellular proteins involved in virus replication and pathogenesis [22, 23, 41, 42] . Therefore, together with the above results, we speculated that the relatively decreased expression of DEPs involved in ribosome structure, protein posttranslational modification and trafficking due to the disrupted nuclear accumulation of M protein affected viral protein synthesis and budding, which might be the third reason responsible for the attenuated replication of rSS1GFP-M/NLSm. Inflammatory responses are important aspects of the innate immune system during virus infection. abstract: Nuclear localization of cytoplasmic RNA virus proteins mediated by intrinsic nuclear localization signal (NLS) plays essential roles in successful virus replication. We previously reported that NLS mutation in the matrix (M) protein obviously attenuates the replication and pathogenicity of Newcastle disease virus (NDV), but the attenuated replication mechanism remains unclear. In this study, we showed that M/NLS mutation not only disrupted M’s nucleocytoplasmic trafficking characteristic but also impaired viral RNA synthesis and transcription. Using TMT-based quantitative proteomics analysis of BSR-T7/5 cells infected with the parental NDV rSS1GFP and the mutant NDV rSS1GFP-M/NLSm harboring M/NLS mutation, we found that rSS1GFP infection stimulated much greater quantities and more expression changes of differentially expressed proteins involved in host cell transcription, ribosomal structure, posttranslational modification, and intracellular trafficking than rSS1GFP-M/NLSm infection. Further in-depth analysis revealed that the dominant nuclear accumulation of M protein inhibited host cell transcription, RNA processing and modification, protein synthesis, posttranscriptional modification and transport; and this kind of inhibition could be weakened when most of M protein was confined outside the nucleus. More importantly, we found that the function of M protein in the cytoplasm effected the inhibition of TIFA expression in a dose-dependent manner, and promoted NDV replication by down-regulating TIFA/TRAF6/NF-κB-mediated production of cytokines. It was the first report about the involvement of M protein in NDV immune evasion. Taken together, our findings demonstrate that NDV replication is closely related to the nucleocytoplasmic trafficking of M protein, which accelerates our understanding of the molecular functions of NDV M protein. url: https://doi.org/10.1080/21505594.2020.1770482 doi: 10.1080/21505594.2020.1770482 id: cord-294108-uvnh0s9r author: Dube, Taru title: Repurposed Drugs, Molecular Vaccines, Immune‐Modulators, and Nanotherapeutics to Treat and Prevent COVID‐19 Associated with SARS‐CoV‐2, a Deadly Nanovector date: 2020-10-25 words: 13885.0 sentences: 845.0 pages: flesch: 44.0 cache: ./cache/cord-294108-uvnh0s9r.txt txt: ./txt/cord-294108-uvnh0s9r.txt summary: [2, [8] [9] [10] This article discusses SARS-CoV-2 nanostructure, the virus biology in connection to its epidemiology, clinical manifestations, and potential and future therapeutic options including repurposed drugs, vaccine/protein therapies, immune therapies, and nanotherapeutics. Mechanisms such as inhibition of viral enzymes (DNA and RNA polymerases, 3CL pro, TMPRSS2, reverse transcriptase, neuraminidase, endonucleases, and other proteases) or processes such as ACE2 cellular receptor inhibitors and endosomal acidification mediators prohibiting viral fusion; molecules interfering with glycosylation of the viral protein, viral assembly, new viral particle transport, and release, and immunomodulation of cytokine release can be potential targets in developing various antiviral drugs for the SARS-CoV-2. [85] A randomized, placebo-controlled, Phase IV clinical trial assessing the safety and efficacy of umifenovir as an adjuvant therapy to the combined therapeutic regimen of IFN 1a, lopinavir/ritonavir and hydroxychloroquine in moderate to severe COVID-19 patients (NCT04350684) is underway. abstract: The deadly pandemic, coronavirus disease 2019 (COVID‐19), caused due to the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has paralyzed the world. Although significant methodological advances have been made in the field of viral detection/diagnosis with 251 in vitro diagnostic tests receiving emergency use approval by the US‐FDA, little progress has been made in identifying curative or preventive therapies. This review discusses the current trends and potential future approaches for developing COVID‐19 therapeutics, including repurposed drugs, vaccine candidates, immune‐modulators, convalescent plasma therapy, and antiviral nanoparticles/nanovaccines/combinatorial nanotherapeutics to surmount the pandemic viral strain. Many potent therapeutic candidates emerging via drug‐repurposing could significantly reduce the cost and duration of anti‐COVID‐19 drug development. Gene/protein‐based vaccine candidates that could elicit both humoral and cell‐based immunity would be on the frontlines to prevent the disease. Many emerging nanotechnology‐based interventions will be critical in the fight against the deadly virus by facilitating early detection and enabling target oriented multidrug therapeutics. The therapeutic candidates discussed in this article include remdesivir, dexamethasone, hydroxychloroquine, favilavir, lopinavir/ritonavir, antibody therapeutics like gimsilumab and TJM2, anti‐viral nanoparticles, and nanoparticle‐based DNA and mRNA vaccines. url: https://doi.org/10.1002/adtp.202000172 doi: 10.1002/adtp.202000172 id: cord-313301-7mkadtp9 author: Duffy, Siobain title: EVOLUTION OF HOST SPECIFICITY DRIVES REPRODUCTIVE ISOLATION AMONG RNA VIRUSES date: 2007-08-23 words: 6091.0 sentences: 273.0 pages: flesch: 45.0 cache: ./cache/cord-313301-7mkadtp9.txt txt: ./txt/cord-313301-7mkadtp9.txt summary: In particular, the high pernucleotide mutation rates of RNA viruses (Drake 1993) provide extensive genetic variation that fuels evolution by natural selection, making the study of reproductive isolation and speciation especially feasible (Holmes 2004) . We tested the plausibility of the no-gene mechanism of speciation by examining the consequences of adaptation to a novel host in laboratory populations of the RNA phage 6, which infects a number of Pseudomonas species. The same microevolutionary processes of mutation and natural selection, which led to the adaptation of 6 populations to a novel host also resulted in a macroevolutionary event: the evolution of a new virus species that is reproductively isolated from the ancestral phage 6 wt . Beyond uniquely demonstrating the evolution of reproductive isolation in the laboratory, our study extends the literature describing the evolutionary genetics of narrowed host range when viruses adapt to a single host. abstract: Ecological speciation hypotheses claim that assortative mating evolves as a consequence of divergent natural selection for ecologically important traits. Reproductive isolation is expected to be particularly likely to evolve by this mechanism in species such as phytophagous insects that mate in the habitats in which they eat. We tested this expectation by monitoring the evolution of reproductive isolation in laboratory populations of an RNA virus that undergoes genetic exchange only when multiple virus genotypes coinfect the same host. We subjected four populations of the RNA bacteriophage φ6 to 150 generations of natural selection on a novel host. Although there was no direct selection acting on host range in our experiment, three of the four populations lost the ability to infect one or more alternative hosts. In the most extreme case, one of the populations evolved a host range that does not contain any of the hosts infectible by the wild‐type φ6. Whole genome sequencing confirmed that the resulting reproductive isolation was due to a single nucleotide change, highlighting the ease with which an emerging RNA virus can decouple its evolutionary fate from that of its ancestor. Our results uniquely demonstrate the evolution of reproductive isolation in allopatric experimental populations. Furthermore, our data confirm the biological credibility of simple “no‐gene” mechanisms of assortative mating, in which this trait arises as a pleiotropic effect of genes responsible for ecological adaptation. url: https://www.ncbi.nlm.nih.gov/pubmed/17908251/ doi: 10.1111/j.1558-5646.2007.00226.x id: cord-269975-1ebmq7t8 author: Duplantier, Allen J. title: Combating biothreat pathogens: ongoing efforts for countermeasure development and unique challenges date: 2020-05-27 words: 12963.0 sentences: 580.0 pages: flesch: 32.0 cache: ./cache/cord-269975-1ebmq7t8.txt txt: ./txt/cord-269975-1ebmq7t8.txt summary: None of the filoviruses or henipaviruses has any FDA-approved therapeutics or vaccines available for prevention or treatment of human disease, and while ribavirin is sometimes used to treat Lassa fever, it is not a terribly effective drug against this viral infection [28] . Many of the therapeutics that are in different stages of either preclinical or clinical development for select biothreat pathogens include small molecule antivirals (Tables 7.3 and 7.4), antibody (or antibody cocktails) against viruses or bacteria/virulence factors (Table 7 .5), and combination drug therapy (Table 7 .6). Although no FDA-approved HDT therapies are yet available for treating infectious diseases, we have summarized in this section the antimicrobial Primary screening of small molecule chemical libraries in the phenotypic HCI assay will identify compounds that inhibit pathogen infection as well as those that may contribute to cellular toxicity. abstract: Research to discover and develop antibacterial and antiviral drugs with potent activity against pathogens of biothreat concern presents unique methodological and process-driven challenges. Herein, we review laboratory approaches for finding new antibodies, antibiotics, and antiviral molecules for pathogens of biothreat concern. Using high-throughput screening techniques, molecules that directly inhibit a pathogen’s entry, replication, or growth can be identified. Alternatively, molecules that target host proteins can be interesting targets for development when countering biothreat pathogens, due to the modulation of the host immune response or targeting proteins that interfere with the pathways required by the pathogen for replication. Monoclonal and cocktail antibody therapies approved by the Food and Drug Administration for countering anthrax and under development for treatment of Ebola virus infection are discussed. A comprehensive tabular review of current in vitro, in vivo, pharmacokinetic and efficacy datasets has been presented for biothreat pathogens of greatest concern. Finally, clinical trials and animal rule or traditional drug approval pathways are also reviewed. Opinions; interpretations; conclusions; and recommendations are those of the authors and are not necessarily endorsed by the US Army. url: https://api.elsevier.com/content/article/pii/B9780128184806000072 doi: 10.1016/b978-0-12-818480-6.00007-2 id: cord-269766-arjoemla author: Dutescu, R. Michael title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs date: 2020-09-08 words: 2141.0 sentences: 124.0 pages: flesch: 57.0 cache: ./cache/cord-269766-arjoemla.txt txt: ./txt/cord-269766-arjoemla.txt summary: title: Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS: We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. CONCLUSIONS: Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. To clarify this, we tested the tear fluid of confirmed hospitalized SARS-CoV-2 patients by PCR using a method not previously used for the collection of tear samples. In this study, we could confirm SARS-CoV-2 RNA positive tear samples by PCR in as many as 28% of determined SARS-CoV-2 patients by oropharyngeal swabs. 13 In a more recent cross-sectional study, only 1 (1.38%) conjunctival swab of 72 confirmed SARS-CoV-2 cases was tested positive. abstract: This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS: We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. Tear samples obtained with a laboratory capillary and oropharyngeal swabs were analyzed by real-time PCR using the Altona SARS-CoV-2 Assay or the Roche SARS-CoV-2 LightMix PCR, depending on the availability. Patient history was documented, and ophthalmoscopy was used to assess for ocular surface disease. RESULTS: Of all 18 patients recruited in April 2020, 5 suffered from respiratory failure and were submitted to an intensive care unit. None of our patients had signs of viral conjunctivitis although all patients in intensive care showed chemosis and conjunctival hyperemia because of third-spacing or fluid overload. The presence of coronavirus RNA was confirmed by PCR in 5 of 18 patients (28%) in tears and 72% for oropharyngeal swabs. CONCLUSIONS: Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. This does not automatically indicate viral shedding in ocular tissue or contagiousness of tear fluid. url: https://doi.org/10.1097/ico.0000000000002562 doi: 10.1097/ico.0000000000002562 id: cord-311982-wkg56xeq author: Dye, Charlotte title: Genomic RNA sequence of feline coronavirus strain FCoV C1Je date: 2007-06-17 words: 5240.0 sentences: 250.0 pages: flesch: 55.0 cache: ./cache/cord-311982-wkg56xeq.txt txt: ./txt/cord-311982-wkg56xeq.txt summary: Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted ''internal mutation theory'' of FIPV pathogenicity. Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted ''internal mutation theory'' of FIPV pathogenicity. Furthermore, the structural and accessory gene regions of viral RNA isolated from the liver of the same cat (FCoV C1Li) were sequenced and the data derived from the enteric (jejunum) and non-enteric (liver) sources were compared. Sequence data previously generated for the laboratory strain FCoV, FIPV 79-1146, were used to design primers for conventional reverse transcriptase polymerase chain reaction (RT-PCR) amplification of short lengths (100e500 bases) of the field strain RNA. Analysis of the accessory gene 7 region of the FCoV C1Je genome identifies two ORFs, which have translation products sharing high amino acid identity with proteins 7a and 7b of FIPV 79-1146. abstract: This paper reports the first genomic RNA sequence of a field strain feline coronavirus (FCoV). Viral RNA was isolated at post mortem from the jejunum and liver of a cat with feline infectious peritonitis (FIP). A consensus sequence of the jejunum-derived genomic RNA (FCoV C1Je) was determined from overlapping cDNA fragments produced by reverse transcriptase polymerase chain reaction (RT-PCR) amplification. RT-PCR products were sequenced by a reiterative sequencing strategy and the genomic RNA termini were determined using a rapid amplification of cDNA ends PCR strategy. The FCoV C1Je genome was found to be 29,255 nucleotides in length, excluding the poly(A) tail. Comparison of the FCoV C1Je genomic RNA sequence with that of the laboratory strain FCoV FIP virus (FIPV) 79-1146 showed that both viruses have a similar genome organisation and predictions made for the open reading frames and cis-acting elements of the FIPV 79-1146 genome hold true for FCoV C1Je. In addition, the sequence of the 3′-proximal third of the liver derived genomic RNA (FCoV C1Li), which encompasses the structural and accessory protein genes of the virus, was also determined. Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted ‘internal mutation theory’ of FIPV pathogenicity. url: https://www.ncbi.nlm.nih.gov/pubmed/17363313/ doi: 10.1016/j.jfms.2006.12.002 id: cord-323987-gh1m05gi author: Dziąbowska, Karolina title: Detection Methods of Human and Animal Influenza Virus—Current Trends date: 2018-10-18 words: 11112.0 sentences: 760.0 pages: flesch: 46.0 cache: ./cache/cord-323987-gh1m05gi.txt txt: ./txt/cord-323987-gh1m05gi.txt summary: RIDTs with digital readout systems showed many similarities to conventional assays like small sample volume (less than 150 µL) and short analysis time (around 15 min) but exhibited much better sensitivities, even one order of magnitude lower limits of detection (LODs). Among methods mentioned, general diagnostic tests for influenza base on virus culture (conventional and shellvial), detection of viral nucleic acid (PCR) or antigens (by neuraminidase enzymatic activity, fluorescent antibody or enzyme/optical immunoassay) and serologic tests. Main trends for influenza virus detection are: (I) modifications of traditional ''gold star'' methods like PCR, RIDTs, ELISA what results in analysis time shortening, costs lowering, LOD and limit of quantification (LOQ) improvement, (II) conjugating of traditional methods and creating new platforms, micro-biochips and others, (III) introducing known solutions to new ones, like smartphone-based analysis control with results data insertion into Google Maps, (IV) reuse of the functions of known devices, like glucometer, smartphone cameras, (V) the most common used detection methods: spectral/optical, electrical, (VI) and entirely new approaches. abstract: The basic affairs connected to the influenza virus were reviewed in the article, highlighting the newest trends in its diagnostic methods. Awareness of the threat of influenza arises from its ability to spread and cause a pandemic. The undiagnosed and untreated viral infection can have a fatal effect on humans. Thus, the early detection seems pivotal for an accurate treatment, when vaccines and other contemporary prevention methods are not faultless. Public health is being attacked with influenza containing new genes from a genetic assortment between animals and humankind. Unfortunately, the population does not have immunity for mutant genes and is attacked in every viral outbreak season. For these reasons, fast and accurate devices are in high demand. As currently used methods like Rapid Influenza Diagnostic Tests lack specificity, time and cost-savings, new methods are being developed. In the article, various novel detection methods, such as electrical and optical were compared. Different viral elements used as detection targets and analysis parameters, such as sensitivity and specificity, were presented and discussed. url: https://doi.org/10.3390/bios8040094 doi: 10.3390/bios8040094 id: cord-022889-lv6fy6e6 author: Dávalos, Alberto title: Literature review of baseline information on non‐coding RNA (ncRNA) to support the risk assessment of ncRNA‐based genetically modified plants for food and feed date: 2019-08-07 words: 96011.0 sentences: 5041.0 pages: flesch: 51.0 cache: ./cache/cord-022889-lv6fy6e6.txt txt: ./txt/cord-022889-lv6fy6e6.txt summary: This report suggests that some plant ncRNAs (e.g miRNAs and siRNAs) show higher stability as compared to other ncRNAs due to peculiar chemical characteristics (2''‐O‐methylation at 3'' end).However, ingested or administered ncRNA must overcome many extracellular and cellular barriers to reach the intended target tissue or functional location in sufficient amount to exert any biological effect. Finally, the publications reporting the outcome of two EFSA procurements aiming respectively at investigating and summarising the state of knowledge on the mode-of-action of dsRNA and miRNA pathways, the potential for non-target gene regulation by dsRNA-derived siRNAs or miRNAs, the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing 6 ; and reviewing relevant scientific information on RNA interference that could serve as baseline information for the environmental risk assessment of RNAi-based GM plants ) 7 were also used. abstract: This report is the outcome of an EFSA procurement (NP/EFSA/GMO/2016/01) reviewing relevant scientific information on ncRNA and on RNA interference(RNAi) that could support the food and feed risk assessment of ncRNA‐based genetically modified (GM) plants. Information was retrieved through key words and key questions covering the stability and degradation of ncRNAs after oral ingestion, the passage of ncRNAs from food and feed to human and animal organs and tissues via the gastrointestinal tract and other barriers, as well as the potential effects on the gastrointestinal tract, the immune system or the entire organism.Full description of the strategy used for the literature search and for studies selectionis provided and the number of retrieved publications is reported. This report is divided into four partsdiscussing the kinetics of exogenous ncRNAs in humans and animals, with focus on ingested ncRNAs (Part 1); the possible effects of ncRNAs on the gastrointestinal tract (Part 2), systemically(Part 3)and on the immune system (Part 4). This report suggests that some plant ncRNAs (e.g miRNAs and siRNAs) show higher stability as compared to other ncRNAs due to peculiar chemical characteristics (2’‐O‐methylation at 3’ end).However, ingested or administered ncRNA must overcome many extracellular and cellular barriers to reach the intended target tissue or functional location in sufficient amount to exert any biological effect. Literature data indicate that chemically unmodified and unformulated ncRNAs exhibit very low stability in the gastrointestinal tract and in biological fluids and, in general, do not elicit major biological effects.This report also provides an overview of the RNA content in plant‐derived foods and diets and discusses the controversies on the presence of dietary exogenous RNAs in the biological fluids of humans and animals and their effects. Finally, gaps in the scientific literature are highlighted and recommendations provided url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163523/ doi: 10.2903/sp.efsa.2019.en-1688 id: cord-353524-3w970ycx author: Dömling, Alexander title: Chemistry and Biology of SARS-CoV-2 date: 2020-05-22 words: 3942.0 sentences: 237.0 pages: flesch: 52.0 cache: ./cache/cord-353524-3w970ycx.txt txt: ./txt/cord-353524-3w970ycx.txt summary: Given that SARS-CoV-2 and SARS-CoV share very high identical sequence in their 3CLpro, these HIV protease inhibitors are currently again repurposed for the treatment of COVID-19 (Chinese Clinical Trial Registry: ChiCTR2000029539). 30, 31 The interplay of the ACE receptor in cardiovascular diseases (with the well-known drug class of ACE inhibitors) and as the docking point for SARS-CoV-2 cellular infection is a current point of intense debate and research. For example, the crystal structure of SARS-CoV-2 N protein RNA-binding domain was just published and will give structural insight as a potential drug target. Potential broad spectrum inhibitors of the coronavirus 3CLpro: A virtual screening and structure-based drug design study Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites abstract: SARS-CoV-2 (previously 2019-nCoV or Wuhan coronavirus) caused an unprecedented fast-spreading worldwide pandemic. Although currently with a rather low mortality rate, the virus spread rapidly over the world using the modern world’s traffic highways. The coronavirus (CoV) family members were responsible for several deadly outbreaks and epidemics during the last decade. Not only governments but also the scientific community reacted promptly to the outbreak, and information is shared quickly. For example, the genetic fingerprint was shared, and the 3D structure of key proteins was rapidly solved, which can be used for the discovery of potential treatments. An overview is given on the current knowledge of the spread, disease course, and molecular biology of SARS-CoV-2. We discuss potential treatment developments in the context of recent outbreaks, drug repurposing, and development timelines. url: https://www.sciencedirect.com/science/article/pii/S2451929420301959 doi: 10.1016/j.chempr.2020.04.023 id: cord-342412-azkamnpa author: Ecker, David J title: The Microbial Rosetta Stone Database: A compilation of global and emerging infectious microorganisms and bioterrorist threat agents date: 2005-04-25 words: 7206.0 sentences: 409.0 pages: flesch: 42.0 cache: ./cache/cord-342412-azkamnpa.txt txt: ./txt/cord-342412-azkamnpa.txt summary: This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. For example, the Centers for Disease Control and Prevention (CDC) maintains an ever-changing list of notifiable diseases, the National Institute of Allergy and Infectious Disease (NIAID) lists agents with potential for use in bioterrorist attacks, and the Department of Health and Human Services (HHS) maintains a list of critical human pathogens. This article focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. It provides a compilation of lists, taken from the database, of important and/or regulated biological agents from a number of agencies including HHS, the United States Department of Agriculture (USDA), the CDC, the World Health Organization (WHO), the NIAID, and other sources. abstract: BACKGROUND: Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks. RESULTS: We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents. CONCLUSION: The Microbial Rosetta Stone is available at . The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases. url: https://www.ncbi.nlm.nih.gov/pubmed/15850481/ doi: 10.1186/1471-2180-5-19 id: cord-291765-97lk5qfo author: Eckerle, Lance D. title: Effects of Mutagenesis of Murine Hepatitis Virus NSP1 and NSP14 on Replication in Culture date: 2006 words: 2187.0 sentences: 105.0 pages: flesch: 50.0 cache: ./cache/cord-291765-97lk5qfo.txt txt: ./txt/cord-291765-97lk5qfo.txt summary: To test the requirements for nsp1 and nsp14 in replication and to probe their functions, deletions or mutations were engineered into the viral genome in nsp1 and nsp14 and mutant viruses were analyzed for virus viability, replication, protein expression, and RNA synthesis. When infectious genome RNA containing these changes was electroporated into permissive cells, only the carboxy-terminal nsp1 deletion allowed recovery of an infectious mutant virus (nsp1 124-242). Based on the above results, systematic mutagenesis of clustered-charged residues was performed, both within the putative essential amino-terminal two-thirds of nsp1 as well as the dispensable carboxy-terminal third of the nsp1 protein domain. Deletions of P1-Gln residues in the flanking cleavage sites between nsp13-14 (VUSS6) and nsp14-15 (VUSS17) were engineered in the infectious clone cDNA and used to generate full-length genome RNA for electroporation into permissive cells. abstract: For nsp1, the fact that the carboxy-terminal but not the amino-terminal half of the protein can be deleted suggests that there may be specific and distinct domains within the protein or that the entire protein is dispensable but that the RNA encoding the amino-terminal half of nsp1 cannot be deleted. The identification of specific required residues support the conclusion that it is the portion of the protein that is required for replication. The results of mutagenesis of the nsp14 coding region and flanking cleavage sites also provided important new insights into this protein and its requirements. Our previous study raised the question as to the essential nature of nsp14 in replication. The results of this study show that putative active site residues cannot be substituted without loss of replication in culture. Interestingly, mutagenesis of Tyr414 showed that while this residue can tolerate a number of substitutions, it was intolerant of Lysine or deletion. The results suggest that nsp14 is required for replication. However, whatever functions nsp14 serves appear to be retained by noncleaved or partially processed nsp14, since abolition of either the amino-terminal or carboxy-terminal cleavage site allowed recovery of viable virus. url: https://www.ncbi.nlm.nih.gov/pubmed/17037504/ doi: 10.1007/978-0-387-33012-9_8 id: cord-334394-qgyzk7th author: Edgar, Robert C. title: Petabase-scale sequence alignment catalyses viral discovery date: 2020-08-10 words: 8134.0 sentences: 423.0 pages: flesch: 51.0 cache: ./cache/cord-334394-qgyzk7th.txt txt: ./txt/cord-334394-qgyzk7th.txt summary: To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To expand the known repertoire of viruses and catalyse global virus discovery, in particular for Coronaviridae (CoV) family, we developed the Serratus cloud computing architecture for ultra-high throughput sequence alignment. We aligned 3,837,755 public RNA-seq, meta-genome, meta-virome and meta-transcriptome datasets (termed a sequencing run [5] ) against a collection of viral family pangenomes comprising all GenBank CoV records clustered at 99% identity plus all non-retroviral RefSeq records for vertebrate viruses (see Methods and Extended Table 1 ). We performed de novo assembly on 52,772 runs potentially containing CoV sequencing reads by combining 37,131 SRA accessions identified by the Serratus search with 18,584 identified by an ongoing cataloguing initiative of the SRA called STAT [5] . abstract: Public sequence data represents a major opportunity for viral discovery, but its exploration has been inhibited by a lack of efficient methods for searching this corpus, which is currently at the petabase scale and growing exponentially. To address the ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 and expand the known sequence diversity of viruses, we aligned pangenomes for coronaviruses (CoV) and other viral families to 5.6 petabases of public sequencing data from 3.8 million biologically diverse samples. To implement this strategy, we developed a cloud computing architecture, Serratus, tailored for ultra-high throughput sequence alignment at the petabase scale. From this search, we identified and assembled thousands of CoV and CoV-like genomes and genome fragments ranging from known strains to putatively novel genera. We generalise this strategy to other viral families, identifying several novel deltaviruses and huge bacteriophages. To catalyse a new era of viral discovery we made millions of viral alignments and family identifications freely available to the research community. Expanding the known diversity and zoonotic reservoirs of CoV and other emerging pathogens can accelerate vaccine and therapeutic developments for the current pandemic, and help us anticipate and mitigate future ones. url: https://doi.org/10.1101/2020.08.07.241729 doi: 10.1101/2020.08.07.241729 id: cord-330847-a84pcc9z author: Edwards, M. C. title: RNA recombination in the genome of Barley stripe mosaic virus date: 1992-07-31 words: 2344.0 sentences: 152.0 pages: flesch: 67.0 cache: ./cache/cord-330847-a84pcc9z.txt txt: ./txt/cord-330847-a84pcc9z.txt summary: Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. A "bandaid" cloning strategy, which exploits the conservation of the 3'' terminal sequence, as well as the unique nature of the 5'' ends of the BSMV RNAs, has been used previously to obtain full-length cDNA clones from which infectious in vitro transcripts can be produced (3, 7). Analysis of the resulting cDNA clones suggested that CV17 RNA y is a naturally occurring chimeric recombinant, composed of a 70nucleotide (nt) a-specific leader sequence preceding a r-specific coding region. 3. ldentrfrcatron of barley stripe mosaic virus strarn CV17 LY and Type strain y-specific leader sequences In 15 putative CV17 y cDNA clones and native RNAs of strains CV17, CV42, and ND1 8. abstract: Abstract Barley stripe mosaic Hordeivirus (BSMV) is a positive-strand RNA virus requiring three single-stranded RNAs (α, β, and γ) for infectivity. A terminal-sequence-dependent cloning strategy was used to clone the entire genome of the CV17 strain. Full-length γ cDNA clones were obtained when oligonucleotides specific for the 5′-terminal sequence of RNA α were used in the cloning procedure, but not when RNA γ-specific oligonucleotides were used. Sequence analysis of six putative γ cDNA clones revealed that nucleotides 1–70 possess 89% homology with the first 70 nucleotides of RNA α. This leader region is separated from the γ-specific coding region by an eight-base intervening sequence common to both CV17 RNAs α and γ. Northern and Southern hybridization with oligonucleotide probes specific for either α or γ leader sequences indicated that CV17 γ cDNA clones are representative of native CV17 γ RNAs. Furthermore, bioassays indicated that in vitro transcripts derived from these γ cDNA clones were infectious when coinoculated with in vitro transcripts of full-length α and β cDNA clones. Thus, the evidence suggests that RNA γ of BSMV strain CV17 is a recombinant molecule which may have arisen as a result of natural recombination between RNAs α and γ. url: https://www.ncbi.nlm.nih.gov/pubmed/1604824/ doi: 10.1016/0042-6822(92)90722-2 id: cord-267377-wyhsxj6g author: Edwards, Michael C. title: Coat protein expression strategy of oat blue dwarf virus() date: 2014-01-14 words: 4709.0 sentences: 231.0 pages: flesch: 54.0 cache: ./cache/cord-267377-wyhsxj6g.txt txt: ./txt/cord-267377-wyhsxj6g.txt summary: The single, large ORF encodes a polyprotein with domains specifying methyltransferase (mtr), protease (pro), helicase/NTpase (hel), and polymerase (pol) activities fused to the sequence encoding the CPs. The major and minor coat proteins map to the same CP sequence and size differences between them are potentially determined by translation initiation at two different start codons (minor, AUG 5581 and major, AUG 5710 ). Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, major CP mutants GH1-7 (premature termination mutant) and KL1-3 (initiation codon mutant), and AB15-25 (marafibox mutant) and incubated for 40 h. Accumulation of viral coat proteins (CPs) and RNA in oat protoplasts inoculated with premature termination and initiation codon mutants of the CP gene. Oat protoplasts were inoculated with capped transcripts of wild type clone pOBDV, premature termination mutants GH1-7 and EF2-2, and initiation codon mutants IJ4-7 (minor CP), and KL1-3 and KL2-5 (major CP) and incubated for 24 h. abstract: Oat blue dwarf virus (OBDV) is a member of the genus Marafivirus whose genome encodes a 227 kDa polyprotein (p227) ostensibly processed post-translationally into its functional components. Encoded near the 3' terminus and coterminal with the p227 ORF are ORFs specifying major and minor capsid proteins (CP). Since the CP expression strategy of marafiviruses has not been thoroughly investigated, we produced a series of point mutants in the OBDV CP encoding gene and examined expression in protoplasts. Results support a model in which the 21 kDa major CP is the product of direct translation of a sgRNA, while the 24 kDa minor CP is a cleavage product derived from both the polyprotein and a larger ~26 kDa precursor translated directly from the sgRNA. Cleavage occurs at an LXG[G/A] motif conserved in many viruses that use papain-like proteases for polyprotein processing and protection against degradation via the ubiquitin-proteasome system. url: https://doi.org/10.1016/j.virol.2013.12.018 doi: 10.1016/j.virol.2013.12.018 id: cord-254895-ym0jsir5 author: Eisenächer, Katharina title: The role of viral nucleic acid recognition in dendritic cells for innate and adaptive antiviral immunity date: 2008-01-18 words: 9040.0 sentences: 465.0 pages: flesch: 47.0 cache: ./cache/cord-254895-ym0jsir5.txt txt: ./txt/cord-254895-ym0jsir5.txt summary: Dendritic cell subpopulations express specific nucleic acid recognition receptors belonging to the Toll-like receptor family (TLR3, 7, 8, 9) and the cytosolic RNA helicase family (RIG-I, MDA5, LGP2). Apart from activating the NFkB and MAPK signaling pathways leading to inflammatory cytokine and chemokine production as well as costimulatory molecule expression, the intracellularly localized nucleic acid recognition receptors TLR3, 7, 8 and 9 specifically trigger type I interferon production via MyD88-and TRIF-dependent signaling pathways. Thus, TRAF6 seems to be required for NFkB activation but not IFN-b induction downstream of IPS-1 which is mainly mediated by TBK1/IKKe. In vitro studies performed with primary cells obtained from RIG-I knockout mice confirmed that RIG-I plays an essential role in eliciting immune responses against specific negative strand and positive strand RNA viruses such as NDV, SeV, VSV, Japanese encephalitis virus (JEV) and Influenza virus in various cell types with the exception of pDCs . abstract: Abstract Dendritic cells which are located at the interface of innate and adaptive immunity are targets for infection by many different DNA and RNA viruses. Dendritic cell subpopulations express specific nucleic acid recognition receptors belonging to the Toll-like receptor family (TLR3, 7, 8, 9) and the cytosolic RNA helicase family (RIG-I, MDA5, LGP2). Activation of dendritic cells by viral DNA and RNA via these receptors is essential for triggering the innate antiviral immune response and shaping the ensuing adaptive antiviral immunity. This review will summarize our current knowledge of viral nucleic acid recognition and signaling by Toll-like receptors and RNA helicases focusing on recent evidence for their specific functions in antiviral defense in vivo. url: https://www.ncbi.nlm.nih.gov/pubmed/18086372/ doi: 10.1016/j.imbio.2007.09.007 id: cord-317851-lj07947c author: Elena, S F title: Experimental evolution of plant RNA viruses date: 2008-02-06 words: 4184.0 sentences: 191.0 pages: flesch: 42.0 cache: ./cache/cord-317851-lj07947c.txt txt: ./txt/cord-317851-lj07947c.txt summary: In this review, we will focus on recent studies that used plant viruses to address evolutionary questions of general interest, such as the rate and fitness effects of deleterious mutations and the role of neutrality as a source of mutational robustness, the evolution of generalist viruses, or the effect of vertical versus horizontal transmission on virulence. Despite mutation rate is still high compared to that of DNA-based microorganisms, a classic field observation is that natural plant virus populations generally exhibit limited genetic variation (García-Arenal et al., 2001) , which may imply either that purifying selection may be strong or that genome replication occurs mainly by Luria''s stamping machine model (Luria, 1951) rather than exponentially (French and Stenger, 2003) , the two hypotheses being nonexclusive. abstract: Undoubtedly, viruses represent a major threat faced by human and veterinary medicines and by agronomy. The rapid evolution of viruses enables them to escape from natural immunities and from state-of-the-art antiviral treatments, with new viruses periodically emerging with deadly consequences. Viruses have also become powerful and are increasingly used tools in the field of experimental evolution. A growing body of evidence points that the evolution of viruses is mainly determined by key features such as their compacted genomes, enormous population sizes, and short generation times. In addition, RNA viruses also present large selection coefficients, antagonistic epistasis, and high mutation rates. Most of this knowledge comes from studies that have used either bacteriophages or animal viruses in cell cultures as experimental systems. However, plant viruses provide almost identical advantages for evolutionary studies and, in addition, offer an invaluable tool for studying the interplay between viruses and pluricellular hosts. Without seeking to be exhaustive, here we summarize some peculiarities of plant viruses and review recent experiments that have explored important questions on evolution, such as the role of deleterious mutation and neutrality, the effect of different transmission modes in the evolution of virulence, and the heterogeneous selective constraints imposed by multiple hosts. url: https://doi.org/10.1038/sj.hdy.6801088 doi: 10.1038/sj.hdy.6801088 id: cord-350189-2su7oqbz author: Elmén, Joacim title: Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality date: 2005-01-14 words: 5415.0 sentences: 322.0 pages: flesch: 55.0 cache: ./cache/cord-350189-2su7oqbz.txt txt: ./txt/cord-350189-2su7oqbz.txt summary: A priori, this suggests that LNA may be used to increase the functional half-life of siRNA in vivo by two different mechanisms, e.g. by enhancing the resistance of the constituent RNA strands against degradation by single-stranded RNases and by stabilizing the siRNA duplex structure that is critical for activity. Next, we examined the effect of making single RNA to LNA exchanges at base-paired positions in the antisense strand of the firefly luciferase siLNA1. Although we cannot exclude that these modifications somehow prevent loading of the antisense strand into RISC, we believe this to be unlikely given the functionality of many significantly more modified siLNAs. Rather, as these positions are all close to the site where RNA target cleavage occurs [between pos. The SARS siRNA (Table 1) has identical closing base-pairs at both ends (A:U) making it likely that enough of both the antisense and sense strand would be incorporated into RISC to observe activity on the respective targets. abstract: Therapeutic application of the recently discovered small interfering RNA (siRNA) gene silencing phenomenon will be dependent on improvements in molecule bio-stability, specificity and delivery. To address these issues, we have systematically modified siRNA with the synthetic RNA-like high affinity nucleotide analogue, Locked Nucleic Acid (LNA). Here, we show that incorporation of LNA substantially enhances serum half-life of siRNA's, which is a key requirement for therapeutic use. Moreover, we provide evidence that LNA is compatible with the intracellular siRNA machinery and can be used to reduce undesired, sequence-related off-target effects. LNA-modified siRNAs targeting the emerging disease SARS, show improved efficiency over unmodified siRNA on certain RNA motifs. The results from this study emphasize LNA's promise in converting siRNA from a functional genomics technology to a therapeutic platform. url: https://www.ncbi.nlm.nih.gov/pubmed/15653644/ doi: 10.1093/nar/gki193 id: cord-255495-xnoppq3y author: Elrashdy, Fatma title: On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity date: 2020-07-09 words: 7523.0 sentences: 353.0 pages: flesch: 47.0 cache: ./cache/cord-255495-xnoppq3y.txt txt: ./txt/cord-255495-xnoppq3y.txt summary: It is possible that this "Trojan horse" strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this "silence" time period and then started to re-spread again. The fact that SARS-CoV-2 can be present within the vacuoles or double membrane vesicles (DMVs) within the host cells was proven by the careful post-mortem histopathological analysis of the renal samples of patients with COVID-19 by light microscopy, electron microscopic examination, and immunostaining (Farkash et al., 2020; Su et al., 2020) . Is this "Trojan horse" strategy of the release of the SARS-CoV-2-loaded exosomes or EDMVs represent a reasonable explanation for the appearance of the viral RNA in the recovered COVID-19 patients 7-14 day post discharge? abstract: We propose here that one of the potential mechanisms for the relapse of the COVID-19 infection could be a cellular transport pathway associated with the release of the SARS-CoV-2-loaded exosomes and other extracellular vesicles. It is possible that this “Trojan horse” strategy represents possible explanation for the re-appearance of the viral RNA in the recovered COVID-19 patients 7–14 day post discharge, suggesting that viral material was hidden within such exosomes or extracellular vesicles during this “silence” time period and then started to re-spread again. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32643586/ doi: 10.1080/07391102.2020.1790426 id: cord-272579-aenuyht0 author: Emmett, Stevan R. title: The Cell Cycle and Virus Infection date: 2005 words: 6456.0 sentences: 388.0 pages: flesch: 60.0 cache: ./cache/cord-272579-aenuyht0.txt txt: ./txt/cord-272579-aenuyht0.txt summary: A number of different viruses interact with the cell cycle in order to subvert host-cell function and increase the efficiency of virus replication; examples can be found from DNA, retro, and RNA viruses. The majority of studies have been conducted on DNA and retroviruses whose primary site of replication is the nucleus, but increasingly a number of researchers are demonstrating that RNA viruses, whose primary site of replication is normally the cytoplasm, also interfere with the cell cycle. Viral interference with the cell cycle can have a myriad of different effects to improve virus infection, for example to promote replication of viral DNA genomes, or to delay the cell cycle to allow sufficient time for RNA virus assembly. Increasingly we have found that proteomic approaches allow the rapid analysis of a whole plethora of cell cycle proteins that may be affected by virus infection. abstract: A number of different viruses interact with the cell cycle in order to subvert host-cell function and increase the efficiency of virus replication; examples can be found from DNA, retro, and RNA viruses. The majority of studies have been conducted on DNA and retroviruses whose primary site of replication is the nucleus, but increasingly a number of researchers are demonstrating that RNA viruses, whose primary site of replication is normally the cytoplasm, also interfere with the cell cycle. Viral interference with the cell cycle can have a myriad of different effects to improve virus infection, for example to promote replication of viral DNA genomes, or to delay the cell cycle to allow sufficient time for RNA virus assembly. Although cell cycle control is fairly well characterized in terms of checkpoints and control molecules (e.g., cyclins), in recent years several researchers have demonstrated that the nucleolus is also involved in cell cycle control. The nucleolus and associated subnuclear structures can sequester cell cycle regulatory complexes, and nucleolar proteins also have a direct and indirect effect on the cycling cell. Viruses also interact with the nucleolus. In order to study the interactions between a virus and the cell cycle and vice versa we have developed and adapted a number of different approaches and strategies. These include determinations of virus yield and measurements of virus replication to flow cytometry and confocal analysis of the host cell. Increasingly we have found that proteomic approaches allow the rapid analysis of a whole plethora of cell cycle proteins that may be affected by virus infection. url: https://www.ncbi.nlm.nih.gov/pubmed/15576934/ doi: 10.1385/1-59259-857-9:197 id: cord-269194-b1wlr3t7 author: Engstrom-Melnyk, Julia title: Chapter 5 Clinical Applications of Quantitative Real-Time PCR in Virology date: 2015-12-31 words: 12542.0 sentences: 501.0 pages: flesch: 36.0 cache: ./cache/cord-269194-b1wlr3t7.txt txt: ./txt/cord-269194-b1wlr3t7.txt summary: Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. With the development and administration of newer drugs that target specific biological processes of HIV, routine and clinical monitoring of viral loads using a real-time quantitative PCR assay continues to be critical to predict treatment failure and early emergence of drug resistance mutations, within a timeframe that would increase subsequent treatment success. abstract: Abstract Since the invention of the polymerase chain reaction (PCR) and discovery of Taq polymerase, PCR has become a staple in both research and clinical molecular laboratories. As clinical and diagnostic needs have evolved over the last few decades, demanding greater levels of sensitivity and accuracy, so too has PCR performance. Through optimisation, the present-day uses of real-time PCR and quantitative real-time PCR are enumerable. The technique, combined with adoption of automated processes and reduced sample volume requirements, makes it an ideal method in a broad range of clinical applications, especially in virology. Complementing serologic testing by detecting infections within the pre-seroconversion window period and infections with immunovariant viruses, real-time PCR provides a highly valuable tool for screening, diagnosing, or monitoring diseases, as well as evaluating medical and therapeutic decision points that allows for more timely predictions of therapeutic failures than traditional methods and, lastly, assessing cure rates following targeted therapies. All of these serve vital roles in the continuum of care to enhance patient management. Beyond this, quantitative real-time PCR facilitates advancements in the quality of diagnostics by driving consensus management guidelines following standardisation to improve patient outcomes, pushing for disease eradication with assays offering progressively lower limits of detection, and rapidly meeting medical needs in cases of emerging epidemic crises involving new pathogens that may result in significant health threats. url: https://api.elsevier.com/content/article/pii/S0580951715000069 doi: 10.1016/bs.mim.2015.04.005 id: cord-326719-p1ma4akz author: Enjuanes, Luis title: Virus-based vectors for gene expression in mammalian cells: Coronavirus date: 2003-12-31 words: 5923.0 sentences: 282.0 pages: flesch: 52.0 cache: ./cache/cord-326719-p1ma4akz.txt txt: ./txt/cord-326719-p1ma4akz.txt summary: Coronaviruses have several advantages as vectors over other viral expression systems: (1) coronaviruses are single-stranded RNA viruses that replicate within the cytoplasm without a DNA intermediary, making integration of the virus genome into the host cell chromosome unlikely, (2) these viruses have the largest RNA virus genome and, in principle, have room for the insertion of large foreign genes, (3) a pleiotropic secretory immune response is best induced by the stimulation of gut-associated lymphoid tissues, (4) the tropism of coronaviruses may be modified by manipulation of the spike (S) protein allowing engineering of the tropism of the vector, (5) non-pathogenic coronavirus strains infecting most species of interest (human, porcine, bovine, canine, feline, and avian) are available to develop expression systems, and (6) infectious coronavirus cDNA clones are available to design expression systems. abstract: Publisher Summary The coronavirus and the torovirus genera form the Coronaviridae family, which is closely related to the Arteriviridae family. Both families are included in the Nidovirales order. Recently, a new group of invertebrate viruses, the Roniviridae, with a genetic structure and replication strategy similar to those of coronaviruses, has been described. This new virus family has been included within the Nidovirales. Coronaviruses have several advantages as vectors over other viral expression systems: (1) coronaviruses are single-stranded RNA viruses that replicate within the cytoplasm without a DNA intermediary, making integration of the virus genome into the host cell chromosome unlikely, (2) these viruses have the largest RNA virus genome and, in principle, have room for the insertion of large foreign genes, (3) a pleiotropic secretory immune response is best induced by the stimulation of gut-associated lymphoid tissues, (4) the tropism of coronaviruses may be modified by manipulation of the spike (S) protein allowing engineering of the tropism of the vector, (5) non-pathogenic coronavirus strains infecting most species of interest (human, porcine, bovine, canine, feline, and avian) are available to develop expression systems, and (6) infectious coronavirus cDNA clones are available to design expression systems. Within the coronavirus two types of expression vectors have been developed: one requires two components (helper–dependent expression system) and the other a single genome that is modified either by targeted recombination or by engineering a cDNA encoding an infectious RNA. This chapter focuses on the advantages and limitations of these coronavirus expression systems, the attempts to increase their expression levels by studying the transcription-regulating sequences (TRSs), and the proven possibility of modifying their tissue and species-specificity. url: https://www.sciencedirect.com/science/article/pii/S016773060338010X doi: 10.1016/s0167-7306(03)38010-x id: cord-015871-1tuf4zxi author: Ergonul, Onder title: Treatment of Crimean-Congo Hemorrhagic Fever date: 2007 words: 8234.0 sentences: 474.0 pages: flesch: 44.0 cache: ./cache/cord-015871-1tuf4zxi.txt txt: ./txt/cord-015871-1tuf4zxi.txt summary: In contrast, a dose of ribavirin at least nine times greater was required to induce a comparable inhibitory effect on the yields of Rift Valley fever virus, for which the drug has been shown to inhibit replication in monkeys and rodents [104] . However hemorrhagic fever virus infections can be approached by the following different therapeutic strategies [6] : (i) administration of high-titered neutralizing antibodies and/or (ii) treatment with antiviral drugs. In recent times, several groups have studied the antiviral activities of interferons against hemorrhagic fever viruses. Human MxA protein inhibits the replication of Crimean-Congo hemorrhagic fever virus Type I interferon inhibits Crimean-Congo hemorrhagic fever virus in human target cells Genotoxic effect of ribavirin in patients with Crimean-Congo hemorrhagic fever Ribavirin efficacy in an in vivo model of Crimean-Congo hemorrhagic fever virus (CCHF) infection Inhibition of Crimean-Congo hemorrhagic fever viral infectivity yields in vitro by ribavirin abstract: Ribavirin is a synthetic purine nucleoside analog with a modified base and D-ribose sugar, also known as virazol, first synthesized by Sidwell and colleagues in 1972 [43, 49] (Fig. 19-1). It is of particular interest, because it was the first synthetic nucleoside to exhibit broad spectrum antiviral activity, and it is one of few antiviral drugs in clinical use effective against agents other than HIV and herpesviruses [43]. It inhibits the replication of a wide range of RNA and DNA viruses in vitro, including orthomyxo, paramyxo, arena, bunya, flavi, herpes, adeno, pox, and retroviruses [49]. In current clinical practice, ribavirin is commonly used for certain viral infections (Table 19-1). Most notably, it is used in combination with interferon-α for treatment of HCV infection [66]. Ribavirin aerosol is used for treatment of pediatric infection by respiratory syncytial virus [19]. It is the only antiviral drug that could be also used in viral hemorrhagic fever syndromes. Besides Crimean- Congo hemorrhagic fever (CCHF), it is used in Lassa fever [70]. Viruses in the Bunyaviridae family are generally sensitive to ribavirin [92]. A prospective, randomized, double-blind, placebo-controlled trial of 242 patients with serologically confirmed Hantaan virus in the People’s Republic of China found a sevenfold decrease in mortality among ribavirin-treated patients [54], other studies did not confirm these benefits. Ribavirin was found to be effective against CCHF virus (CCHFV) in vitro [99, 104]. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119965/ doi: 10.1007/978-1-4020-6106-6_19 id: cord-293215-6flf5ig0 author: Eriksson, Klara Kristin title: Generation of Recombinant Coronaviruses Using Vaccinia Virus as the Cloning Vector and Stable Cell Lines Containing Coronaviral Replicon RNAs date: 2007-11-28 words: 4682.0 sentences: 325.0 pages: flesch: 58.0 cache: ./cache/cord-293215-6flf5ig0.txt txt: ./txt/cord-293215-6flf5ig0.txt summary: title: Generation of Recombinant Coronaviruses Using Vaccinia Virus as the Cloning Vector and Stable Cell Lines Containing Coronaviral Replicon RNAs Based on cloned coronaviral cDNA, we describe the generation of recombinant coronaviruses and stable cell lines containing coronaviral replicon RNAs. Initially, the vaccinia virus-based reverse genetic system was established for the generation of recombinant human coronavirus 229E. This section describes the preparation of purified vaccinia virus DNA that can be used: (i) for the in vitro ligation with the assembled coronavirus full-length cDNA (see Section 3.1.4), and (ii) as template for in vitro transcription reactions (see Section 3.3.1). First, a fulllength coronavirus RNA is produced using the genomic DNA of a vaccinia virus containing the full-length coronavirus cDNA insert as a template for in vitro transcription. 1. Based on a full-length coronavirus cDNA cloned in vaccinia virus, a replicon RNA-encoding cDNA can be generated using vaccinia virus-mediated homologous recombination as described in Section 3.2. abstract: Coronavirus reverse genetic systems have become valuable tools for studying the molecular biology of coronavirus infections. They have been applied to the generation of recombinant coronaviruses, selectable replicon RNAs, and coronavirus-based vectors for heterologous gene expression. Here we provide a collection of protocols for the generation, cloning, and modification of full-length coronavirus cDNA using vaccinia virus as a cloning vector. Based on cloned coronaviral cDNA, we describe the generation of recombinant coronaviruses and stable cell lines containing coronaviral replicon RNAs. Initially, the vaccinia virus-based reverse genetic system was established for the generation of recombinant human coronavirus 229E. However, it is also applicable to the generation of other coronaviruses, such as the avian infectious bronchitis virus, mouse hepatitis virus, and SARS coronavirus. url: https://www.ncbi.nlm.nih.gov/pubmed/19057873/ doi: 10.1007/978-1-59745-181-9_18 id: cord-331076-ak481qew author: Eskier, Doğa title: Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load date: 2020-10-12 words: 3858.0 sentences: 192.0 pages: flesch: 52.0 cache: ./cache/cord-331076-ak481qew.txt txt: ./txt/cord-331076-ak481qew.txt summary: In our previous study, we examined the top 10 most frequent mutations in the SARS-CoV-2 nsp12, and identified that four of them are associated with an increase in mutation density in two genes, the membrane glycoprotein (M) and the envelope glycoprotein (E) (the combination of which is hereafter referred to as MoE, as we previously described), which are under less selective pressure, and mutations in these genes are potential markers of reduced replication fidelity (Eskier et al., 2020a) . To identify the trends in SARS-CoV-2 mutation load over time, we calculated the average mutation density per day for all isolates for whole genome, S gene and MoE regions, capping outliers at the 95th and 5th percentile values to minimize the potential effects of sequencing errors (Fig. 1) . Three of the five most common nsp14 mutations, namely 18060C>T, 18736T>C and 18877C>T are associated with increases in both genome-wide mutational load, as well as MoE status, an alternative indicator of mutational rate and virus evolution. abstract: SARS-CoV-2 is a betacoronavirus responsible for COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load without selective pressure and across the genome, compared to nsp7, nsp8 and nsp12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates and nsp14 mutations as potential predictors for high mutability strains. url: https://doi.org/10.7717/peerj.10181 doi: 10.7717/peerj.10181 id: cord-285159-gytebbua author: Eydoux, Cecilia title: A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex date: 2020-07-07 words: 3603.0 sentences: 215.0 pages: flesch: 59.0 cache: ./cache/cord-285159-gytebbua.txt txt: ./txt/cord-285159-gytebbua.txt summary: Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights A new SARS-CoV non radioactive RNA polymerase assay is described The robotized assay is suitable to identify RdRp inhibitors based on HTS -A new SARS-CoV non radioactive RNA polymerase assay is described -The robotized assay is suitable to identify RdRp inhibitors based on HTS the RdRp core nsp12 and shown to confer full activity and processivity to nsp12 (Subissi et al., 2014) . Picogreen kinetic assay was based on polymerase activity of SARS nsp12 in complex with nsp7L8, which catalyzed the reaction using a poly (A) template and uridine triphosphate (UTP). abstract: The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) emergence in 2003 introduced the first serious human coronavirus pathogen to an unprepared world. To control emerging viruses, existing successful anti(retro)viral therapies can inspire antiviral strategies, as conserved viral enzymes (eg., viral proteases and RNA-dependent RNA polymerases) represent targets of choice. Since 2003, much effort has been expended in the characterization of the SARS-CoV replication/transcription machinery. Until recently, a pure and highly active preparation of SARS-CoV recombinant RNA synthesis machinery was not available, impeding target-based high throughput screening of drug candidates against this viral family. The current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic revealed a new pathogen whose RNA synthesis machinery is highly (>96% aa identity) homologous to SARS-CoV. This phylogenetic relatedness highlights the potential use of conserved replication enzymes to discover inhibitors against this significant pathogen, which in turn, contributes to scientific preparedness against emerging viruses. Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. The screening of a small (1,520 compounds) chemical library of FDA-approved drugs demonstrates the robustness of our assay and will allow to speed-up drug repositioning or novel drug discovery against the SARS-CoV-2. Principle of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay Highlights - A new SARS-CoV non radioactive RNA polymerase assay is described - The robotized assay is suitable to identify RdRp inhibitors based on HTS url: https://doi.org/10.1101/2020.07.07.192005 doi: 10.1101/2020.07.07.192005 id: cord-321607-3r736dnk author: Ezelle, Heather J. title: The Roles of RNase-L in Antimicrobial Immunity and the Cytoskeleton-Associated Innate Response date: 2016-01-08 words: 11694.0 sentences: 588.0 pages: flesch: 42.0 cache: ./cache/cord-321607-3r736dnk.txt txt: ./txt/cord-321607-3r736dnk.txt summary: The active nuclease then cleaves ssRNAs, both cellular and viral, leading to downregulation of their expression and the generation of small RNAs capable of activating retinoic acid-inducible gene-I (RIG-I)-like receptors or the nucleotide-binding oligomerization domain-like receptor 3 (NLRP3) inflammasome. Although cleavage of RNA virus genomes appeared as the most direct mechanism of action, other important pathways have become evident, such as the regulation of host gene expression, stimulation of IFNβ production, activation of the NACHT, LRR, and PYD-containing protein-3 (NLRP3) inflammasome, and maintenance of the cell''s structural barrier to infection [27, 55, 83, 84] . These small RNAs are capable of stimulating RIG-I and MDA5 (melanoma differentiation associated gene-5) to activate mitochondrial antiviral signaling protein (MAVS) and induce the subsequent translocation of interferon regulatory factor 3 (IRF3) to the nucleus to drive transcription of IFNβ. abstract: The interferon (IFN)-regulated endoribonuclease RNase-L is involved in multiple aspects of the antimicrobial innate immune response. It is the terminal component of an RNA cleavage pathway in which dsRNA induces the production of RNase-L-activating 2-5A by the 2′-5′-oligoadenylate synthetase. The active nuclease then cleaves ssRNAs, both cellular and viral, leading to downregulation of their expression and the generation of small RNAs capable of activating retinoic acid-inducible gene-I (RIG-I)-like receptors or the nucleotide-binding oligomerization domain-like receptor 3 (NLRP3) inflammasome. This leads to IFNβ expression and IL-1β activation respectively, in addition to broader effects on immune cell function. RNase-L is also one of a growing number of innate immune components that interact with the cell cytoskeleton. It can bind to several cytoskeletal proteins, including filamin A, an actin-binding protein that collaborates with RNase-L to maintain the cellular barrier to viral entry. This antiviral activity is independent of catalytic function, a unique mechanism for RNase-L. We also describe here the interaction of RNase-L with the E3 ubiquitin ligase and scaffolding protein, ligand of nump protein X (LNX), a regulator of tight junction proteins. In order to better understand the significance and context of these novel binding partners in the antimicrobial response, other innate immune protein interactions with the cytoskeleton are also discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/26760998/ doi: 10.3390/ijms17010074 id: cord-022196-1tionxun author: FENNER, FRANK title: The Nature and Classification of Animal Viruses date: 2013-11-17 words: 9588.0 sentences: 406.0 pages: flesch: 46.0 cache: ./cache/cord-022196-1tionxun.txt txt: ./txt/cord-022196-1tionxun.txt summary: With most isometric particles and in all complex virions, the capsid encloses another protein structure containing the viral genome, called the core. All animal viruses with tubular nucleocapsids are enveloped, and in these the lipid layer from which glycoprotein peplomers project is probably applied to a protein shell (the membrane protein; see Fig. 1 -1), which may be relatively rigid, as in Rhabdovirus, or readily distorted (as in the myxoviruses) so that in negatively stained electron micrographs the virions appear to be pleomorphic. The RNA viruses that have the largest (single-stranded) genomes, those of the Leukovirus genus, also have a highly complex structure with an envelope enclosing an icosahedral capsid that, in turn, surrounds a tubular nucleocapsid. The conventional physicochemical criteria [(a) nucleic acid: type, strandedness, fragmentation, and molecular weight; (b) virion: shape, size, and symmetry] are suitable for classification at this level of family/genus, perhaps assisted by the serological cross-reactivity of "group" antigens where these have been recognized. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155428/ doi: 10.1016/b978-0-12-253040-1.50006-3 id: cord-023705-3q9yr6np author: FENNER, FRANK title: Viral Replication date: 2014-06-27 words: 8331.0 sentences: 424.0 pages: flesch: 51.0 cache: ./cache/cord-023705-3q9yr6np.txt txt: ./txt/cord-023705-3q9yr6np.txt summary: Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. Many important biochemical phenomena, such as splicing and other types of posttranscriptional processing of RNA, posttranslational cleavage and glycosylation of proteins, replica tion of RNA, reverse transcription, integration, and transposition of viral genes and cellular oncogenes, were first elucidated by virologists and have general application in cell biology. The proteins translated from the early transcripts of DNA viruses include enzymes and other proteins required for the replication of viral nucleic acid, as well as proteins that suppress host cell RNA and protein synthesis. abstract: Viral replication is the central focus of much experimental virology and is a significant part of molecular biology. Studies with bacteriophages in their prokaryotic host cells in the 1940s and 1950s provided the first insights into the complexities of viral replication. With the development of mammalian cell culture procedures, the techniques used for the study of bacteriophages were adapted to animal viruses. Progress has been such that the basic mechanisms of transcription, translation, and nucleic acid replication have been characterized for all the major families of animal viruses and the strategy of gene expression and its regulation clarified. Many important biochemical phenomena such as the splicing and other types of posttranscriptional processing of RNA, the posttranslational cleavage and glycosylation of proteins, the replication of RNA, reverse transcription, integration, and the transposition of viral genes and cellular oncogenes were first elucidated by virologists and have general application in cell biology. The chapter provides a general overview on viral replication for understanding pathogenesis, immunity, chemotherapy, and the role of viruses in cancer. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173495/ doi: 10.1016/b978-0-12-253055-5.50008-6 id: cord-266585-jfjrk9gy author: Fang, Shouguo title: An arginine-to-proline mutation in a domain with undefined functions within the helicase protein (Nsp13) is lethal to the coronavirus infectious bronchitis virus in cultured cells date: 2007-02-05 words: 7152.0 sentences: 356.0 pages: flesch: 56.0 cache: ./cache/cord-266585-jfjrk9gy.txt txt: ./txt/cord-266585-jfjrk9gy.txt summary: During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation blocks the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid (Lys) affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. To further demonstrate that the failure to rescue infectious virus from the G15526C mutant transcripts is due to a defect in subgenomic RNA transcription, the full-length clones with and without the G15526C mutation were used to generate recombinant IBV expressing the enhanced green fluorescent protein (EGFP) by replacing the 5a gene with EGFP. abstract: Genetic manipulation of the RNA genomes by reverse genetics is a powerful tool to study the molecular biology and pathogenesis of RNA viruses. During construction of an infectious clone from a Vero cell-adapted coronavirus infectious bronchitis virus (IBV), we found that a G–C point mutation at nucleotide position 15526, causing Arg-to-Pro mutation at amino acid position 132 of the helicase protein, is lethal to the infectivity of IBV on Vero cells. When the in vitro-synthesized full-length transcripts containing this mutation were introduced into Vero cells, no infectious virus was rescued. Upon correction of the mutation, infectious virus was recovered. Further characterization of the in vitro-synthesized full-length transcripts containing the G15526C mutation demonstrated that this mutation may block the transcription of subgenomic RNAs. Substitution mutation of the Arg132 residue to a positively charged amino acid Lys affected neither the infectivity of the in vitro-synthesized transcripts nor the growth properties of the rescued virus. However, mutation of the Arg132 residue to Leu, a conserved residue in other coronaviruses at the same position, reduced the recovery rate of the in vitro-synthesized transcripts. The recovered mutant virus showed much smaller-sized plaques. On the contrary, a G–C and a G–A point mutations at nucleotide positions 4330 and 9230, respectively, causing Glu–Gln and Gly–Glu mutations in or near the catalytic centers of the papain-like (Nsp3) and 3C-like (Nsp5) proteinases, did not show detectable detrimental effect on the rescue of infectious viruses and the infectivity of the rescued viruses. url: https://api.elsevier.com/content/article/pii/S0042682206005745 doi: 10.1016/j.virol.2006.08.020 id: cord-000088-1xgjdhkx author: Faria, Nuno R title: Rooting human parechovirus evolution in time date: 2009-07-15 words: 4011.0 sentences: 214.0 pages: flesch: 51.0 cache: ./cache/cord-000088-1xgjdhkx.txt txt: ./txt/cord-000088-1xgjdhkx.txt summary: Using both strict and relaxed clock Bayesian phylogenetics we investigated 1) the substitutions rates of the structural P1 and capsid VP1 regions and 2) evolutionary timescale of currently circulating HPeV lineages. Their evolutionary history and population dynamics can be reconstructed by means of genealogy-based coalescent approaches using nucleotide sequences sampled over an epidemiological time frame in order to estimate timed viral ancestry as well as the rates of genetic change [27, 29] . We first identified the best-fitting substitution model for the HPeV sequences using the Modelgenerator package (GTR + Γ) [35] , and tested whether the evolution of the P1 and VP1 genetic regions was better described by a strict or relaxed lognormal molecular clock. The Bayesian analysis presented here first indicates that the structural P1 and the capsid VP1 region of this viral species evolve at a high rate of evolutionary change (~10 -3 substitutions per site per year). abstract: BACKGROUND: The Picornaviridae family contains a number of important pathogenic viruses, among which the recently reclassified human parechoviruses (HPeVs). These viruses are widespread and can be grouped in several types. Understanding the evolutionary history of HPeV could answer questions such as how long the circulating lineages last shared a common ancestor and how the evolution of this viral species is shaped by its population dynamics. Using both strict and relaxed clock Bayesian phylogenetics we investigated 1) the substitutions rates of the structural P1 and capsid VP1 regions and 2) evolutionary timescale of currently circulating HPeV lineages. RESULTS: Our estimates reveal that human parechoviruses exhibit high substitution rates for both structural P1 and capsid VP1 regions, respectively 2.21 × 10(-3 )(0.48 – 4.21 × 10(-3)) and 2.79 × 10(-3 )(2.05 – 3.66 × 10(-3)) substitutions per site per year. These are within the range estimated for other picornaviruses. By employing a constant population size coalescent prior, the date of the most recent common ancestor was estimated to be at around 1600 (1427–1733). In addition, by looking at the frequency of synonymous and non-synonymous substitutions within the VP1 gene we show that purifying selection constitutes the dominating evolutionary force leading to strong amino acid conservation. CONCLUSION: In conclusion, our estimates provide a timescale for the evolution of HPeVs and suggest that genetic diversity of current circulating HPeV types has arisen about 400 years ago. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723090/ doi: 10.1186/1471-2148-9-164 id: cord-283168-kl1hoa1x author: Farkas, Tibor title: Molecular detection of novel picornaviruses in chickens and turkeys date: 2011-12-13 words: 4034.0 sentences: 196.0 pages: flesch: 52.0 cache: ./cache/cord-283168-kl1hoa1x.txt txt: ./txt/cord-283168-kl1hoa1x.txt summary: Fecal specimens, including swabs and litter extracts, collected from chickens, domestic ducks, turkeys, and Canadian geese were tested using degenerate primers targeting regions encoding for conserved amino acid motifs (YGDD and DY(T/S)(R/K/G)WDST) in calicivirus RNA-dependent RNA polymerases. Analysis of 2.2–3.2 kb extended genome sequences including the partial P2 (2C) and complete P3 (3A, 3B (VPg), 3C(pro), and 3D(pol)) regions of selected strains indicated that viruses yielding the 280/283 bp amplicons represent a putative new genus of Picornaviridae. This study utilized a broadly reactive primer set targeting conserved amino acid motifs encoding regions present in calicivirus RNA-dependent RNA polymerases (RdRp) and are partially also present in other viral RdRps. As part of the study here we report the serendipitous detection of novel picornaviruses in chicken and turkey samples that included diagnostic cases with runting-stunting syndrome (RSS). abstract: Fecal specimens, including swabs and litter extracts, collected from chickens, domestic ducks, turkeys, and Canadian geese were tested using degenerate primers targeting regions encoding for conserved amino acid motifs (YGDD and DY(T/S)(R/K/G)WDST) in calicivirus RNA-dependent RNA polymerases. Similar motifs are also present in other RNA viruses. Two fecal specimens and 18 litter extracts collected from chickens and turkeys yielded RT-PCR products. BLAST search and phylogenetic analysis revealed that all amplicons represented picornaviruses that clustered into two major groups. Four chicken and one turkey samples yielded 250 bp amplicons with 84–91% nucleotide identity to the recently described turkey hepatitis viruses, while 280 and 283 bp amplicons obtained from 11 chicken and 4 turkey samples represented novel picornaviruses with the closest nucleotide identity to kobuviruses (54–61%) and turdiviruses (47–54%). Analysis of 2.2–3.2 kb extended genome sequences including the partial P2 (2C) and complete P3 (3A, 3B (VPg), 3C(pro), and 3D(pol)) regions of selected strains indicated that viruses yielding the 280/283 bp amplicons represent a putative new genus of Picornaviridae. The 3′-non-translated region (NTR) of the turkey hepatitis-like viruses described in this study was significantly longer (641–654 nt) than that of any of the other piconaviruses and included a putative short open reading frame (ORF). In summary, we report the molecular detection of novel picornaviruses that appear to be endemic in both chickens and turkeys. url: https://doi.org/10.1007/s11262-011-0695-4 doi: 10.1007/s11262-011-0695-4 id: cord-122092-gdyt02er author: Fatehi, Farzad title: Comparing antiviral strategies against COVID-19 via multi-scale within host modelling date: 2020-10-18 words: 10080.0 sentences: 511.0 pages: flesch: 55.0 cache: ./cache/cord-122092-gdyt02er.txt txt: ./txt/cord-122092-gdyt02er.txt summary: Comparison of different scenarios is based on tissue damage and viral load, highlighting the impact(s) of antibodies and adaptive cell-mediated immune response on infection dynamics. Surprisingly, our model also suggests that early treatment by either therapy alone can actually increase the duration of infection compared with a later therapy start, likely because suppressing virus production results in a reduced immune response. The model also includes non-structural proteins that are important for the viral life cycle, such as the replicase-transcriptase complex (RTC), and keeps track of the numbers of gRNAs (and subgenomic sgRNAs) at different stages of the replication process. We have included additional reactions into the model that describe remdesivir binding to the RTC complexes on the gRNAs and sgRNAs to capture this (see SI for details), and track the effect of a given, fixed number of remdesivir molecules per cell on the release of viral particles from an infected host cell. abstract: Within-host models of COVID-19 infection dynamics enable the merits of different forms of antiviral therapy to be assessed in individual patients. A stochastic agent-based model of COVID-19 intracellular dynamics is introduced here, that incorporates essential steps of the viral life cycle targeted by treatment options. Integration of model predictions with an intercellular model of within-host infection dynamics, fitted to patient data, generates a generic profile of disease progression in patients that have recovered in the absence of treatment. This is contrasted with the profiles obtained after variation of model parameters pertinent to the immune response, such as effector cell and antibody proliferation rates, mimicking disease progression in immunocompromised patients. These profiles are then compared with disease progression in the presence of antiviral and convalescent plasma therapy against COVID-19 infections. The model reveals that using both therapies in combination can be very effective in reducing the length of infection, but these synergistic effects decline with a delayed treatment start. Conversely, early treatment with either therapy alone can actually increase the duration of infection, with infectious virions still present after the decline of other markers of infection. This suggests that usage of these treatments should remain carefully controlled in a clinical environment. url: https://arxiv.org/pdf/2010.08957v1.pdf doi: nan id: cord-002994-1zjrunzc author: Faye, Martin title: Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus date: 2018-04-13 words: 11495.0 sentences: 517.0 pages: flesch: 45.0 cache: ./cache/cord-002994-1zjrunzc.txt txt: ./txt/cord-002994-1zjrunzc.txt summary: Based on these alignments, we investigated the genetic properties of these different isolates circulating in West Africa, such as genome length and location of main conserved amino acid motifs previously described in mosquito-borne flaviviruses (MBFVs) with sometimes mutations which include no physicochemical properties changes [3] . The RNAz method [21] implemented in the Vienna RNA Websuite (http://rna.tbi.univie.ac.at/) [22] was used to detect thermodynamically stable and evolutionarily conserved structural RNA domains on complete non-coding regions of the 11 West African BAGV isolates characterized in this study and the isolates from Spain and CAR, because complete non-coding sequences are not currently available for the isolate from India. Here, we described location of main conserved amino acid motifs on BAGV proteins using in silico analysis of complete genome sequences of the 11 West African BAGV isolates characterized in this study and sequences from India, CAR and Spain. abstract: Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923487/ doi: 10.3390/v10040193 id: cord-313439-cadyykks author: Felten, Sandra title: Diagnosis of Feline Infectious Peritonitis: A Review of the Current Literature date: 2019-11-15 words: 12466.0 sentences: 522.0 pages: flesch: 44.0 cache: ./cache/cord-313439-cadyykks.txt txt: ./txt/cord-313439-cadyykks.txt summary: Studies evaluating sensitivity and specificity of the detection of serum antibodies in comparison to either histopathology, a combination of diagnostic tests or clinical suspicion of feline infectious peritonitis (FIP). Recent studies evaluated the use of a quantitative RT-PCR (RT-qPCR) to detect FCoV RNA in FNA samples of the mesenteric lymph nodes and other abnormal tissues of clinical cases [119, 140] and hypothesized that this technique would be a useful tool to diagnose FIP for veterinary practitioners, especially in cats without effusion. Sensitivity and specificity from different studies evaluating the detection of feline coronavirus (FCoV) spike (S) gene mutations in tissue samples. RT-nPCR and subsequent S gene sequencing of serum and plasma samples from cats with FIP (diagnosed by histopathology ± IHC or by positive immunofluorescence in effusion) and control cats (diagnosed with another disease either ante or post mortem) revealed a sensitivity of only 7%, which confirms the very low virus load in blood. abstract: Feline infectious peritonitis (FIP) is a fatal disease that poses several challenges for veterinarians: clinical signs and laboratory changes are non-specific, and there are two pathotypes of the etiologic agent feline coronavirus (FCoV), sometimes referred to as feline enteric coronavirus (FECV) and feline infectious peritonitis virus (FIPV) that vary fundamentally in their virulence, but are indistinguishable by a number of diagnostic methods. This review focuses on all important steps every veterinary practitioner has to deal with and new diagnostic tests that can be considered when encountering a cat with suspected FIP with the aim to establish a definitive diagnosis. It gives an overview on all available direct and indirect diagnostic tests and their sensitivity and specificity reported in the literature in different sample material. By providing summarized data for sensitivity and specificity of each diagnostic test and each sample material, which can easily be accessed in tables, this review can help to facilitate the interpretation of different diagnostic tests and raise awareness of their advantages and limitations. Additionally, diagnostic trees depict recommended diagnostic steps that should be performed in cats suspected of having FIP based on their clinical signs or clinicopathologic abnormalities. These steps can easily be followed in clinical practice. url: https://doi.org/10.3390/v11111068 doi: 10.3390/v11111068 id: cord-314019-8n0jafsk author: Feng, Qian title: Induction and suppression of innate antiviral responses by picornaviruses date: 2014-07-18 words: 7215.0 sentences: 358.0 pages: flesch: 43.0 cache: ./cache/cord-314019-8n0jafsk.txt txt: ./txt/cord-314019-8n0jafsk.txt summary: We focus on two important and well-studied genera of picornaviruses, namely Enterovirus and Cardiovirus, and discuss how their RNAs are recognized by RLRs, and how they antagonize the IFN-a/b induction pathway and SG formation in infected cells. Picornavirus infections activate a cytosolic RNA sensor, MDA5, which in turn, induces a type I interferon response, a crucial component of antiviral immunity. Picornavirus infections activate a cytosolic RNA sensor, MDA5, which in turn, induces a type I interferon response, a crucial component of antiviral immunity. However, it is important to point out that the caspase-and proteasome-mediated MDA5 cleavage events were observed under conditions where MDA5 expression level was artificially upregulated prior to infection (either by poly(I:C) or viral RNA transfections) [39, 42] , which may sensitize cells for virus-induced apoptosis, thereby promote caspase-and proteasome-mediated protein degradations. abstract: The family Picornaviridae comprises of small, non-enveloped, positive-strand RNA viruses and contains many human and animal pathogens including enteroviruses (e.g. poliovirus, coxsackievirus, enterovirus 71 and rhinovirus), cardioviruses (e.g. encephalomyocarditis virus), hepatitis A virus and foot-and-mouth disease virus. Picornavirus infections activate a cytosolic RNA sensor, MDA5, which in turn, induces a type I interferon response, a crucial component of antiviral immunity. Moreover, picornaviruses activate the formation of stress granules (SGs), large aggregates of preassembled mRNPs (messenger ribonucleoprotein particles) to temporarily store these molecules upon cellular stress. Meanwhile, picornaviruses actively suppress these antiviral responses to ensure efficient replication. In this review we provide an overview of the induction and suppression of the MDA5-mediated IFN-α/β response and the cellular stress pathway by picornaviruses. url: https://www.sciencedirect.com/science/article/pii/S1359610114000653 doi: 10.1016/j.cytogfr.2014.07.003 id: cord-000660-tsvzg0ax author: Fensterl, Volker title: Interferon-Induced Ifit2/ISG54 Protects Mice from Lethal VSV Neuropathogenesis date: 2012-05-17 words: 8283.0 sentences: 446.0 pages: flesch: 55.0 cache: ./cache/cord-000660-tsvzg0ax.txt txt: ./txt/cord-000660-tsvzg0ax.txt summary: Interferon protects mice from vesicular stomatitis virus (VSV) infection and pathogenesis; however, it is not known which of the numerous interferon-stimulated genes (ISG) mediate the antiviral effect. In contrast, in acute infection by viruses that cause severe pathogenesis and death within a few days after infection, protection is primarily provided by the intrinsic antiviral actions of IFN-induced proteins encoded by the hundreds of IFN-stimulated genes (ISGs) [10] [11] [12] , several of which often contribute to the overall effect of IFN against a given virus. From the above observations, we conclude that after intranasal infection by VSV, Ifit2 protects mice from neuropathogenesis by suppressing replication or spread of the virus in brain neurons. In the complete absence of type I IFN action in the IFNAR 2/2 mice, intranasally infected VSV replicated vigorously not only in brains, but also in livers and lungs ( Figure 7A-C) . abstract: Interferon protects mice from vesicular stomatitis virus (VSV) infection and pathogenesis; however, it is not known which of the numerous interferon-stimulated genes (ISG) mediate the antiviral effect. A prominent family of ISGs is the interferon-induced with tetratricopeptide repeats (Ifit) genes comprising three members in mice, Ifit1/ISG56, Ifit2/ISG54 and Ifit3/ISG49. Intranasal infection with a low dose of VSV is not lethal to wild-type mice and all three Ifit genes are induced in the central nervous system of the infected mice. We tested their potential contributions to the observed protection of wild-type mice from VSV pathogenesis, by taking advantage of the newly generated knockout mice lacking either Ifit2 or Ifit1. We observed that in Ifit2 knockout (Ifit2 (−/−)) mice, intranasal VSV infection was uniformly lethal and death was preceded by neurological signs, such as ataxia and hind limb paralysis. In contrast, wild-type and Ifit1 (−/−) mice were highly protected and survived without developing such disease. However, when VSV was injected intracranially, virus replication and survival were not significantly different between wild-type and Ifit2(−/−) mice. When administered intranasally, VSV entered the central nervous system through the olfactory bulbs, where it replicated equivalently in wild-type and Ifit2 (−/−) mice and induced interferon-β. However, as the infection spread to other regions of the brain, VSV titers rose several hundred folds higher in Ifit2 (−/−) mice as compared to wild-type mice. This was not caused by a broadened cell tropism in the brains of Ifit2 (−/−) mice, where VSV still replicated selectively in neurons. Surprisingly, this advantage for VSV replication in the brains of Ifit2(−/−) mice was not observed in other organs, such as lung and liver. Pathogenesis by another neurotropic RNA virus, encephalomyocarditis virus, was not enhanced in the brains of Ifit2 (−/−) mice. Our study provides a clear demonstration of tissue-, virus- and ISG-specific antiviral action of interferon. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355090/ doi: 10.1371/journal.ppat.1002712 id: cord-314567-purplsjn author: Fernández-Ponce, Cecilia title: Ultrastructural Localization and Molecular Associations of HCV Capsid Protein in Jurkat T Cells date: 2018-01-04 words: 7978.0 sentences: 382.0 pages: flesch: 41.0 cache: ./cache/cord-314567-purplsjn.txt txt: ./txt/cord-314567-purplsjn.txt summary: HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4 + T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. As studies using the whole virus do not allow for the elucidation of the specific molecular mechanisms in which each protein is implicated, in this work, we focused on a single viral protein, showing that in CD4 + T cells, HCV core protein mostly localizes in the nucleus and specifically in the nucleolus where it is greatly enriched. abstract: Hepatitis C virus core protein is a highly basic viral protein that multimerizes with itself to form the viral capsid. When expressed in CD4(+) T lymphocytes, it can induce modifications in several essential cellular and biological networks. To shed light on the mechanisms underlying the alterations caused by the viral protein, we have analyzed HCV-core subcellular localization and its associations with host proteins in Jurkat T cells. In order to investigate the intracellular localization of Hepatitis C virus core protein, we have used a lentiviral system to transduce Jurkat T cells and subsequently localize the protein using immunoelectron microscopy techniques. We found that in Jurkat T cells, Hepatitis C virus core protein mostly localizes in the nucleus and specifically in the nucleolus. In addition, we performed pull-down assays combined with Mass Spectrometry Analysis, to identify proteins that associate with Hepatitis C virus core in Jurkat T cells. We found proteins such as NOLC1, PP1γ, ILF3, and C1QBP implicated in localization and/or traffic to the nucleolus. HCV-core associated proteins are implicated in RNA processing and RNA virus infection as well as in functions previously shown to be altered in Hepatitis C virus core expressing CD4(+) T cells, such as cell cycle delay, decreased proliferation, and induction of a regulatory phenotype. Thus, in the current work, we show the ultrastructural localization of Hepatitis C virus core and the first profile of HCV core associated proteins in T cells, and we discuss the functions and interconnections of these proteins in molecular networks where relevant biological modifications have been described upon the expression of Hepatitis C virus core protein. Thereby, the current work constitutes a necessary step toward understanding the mechanisms underlying HCV core mediated alterations that had been described in relevant biological processes in CD4(+) T cells. url: https://www.ncbi.nlm.nih.gov/pubmed/29354102/ doi: 10.3389/fmicb.2017.02595 id: cord-271130-6s79q1c1 author: Filoni, Claudia title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) date: 2017-11-17 words: 6584.0 sentences: 337.0 pages: flesch: 47.0 cache: ./cache/cord-271130-6s79q1c1.txt txt: ./txt/cord-271130-6s79q1c1.txt summary: title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) Thus, the aim of this study was to perform additional serological and molecular tests and monitor the population of jaguarundis at FPZSP for FeLV infection and development of FeLV-related diseases for 5 years (2003) (2004) (2005) (2006) (2007) . Two captive-born male jaguarundis, the geriatric #1 and the mature adult #4, presented serological and molecular FeLV test results similar to the progressive FeLV infection outcome in domestic cats [25] . Moreover, consistent with findings in domestic cats with a progressive FeLV infection, no antibodies to FeLV antigens were detected in jaguarundis #1 and #4. Two captive-born jaguarundis, #2 and #22, presented test results similar to those reported for domestic cats with abortive FeLV infection and seroconversion as the only marker of FeLV exposure [28] . abstract: BACKGROUND: Feline leukemia virus (FeLV) is an exogenous gammaretrovirus of domestic cats (Felis catus) and some wild felids. The outcomes of FeLV infection in domestic cats vary according to host susceptibility, virus strain, and infectious challenge dose. Jaguarundis (Puma yagouaroundi) are small wild felids from South and Central America. We previously reported on FeLV infections in jaguarundis. We hypothesized here that the outcomes of FeLV infection in P. yagouaroundi mimic those observed in domestic cats. The aim of this study was to investigate the population of jaguarundis at Fundação Parque Zoológico de São Paulo for natural FeLV infection and resulting outcomes. METHODS: We investigated the jaguarundis using serological and molecular methods and monitored them for FeLV-related diseases for 5 years. We retrieved relevant biological and clinical information for the entire population of 23 jaguarundis held at zoo. Post-mortem findings from necropsies were recorded and histopathological and immunohistopathological analyses were performed. Sequencing and phylogenetic analyses were performed for FeLV-positive samples. For sample prevalence, 95% confidence intervals (CI) were calculated. Fisher’s exact test was used to compare frequencies between infected and uninfected animals. P-values <0.05 were considered significant. RESULTS: In total, we detected evidence of FeLV exposure in four out of 23 animals (17%; 95% CI 5–39%). No endogenous FeLV (enFeLV) sequences were detected. An intestinal B-cell lymphoma in one jaguarundi was not associated with FeLV. Two jaguarundis presented FeLV test results consistent with an abortive FeLV infection with seroconversion, and two other jaguarundis had results consistent with a progressive infection and potentially FeLV-associated clinical disorders and post-mortem changes. Phylogenetic analysis of env revealed the presence of FeLV-A, a common origin of the virus in both animals (100% identity) and the closest similarity to FeLV-FAIDS and FeLV-3281 (98.4% identity), originally isolated from cats in the USA. CONCLUSIONS: We found evidence of progressive and abortive FeLV infection outcomes in jaguarundis, and domestic cats were probably the source of infection in these jaguarundis. url: https://www.ncbi.nlm.nih.gov/pubmed/29149857/ doi: 10.1186/s12985-017-0889-z id: cord-341321-paucodwz author: Finkbeiner, Stacy R title: Complete genome sequence of a highly divergent astrovirus isolated from a child with acute diarrhea date: 2008-10-14 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: BACKGROUND: Astroviruses infect a variety of mammals and birds and are causative agents of diarrhea in humans and other animal hosts. We have previously described the identification of several sequence fragments with limited sequence identity to known astroviruses in a stool specimen obtained from a child with acute diarrhea, suggesting that a novel virus was present. RESULTS: In this study, the complete genome of this novel virus isolate was sequenced and analyzed. The overall genome organization of this virus paralleled that of known astroviruses, with 3 open reading frames identified. Phylogenetic analysis of the ORFs indicated that this virus is highly divergent from all previously described animal and human astroviruses. Molecular features that are highly conserved in human serotypes 1–8, such as a 3'NTR stem-loop structure and conserved nucleotide motifs present in the 5'NTR and ORF1b/2 junction, were either absent or only partially conserved in this novel virus. CONCLUSION: Based on the analyses described herein, we propose that this newly discovered virus represents a novel species in the family Astroviridae. It has tentatively been named Astrovirus MLB1. url: https://doi.org/10.1186/1743-422x-5-117 doi: 10.1186/1743-422x-5-117 id: cord-000435-2u49b7xo author: Firth, Andrew E. title: Stimulation of stop codon readthrough: frequent presence of an extended 3′ RNA structural element date: 2011-04-27 words: 7256.0 sentences: 324.0 pages: flesch: 50.0 cache: ./cache/cord-000435-2u49b7xo.txt txt: ./txt/cord-000435-2u49b7xo.txt summary: With respect to the non-structural polyprotein, SINV and Aura virus (AURAV) form a separate clade from VEEV, WEEV and EEEV but, again, the conservation analysis revealed striking tandem conservation peaks 3 0 of the RT site ( Figure 1B ) and, again, the conservation peaks corresponded to sequences with the potential to base pair to form an RNA structure-this time comprising an 11 bp stem with a 1 nt asymmetric 3 0 bulge, a 12 nt ''spacer'' from the RT stop codon, and a 154 nt ''loop'' region ( Figure 2 ). The potential to form an extended stemloop structure 3 0 -adjacent to a RT stop codon-phylogenetically conserved and supported by a pair of peaks in synonymous site conservation-was also found in a number of plant virus RT cases, for example, in the replicase gene in the genera (Figures 3 and 4) . abstract: In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3′-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the ∼150 nt 3′-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem–loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem–loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3′ RNA stimulatory structures feature in a much larger proportion of readthrough cases than previously anticipated, and provide a new criterion for assessing the large number of cellular readthrough candidates that are currently being revealed by comparative sequence analysis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159437/ doi: 10.1093/nar/gkr224 id: cord-003104-9cx1gdze author: Fitzsimmons, William J. title: A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus date: 2018-06-28 words: 8643.0 sentences: 457.0 pages: flesch: 55.0 cache: ./cache/cord-003104-9cx1gdze.txt txt: ./txt/cord-003104-9cx1gdze.txt summary: Here, we present data for an alternative model whereby RNA viruses evolve high mutation rates as a byproduct of selection for increased replicative speed. However, the observed attenuation of antimutator RNA viruses in vivo has led many to argue for the adaptive benefit of high mutation rates, as genetic diversity provides a rich substrate for a virus''s evolution in the face of varying intrahost environments [7, 10, [34] [35] [36] [37] [38] . This is a moderate fitness defect, falling in the 64th percentile in a dataset of 8,970 fitness values obtained for point mutants of poliovirus under similar conditions [16] (e.g., human epithelial cells [HeLa] multiplicity of infection [MOI] 0.1, 8-hour infection cycle, and 6 passages; Fig 1B) . The adaptability of WT and high-fidelity viruses have generally been compared using assays that measure the acquisition of drug resistance, the reversion of an attenuating point mutation, or escape from microRNA in a limited number of replication cycles [5] [6] [7] 34, 36] . abstract: Mutation rates can evolve through genetic drift, indirect selection due to genetic hitchhiking, or direct selection on the physicochemical cost of high fidelity. However, for many systems, it has been difficult to disentangle the relative impact of these forces empirically. In RNA viruses, an observed correlation between mutation rate and virulence has led many to argue that their extremely high mutation rates are advantageous because they may allow for increased adaptability. This argument has profound implications because it suggests that pathogenesis in many viral infections depends on rare or de novo mutations. Here, we present data for an alternative model whereby RNA viruses evolve high mutation rates as a byproduct of selection for increased replicative speed. We find that a poliovirus antimutator, 3D(G64S), has a significant replication defect and that wild-type (WT) and 3D(G64S) populations have similar adaptability in 2 distinct cellular environments. Experimental evolution of 3D(G64S) under selection for replicative speed led to reversion and compensation of the fidelity phenotype. Mice infected with 3D(G64S) exhibited delayed morbidity at doses well above the lethal level, consistent with attenuation by slower growth as opposed to reduced mutational supply. Furthermore, compensation of the 3D(G64S) growth defect restored virulence, while compensation of the fidelity phenotype did not. Our data are consistent with the kinetic proofreading model for biosynthetic reactions and suggest that speed is more important than accuracy. In contrast with what has been suggested for many RNA viruses, we find that within-host spread is associated with viral replicative speed and not standing genetic diversity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6040757/ doi: 10.1371/journal.pbio.2006459 id: cord-293038-pjjvfdnq author: Fontana, Juan title: The unique architecture of Bunyamwera virus factories around the Golgi complex date: 2008-06-10 words: 7389.0 sentences: 386.0 pages: flesch: 50.0 cache: ./cache/cord-293038-pjjvfdnq.txt txt: ./txt/cord-293038-pjjvfdnq.txt summary: We propose that this new structure, unique among enveloped viruses, assembles in association with the most stable component of Golgi stacks, the actin‐containing matrix scaffold, connecting viral replication and morphogenesis inside viral factories. Modified membranes harbouring viral replication complexes (RCs) frequently integrate into a complex structure known as the ''viral factory'' where the cytoskeleton participates, cell organelles are recruited and the different steps of the virus life cycle are sequentially connected. We propose that this new multifunctional structure associates with the actin-containing matrix of the Golgi stacks providing a stable scaffold for viral replication and early morphogenesis. LtA and CyD had very little or no effect, respectively, on viral replication and assembly as determined by measurement of infectious viral particles released to the culture supernatants at 6 and 10 h p.i. Complete tubes, virus budding profiles and viral particles assembled in Golgi stacks of cells treated with LtA, as observed in thin sections of treated cells studied by EM (not shown). abstract: Viral factories are novel structures built by viruses in infected cells. During their construction organelles are recruited and build a large scaffold for viral replication and morphogenesis. We have studied how a bunyavirus uses the Golgi to build the factory. With the help of confocal and 3D ultrastructural imaging together with molecular mapping in situ and in vitro we have characterized a tubular structure that harbours the viral replication complexes in a globular domain. Numerous ribonucleoproteins were released from purified tubes disrupted in vitro. Actin and myosin I were identified by peptide mass fingerprinting in isolated tubes while actin and the viral NSm non‐structural protein were detected in the tubes' internal proteinaceous scaffold by immunogold labelling. Studies with NSm deletion mutants and drugs affecting actin showed that both NSm and actin are key factors for tube and virus assembly in Golgi. Three‐dimensional reconstructions based on oriented serial sections of infected cells showed that tubes anchor cell organelles to Golgi stacks and make contacts with intracellular viruses. We propose that this new structure, unique among enveloped viruses, assembles in association with the most stable component of Golgi stacks, the actin‐containing matrix scaffold, connecting viral replication and morphogenesis inside viral factories. url: https://www.ncbi.nlm.nih.gov/pubmed/18547336/ doi: 10.1111/j.1462-5822.2008.01184.x id: cord-000113-d0eur1hq author: Fooks, Anthony R. title: Emerging Technologies for the Detection of Rabies Virus: Challenges and Hopes in the 21st Century date: 2009-09-29 words: 6937.0 sentences: 319.0 pages: flesch: 38.0 cache: ./cache/cord-000113-d0eur1hq.txt txt: ./txt/cord-000113-d0eur1hq.txt summary: The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. Another method for the detection of rabies virus antigen from postmortem samples is a recently developed rapid immunodiagwww.plosntds.org nostic test (RIDT) based on the principles of immunochromatography [13] . Development of RT-LAMP assays for use in diagnosis and surveillance is challenged by the considerable sequence variation observed within the rabies virus genome [44] that can frustrate specific primer design. Currently, high-throughput rabies virus molecular detection methods augment standard diagnostic tests or are in the process of development and refinement for use alone. abstract: The diagnosis of rabies is routinely based on clinical and epidemiological information, especially when exposures are reported in rabies-endemic countries. Diagnostic tests using conventional assays that appear to be negative, even when undertaken late in the disease and despite the clinical diagnosis, have a tendency, at times, to be unreliable. These tests are rarely optimal and entirely dependent on the nature and quality of the sample supplied. In the course of the past three decades, the application of molecular biology has aided in the development of tests that result in a more rapid detection of rabies virus. These tests enable viral strain identification from clinical specimens. Currently, there are a number of molecular tests that can be used to complement conventional tests in rabies diagnosis. Indeed the challenges in the 21st century for the development of rabies diagnostics are not of a technical nature; these tests are available now. The challenges in the 21st century for diagnostic test developers are two-fold: firstly, to achieve internationally accepted validation of a test that will then lead to its acceptance by organisations globally. Secondly, the areas of the world where such tests are needed are mainly in developing regions where financial and logistical barriers prevent their implementation. Although developing countries with a poor healthcare infrastructure recognise that molecular-based diagnostic assays will be unaffordable for routine use, the cost/benefit ratio should still be measured. Adoption of rapid and affordable rabies diagnostic tests for use in developing countries highlights the importance of sharing and transferring technology through laboratory twinning between the developed and the developing countries. Importantly for developing countries, the benefit of molecular methods as tools is the capability for a differential diagnosis of human diseases that present with similar clinical symptoms. Antemortem testing for human rabies is now possible using molecular techniques. These barriers are not insurmountable and it is our expectation that if such tests are accepted and implemented where they are most needed, they will provide substantial improvements for rabies diagnosis and surveillance. The advent of molecular biology and new technological initiatives that combine advances in biology with other disciplines will support the development of techniques capable of high throughput testing with a low turnaround time for rabies diagnosis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745658/ doi: 10.1371/journal.pntd.0000530 id: cord-316179-kmdxltie author: Fozouni, P. title: Direct detection of SARS-CoV-2 using CRISPR-Cas13a and a mobile phone date: 2020-09-30 words: 8244.0 sentences: 507.0 pages: flesch: 58.0 cache: ./cache/cord-316179-kmdxltie.txt txt: ./txt/cord-316179-kmdxltie.txt summary: Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. When the SARS-CoV-2 sequence became public in January 2020, we set out to develop a Cas13-based direct-detection assay for viral RNA that would avoid the need for amplification and enable point-of-care testing. We tested the performance of the device for detecting SARS-CoV-2 RNA using the triple-crRNA Cas13a assay and a dilution series with full viral RNA isolated from supernatants of infected Vero CCL-81 cells . (B) RNPs made with crRNA 2 and crRNA 4 individually and in combination (50 nM total RNP concentration for each reaction) were tested against 2.9 x 10 5 copies/µL (480 fM) of SARS-CoV-2 IVT N gene RNA, and compared to fluorescence from no target RNA RNP alone controls ("RNP 2," "RNP 4," and "RNP 2+4"). abstract: The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic and pre- symptomatic carriers of the virus. CRISPR-based diagnostics that utilize RNA and DNA-targeting enzymes can augment gold-standard PCR-based testing if they can be made rapid, portable and accurate. Here we report the development of an amplification-free CRISPR-Cas13a-based mobile phone assay for direct detection of SARS-CoV-2 from nasal swab RNA extracts. The assay achieved ~100 copies/L sensitivity in under 30 minutes and accurately detected a set of positive clinical samples in under 5 minutes. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity, and we directly quantified viral load using enzyme kinetics. Combined with mobile phone-based quantification, this assay can provide rapid, low-cost, point-of-care screening to aid in the control of SARS-CoV-2. url: https://doi.org/10.1101/2020.09.28.20201947 doi: 10.1101/2020.09.28.20201947 id: cord-013854-wadpugbj author: Fratter, Carl title: EMQN best practice guidelines for genetic testing in dystrophinopathies date: 2020-05-18 words: 12725.0 sentences: 536.0 pages: flesch: 38.0 cache: ./cache/cord-013854-wadpugbj.txt txt: ./txt/cord-013854-wadpugbj.txt summary: Since whole-exon deletions or duplications are the predominant type of pathogenic variant in the DMD gene (~78%; Table 1 ), an initial screen which detects the majority of these copy number variations (CNVs) should be the first diagnostic test offered (refer to Genetic testing strategy section and Fig. 1 ). In patients with an ascertained clinical diagnosis of dystrophinopathy but no CNVs or small variants identified, RNA-based methods offer a valuable tool with a high likelihood of being able to detect variants that escape detection using level 1 and 2 DNA approaches, such as complex rearrangements or deep intronic variants leading to pseudo-exon insertion or cryptic splice site recognition in the mature transcripts. If a pathogenic DMD variant is not identified by analysis for whole-exon deletions and duplications or after DMD gene sequencing, then in some cases alternative diagnoses should be considered, depending on the available clinical evidence and test results. abstract: Dystrophinopathies are X-linked diseases, including Duchenne muscular dystrophy and Becker muscular dystrophy, due to DMD gene variants. In recent years, the application of new genetic technologies and the availability of new personalised drugs have influenced diagnostic genetic testing for dystrophinopathies. Therefore, these European best practice guidelines for genetic testing in dystrophinopathies have been produced to update previous guidelines published in 2010. These guidelines summarise current recommended technologies and methodologies for analysis of the DMD gene, including testing for deletions and duplications of one or more exons, small variant detection and RNA analysis. Genetic testing strategies for diagnosis, carrier testing and prenatal diagnosis (including non-invasive prenatal diagnosis) are then outlined. Guidelines for sequence variant annotation and interpretation are provided, followed by recommendations for reporting results of all categories of testing. Finally, atypical findings (such as non-contiguous deletions and dual DMD variants), implications for personalised medicine and clinical trials and incidental findings (identification of DMD gene variants in patients where a clinical diagnosis of dystrophinopathy has not been considered or suspected) are discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608854/ doi: 10.1038/s41431-020-0643-7 id: cord-016343-wc3i54fc author: Frese, Michael title: Interferon-Induced Effector Proteins and Hepatitis C Virus Replication date: 2008 words: 10097.0 sentences: 503.0 pages: flesch: 45.0 cache: ./cache/cord-016343-wc3i54fc.txt txt: ./txt/cord-016343-wc3i54fc.txt summary: RdRp, RNA-dependent RNA polymerase; IRES, internal ribosome entry site; 5BSL3.2, stem loop 3.2 within the coding sequence of NS5B normally result in the production of type I IFNs and the subsequent expression of IFN-induced effector proteins, which in turn would establish an antiviral state in the IFN-producing cell itself and in neighboring cells. Since MxA has the ability to efficiently inhibit a variety of different RNA viruses, MxA was the first IFN-induced effector protein to be analyzed for its antiviral activity in the HCV replicon system (Frese et al., 2001) . Rather indirect evidence that the OAS/RNase L pathway may indeed target HCV replication/translation was recently provided by Taguchi and co-workers, who reported that the N-terminal portion of NS5A (amino acids 1 to 148), which lacks the so-called PKR-binding domain, binds to OAS proteins and there by counteract the antiviral activity of IFN-α (Taguchi et al., 2004) . abstract: Hepatitis C virus (HCV) is a small, enveloped RNA virus that is often capable of establishing a persistent infection, which may lead to chronic liver disease, cirrhosis, hepatocellular carcinoma, and eventually death. For more than 20 years, hepatitis C patients have been treated with interferon-alpha (IFN-α). Current treatment usually consists of polyethylene glycol-conjugated IFN-α that is combined with ribavirin, but even the most advanced IFN-based therapies are still ineffective in eliminating the virus from a large proportion of individuals. Therefore, a better understanding of the IFN-induced innate immune response is urgently needed. By using selectable self-replicating RNAs (replicons) and, more recently, recombinant full-length genomes, many groups have tried to elucidate the mechanism(s) by which IFNs inhibit HCV replication. This chapter attempts to summarize the current state of knowledge in this interesting field of HCV research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120596/ doi: 10.1007/978-0-387-71376-2_6 id: cord-320212-fw51w4nm author: Friedman, Stephanie D. title: Genomic Sequences of two Novel Levivirus Single-Stranded RNA Coliphages (Family Leviviridae): Evidence for Recombinationin Environmental Strains date: 2012-09-13 words: 5349.0 sentences: 296.0 pages: flesch: 51.0 cache: ./cache/cord-320212-fw51w4nm.txt txt: ./txt/cord-320212-fw51w4nm.txt summary: When the novel strains were compared to nine Levivirus genogroup I strains, they shared 95–100% similarity among the maturation, capsid and lysis proteins, but only 84–85% in the RNA-dependent RNA polymerase gene. In all analysis programs, the nucleotide or amino acid sequences were aligned to other strains and were therefore approximate positions on the replicase gene. Breakpoint nucleotides for strains DL52 and DL54 (when aligned to genogroup I strains) occurred between nt 84-592 and 84-401, respectively ( Figure 5 a, b) , corresponding to the approximate amino acid breakpoint positions of 133-197 within the replicase gene. Human Noroviruses, a positive sense ssRNA virus with a genome length of 7400-8300 nt, are considered to belong to a prototype strain if they share approximately 85% overall nucleotide sequence identity and a high amino acid sequence identity (>95%) in the polymerase gene [20] . abstract: Bacteriophages are likely the most abundant entities in the aquatic environment, yet knowledge of their ecology is limited. During a fecal source-tracking study, two genetically novel Leviviridae strains were discovered. Although the novel strains were isolated from coastal waters 1130 km apart (North Carolina and Rhode Island, USA), these strains shared 97% nucleotide similarity and 97–100% amino acid similarity. When the novel strains were compared to nine Levivirus genogroup I strains, they shared 95–100% similarity among the maturation, capsid and lysis proteins, but only 84–85% in the RNA-dependent RNA polymerase gene. Further bioinformatic analyses suggested a recombination event occurred. To the best of our knowledge, this is the first description of viral recombinants in environmental Leviviridae ssRNA bacteriophages. url: https://doi.org/10.3390/v4091548 doi: 10.3390/v4091548 id: cord-253024-b393ea2u author: Fu, Kaisong title: Evidence for variable rates of recombination in the MHV genome date: 1992-07-31 words: 8420.0 sentences: 488.0 pages: flesch: 56.0 cache: ./cache/cord-253024-b393ea2u.txt txt: ./txt/cord-253024-b393ea2u.txt summary: Six RNA+ mutants that reside within a single complementation group mapping within the S glycoprotein gene of MHV-A59 were isolated which did not cause syncytium at the restrictive temperature. Since these mutants do not produce syncytium at the restrictive temperature ( Fig. 1) and sequence analysis of RNA recombinant viruses suggested that the defect in LA7 mapped within the first 1 .l kb of the S glycoprotein gene (Banner et al., 1990; Keck eta/., 1987 Keck eta/., , 1988a Makino eta/., 1986b Makino eta/., , 1987 , these data provided an anchor for mapping the location of the remaining group F RNA+ mutants. Since the distance between the group Fl and F2 mutants would have required sizable deletions (>lOO bp) to result in ts+ virus (Fig. 4) these data suggested that large deletions were rare events in these crosses, and did not contribute to an increase in the recombination frequency within the S glycoprotein gene. abstract: Abstract Mouse hepatitis virus has been shown to undergo RNA recombination at high frequency during mixed infection. Temperature-sensitive mutants were isolated using 5-fluorouracil and 5-azacytidine as mutagen. Six RNA+ mutants that reside within a single complementation group mapping within the S glycoprotein gene of MHV-A59 were isolated which did not cause syncytium at the restrictive temperature. Using standard genetic techniques, a recombination map was established that indicated that these mutants mapped into two distinct domains designated F1 and F2. These genetic domains may correspond to mutations mapping within the S1 and S2 glycoproteins, respectively, and suggest that both the S1 and S2 domains are important in eliciting the fusogenic activity of the S glycoprotein gene. In addition, assuming that most distal is alleles map roughly 4.0 kb apart, a recombination frequency of 1 % per 575–676 by was predicted through the S glycoprotein gene. Interestingly, this represents a threefold increase in the recombination frequency as compared to rates predicted through the polymerase region. The increase in the recombination rate was probably not due to recombination events resulting in large deletions or insertions (>50 bp), but rather was probably due to a combination of homologous and nonhomologous recombination. A variety of explanations could account for the increased rates of recombination in the S gene. url: https://www.sciencedirect.com/science/article/pii/004268229290684H doi: 10.1016/0042-6822(92)90684-h id: cord-310086-9e4txeck author: Fu, Wei title: Letter to the Editor: Three cases of re‐detectable positive SARS‐CoV‐2 RNA in recovered COVID‐19 patients with antibodies date: 2020-05-05 words: 1149.0 sentences: 86.0 pages: flesch: 55.0 cache: ./cache/cord-310086-9e4txeck.txt txt: ./txt/cord-310086-9e4txeck.txt summary: Here, we report three confirmed cases of COVID‐19 whose IgM was negative and IgG was positive before the first discharge, while nasopharyngeal swab test of SARS‐CoV‐2 RNA turned positive again during hotel isolation. The SARS-CoV-2 RNA test of all three patients was positive before being admitted to hospital. The results of SARS-CoV-2 RNA test during the two periods of hospitalization were shown in Table 1 . Although no special discomfort was found, all patient''s nasopharyngeal swab test of SARS-CoV-2 RNA were positive during the isolation. The detoxification procedure does occur which will cause re-detectable positive SARS-CoV-2 RNA in recovered COVID-19 Accepted Article patients [6] . However, these patients re-detectable positive for SARS-CoV-2 RNA displayed high levels of IgG and negative IgM in the plasma during two hospitalization periods. Results of SARS-CoV-2 RNA and Antibody tests of re-admission patients Recurrence of positive SARS-CoV-2 RNA in COVID-19: A case report abstract: The number of hospitalized cases has declined significantly in Wuhan. However, there have been reports that several cases of re‐detectable positive SARS‐CoV‐2 RNA in recovered COVID‐19 patients, the potential reasons of re‐detectable positive patients remained elusive. Here, we report three confirmed cases of COVID‐19 whose IgM was negative and IgG was positive before the first discharge, while nasopharyngeal swab test of SARS‐CoV‐2 RNA turned positive again during hotel isolation. In addition, all three cases presented negative results for IgM antibodies and positive results for IgG antibodies during re‐admission period. These cases suggested that the reasons for re‐detectable positive patients with profile of antibodies may be related to several factors. It is necessary to quarantine COVID‐19 patients for 14 days after discharge, and the role of antibodies in anti‐SARS‐CoV‐2 warrants further investigation. This article is protected by copyright. All rights reserved. url: https://www.ncbi.nlm.nih.gov/pubmed/32369214/ doi: 10.1002/jmv.25968 id: cord-311628-ep795pil author: Fu, Yu title: A novel delivery platform based on Bacteriophage MS2 virus-like particles date: 2016-01-04 words: 6014.0 sentences: 309.0 pages: flesch: 51.0 cache: ./cache/cord-311628-ep795pil.txt txt: ./txt/cord-311628-ep795pil.txt summary: Our objective here is to review the novel delivery platform based on Bacteriophage MS2 virus-like particles (VLPs), including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. A series of research findings showed that an MS2 VLP-based vaccine can effectively induce innate and cognate immune responses and can be used as a specific preventive intervention in some diseases, such as foot-and-mouth disease (Bittle et al., 1982; Dong et al., 2015; Van Lierop et al., 1992; Wong et al., 2000) , prostate cancer (Li et al., 2014) , and illnesses caused by human papilloma virus (HPV) (Tumban et al., 2012) . These particles offer an effective and convenient way to package RNAs, DNAs, epitope peptides, and drugs into bacteriophage capsids, forming different kinds of VLPs. MS2 VLPs can not only deliver various kinds of agents with a good safety profile and strong immunogenicity but also ensure tissue-specific targeting, which is determined by the species of the virus. abstract: Our objective here is to review the novel delivery platform based on Bacteriophage MS2 virus-like particles (VLPs), including introduction to their structure, their potential as a delivery platform, and their expected use in medicine and other fields. Bacteriophage MS2 VLPs are nanoparticles devoid of viral genetic material and can self-assemble from the coat protein into an icosahedral capsid. As a novel delivery platform, they possess numerous features that make them suitable and attractive for targeted delivery of RNAs or DNAs, epitope peptides, and drugs within the protein capsid. In short, as a novel delivery platform, MS2 VLPs are suitable for delivery of targeted agents and hold promise for use in diagnostics, vaccines, and therapeutic modalities. url: https://www.sciencedirect.com/science/article/pii/S016817021530054X doi: 10.1016/j.virusres.2015.08.022 id: cord-289192-1ecr16a3 author: Fujita, Motomichi title: Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA date: 2019-02-01 words: 2374.0 sentences: 160.0 pages: flesch: 54.0 cache: ./cache/cord-289192-1ecr16a3.txt txt: ./txt/cord-289192-1ecr16a3.txt summary: title: Development of a homogeneous time-resolved fluorescence assay for detection of viral double-stranded RNA Here, we describe a simple, rapid, cost-effective, high-throughput method using a homogeneous time-resolved fluorescence (HTRF) assay [2] focusing on viral dsRNA. The dsRNA-HTRF assay may be a useful method for screening of antiviral agents against (+) ssRNA viruses. Moreover, we determined whether the dsRNA-HTRF assay could detect the concentration-and time-dependent signals. Therefore, to evaluate whether the dsRNA-HTRF assay can detect (+) ssRNA viruses, we focused on infection by picornaviruses represented by HRV. Schematic diagram of the double-stranded RNA (dsRNA) -homogeneous time-resolved fluorescence (HTRF)-based assay. In addition, we examined whether the dsRNA-HTRF assay could detect a single cycle of viral replication. H1-HeLa cells were infected with HRV-B14 at MOI of 10 to achieve single-cycle growth, and viral dsRNA was detected at 6 h post-infection using the dsRNA-HTRF assay ( Supplementary Fig. 2) , indicating that this assay could evaluate the single-cycle growth of HRV-B14. abstract: The group of positive-sense single-stranded RNA ((+) ssRNA) viruses includes many important human pathogens. However, specific antiviral agents are not currently available for many RNA viruses. For screening of antiviral agents, methods that are simple, rapid, and compatible with high-throughput are required. Here, we describe a novel method for measurement of double-stranded RNA using a homogeneous time-resolved fluorescence assay. This method allowed detection of human rhinovirus (HRV), enterovirus, coxsackievirus, and murine norovirus. Furthermore, this method detected antiviral activity of a HRV 3C protease inhibitor. The assay may be useful for discovery of antiviral agents against (+) ssRNA viruses. url: https://www.sciencedirect.com/science/article/pii/S0003269718308364 doi: 10.1016/j.ab.2018.10.021 id: cord-306076-ygfnkgqp author: Fujita, Yu title: RNAi Therapeutic Platforms for Lung Diseases date: 2013-02-06 words: 8419.0 sentences: 495.0 pages: flesch: 43.0 cache: ./cache/cord-306076-ygfnkgqp.txt txt: ./txt/cord-306076-ygfnkgqp.txt summary: Although the success in delivering siRNAs intranasally in rodents cannot be completely extrapolated to human use because of the significant differences in lung anatomy [37] , this approach has potential for the clinical application of siRNAs. Phase II clinical trials have been initiated for the treatment of respiratory syncytial virus (RSV) infection, making use of intranasal application of naked chemically modified siRNA molecules that target viral gene products [17, 38] (see Section 3.1.1. The simultaneously inhibition of several genes would also minimize the risk of drug resistance normally encountered with small molecule-based therapies, involving siRNAs and miRNAs. There have already been significant improvements in siRNAs for primary or metastatic lung cancer treatment by targeting oncogenes such as Akt1 [9] , Wilms tumor 1 (WT1) [12] , overexpressed genes such as the insulin-like growth factor receptor 1 (IGF-1R) [77] , NUPR1 [53] and EZH2 [78] . abstract: RNA interference (RNAi) is rapidly becoming an important method for analyzing gene functions in many eukaryotes and holds promise for the development of therapeutic gene silencing. The induction of RNAi relies on small silencing RNAs, which affect specific messenger RNA (mRNA) degradation. Two types of small RNA molecules, i.e. small interfering RNAs (siRNAs) and microRNAs (miRNAs), are central to RNAi. Drug discovery studies and novel treatments of siRNAs are currently targeting a wide range of diseases, including various viral infections and cancers. Lung diseases in general are attractive targets for siRNA therapeutics because of their lethality and prevalence. In addition, the lung is anatomically accessible to therapeutic agents via the intrapulmonary route. Recently, increasing evidence indicates that miRNAs play an important role in lung abnormalities, such as inflammation and oncogenesis. Therefore, miRNAs are being targeted for therapeutic purposes. In this review, we present strategies for RNAi delivery and discuss the current state-of-the-art RNAi-based therapeutics for various lung diseases. url: https://doi.org/10.3390/ph6020223 doi: 10.3390/ph6020223 id: cord-317591-qa6oxy4j author: Fukushima, Akiko title: Development of a Chimeric DNA-RNA Hammerhead Ribozyme Targeting SARS Virus date: 2009-05-07 words: 3605.0 sentences: 196.0 pages: flesch: 53.0 cache: ./cache/cord-317591-qa6oxy4j.txt txt: ./txt/cord-317591-qa6oxy4j.txt summary: To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. A chimeric DNA-RNA hammerhead ribozyme was designed and synthesized to target a common nucleotide sequence between SARS-CoV and mouse hepatitis virus (MHV), and its effectiveness on suppression of MHV and SARS-CoV RNA expression evaluated in vitro. Figure 4 shows effect of the chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV RNA on the multiplication of MHV in DBT cells. Therefore, the chimeric DNA-RNA hammerhead ribozyme was designed with complementarity to common regions of SARS-CoV and MHV that included the target GUC sequence. In the present study, inhibition on the multiplication of MVH was approximately 60%, with 60% transfection efficiency of the chimeric DNA-RNA ribozyme targeting SARS-CoV into DBT cells. abstract: OBJECTIVE: Severe acute respiratory syndrome (SARS) is a severe pulmonary infectious disease caused by a novel coronavirus. To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). METHOD: Chimeric DNA-RNA hammerhead ribozyme targeting MHV and SARS-CoV were designed and synthesized. To confirm its activity, in vitro cleavage reactions were performed with the synthesized ribozyme. Effects of the chimeric ribozyme were evaluated on multiplication of MHV. Effects of the chimeric ribozyme on expression of SARS-CoV were evaluated in cultured 3T3 cells. RESULT: The synthetic ribozyme cleaved the synthetic target MHV and SARS-CoV RNA into fragments of predicted length. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited the expression of SARS-CoV RNA in 3T3 cells transfected with the recombinant plasmid. The chimeric DNA-RNA ribozyme targeting SARS-CoV significantly inhibited MHV viral activity and expression of recombinant SARS RNA in vitro. CONCLUSION: These findings indicate that the synthetic chimeric DNA-RNA ribozyme could provide a feasible treatment for SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/19420961/ doi: 10.1159/000215946 id: cord-314891-brgtwxhe author: Fumian, Tulio M. title: Potential Therapeutic Agents for Feline Calicivirus Infection date: 2018-08-16 words: 5483.0 sentences: 278.0 pages: flesch: 47.0 cache: ./cache/cord-314891-brgtwxhe.txt txt: ./txt/cord-314891-brgtwxhe.txt summary: Using cell culture assays, PPNDS, quercetagetin and GC376 did not display antivirals effects, however, we identified nitazoxanide and 2′-C-methylcytidine (2CMC) as potent inhibitors of FCV replication, with EC(50) values in the low micromolar range (0.6 μM and 2.5 μM, respectively). The combined inhibitory effects of nitazoxanide (0 to 0.6 µM) and 2CMC (0 to 4 µM) were tested over a range of combinations against FCV in the cell culture using the plaque reduction assay. Of the six NNI compounds tested in the current study, PPNDS and quercetagetin showed an inhibition of FCV RdRp activity with IC 50 values in the low micromolar range (Figure 2 and Table 1 ). Finally, we reported the identification of two compounds (nitazoxanide and 2CMC) with antiviral activity against FCV in cell culture at low micromolar concentrations with a potential combinational therapeutic utility to treat FCV-infected cats. abstract: Feline calicivirus (FCV) is a major cause of upper respiratory tract disease in cats, with widespread distribution in the feline population. Recently, virulent systemic diseases caused by FCV infection has been associated with mortality rates up to 50%. Currently, there are no direct-acting antivirals approved for the treatment of FCV infection. Here, we tested 15 compounds from different antiviral classes against FCV using in vitro protein and cell culture assays. After the expression of FCV protease-polymerase protein, we established two in vitro assays to assess the inhibitory activity of compounds directly against the FCV protease or polymerase. Using this recombinant enzyme, we identified quercetagetin and PPNDS as inhibitors of FCV polymerase activity (IC(50) values of 2.8 μM and 2.7 μM, respectively). We also demonstrate the inhibition of FCV protease activity by GC376 (IC(50) of 18 µM). Using cell culture assays, PPNDS, quercetagetin and GC376 did not display antivirals effects, however, we identified nitazoxanide and 2′-C-methylcytidine (2CMC) as potent inhibitors of FCV replication, with EC(50) values in the low micromolar range (0.6 μM and 2.5 μM, respectively). In conclusion, we established two in vitro assays that will accelerate the research for FCV antivirals and can be used for the high-throughput screening of direct-acting antivirals. url: https://doi.org/10.3390/v10080433 doi: 10.3390/v10080433 id: cord-271972-qhr6iir6 author: Gaglia, Marta Maria title: Viruses and the cellular RNA decay machinery date: 2010-05-06 words: 6580.0 sentences: 393.0 pages: flesch: 48.0 cache: ./cache/cord-271972-qhr6iir6.txt txt: ./txt/cord-271972-qhr6iir6.txt summary: [10] [11] [12] [13] [14] While the role of the Lsm proteins in eukaryotes is closely linked to mRNA degradation, several viruses use this complex instead to facilitate viral replication and, surprisingly, to enhance viral RNA stability. 25 It is notable that the virus-associated roles of the Lsm complex in mRNA stabilization, enhanced translation, and replication are at odds with its established cellular function in activating mRNA decapping to facilitate message degradation. However, the zinc-finger antiviral protein (ZAP), an important mediator of cellular response to retroviruses, 39 alphaviruses, 40 and filoviruses, 41 has been shown to bind the hRrp46 component of the exosome and to recruit the complex to viral mRNAs to promote their degradation. Nonetheless, given the widespread roles for the exosome in RNA quality control and turnover, viruses presumably activate this complex at least indirectly when triggering turnover of cellular mRNAs. For example, infection by select herpes and coronaviruses results in a global destruction of host messages. abstract: The ability to control cellular and viral gene expression, either globally or selectively, is central to a successful viral infection, and it is also crucial for the host to respond and eradicate pathogens. In eukaryotes, regulation of message stability contributes significantly to the control of gene expression and plays a prominent role in the normal physiology of a cell as well as in its response to environmental and pathogenic stresses. Not surprisingly, emerging evidence indicates that there are significant interactions between the eukaryotic RNA turnover machinery and a wide variety of viruses. Interestingly, in many cases viruses have evolved mechanisms not only to evade eradication by these pathways, but also to manipulate them for enhanced viral replication and gene expression. Given our incomplete understanding of how many of these pathways are normally regulated, viruses should be powerful tools to help deconstruct the complex networks and events governing eukaryotic RNA stability. Copyright © 2010 John Wiley & Sons, Ltd. 1.. RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms; 2.. RNA in Disease and Development > RNA in Disease. url: https://doi.org/10.1002/wrna.3 doi: 10.1002/wrna.3 id: cord-275307-d7htyfcl author: Gaglia, Marta Maria title: Transcriptome-Wide Cleavage Site Mapping on Cellular mRNAs Reveals Features Underlying Sequence-Specific Cleavage by the Viral Ribonuclease SOX date: 2015-12-08 words: 10860.0 sentences: 537.0 pages: flesch: 57.0 cache: ./cache/cord-275307-d7htyfcl.txt txt: ./txt/cord-275307-d7htyfcl.txt summary: Development of a novel bioinformatics pipeline to detect highconfidence SOX cleavage sites across the transcriptome following PARE Prior analyses of individual mRNAs indicated that the KSHV RNase SOX cuts at specific locations within the RNA, in a manner dependent on the sequence surrounding the cleavage site [5] . This example shows the expected distribution for a cut site followed by exonucleolytic degradation due PARE libraries from two replicates of SOX-expressing or GFP control cells and extracted the 5'' end of each mapped read, which represents the cleavage site (S1 Table) . Indeed, the sequences flanking the set of reproducible SOX cut sites (identified with a confidence level of 99.99%) were a closer match to the motif compared to those surrounding GFP-specific fragment ends, as shown by the distribution of the log likelihood scores (Fig 6A) . abstract: Many viruses express factors that reduce host gene expression through widespread degradation of cellular mRNA. An example of this class of proteins is the mRNA-targeting endoribonuclease SOX from the gamma-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV). Previous studies indicated that cleavage of messenger RNAs (mRNA) by SOX occurs at specific locations defined by the sequence of the target RNA, which is at odds with the down-regulation of a large portion of cellular transcripts. In this study, we address this paradox by using high-throughput sequencing of cleavage intermediates combined with a custom bioinformatics-based analysis pipeline to identify SOX cleavage sites across the mRNA transcriptome. These data, coupled with targeted mutagenesis, reveal that while cleavage sites are specific and reproducible, they are defined by a degenerate sequence motif containing a small number of conserved residues rather than a strong consensus sequence. This degenerate element is well represented in both human and KSHV mRNA, and its presence correlates with RNA destabilization by SOX. This represents a new endonuclease targeting strategy, in which use of a degenerate targeting element enables RNA cleavage at specific locations without restricting the range of targets. Furthermore, it shows that strong target selectivity can be achieved without a high degree of sequence specificity. url: https://www.ncbi.nlm.nih.gov/pubmed/26646420/ doi: 10.1371/journal.ppat.1005305 id: cord-300963-1n1f8mf2 author: Gajendran, Mahesh title: Inflammatory bowel disease amid the COVID-19 pandemic: impact, management strategies, and lessons learned date: 2020-10-12 words: 6681.0 sentences: 350.0 pages: flesch: 46.0 cache: ./cache/cord-300963-1n1f8mf2.txt txt: ./txt/cord-300963-1n1f8mf2.txt summary: Previous studies based on SARS-CoV-1 showed that the "cytokine storm" was strongly associated with viral sepsis, inflammation-induced lung injury, and acute respiratory distress syndrome (ARDS) [32, 34] . With regard to IBD-specific risk factors, it is speculated that patients on immunosuppressive agents, those with active IBD symptoms, malnutrition, and frequent visits to clinics or hospitals are at greater risk of acquiring SARS-CoV-2 infection [50] . The International Organization for the Study of Inflammatory Bowel Diseases (IOIBD) maintains a registry for reporting COVID-19 in IBD patients called SECURE-IBD registry. Hence, all the societies have recommended that patients continue their IBD medications to sustain remission, because the risk of disease flare-up outweighs the chance of contracting SARS-CoV-2 infection. The management strategy will depend on multiple factors, such as the patient''s age, the severity of the COVID-19 infection, the clinical status of the IBD, and the presence of other comorbid conditions. abstract: The current outbreak of COVID-19 pandemic caused by SARS-CoV-2 has affected nearly 188 countries. Patients with severe COVID-19 are more commonly elderly and suffer from comorbidities such as hypertension, diabetes mellitus, coronary artery disease, chronic pulmonary disease, obesity, and cancer. Inflammatory bowel disease (IBD) affects as many as 6.8 million people globally, and a significant proportion of them are treated with immunosuppressants. Hence, there is an ongoing concern over the impact of COVID-19 on IBD patients and their susceptibility to it. So far, there are about 1439 IBD patients in the Surveillance Epidemiology of Coronavirus under Research Exclusion (SECURE-IBD) registry reported to be infected with SARS-CoV-2. There are many unique challenges and dilemmas that need to be taken into account when managing an IBD patient with COVID-19. The management of each patient should be individualized. The IBD societies and experts have strongly recommended that patients should not discontinue their IBD medications. If the patients have symptoms of COVID-19 or IBD flare-up, they are recommended to call their IBD physician first to discuss their medication. In addition, IBD patients are urged to practice social distancing strictly to minimize the chances of infection. As COVID-19 is rapidly evolving, our experience and understanding of its impact on the IBD population may potentially change in the near future. url: https://doi.org/10.20524/aog.2020.0547 doi: 10.20524/aog.2020.0547 id: cord-271091-ffn59sgf author: Galao, Rui P title: Saccharomyces cerevisiae: a versatile eukaryotic system in virology date: 2007-10-10 words: 6539.0 sentences: 318.0 pages: flesch: 42.0 cache: ./cache/cord-271091-ffn59sgf.txt txt: ./txt/cord-271091-ffn59sgf.txt summary: These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. Although the expression of viral proteins in yeast not always necessarily reflects their role in higher eukaryotes, here we selected some examples in which the analysis in yeast of their effect on highly conserved cellular processes such as cell cycle control, apoptosis or mRNA degradation have contributed to the current understanding of the pathogenesis of important viral pathogens such as HIV-1 and HCV. The identification of the host factors involved in viral RNA replication is a priority area of research in virology because it can provide new targets for antiviral drug development. abstract: The yeast Saccharomyces cerevisiae is a well-established model system for understanding fundamental cellular processes relevant to higher eukaryotic organisms. Less known is its value for virus research, an area in which Saccharomyces cerevisiae has proven to be very fruitful as well. The present review will discuss the main achievements of yeast-based studies in basic and applied virus research. These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production. url: https://www.ncbi.nlm.nih.gov/pubmed/17927824/ doi: 10.1186/1475-2859-6-32 id: cord-266985-9qwttt2y author: Gale, P. title: Applications of omics approaches to the development of microbiological risk assessment using RNA virus dose–response models as a case study date: 2014-11-04 words: 8073.0 sentences: 341.0 pages: flesch: 43.0 cache: ./cache/cord-266985-9qwttt2y.txt txt: ./txt/cord-266985-9qwttt2y.txt summary: At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. The binding of NoV capsid protein to its HBGA receptor Table 1 Breakdown of the initial infection process into four steps for building a mechanistic dose-response relationship for RNA viruses through the oral route: information needs Host glycans play a central role in the pathogen infection process including binding of virus to specific receptors in steps 1 and 2 and also in the immune system. abstract: T e in the amount of ‘omics’ data available and in our ability to interpret those data. The aim of this paper was to consider how omics techniques can be used to improve and refine microbiological risk assessment, using dose–response models for RNA viruses, with particular reference to norovirus through the oral route as the case study. The dose–response model for initial infection in the gastrointestinal tract is broken down into the component steps at the molecular level and the feasibility of assigning probabilities to each step assessed. The molecular mechanisms are not sufficiently well understood at present to enable quantitative estimation of probabilities on the basis of omics data. At present, the great strength of gene sequence data appears to be in giving information on the distribution and proportion of susceptible genotypes (for example due to the presence of the appropriate pathogen‐binding receptor) in the host population rather than in predicting specificities from the amino acid sequences concurrently obtained. The nature of the mutant spectrum in RNA viruses greatly complicates the application of omics approaches to the development of mechanistic dose–response models and prevents prediction of risks of disease progression (given infection has occurred) at the level of the individual host. However, molecular markers in the host and virus may enable more broad predictions to be made about the consequences of exposure in a population. In an alternative approach, comparing the results of deep sequencing of RNA viruses in the faeces/vomitus from donor humans with those from their infected recipients may enable direct estimates of the average probability of infection per virion to be made. url: https://doi.org/10.1111/jam.12656 doi: 10.1111/jam.12656 id: cord-283097-rlf5nv5q author: Ganar, Ketan title: Newcastle disease virus: Current status and our understanding date: 2014-05-12 words: 8613.0 sentences: 415.0 pages: flesch: 46.0 cache: ./cache/cord-283097-rlf5nv5q.txt txt: ./txt/cord-283097-rlf5nv5q.txt summary: Newcastle disease virus-vectored vaccines expressing the hemagglutinin or neuraminidase protein of H5N1 highly pathogenic avian influenza virus protect against virus challenge in monkeys Quantitative basic residue requirements in the cleavage-activation site of the fusion glycoprotein as a determinant of virulence for Newcastle disease virus Role of C596 in the Cterminal extension of the haemagglutinin-neuraminidase protein in replication and pathogenicity of a highly virulent Indonesian strain of Newcastle disease virus Role of the cytoplasmic tail amino acid sequences of Newcastle disease virus hemagglutinin-neuraminidase protein in virion incorporation, cell fusion, and pathogenicity Evaluation of the Newcastle disease virus F and HN proteins in protective immunity by using a recombinant avian paramyxovirus type 3 vector in chickens Role of fusion protein cleavage site in the virulence of Newcastle disease virus A single amino acid change, Q114R, in the cleavage-site sequence of Newcastle disease virus fusion protein attenuates viral replication and pathogenicity abstract: Abstract Newcastle disease (ND) is one of the highly pathogenic viral diseases of avian species. ND is economically significant because of the huge mortality and morbidity associated with it. The disease is endemic in many third world countries where agriculture serves as the primary source of national income. Newcastle disease virus (NDV) belongs to the family Paramyxoviridae and is well characterized member among the avian paramyxovirus serotypes. In recent years, NDV has lured the virologists not only because of its pathogenic potential, but also for its oncolytic activity and its use as a vaccine vector for both humans and animals. The NDV based recombinant vaccine offers a pertinent choice for the construction of live attenuated vaccine due to its modular nature of transcription, minimum recombination frequency, and lack of DNA phase during replication. Our current understanding about the NDV biology is expanding rapidly because of the availability of modern molecular biology tools and high-throughput complete genome sequencing. url: https://api.elsevier.com/content/article/pii/S016817021400080X doi: 10.1016/j.virusres.2014.02.016 id: cord-312431-de7zhswl author: Ganesh, Atheesha title: Detecting Virus‐Like Particles from the Umgeni River, South Africa date: 2013-08-30 words: 7112.0 sentences: 376.0 pages: flesch: 48.0 cache: ./cache/cord-312431-de7zhswl.txt txt: ./txt/cord-312431-de7zhswl.txt summary: These results indicate the potential of viruses in the water samples especially from the lower catchment areas of the Umgeni River to infect human hosts throughout the year. It is well recognised that monitoring the presence of enteric viruses could be challenging due to the relatively low level of infectious viral particles towards the respective host species and small viral particle size existing in environmental waters, thus making it essential to start with a large water sample volume and concentrate it to several orders of magnitude [27] [28] [29] [30] [31] . The present study was conducted to optimise procedures to extract and enumerate indigenous virus-like particles (VLPs) and to determine the community structures and infectivity of these viruses from river water. Canonical correspondence analysis (CCA) was used to reveal the association amongst the bacteriophages, VLPs and the physical and chemical water quality variables, which were measured from the same sites and seasons in concurrent studies performed in this laboratory [46] , with a view to defining the significant variables accountable for the observed spatial and temporal distribution of the communities. abstract: It is important to consider viruses in water quality because of their incidence as causal agents for diarrhoeal disease, and due to their characteristics, which allow them to survive in changing environmental conditions indefinitely. This study assessed the viral quality of the Umgeni River in South Africa seasonally. A two‐step tangential flow filtration process was setup to remove the bacteria and to concentrate the virus populations from large volume water samples. The concentrated water samples contained up to 659 and 550 pfu/mL of somatic and F‐RNA coliphages, respectively. Several virus families including Adenoviridae, Herpesviridae, Orthomyxoviridae, Picornaviridae, Poxviridae and Reoviridae were found in the river based on the morphologies examined under transmission electron microscopy. All concentrated water samples produced substantial cytopathic effects on the Vero, HEK 293, Hela and A549 cell lines. These results indicate the potential of viruses in the water samples especially from the lower catchment areas of the Umgeni River to infect human hosts throughout the year. The present study highlights the importance of routine environmental surveillance of human enteric viruses in water sources. This can contribute to a better understanding of the actual burden of disease on those who might be using the water directly without treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/32313584/ doi: 10.1002/clen.201200564 id: cord-293913-frkb8iso author: Gao, Hong-Qiang title: Identification of the polymerase polyprotein products p72 and p65 of the murine coronavirus MHV-JHM date: 1996-12-31 words: 3624.0 sentences: 176.0 pages: flesch: 53.0 cache: ./cache/cord-293913-frkb8iso.txt txt: ./txt/cord-293913-frkb8iso.txt summary: Abstract The RNA polymerase gene of murine coronavirus MHV-JHM encodes a polyprotein of greater than 750 kDa. This polyprotein is proposed to be processed by two papain-like cysteine proteinases, PCP-1 and PCP-2, and a poliovirus 3C-like proteinase domain, 3C-pro, to generate protein products. To investigate which viral proteinase may be responsible for generating p72 and p65, we expressed the 5′-region of the MHV-JHM RNA polymerase gene including the two papain-like cysteine proteinase domains in an in vitro transcription/translation system and analyzed the translation products for proteolytic processing. To determine how p72 and p65 are generated from the polymerase polyprotein, we expressed cDNA clones encoding the 5''-end of ORF l a, including the 2 papain-like cysteine proteinase domains, and analyzed the translation reactions for the presence of proteolytic products. abstract: Abstract The RNA polymerase gene of murine coronavirus MHV-JHM encodes a polyprotein of greater than 750 kDa. This polyprotein is proposed to be processed by two papain-like cysteine proteinases, PCP-1 and PCP-2, and a poliovirus 3C-like proteinase domain, 3C-pro, to generate protein products. The amino-terminal product of the MHV polymerase polyprotein, p28, is generated by cleavage of the polyprotein by PCP-1. To identify the viral products downstream of p28, we generated a fusion-protein specific antiserum directed against the region adjacent to p28 and used the antiserum to detect virus-specific proteins from MHV-JHM infected cells. When this antiserum was used to immunoprecipitate radiolabeled proteins from MHV-JHM infected cell lysates, virus-specific proteins of 72 and 65 kDa were detected. Furthermore, pulse and chase experiments demonstrated that p72 is likely a precursor to the mature protein product, p65. To investigate which viral proteinase may be responsible for generating p72 and p65, we expressed the 5′-region of the MHV-JHM RNA polymerase gene including the two papain-like cysteine proteinase domains in an in vitro transcription/translation system and analyzed the translation products for proteolytic processing. We also cloned and expressed the 72 kDa region immediately downstream from p28, and tested the ability of in vitro translated PCP-1 and PCP-2 to cleave p72 to p65 in trans. Our results indicate that neither viral proteinase domain PCP-1 nor PCP-2 is capable of cleavage of p72 to produce p65 in vitro. The role of MHV proteinases in the processing of p72 and p65 is discussed. url: https://www.sciencedirect.com/science/article/pii/S0168170296013688 doi: 10.1016/s0168-1702(96)01368-8 id: cord-353703-u86ggw11 author: Gao, Peng title: Reprogramming the unfolded protein response for replication by porcine reproductive and respiratory syndrome virus date: 2019-11-18 words: 8258.0 sentences: 412.0 pages: flesch: 49.0 cache: ./cache/cord-353703-u86ggw11.txt txt: ./txt/cord-353703-u86ggw11.txt summary: We provide evidence that the virus targets the UPR central regulator GRP78 for proteasomal degradation via a mechanism that requires viral glycoprotein GP2a, while both IRE1-XBP1s and PERK-eIF2α-ATF4 signaling branches of the UPR are turned on at early stage of infection. In support of our hypothesis, antibodies to ATF4, but not the isotype control (IgG), could immunoprecipitate viral RNA from infected MARC-145 cells, as detected by RT-qPCR of the PRRSV 5''UTR region ( Fig 7D) . Because GRP78 is the master regulator, its reduced accumulation likely prevents any modulation of the UPR, keeping the ER stress pathways induced for The abundance of viral RNA was assessed by RT-PCR of ORF7, normalized against the house-keeping gene GAPDH, and then compared the benefit of the virus. abstract: The unfolded protein response (UPR) in the endoplasmic reticulum (ER) constitutes a critical component of host innate immunity against microbial infections. In this report, we show that porcine reproductive and respiratory syndrome virus (PRRSV) utilizes the UPR machinery for its own benefit. We provide evidence that the virus targets the UPR central regulator GRP78 for proteasomal degradation via a mechanism that requires viral glycoprotein GP2a, while both IRE1-XBP1s and PERK-eIF2α-ATF4 signaling branches of the UPR are turned on at early stage of infection. The activated effector XBP1s was found to enter the nucleus, but ATF4 was unexpectedly diverted to cytoplasmic viral replication complexes by means of nonstructural proteins nsp2/3 to promote viral RNA synthesis. RNAi knockdown of either ATF4 or XBP1s dramatically attenuated virus titers, while overexpression caused increases. These observations reveal attractive host targets (e.g., ATF4 and XBP1s) for antiviral drugs and have implications in vaccine development. url: https://www.ncbi.nlm.nih.gov/pubmed/31738790/ doi: 10.1371/journal.ppat.1008169 id: cord-000265-llilwq1u author: Gao, Rongbao title: A Systematic Molecular Pathology Study of a Laboratory Confirmed H5N1 Human Case date: 2010-10-12 words: 4896.0 sentences: 253.0 pages: flesch: 46.0 cache: ./cache/cord-000265-llilwq1u.txt txt: ./txt/cord-000265-llilwq1u.txt summary: Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Although H5N1 virus infection of humans is primarily one of the lower respiratory tract, more recent reports suggested that influenza A H5N1 may in rare, severe cases, disseminate beyond the lungs and infect brain [26, 27] , intestines [20, 27] and lymphoid tissues [27] , and result in extra-pulmonary clinical manifestations including encephalopathy or encephalitis [15, 28] . To better understand the pathogenesis of human H5N1 virus infection, and investigate the route of virus dissemination in vivo, we report on the use of different techniques to detect virus distribution and infection of 5 organ systems in a laboratory confirmed fatal human H5N1 virus infection, and analyze the relationship between viral load in tissues and host response. abstract: Autopsy studies have shown that human highly pathogenic avian influenza virus (H5N1) can infect multiple human organs other than just the lungs, and that possible causes of organ damage are either viral replication and/or dysregulation of cytokines and chemokines. Uncertainty still exists, partly because of the limited number of cases analysed. In this study, a full autopsy including 5 organ systems was conducted on a confirmed H5N1 human fatal case (male, 42 years old) within 18 hours of death. In addition to the respiratory system (lungs, bronchus and trachea), virus was isolated from cerebral cortex, cerebral medullary substance, cerebellum, brain stem, hippocampus ileum, colon, rectum, ureter, aortopulmonary vessel and lymph-node. Real time RT-PCR evidence showed that matrix and hemagglutinin genes were positive in liver and spleen in addition to positive tissues with virus isolation. Immunohistochemistry and in-situ hybridization stains showed accordant evidence of viral infection with real time RT-PCR except bronchus. Quantitative RT-PCR suggested that a high viral load was associated with increased host responses, though the viral load was significantly different in various organs. Cells of the immunologic system could also be a target for virus infection. Overall, the pathogenesis of HPAI H5N1 virus was associated both with virus replication and with immunopathologic lesions. In addition, immune cells cannot be excluded from playing a role in dissemination of the virus in vivo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953511/ doi: 10.1371/journal.pone.0013315 id: cord-345647-h3imwhss author: Gao, Wen-Hua title: Newly identified viral genomes in pangolins with fatal disease date: 2020-04-12 words: 5018.0 sentences: 287.0 pages: flesch: 53.0 cache: ./cache/cord-345647-h3imwhss.txt txt: ./txt/cord-345647-h3imwhss.txt summary: To identify the possible etiologic agents of disease in the four pangolins, eight meta-transcriptomic libraries from blood, liver, spleen, lung, kidney, and fecal samples were constructed, generating a total of 306,908,179 paired-end sequence reads. De novo assembly revealed the high abundance of a pestivirusand coltivirus-like virus in all the meta-transcriptomic libraries of the pangolin 1-Dongyang and 2-Lishui, representing 6-80 and 1-29 per cent of total viral contigs, respectively (Supplementary Table S2 ). Considering that they are related, yet clearly genetically distinct, from known members of Pestivirus and Coltivirus (see below), we designated these two newly identified viruses as Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV), respectively, reflecting their hosts species and the geographic location of sampling. Consequently, DYPV was identified in the heart, liver, spleen, lung, kidney, brain, blood, throat swab, and fecal sampled from pangolin 1-Dongyang, as well as the nymph ticks (Amblyomma javanense) collected from this animal. abstract: Epizootic pathogens pose a major threat to many wildlife species, particularly in the context of rapidly changing environments. Pangolins (order Pholidota) are highly threatened mammals, in large part due to the trade in illegal wildlife. During July to August 2018 four sick wild pangolins (three Manis javanica and one Manis pentadactyla) exhibiting a variety of clinical symptoms were rescued by the Jinhua Wildlife Protection Station in Zhejiang province, China. Although three of these animals died, fortunately one recovered after 2 weeks of symptomatic treatment. Using meta-transcriptomics combined with reverse transcription polymerase chain reaction (RT-PCR), we identified two novel RNA viruses in two of the dead pangolins. Genomic analysis revealed that these viruses were most closely related to pestiviruses and coltiviruses, although still highly genetically distinct, with more than 48 and 25 per cent sequence divergence at the amino acid level, respectively. We named these Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV) based on the sampling site and hosts. Although coltiviruses (LSPV) are known to be transmitted by ticks, we found no evidence of LSPV in ticks sampled close to where the pangolins were collected. In addition, although DYPV was present in nymph ticks (Amblyomma javanense) collected from a diseased pangolin, they were not found in the local tick population. Epidemiological investigation revealed that both novel viruses might have been imported following the illegal international trade of pangolins. Hence, these data indicate that illegal wildlife trafficking not only threatens the status of pangolin populations, but may also spread epizootic pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/32296543/ doi: 10.1093/ve/veaa020 id: cord-103787-qhftb6d7 author: Garcia, Elizabeth P. title: Scalable Transcriptional Analysis Routine—Multiplexed Quantitative Real-Time Polymerase Chain Reaction Platform for Gene Expression Analysis and Molecular Diagnostics date: 2005-10-31 words: 7354.0 sentences: 355.0 pages: flesch: 47.0 cache: ./cache/cord-103787-qhftb6d7.txt txt: ./txt/cord-103787-qhftb6d7.txt summary: Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. We have developed STAR (scalable transcription analysis routine), a gene expression analysis platform that represents an innovative integration of real-time multiplex PCR and capillary electrophoresis (CE), allowing the simultaneous quantitative measurement of multiple targets in a single sample with high sensitivity. In a typical STAR experiment (diagrammatically shown in Figure 1A ), a PCR reaction is set up in a single tube containing the analyte, common PCR reagents (eg, DNA polymerase, dNTPs), and, for each target to be amplified, gene-specific primers where at least one of each pair is labeled with a fluorophore. abstract: We report the development of a new technology for simultaneous quantitative detection of multiple targets in a single sample. Scalable transcriptional analysis routine (STAR) represents a novel integration of reverse transcriptase-polymerase chain reaction and capillary electrophoresis that allows detection of dozens of gene transcripts in a multiplexed format using amplicon size as an identifier for each target. STAR demonstrated similar or better sensitivity and precision compared to two commonly used methods, SYBR Green-based and TaqMan probe-based real-time reverse transcriptase-polymerase chain reaction. STAR can be used as a flexible platform for building a variety of applications to monitor gene expression, from single gene assays to assays analyzing the expression level of multiple genes. Using severe acute respiratory syndrome (SARS) corona virus as a model system, STAR technology detected single copies of the viral genome in a two-gene multiplex. Blinded studies using RNA extracted from various tissues of a SARS-infected individual showed that STAR correctly identified all samples containing SARS virus and yielded negative results for non-SARS control samples. Using alternate priming strategies, STAR technology can be adapted to transcriptional profiling studies without requiring a priori sequence information. Thus, STAR technology offers a flexible platform for development of highly multiplexed assays in gene expression analysis and molecular diagnostics. url: https://api.elsevier.com/content/article/pii/S1525157810605752 doi: 10.1016/s1525-1578(10)60575-2 id: cord-267588-ruuzr6l1 author: Garnett, Lauren title: Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages date: 2020-08-08 words: 3093.0 sentences: 156.0 pages: flesch: 51.0 cache: ./cache/cord-267588-ruuzr6l1.txt txt: ./txt/cord-267588-ruuzr6l1.txt summary: This study aimed to examine the efficacy of six different swabs that are commonly found in hospital settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6" cotton tipped applicators, and HOLOGIC Aptima), along with more readily available alternative transport mediums (DMEM, PBS, 100% ethanol, 0.9% normal saline and VTM) for their use in molecular detection of SARS-CoV-2. Therefore, our results suggest that the cotton and wood For the portion of the study focusing on alternative transport media, we assessed the ability of DMEM, PBS, 0.9% Normal Saline, and 100% ethanol compared to VTM to be used as medium for the preservation and recovery of viral RNA to be quantified by molecular detection. Despite finding similar levels of viral RNA collected using different swabs and transport media, there is variation when evaluating different respiratory clinical samples while testing for SARS-CoV-2. abstract: On March 11, 2020, the World Health Organization (WHO) assessed COVID-19, caused by SARS-CoV-2, as a pandemic. As of June 1, 2020, SARS-CoV-2 has had a documented effect of over 6 million cases world-wide, amounting to over 370,000 deaths (World Health Organization, 2020. Novel Coronavirus (COVID-19) Situation. http://https://covid19.who.int/). Consequently, the high demand for testing has resulted in a depletion of commercially available consumables, including the recommended swabs and viral transport media (VTM) required for nasopharyngeal sampling. Therefore, the potential use of unvalidated alternatives must be explored to address the global shortage of testing supplies. To tackle this issue, we evaluated the utility of different swabs and transport mediums for the molecular detection of SARS-CoV-2. This study compared the performance of six swabs commonly found in primary and tertiary health care settings (PurFlock Ultra, FLOQSwab, Puritan Pur-Wraps cotton tipped applicators, Puritan polyester tipped applicators, MedPro 6” cotton tipped applicators, and HOLOGIC Aptima) for their efficacy in testing for SARS-CoV-2. Separately, the molecular detection of SARS-CoV-2 was completed from different transport mediums (DMEM, PBS, 100 % ethanol, 0.9 % normal saline and VTM), which were kept up to three days at room temperature (RT). The results indicate that there is no meaningful difference in viral yield from different swabs and most transport mediums for the collection and detection of SARS-CoV-2, indicating swab and medium alternatives could be used if supplies run out. url: https://api.elsevier.com/content/article/pii/S0166093420301993 doi: 10.1016/j.jviromet.2020.113947 id: cord-014397-7b88ycv8 author: Gavora, JS title: Resistance of livestock to viruses: mechanisms and strategies for genetic engineering date: 1996-12-15 words: 11583.0 sentences: 528.0 pages: flesch: 41.0 cache: ./cache/cord-014397-7b88ycv8.txt txt: ./txt/cord-014397-7b88ycv8.txt summary: Thus introduction of new mechanisms of disease resistance in livestock by gene transfer may be viewed as a logical continuation of the creative influence of humans on the evolution of farm animals and birds that could benefit mankind by improvements in food safety and production efficiency. As background for the discussion of the subject, the article deals briefly with coevolution of hosts and parasites and principal elements of virus-host interactions, and reviews past improvement of disease resistance in plants and livestock by conventional breeding and genetic engineering, as well as the potential ''biological cost'' of genetic manipulation. Basic understanding of the parallel evolution of viruses and their hosts provides a useful starting point for the consideration of strategies for genetic engineering of new mechanisms of resistance. Genetic engineering strategies that prevent entry of viruses into host cells would be effective against all three types of viral infection. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708302/ doi: 10.1186/1297-9686-28-5-385 id: cord-255738-r8zfdsix author: Ge, Feng title: Derivation of a novel SARS–coronavirus replicon cell line and its application for anti-SARS drug screening date: 2007-03-30 words: 5103.0 sentences: 242.0 pages: flesch: 49.0 cache: ./cache/cord-255738-r8zfdsix.txt txt: ./txt/cord-255738-r8zfdsix.txt summary: Sequence analysis of the replicon RNA purified from SCR-1 cells soon after selection in blasticidin (passage number 6) found no sequence differences compared with the published sequence of SARS-CoV strain SIN2774 (GenBank Accession Number AY283798). Baric''s group constructed a transmissible gastroenteritis virus (TGEV) replicon for the expression of heterologous GFP gene (Curtis et al., 2002) and Thiel''s group generated a non-cytopathic, selectable replicon RNA (based on HCoV 229E) for the identification of coronavirus replicase inhibitors (Hertzig et al., 2004) . Compared to anti-viral agent identification systems based on purified proteins or nucleic acids, our SARS-CoV replicon cell line has two advantages: first, if a candidate inhibitor can inhibit replication of our replicon RNA, which occurs intracellularly, it thus demonstrates that this agent can permeate the cell. To obtain the complete sequence of the SARS-CoV replicon persisting in the SCR-1 cells, the total cellular RNAs isolated from SRC-1 cells at passage number 6 and 40 were used as the templates. abstract: The severe acute respiratory syndrome (SARS) outbreak in 2002, which had a high morbidity rate and caused worldwide alarm, remains untreated today even though SARS was eventually isolated and controlled. Development and high-throughput screening of efficacious drugs is therefore critical. However, currently there remains a lack of such a safe system. Here, the generation and characterization of the first selectable, SARS–coronavirus (SARS–CoV)-based replicon cell line which can be used for screening is described. Partial SARS–CoV cDNAs and antibiotic resistance/reporter gene DNA were generated and assembled in vitro to produce the replicon transcription template, which was then transcribed in vitro to generate the replicon RNA. The latter was introduced into a mammalian cell line and the transfected cells were selected for by antibiotic application. For the antibiotic-resistant cell lines thus generated, the expression of reporter gene was ensured by continued monitoring using fluorescent microscopy and flow cytometry. The suitability of this replicon cell line in drug screening was demonstrated by testing the inhibitory effect of several existing drugs and the results demonstrate that the SARS–CoV replicon cell lines provide a safe tool for the identification of SARS–CoV replicase inhibitors. The replicon cell lines thus developed can be applied to high-throughput screening for anti-SARS drugs without the need to grow infectious SARS–CoV. url: https://api.elsevier.com/content/article/pii/S0042682206007410 doi: 10.1016/j.virol.2006.10.016 id: cord-295733-f3rt1fyk author: Ge, Tianxiang title: Evaluation of disinfection procedures in a designated hospital for COVID-19 date: 2020-08-22 words: 2492.0 sentences: 142.0 pages: flesch: 49.0 cache: ./cache/cord-295733-f3rt1fyk.txt txt: ./txt/cord-295733-f3rt1fyk.txt summary: When compared with previous study, more places that could be potentially contaminated by COVID-19 patients were sampled for viral RNA detection, such as the flush button of the toilet bowl, medical refuse transfer trolley, elevators, and the examination rooms for these patients. These areas could not be used for non-COVID-19 patients until all the environmental samples collected were negative for SARS-CoV-2 RNA detection. In this study, surface samples collected from the examination rooms were all negative for SARS-CoV-2 RNA detection, and the samples collected from isolation wards and other places were also negative for viral RNA detection, which indicated that the terminal disinfection was effective. Other researches had revealed the presence of SARS-CoV-2 RNA in aerosol, which indicated the air could be contaminated by the virus, and patients could be infected in the isolation wards [12, 28] . Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients abstract: BACKGROUND: Coronavirus disease 2019 (COVID-19) has spread globally and been a public health emergency worldwide. It is important to reduce the risk of healthcare associated infections among the healthcare workers and patients. This study aimed to investigate the contamination of environment in isolation wards and sewage, and assess the quality of routine disinfection procedures in our hospital. METHODS: Routine disinfection procedures were performed three-times a day in general isolation wards and six-times a day in isolated ICU wards in our hospital. Environmental surface samples and sewage samples were collected for viral RNA detection. SARS-CoV-2 RNA detection were performed with quantitative reverse transcription PCR (qRT-PCR). RESULTS: A total of 163 samples were collected from February 6th to April 4th. Among 122 surface samples, two were positive for SARS-CoV-2 RNA detection. One was collected from the flush button of the toilet bowl, and the other was collected from a hand-basin. Although 10 of the sewage samples were positive for viral RNA detection, all positive samples were negative for viral culture. CONCLUSION: These results revealed the routine disinfection procedures in our hospital were effective in reducing the potential risk of healthcare associated infection. Two surface samples were positive for viral detection, suggesting that more attention should be paid when disinfecting places easy to be ignored. url: https://www.sciencedirect.com/science/article/pii/S0196655320308129?v=s5 doi: 10.1016/j.ajic.2020.08.028 id: cord-002423-1u44tdrj author: Geoghegan, Jemma L. title: Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families date: 2017-02-08 words: 6186.0 sentences: 267.0 pages: flesch: 44.0 cache: ./cache/cord-002423-1u44tdrj.txt txt: ./txt/cord-002423-1u44tdrj.txt summary: While this method does not explicitly model host-switching events, it does provide a simple means to compare multiple topologies of virus-host pairs, and accounts for differences in sample size and the fact that several viruses from a specific family can infect a single host species. Across the data set as a whole we found that all virus families displayed relatively large tree topological distances with nPH85 values of !0.6, suggesting that cross-species transmission is widespread, at least at the family-level (Fig 2; S3 Table) . As with the analysis of topological distances, this revealed that cross-species transmission was the most common evolutionary event in all virus families studied here, with co-divergence consistently less frequent (with the possible exception of the Hepadnaviridae-see below), and lineage duplication and extinction playing a much more minor role. To investigate the comparative prevalence of cross-species transmission among viruses we measured the congruence between virus and host phylogenetic trees using a normalized tree topological distance-based approach (nPH85, [14] ). abstract: The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319820/ doi: 10.1371/journal.ppat.1006215 id: cord-321053-lgae22f8 author: Gerold, Gisa title: Opportunities and Risks of Host-targeting Antiviral Strategies for Hepatitis C date: 2013-10-04 words: 9393.0 sentences: 470.0 pages: flesch: 42.0 cache: ./cache/cord-321053-lgae22f8.txt txt: ./txt/cord-321053-lgae22f8.txt summary: Numerous in vitro studies in combination with a growing number of HCV sequencing data from patients undergoing DAA treatment underline that the virus can develop drug-resistance and fitness restoring compensatory mutations [11] . An emerging third group of antivirals, so called hosttargeting antivirals (HTA), may be part of such future combination therapies, in particular as HTAs hold the promise of overcoming some of the caveats of DAAs. HTAs are antibodies, RNAs or small molecules, which interfere with host factors needed for HCV propagation. On the one hand, this demonstrates that HCV can in theory evade HTA therapy by mutating the viral binding partner of the targeted host factor and in fact suggests a low genetic barrier to resistance. Targeting HCV RNA Replication: Phosphatidylinositol 4-kinase III alpha (PI4KIIIα) Genome wide RNA interference screens and in depth cell culture replication assays with HCV replicons and full length infectious virus have revealed numerous additional host dependency factors, that could in principle serve as antiviral targets [99] [100] [101] [102] [103] [104] [105] [106] [107] . abstract: Hepatitis C virus (HCV) infects more than 2 % of the world population with highest prevalence in parts of Africa and Asia. Past standard of care using interferon α and ribavirin had adverse effects and showed modest efficacy for some HCV genotypes spurring the development of direct acting antivirals (DAAs). Such DAAs target viral proteins and are thus better tolerated but they suffer from emergence of vial resistance. Furthermore, DAAs are often HCV genotype specific. Novel drug candidates targeting host factors required for HCV propagation, so called host-targeting antivirals (HTAs), promise to overcome both caveats. The genetic barrier to resistance is usually considered to be high for HTAs and all HCV genotypes presumably use the same host factors. Recent data, however, challenge these assumptions, at least for some HTAs. Here, we highlight the most important host-targeting strategies against hepatitis C and critically discuss their opportunities and risks. url: https://www.ncbi.nlm.nih.gov/pubmed/32214912/ doi: 10.1007/s11901-013-0187-1 id: cord-355743-vjiecd4k author: Ghosh, Sabyasachi title: Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing date: 2020-04-29 words: 4826.0 sentences: 279.0 pages: flesch: 63.0 cache: ./cache/cord-355743-vjiecd4k.txt txt: ./txt/cord-355743-vjiecd4k.txt summary: The decoding algorithm takes as input cycle threshold values from qPCR tests on the pools, and returns a result for each sample, along with an estimate of viral load if positive. Once pooled tests are run, the cycle threshold values can be entered into the app which solves for and displays the list of positive and negative samples along with an estimate of viral loads. 16 × 40 pooling matrix: Table 2 shows the emulated cycle threshold (Ct) values for the 16 RT-qPCR tests corresponding to five different trials (0, 1, 2, 3 or 4 positive samples out of a total of 40 samples). 24 × 60 pooling matrix: Table 3 shows the cycle threshold (Ct) values obtained for the 24 RT-qPCR tests corresponding to a trial with 2 positive samples out of a total of 60 samples. abstract: The COVID-19 pandemic has strained testing capabilities worldwide. There is an urgent need to find economical and scalable ways to test more people. We present Tapestry, a novel quantitative nonadaptive pooling scheme to test many samples using only a few tests. The underlying molecular diagnostic test is any real-time RT-PCR diagnostic panel approved for the detection of the SARS-CoV-2 virus. In cases where most samples are negative for the virus, Tapestry accurately identifies the status of each individual sample with a single round of testing in fewer tests than simple two-round pooling. We also present a companion Android application BYOM Smart Testing which guides users through the pipetting steps required to perform the combinatorial pooling. The results of the pooled tests can be fed into the application to recover the status and estimated viral load for each individual sample. url: https://doi.org/10.1101/2020.04.23.20077727 doi: 10.1101/2020.04.23.20077727 id: cord-269726-z0frgm7s author: Gidari, Anna title: Is recurrence possible in coronavirus disease 2019 (COVID-19)? Case series and systematic review of literature date: 2020-10-10 words: 6678.0 sentences: 441.0 pages: flesch: 54.0 cache: ./cache/cord-269726-z0frgm7s.txt txt: ./txt/cord-269726-z0frgm7s.txt summary: Criteria for patients'' selection were diagnosis of SARS-CoV-2 infection [5] ; the subsequent meeting of criteria for hospital discharge (improvement of symptoms and two negative swabs collected at least 24 h apart) [4] ; and a positive respiratory sample collected after discharge. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement protocol [8] , a systematic review has been performed concerning the patients with a diagnosis of COVID-19 that, after clinical and virological recovery, presented a new positive respiratory sample (swab, sputum, saliva, tracheal aspirate, or BAL). The patient was discharged in good clinical conditions with indication to repeat quarantine and swab tests that came negative for SARS-CoV-2 (Allplex™ 2019-nCoV Assay) on April 27 and 28 (Fig. 1b) . abstract: Can a patient diagnosed with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) be infected again? This question is still unsolved. We tried to analyze local and literature cases with a positive respiratory swab after recovery. We collected data from symptomatic patients diagnosed with SARS-CoV-2 infection in the Italian Umbria Region that, after recovery, were again positive for SARS-CoV-2 in respiratory tract specimens. Samples were also assessed for infectivity in vitro. A systematic review of similar cases reported in the literature was performed. The study population was composed of 9 patients during a 4-month study period. Among the new positive samples, six were inoculated in Vero-E6 cells and showed no growth and negative molecular test in culture supernatants. All patients were positive for IgG against SARS-CoV-2 nucleoprotein and/or S protein. Conducting a review of the literature, 1350 similar cases have been found. The presumptive reactivation occurred in 34.5 days on average (standard deviation, SD, 18.7 days) after COVID-19 onset, when the 5.6% of patients presented fever and the 27.6% symptoms. The outcome was favorable in 96.7% of patients, while the 1.1% of them were still hospitalized at the time of data collection and the 2.1% died. Several hypotheses have been formulated to explain new positive respiratory samples after confirmed negativity. According to this study, the phenomenon seems to be due to the prolonged detection of SARS-CoV-2 RNA traces in respiratory samples of recovered patients. The failure of the virus to replicate in vitro suggests its inability to replicate in vivo. url: https://doi.org/10.1007/s10096-020-04057-6 doi: 10.1007/s10096-020-04057-6 id: cord-260345-ugd8kkor author: Giles, Ian G. title: A compendium of reviews in biochemistry and molecular biology published in the first half of 1992 date: 1992-12-31 words: 5327.0 sentences: 701.0 pages: flesch: 45.0 cache: ./cache/cord-260345-ugd8kkor.txt txt: ./txt/cord-260345-ugd8kkor.txt summary: 203, sodium dodecyl-sulfate.; ted blood-cells; phosphoenolpyruvate carboxylase activity; nucleotide-linked dehydrogenases; alkaline-phosphatase isoenzymes; pathogenesis-related proteins; cr-L-fucosidase; polyactylamide-gel; produce phosphate; general-method. low-density~l&protein; high-performance liquid; chrcmatogmphy mass spectmmetry; chicken vitellogam gene; thin-layer chmmatography; apolipoprotein-VLDL-II; fatty-acid composition; laying turkey hens; egg-yolk; plasma-lipoproteins. human-skin fibroblests; IGF binding-protein; messenger ribonucleic-acid; cooh-teminal truncation; monoclonal-antibody; endothelial-cells; factor receptoc amniotic-fluid; DNA-synthesis; rat-heart. factor-binding-protein; erythroid colony formation; cultured human-tibroblasts; factor messenger-RNA, N-terminal sequence; fetal bovine serum; IGF-I; somatomedin C, clinical-applicstians; stimulating factors. shon-hved protein; dependent pmteolytic system; ubiquitin-conjugating enzyme; repair gene ra&, Escherichia coli; transfer RNA; Sacclurroqces cercvisiue; endoplasmic-reticulum; cell-cycle; amino-acid. polymense chain-reaction; fragment length polymorphisms; dependent diabetes-mellitus; sickle-cell anemia; factor-M gene; enzymatic AMPlificatiat; genomic DNA; mutations; sequence; diagnosis; predisposition; genetics. T-cell receptor; messenger-RNA degradation; gamma-delta; stress proteins; antigen-receptor, lymphocytes-T; ~ycobactcrium fuberc&arir. Wiskott-Aldrich syndrome; heat-shock proteins; receptor-delta; ataxia telangiectasia; transgenic mice; lymphocytes T; bearing cells; recognition; expression; incmase. human granulocyte-macmphage; protein kinase-c; recombinant human interleukin-3; cell growth-factor, murine bone-marrow; express functional receptors; acute lymphocytic-leukemia; GTPase-activating pm&n; factor-independent growth. abstract: Abstract 1. 1. A compendium of reviews and mini-reviews in Biochemistry and Molecular Biology published in the first half of 1992 is presented. In all 499 titles are listed from 95 different publications. 2. 2. This compendium presents the references by Journal Name. Keywords have been included with each reference to increase the value of the collection. Keyword and author cross-reference indexes are not included but are available in the electronic database from which this version was constructed. Should anyone wish to have this information in electronic form it can be distributed on MS-DOS formatted flopppy disks in either Reference Manager or Medline format. The author should be contacted for details of the number of preformatted floppy disks required. url: https://www.sciencedirect.com/science/article/pii/0020711X92902837 doi: 10.1016/0020-711x(92)90283-7 id: cord-260782-1lm8tzbc author: Giles, Julia title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) date: 2018-07-14 words: 6575.0 sentences: 319.0 pages: flesch: 43.0 cache: ./cache/cord-260782-1lm8tzbc.txt txt: ./txt/cord-260782-1lm8tzbc.txt summary: title: Viral RNA load and histological changes in tissues following experimental infection with an arterivirus of possums (wobbly possum disease virus) The aim of the current study was to describe histological lesions and viral RNA levels in tissues from possum experimentally infected with WPDV. Histology of brain, kidney and liver tissue from wobbly possum disease virus (WPDV)-infected possums. Whilst RNA levels in selected tissues (liver, spleen, brain and kidney) from WPD-infected possums have been previously reported (Dunowska et al., 2013) , we have expanded both the number of possums and the tissue types tested to provide a greater understanding of the tissues targeted by the virus in-vivo. Detection of moderate to high levels of viral RNA from the sera of all but one infected possum in this study also supports the use of blood or serum samples for detection of WPDV. abstract: Tissues from Australian brushtail possums (Trichosurus vulpecula) that had been experimentally infected with wobbly possum disease (WPD) virus (WPDV) were examined to elucidate pathogenesis of WPDV infection. Mononuclear inflammatory cell infiltrates were present in livers, kidneys, salivary glands and brains of WPD-affected possums. Specific staining was detected by immunohistochemistry within macrophages in the livers and kidneys, and undefined cell types in the brains. The highest viral RNA load was found in macrophage-rich tissues. The detection of viral RNA in the salivary gland, serum, kidney, bladder and urine is compatible with transmission via close physical contact during encounters such as fighting or grooming, or by contact with an environment that has been contaminated with saliva or urine. Levels of viral RNA remained high in all tissues tested throughout the study, suggesting that on-going virus replication and evasion of the immune responses may be important in the pathogenesis of disease. url: https://www.ncbi.nlm.nih.gov/pubmed/30014860/ doi: 10.1016/j.virol.2018.07.003 id: cord-267115-6jqdi417 author: Giobbe, Giovanni Giuseppe title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids date: 2020-06-24 words: 8080.0 sentences: 408.0 pages: flesch: 47.0 cache: ./cache/cord-267115-6jqdi417.txt txt: ./txt/cord-267115-6jqdi417.txt summary: Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. Principal component analysis (PCA) showed smaller heterogeneity in the organoid groups derived at different stages of fetal and pediatric development with respect to the primary tissues analyzed at the same stages, which may also include some heterogeneity from the surrounding cells as a result of the isolation procedure (Fig. 3a) . In order to validate both fetal and pediatric gastric organoids as functional in vitro models of SARS-CoV-2 infection and replication, we optimized the culture condition for viral infection in a 3D system (Fig. 4a) . abstract: Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global public health emergency. COVID-19 typically manifests as a respiratory illness but an increasing number of clinical reports describe gastrointestinal (GI) symptoms. This is particularly true in children in whom GI symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. By contrast, fetuses seem to be rarely affected by COVID-19, although the virus has been detected in placentas of affected women. These observations raise the question of whether the virus can infect and replicate within the stomach once ingested. Moreover, it is not yet clear whether active replication of SARS-CoV-2 is possible in the stomach of children or in fetuses at different developmental stages. Here we show the novel derivation of fetal gastric organoids from 8-21 post-conception week (PCW) fetuses, and from pediatric biopsies, to be used as an in vitro model for SARS-CoV-2 gastric infection. Gastric organoids recapitulate human stomach with linear increase of gastric mucin 5AC along developmental stages, and expression of gastric markers pepsinogen, somatostatin, gastrin and chromogranin A. In order to investigate SARS-CoV-2 infection with minimal perturbation and under steady-state conditions, we induced a reversed polarity in the gastric organoids (RP-GOs) in suspension. In this condition of exposed apical polarity, the virus can easily access viral receptor angiotensin-converting enzyme 2 (ACE2). The pediatric RP-GOs are fully susceptible to infection with SARS-CoV-2, where viral nucleoprotein is expressed in cells undergoing programmed cell death, while the efficiency of infection is significantly lower in fetal organoids. The RP-GOs derived from pediatric patients show sustained robust viral replication of SARS-CoV-2, compared with organoids derived from fetal stomachs. Transcriptomic analysis shows a moderate innate antiviral response and the lack of differentially expressed genes belonging to the interferon family. Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. However, the virus can efficiently infect gastric epithelium in pediatric patients, suggesting that the stomach might have an active role in fecal-oral transmission of SARS-CoV-2. url: https://doi.org/10.1101/2020.06.24.167049 doi: 10.1101/2020.06.24.167049 id: cord-315072-b28yikvj author: Giotis, Efstathios S. title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) date: 2016-08-05 words: 5878.0 sentences: 285.0 pages: flesch: 48.0 cache: ./cache/cord-315072-b28yikvj.txt txt: ./txt/cord-315072-b28yikvj.txt summary: title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α) To generate a chicken ISG database we have compared data from three transcriptomic technology platforms: (i) the classical 3′-biased GeneChip Chicken Genome Array (32K; Affymetrix, High Wycombe, UK), (ii) the Chicken Gene 1.0 Sense Target (ST) whole transcriptome Array (Affymetrix) and (iii) Illumina (Little Chesterford, UK) RNA-seq. One of the most highly-expressed contigs was one which, when analysed by BLAST, proved to represent a homologue of STAT2, which is missing from the current ENSEMBL annotated reference chicken genome In (B) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5. Technologies identifying significant IRGs are listed as "1" RNA-seq (using Kal''s Z test); "2" Affymetrix 32K GeneChip Chicken Genome Array and "3" Chicken Gene 1.0 ST Array'' . abstract: Viruses that infect birds pose major threats—to the global supply of chicken, the major, universally-acceptable meat, and as zoonotic agents (e.g. avian influenza viruses H5N1 and H7N9). Controlling these viruses in birds as well as understanding their emergence into, and transmission amongst, humans will require considerable ingenuity and understanding of how different species defend themselves. The type I interferon-coordinated response constitutes the major antiviral innate defence. Although interferon was discovered in chicken cells, details of the response, particularly the identity of hundreds of stimulated genes, are far better described in mammals. Viruses induce interferon-stimulated genes but they also regulate the expression of many hundreds of cellular metabolic and structural genes to facilitate their replication. This study focusses on the potentially anti-viral genes by identifying those induced just by interferon in primary chick embryo fibroblasts. Three transcriptomic technologies were exploited: RNA-seq, a classical 3′-biased chicken microarray and a high density, “sense target”, whole transcriptome chicken microarray, with each recognising 120–150 regulated genes (curated for duplication and incorrect assignment of some microarray probesets). Overall, the results are considered robust because 128 of the compiled, curated list of 193 regulated genes were detected by two, or more, of the technologies. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13567-016-0363-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/27494935/ doi: 10.1186/s13567-016-0363-8 id: cord-001152-v6uc0ijw author: Girardi, Erika title: Identification of RNase L-Dependent, 3′-End-Modified, Viral Small RNAs in Sindbis Virus-Infected Mammalian Cells date: 2013-11-19 words: 7021.0 sentences: 383.0 pages: flesch: 52.0 cache: ./cache/cord-001152-v6uc0ijw.txt txt: ./txt/cord-001152-v6uc0ijw.txt summary: Here, we provide evidence for the presence of discrete small RNAs of viral origin that are not associated with the RNA-induced silencing complex (RISC), that are highly expressed and detected by Northern blot analysis, and that accumulate as 21to 28-nucleotide (nt) species during infection. We report that the cellular antiviral endoribonuclease RNase L cleaves the viral genome, producing in turn the small RNAs. Surprisingly, we uncovered the presence of a modification on the 3′-end nucleotide of SINV-derived viral small RNAs (SvsRNAs) that might be at the origin of their stability. The identification of small RNAs from RNA viruses could be seen either as a result of a productive mechanism for the pathogen (as for virus-encoded miRNAs) or as the consequence of a host response to control the infection by degrading viral RNAs. SINV expresses four enzymes that play key functions during the viral replicative cycle. abstract: Small RNAs play a critical role in host-pathogen interaction. Indeed, small RNA-mediated silencing or RNA interference (RNAi) is one of the earliest forms of antiviral immunity. Although it represents the main defense system against viruses in many organisms, the antiviral role of RNAi has not been clearly proven in higher vertebrates. However, it is well established that their response to viral infection relies on the recognition of viral RNAs by host pattern recognition receptors (PRRs) to trigger activation of the interferon pathway. In the present work, we report the existence of a novel small noncoding RNA population produced in mammalian cells upon RNA virus infection. Using Sindbis virus (SINV) as a prototypic arbovirus model, we profiled the small RNA population of infected cells in both human and African green monkey cell lines. Here, we provide evidence for the presence of discrete small RNAs of viral origin that are not associated with the RNA-induced silencing complex (RISC), that are highly expressed and detected by Northern blot analysis, and that accumulate as 21- to 28-nucleotide (nt) species during infection. We report that the cellular antiviral endoribonuclease RNase L cleaves the viral genome, producing in turn the small RNAs. Surprisingly, we uncovered the presence of a modification on the 3′-end nucleotide of SINV-derived viral small RNAs (SvsRNAs) that might be at the origin of their stability. Altogether, our findings show that stable modified small viral RNAs could represent a novel way to modulate host-virus interaction upon SINV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3870239/ doi: 10.1128/mbio.00698-13 id: cord-346916-jj4l9ydl author: Girardi, Erika title: Roadblocks and fast tracks: How RNA binding proteins affect the viral RNA journey in the cell date: 2020-08-23 words: 13119.0 sentences: 728.0 pages: flesch: 45.0 cache: ./cache/cord-346916-jj4l9ydl.txt txt: ./txt/cord-346916-jj4l9ydl.txt summary: Moreover, despite the molecular mimicry set by RNA viruses to resemble cellular mRNAs and escape host recognition, the viral nucleic acid still needs to embark on a long journey through a hostile cell environment and must overcome the obstacles put in place by the host antiviral system in order to be translated and replicated. Another example, is the zinc-finger antiviral protein (ZAP), which binds vRNAs containing a ZAP response element (ZRE) and induces RNA degradation via interaction of its N-terminal domain with host decay machinery mediated [75] (Fig. 1 ). In fact, IRES elements present in the genome of different families of RNA viruses lack overall conserved features [146, 147] .The classification of viral IRESs in four types stems from their structural organization, their respective dependence on sets of translation initiation factors, and whether they use scanning or instead directly recruit ribosomes to the start codon [148] (Fig. 2) . abstract: As obligate intracellular parasites with limited coding capacity, RNA viruses rely on host cells to complete their multiplication cycle. Viral RNAs (vRNAs) are central to infection. They carry all the necessary information for a virus to synthesize its proteins, replicate and spread and could also play essential non-coding roles. Regardless of its origin or tropism, vRNA has by definition evolved in the presence of host RNA Binding Proteins (RBPs), which resulted in intricate and complicated interactions with these factors. While on one hand some host RBPs recognize vRNA as non-self and mobilize host antiviral defenses, vRNA must also co-opt other host RBPs to promote viral infection. Focusing on pathogenic RNA viruses, we will review important scenarios of RBP-vRNA interactions during which host RBPs recognize, modify or degrade vRNAs. We will then focus on how vRNA hijacks the largest ribonucleoprotein complex (RNP) in the cell, the ribosome, to selectively promote the synthesis of its proteins. We will finally reflect on how novel technologies are helping in deepening our understanding of vRNA-host RBPs interactions, which can be ultimately leveraged to combat everlasting viral threats. url: https://api.elsevier.com/content/article/pii/S1084952120300914 doi: 10.1016/j.semcdb.2020.08.006 id: cord-350286-n7ylgqfu author: Giri, Rajanish title: When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses date: 2020-04-03 words: 15827.0 sentences: 874.0 pages: flesch: 56.0 cache: ./cache/cord-350286-n7ylgqfu.txt txt: ./txt/cord-350286-n7ylgqfu.txt summary: The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) . abstract: Recently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 9,00,000 cases of SARS-CoV-2 infection and more than 47,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted that the COVID-19 is a pandemic now. The multiple sequence alignment data correlated with the already published reports on the SARS-CoV-2 evolution and indicated that this virus is closely related to the bat Severe Acute Respiratory Syndrome-like coronavirus (bat SARS-like CoV) and the well-studied Human SARS coronavirus (SARS CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for Nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins were shown to contain molecular recognition features (MoRFs), which are intrinsic disorder-based protein-protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of the SARS-CoV-2 proteome will have important implications for the structural and non-structural biology of SARS or SARS-like coronaviruses. Significance The infection caused by a novel coronavirus (SARS-CoV-2) that causes severe respiratory disease with pneumonia-like symptoms in humans is responsible for the current COVID-19 pandemic. No in-depth information on structures and functions of SARS-CoV-2 proteins is currently available in the public domain, and no effective anti-viral drugs and/or vaccines are designed for the treatment of this infection. Our study provides the first comparative analysis of the order- and disorder-based features of the SARS-CoV-2 proteome relative to human SARS and bat CoV that may be useful for structure-based drug discovery. url: https://doi.org/10.1101/2020.03.13.990598 doi: 10.1101/2020.03.13.990598 id: cord-273019-hbpfz8rt author: Glingston, R. Sahaya title: Organelle dynamics and viral infections: at cross roads date: 2018-06-25 words: 9513.0 sentences: 486.0 pages: flesch: 35.0 cache: ./cache/cord-273019-hbpfz8rt.txt txt: ./txt/cord-273019-hbpfz8rt.txt summary: Studies on the herpes simplex virus-1 (HSV-1) infection on Vero, BHK-21 and PtK 2 cells reported transportation of viral tegument-capsid by dynein to the cytoplasmic side of NPC [22, 23] . In order to construct these compartments, viruses alter host''s fatty acid metabolism, induce rearrangement of the membrane constituents and also recruit cellular machinery to produce proteins essential for its replication [59, 60] . Upregulation of mitophagy and degradation of the mitochondrial antiviral signalling protein (MAVS) in order to attenuate the antiviral immune response in non-small cell lung cancer (NSCLC) cells was reported upon measles virus infection [83] . The expression of matrix protein (M) of human parainfluenza virus type 3 (HPIV3) in HEK293T and HeLa cells was reported to induce mitophagy resulting in the suppression of type1 interferon response [84] . Many viruses or viral proteins are reported to localize to peroxisomes and/or exploit their functions to facilitate their replication in the host cells [108] . abstract: Viruses are obligate intracellular parasites of the host cells. A commonly accepted view is the requirement of internal membranous structures for various aspects of viral life cycle. Organelles enable favourable intracellular environment for several viruses. However, studies reporting organelle dynamics upon viral infections are scant. In this review, we aim to summarize and highlight modulations caused to various organelles upon viral infection or expression of its proteins. url: https://api.elsevier.com/content/article/pii/S1286457918301412 doi: 10.1016/j.micinf.2018.06.002 id: cord-350747-5t5xthk6 author: Gmyl, A. P. title: Diverse Mechanisms of RNA Recombination date: 2005 words: 8187.0 sentences: 463.0 pages: flesch: 41.0 cache: ./cache/cord-350747-5t5xthk6.txt txt: ./txt/cord-350747-5t5xthk6.txt summary: It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. An illustrative example of deletions is provided by defective interfering (DI) genomes, which accumulate in a virus population upon high-multiplicity infections and lack a fragment of the sequence coding for viral proteins [5] [6] [7] . A special role in the variation of RNA viruses is played by recombination, the generation of new genomes from two or more parental RNAs. Recombination between viral RNA molecules was observed for the first time as early as in the 1960s in the poliovirus [14, 15] . In other words, it is possible to assume that some of the mechanisms of nonreplicative RNA recombination play an important role in the evolution of not only viral, but also cell genomes [51, 90] . abstract: Recombination is widespread among RNA viruses, but many molecular mechanisms of this phenomenon are still poorly understood. It was believed until recently that the only possible mechanism of RNA recombination is replicative template switching, with synthesis of a complementary strand starting on one viral RNA molecule and being completed on another. The newly synthesized RNA is a primary recombinant molecule in this case. Recent studies have revealed other mechanisms of replicative RNA recombination. In addition, recombination between the genomes of RNA viruses can be nonreplicative, resulting from a joining of preexisting parental molecules. Recombination is a potent tool providing for both the variation and conservation of the genome in RNA viruses. Replicative and nonreplicative mechanisms may contribute differently to each of these evolutionary processes. In the form of trans splicing, nonreplicative recombination of cell RNAs plays an important role in at least some organisms. It is conceivable that RNA recombination continues to contribute to the evolution of DNA genomes. url: https://doi.org/10.1007/s11008-005-0069-x doi: 10.1007/s11008-005-0069-x id: cord-354733-qxivrhj8 author: Gniazdowski, V. title: Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity date: 2020-08-06 words: 3924.0 sentences: 251.0 pages: flesch: 56.0 cache: ./cache/cord-354733-qxivrhj8.txt txt: ./txt/cord-354733-qxivrhj8.txt summary: Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Whole genome sequencing confirmed the virus genotype in patients with prolonged 28 viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false 29 negative standard of care PCR results. Prolonged viral RNA shedding was associated with recovery of infectious 31 virus in specimens collected up to 20 days after the first positive result in patients who were 32 symptomatic at the time of specimen collection. Infection control personnel and physicians managing COVID-19 patients and patients under 43 investigation (PUI) continue to face several diagnostic dilemmas related to a lack of 44 understanding of the clinical sensitivities of SARS-CoV-2 molecular diagnostics and the 45 correlation between viral RNA detection and shedding of infectious virus. abstract: Repeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Consecutively collected specimens from a retrospective cohort of COVID-19 patients at the Johns Hopkins Hospital were assessed for RNA and infectious virus shedding. Whole genome sequencing confirmed the virus genotype in patients with prolonged viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false negative standard of care PCR results. Recovery of infectious virus was associated with Ct values of 18.8 {+/-} 3.4. Prolonged viral RNA shedding was associated with recovery of infectious virus in specimens collected up to 20 days after the first positive result in patients who were symptomatic at the time of specimen collection. The use of Ct values and clinical symptoms provides a more accurate assessment of the potential for infectious virus shedding. url: https://doi.org/10.1101/2020.08.05.20168963 doi: 10.1101/2020.08.05.20168963 id: cord-260422-z22t57ju author: Godet, Julien title: Comparative nucleic acid chaperone properties of the nucleocapsid protein NCp7 and Tat protein of HIV-1 date: 2012-06-26 words: 9180.0 sentences: 486.0 pages: flesch: 49.0 cache: ./cache/cord-260422-z22t57ju.txt txt: ./txt/cord-260422-z22t57ju.txt summary: Today''s view is that RNA chaperones are nucleic acid binding proteins present in all living organisms, including viruses, where they Abbreviations: HIV-1, human immunodeficiency virus-type I; NCp7, nucleocapsid protein of HIV-1; ZF, zinc finger; NA, nucleic acid; TAR, transactivation response element; PBS, primer binding site; AA, amino acids. The substantial nucleic acid chaperone properties exhibited by Tat may account for its ability to promote the annealing of the primer tRNA to the viral RNA (Kameoka et al., 2002) and intervene in the first strand transfer (Boudier et al., 2010) and by this way, to stimulate RTion as does NCp7 (Harrich et al., 1997; Ulich et al., 1999; Apolloni et al., 2007) . Human immunodeficiency virus Type 1 nucleocapsid protein (NCp7) directs specific initiation of minusstrand DNA synthesis primed by human tRNA(Lys3) in vitro: studies of viral RNA molecules mutated in regions that flank the primer binding site abstract: RNA chaperones are proteins able to rearrange nucleic acid structures towards their most stable conformations. In retroviruses, the reverse transcription of the viral RNA requires multiple and complex nucleic acid rearrangements that need to be chaperoned. HIV-1 has evolved different viral-encoded proteins with chaperone activity, notably Tat and the well described nucleocapsid protein NCp7. We propose here an overview of the recent reports that examine and compare the nucleic acid chaperone properties of Tat and NCp7 during reverse transcription to illustrate the variety of mechanisms of action of the nucleic acid chaperone proteins. url: https://www.sciencedirect.com/science/article/pii/S0168170212002183 doi: 10.1016/j.virusres.2012.06.021 id: cord-278684-txlvla0j author: Gonzalez–Dunia, Daniel title: Borna Disease Virus and the Brain date: 1998-01-30 words: 13952.0 sentences: 784.0 pages: flesch: 43.0 cache: ./cache/cord-278684-txlvla0j.txt txt: ./txt/cord-278684-txlvla0j.txt summary: The BDV paradigm is amenable to study virus–cell interactions in the CNS that can lead to neurodevelopmental abnormalities, immune-mediated damage, as well as alterations in cell differentiated functions that affect brain homeostasis. Evidence provided by epidemiological and clinical data, together with virological studies, have led to the hypothesis that chronic viral infections of the CNS contribute to human mental disorders of unknown etiology. Therefore, neuronal damage seen in BD appears to be mediated by the cytotoxic activity of CD8 ϩ T-cells present in the brain parenchyma of BDV-infected rats. Studies on PTI-NB rats may provide valuable information regarding the contribution of CNS resident cells to disturbances in cytokine gene expression caused by BDV. Borna disease virus replicates in astrocytes, Schwann cells and ependymal cells in persistently infected rats: Location of viral genomic and messenger RNAs by in situ hybridization Expression of tissue factor is increased in astrocytes within the central nervous system during persistent infection with Borna disease virus abstract: Viruses with the ability to establish persistent infection in the central nervous system (CNS) can induce progressive neurologic disorders associated with diverse pathological manifestations. Clinical, epidemiological, and virological evidence supports the hypothesis that viruses contribute to human mental diseases whose etiology remains elusive. Therefore, the investigation of the mechanisms whereby viruses persist in the CNS and disturb normal brain function represents an area of research relevant to clinical and basic neurosciences. Borna disease virus (BDV) causes CNS disease in several vertebrate species characterized by behavioral abnormalities. Based on its unique features, BDV represents the prototype of a new virus family. BDV provides an important model for the investigation of the mechanisms and consequences of viral persistence in the CNS. The BDV paradigm is amenable to study virus–cell interactions in the CNS that can lead to neurodevelopmental abnormalities, immune-mediated damage, as well as alterations in cell differentiated functions that affect brain homeostasis. Moreover, seroepidemiological data and recent molecular studies indicate that BDV is associated with certain neuropsychiatric diseases. The potential role of BDV and of other yet to be uncovered BDV-related viruses in human mental health provides additional impetus for the investigation of this novel neurotropic infectious agent. url: https://api.elsevier.com/content/article/pii/S0361923097002761 doi: 10.1016/s0361-9230(97)00276-1 id: cord-266634-bww62vx8 author: Gopinath, M. title: Evidence for N(7) guanine methyl transferase activity encoded within the modular domain of RNA-dependent RNA polymerase L of a Morbillivirus date: 2015-10-07 words: 2304.0 sentences: 104.0 pages: flesch: 53.0 cache: ./cache/cord-266634-bww62vx8.txt txt: ./txt/cord-266634-bww62vx8.txt summary: In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Considering the presence of both KDKE tetrad, responsible for 2 0 -O-methyl transferase as well as GXGXG motif for SAM substrate binding, domain III could likely represent the methyl transfer module (both N 7 -guanine and 2 0 -Omethyl) of RPV L protein. Consensus sequence between the viral mRNAs is given in bold the capped RNA with the partially purified L-P complex from insect cells resulted in a concentration dependent N 7 guanine methylation of 6 bp substrate (Fig. 2b , marked as rL) which was not detected in a mock-purified high-density fraction from insect cells infected with non-recombinant baculovirus (Fig. 2b, mock) . Further, to functionally validate the methyl transferase activity of domain III (aa 1717-2183, LD3) of RPV L protein, LD3 was purified from insect cells using metal chelate affinity chromatography as described earlier [8] . abstract: Post-transcriptional modification of viral mRNA is essential for the translation of viral proteins by cellular translation machinery. Due to the cytoplasmic replication of Paramyxoviruses, the viral-encoded RNA-dependent RNA polymerase (RdRP) is thought to possess all activities required for mRNA capping and methylation. In the present work, using partially purified recombinant RNA polymerase complex of rinderpest virus expressed in insect cells, we demonstrate the in vitro methylation of capped mRNA. Further, we show that a recombinant C-terminal fragment (1717–2183 aa) of L protein is capable of methylating capped mRNA, suggesting that the various post-transcriptional activities of the L protein are located in independently folding domains. url: https://doi.org/10.1007/s11262-015-1252-3 doi: 10.1007/s11262-015-1252-3 id: cord-343918-5yk1j4ms author: Gorbalenya, A.E. title: Phylogeny of Viruses date: 2008-07-30 words: 3892.0 sentences: 182.0 pages: flesch: 40.0 cache: ./cache/cord-343918-5yk1j4ms.txt txt: ./txt/cord-343918-5yk1j4ms.txt summary: For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. Phylogenetic analysis is used in a wide range of studies to address both applied and fundamental issues of virus research, including epidemiology, diagnostics, forensic studies, phylogeography, origin, evolution, and taxonomy of viruses. With the latter virus, poor sampling of the coronavirus diversity in the SARS-CoV lineage at the time, some uncertainty over the relationship between phylogeny and taxonomy of coronaviruses, and the complexity of phylogenetic analysis of a virus data set including isolated distant lineages led to considerable controversy over the exact evolutionary position of SARS-CoV among coronaviruses. abstract: Biological species, including viruses, change through generations and over time in the process known as evolution. Viruses may evolve at high, uneven, and fluctuating rates among genome sites. The accumulated changes, through either mutation or recombination with other species, are first fixed in the genome of successful individuals that give rise to genetic lineages. The relationship between biological lineages related by common descent is called ‘phylogeny’. For inferring phylogeny, the differences between aligned sequences of genomes and proteins are quantified and depicted in the form of a tree, in which contemporary species and their intermediate and common ancestors occupy, respectively, the terminal nodes, internal nodes, and the root. The tree is characterized by a topology, length of branches, shape, and the root position. A complex mathematical apparatus has been developed for phylogeny inference that can evaluate inter-species differences, facilitate tree building and comparison of trees, and assess the fit between data and tree through, typically, computationally intensive calculations. A reconstructed tree is an approximation of the true phylogeny that practically remains unknown. The phylogenetic analysis is used in applied and fundamental virus research, including epidemiology, diagnostics, forensic studies, phylogeography, evolutionary studies, and virus taxonomy. It can provide an evolutionary perspective on variation of any trait that can be measured for a group of viruses. url: https://www.sciencedirect.com/science/article/pii/B9780123744104007123 doi: 10.1016/b978-012374410-4.00712-3 id: cord-006935-wzz5t3sv author: Gorbalenya, Alexander E. title: Viral cysteine proteinases date: 1996 words: 8112.0 sentences: 460.0 pages: flesch: 59.0 cache: ./cache/cord-006935-wzz5t3sv.txt txt: ./txt/cord-006935-wzz5t3sv.txt summary: Only one conserved cysteine residue, thought to be the catalytic nucleophile, was identified in 3C p~° sequences of different origin [41, 47] and its indispensability for the PV 3C pr° proteolytic activity was proven by site-directed mutagenesis [48] . All RNA viral cysteine proteinases are synthesized as a domain in a polyprotein [17] and three major trends were discovered with respect to the position occupied by these enzymes. However, in an N-terminally extended precursor of 3C pr°, the Nterminal region of the proteinase could adopt a different structure that would fit the substrate binding pocket and might be processed in cis [5] . The $5-$2 subsites of the substrate-binding pocket, which interact with the less conserved P5-P2 positions of the cleavage sites, were recognized in the enzyme-substrate model of the HRV-14 3C pr° as well [5] . abstract: Dozens of novel cysteine proteinases have been identified in positive single-stranded RNA viruses and, for the first time, in large double-stranded DNA viruses. The majority of these proteins are distantly related to papain or chymotrypsin and may be direct descendants of primordial proteolytic enzymes. Virus genome synthesis and expression, virion formation, virion entry into the host cell, as well as cellular architecture and functioning can be under the control of viral cysteine proteinases during infection. RNA virus proteinases mediate their liberation from giant multidomain precursors in which they tend to occupy conserved positions. These proteinases possess a narrow substrate specificity, can cleave in cis and in trans, and may also have additional, nonproteolytic functions. The mechanisms of catalysis, substrate recognition and RNA binding were highlighted by the recent analysis of the three-dimensional structure of the chymotrypsin-like cysteine proteinases of two RNA viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104566/ doi: 10.1007/bf02174046 id: cord-325043-vqjhiv7p author: Gorbalenya, Alexander E. title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication date: 1989 words: 6805.0 sentences: 361.0 pages: flesch: 52.0 cache: ./cache/cord-325043-vqjhiv7p.txt txt: ./txt/cord-325043-vqjhiv7p.txt summary: title: An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication These observations, taken together with the results of comparative analysis of the positions occupied by respective proteins (domains) in viral multidomain proteins, suggest that all the NTP-motif-containing proteins of positive-strand RNA viruses are homologous, constituting a highly diverged monophyletic group. Preliminary comparative analysis of the amino acid sequences of the NTP-motif-eontaining proteins of positive-strand RNA viruses by use of the programs DIAGON and OPTAL (see Methods) revealed three distinct families and some additional proteins in whose close relatives the motif was not conserved. In the present study we demonstrate that in a highly diverged group including similar proteins of positive-strand RNA viruses, the consensus sequences of the NTP-motif constitute the most strictly conserved stretches, encompassing four of the five invariant amino acid residues. abstract: NTP-motif, a consensus sequence previously shown to be characteristic of numerous NTP-utilizing enzymes, was identified in nonstructural proteins of several groups of positive-strand RNA viruses. These groups include picorna-, alpha-, and coronaviruses infecting animals and como-, poty-, tobamo-, tricorna-, hordei-, and furoviruses of plants, totalling 21 viruses. It has been demonstrated that the viral NTP-motif-containing proteins constitute three distinct families, the sequences within each family being similar to each other at a statistically highly significant level. A lower, but still valid similarity has also been revealed between the families. An overall alignment has been generated, which includes several highly conserved sequence stretches. The two most prominent of the latter contain the socalled “A” and “B” sites of the NTP-motif, with four of the five invariant amino acid residues observed within these sequences. These observations, taken together with the results of comparative analysis of the positions occupied by respective proteins (domains) in viral multidomain proteins, suggest that all the NTP-motif-containing proteins of positive-strand RNA viruses are homologous, constituting a highly diverged monophyletic group. In this group the “A” and “B” sites of the NTP-motif are the most conserved sequences and, by inference, should play the principal role in the functioning of the proteins. A hypothesis is proposed that all these proteins posses NTP-binding capacity and possibly NTPase activity, performing some NTP-dependent function in viral RNA replication. The importance of phylogenetic analysis for the assessment of the significance of the occurrence of the NTP-motif (and of sequence motifs of this sort in general) in proteins is emphasized. url: https://www.ncbi.nlm.nih.gov/pubmed/2522556/ doi: 10.1007/bf02102483 id: cord-331680-qlzhtxs0 author: Goryachev, A.N. title: Potential Opportunity of Antisense Therapy of COVID-19 on an in Vitro Model date: 2020-11-03 words: 4106.0 sentences: 200.0 pages: flesch: 51.0 cache: ./cache/cord-331680-qlzhtxs0.txt txt: ./txt/cord-331680-qlzhtxs0.txt summary: In accordance with the purpose of the study, the following tasks were set: -to select the nucleotide sequence of the virus that is supposed to be inhibited, -to carry out the synthesis of oligonucleotide, -to determine cytotoxicity and antiviral activity in an in vitro experiment on cell culture. The assessment of antiviral activity of the drug in addition to cytopathic action was also taken into account by reducing the infectious titer of the virus in the culture of Vero cells E6 according to PCR RNA SARS-CoV-2, determined by the threshold of the number of reaction cycles (cycle treshold, Ct) in various dilutions of the study drug. Determination of the antiviral efficacy of the antisense oligonucleotide according to the treatment scheme (administration of the drug 24 hours after infection) was taken into account by the decrease in the infectious titer of the virus in the culture of Vero E6 cells by the cytopathic effect. abstract: Data on potential effectiveness and prospects of treatment of new coronavirus infection of COVID-19 caused by virus SARS-CoV-2 with the help of antisense oligonucleotides acting against RNA of virus on an in vitro model are given. The ability of antisense oligonucleotides to suppress viral replication in diseases caused by coronaviruses using the example of SARS and MERS is shown. The identity of the initial regulatory section of RNA of various coronaviruses was found within 50 - 100 nucleotides from the 5’-end, which allows using antisense suppression of this RNA fragment. A new RNA fragment of the virus present in all samples of coronovirus SARS-CoV-2 has been identified, the suppression of which with the help of an antisense oligonucleotide can be effective in the treatment of COVID-19. The study of the synthesized antisense oligonucleotide 5’ - AGCCGAGTGACAGCC ACACAG, complementary to the selected virus RNA sequence, was carried out. The low toxicity of the preparations of this group in the cell culture study and the ability to reduce viral load at high doses according to real time-PCR data are shown. The cytopathogenic dose exceeds 2 mg / ml. At a dosage of 1 mg / ml, viral replication is reduced by 5-13 times. Conclusions are made about the prospects of this direction and the feasibility of using the inhalation way of drug administration into the body. url: https://doi.org/10.1101/2020.11.02.363598 doi: 10.1101/2020.11.02.363598 id: cord-298938-xemarhlv author: Goswami, Biswendu B. title: Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase date: 2004-04-07 words: 7455.0 sentences: 369.0 pages: flesch: 51.0 cache: ./cache/cord-298938-xemarhlv.txt txt: ./txt/cord-298938-xemarhlv.txt summary: title: Apoptosis induced by a cytopathic hepatitis A virus is dependent on caspase activation following ribosomal RNA degradation but occurs in the absence of 2′–5′ oligoadenylate synthetase We have presented previously evidence that the cytopathogenic 18f strain of hepatitis A virus (HAV) induced degradation of ribosomal RNA (rRNA) in infected cells [Arch. Based on the pattern of rRNA degradation in intact ribosomes, we suggested that the 18f virus activates the interferon (IFN) controlled 2 -5 oligoadenylic acid-dependent RNase L pathway (for recent reviews, see Stark et al., 1998; Barber, 2001; Sen, 2001) . First, the level of IFN, 2 -5 OAS and RNase L mRNAs were investigated by RT-PCR to determine if any of these RNAs were induced following virus infection (Fig. 8) . RT-PCR amplification of selected cellular and viral mRNAs. Two microgram of RNA isolated from virus infected, IFN-␤, or dsRNA treated cells were reverse transcribed in a volume of 20 l using oligo(dT) 15 as primer as described in Section 2. abstract: We have presented previously evidence that the cytopathogenic 18f strain of hepatitis A virus (HAV) induced degradation of ribosomal RNA (rRNA) in infected cells [Arch. Virol. 148 (2003) 1275–1300]. In contrast, the non-cytopathogenic parent virus HM175 clone 1 had no effect on rRNA integrity. We present here data showing that rRNA degradation is followed by apoptosis accompanied by characteristic DNA laddering in the cytoplasm of 18f infected cells. The DNA laddering coincided with the detection of caspase 3 and PARP-1 cleavage and was dependent upon activation of the caspase pathway, since treatment with Z-VAD-FMK, a pan-caspase inhibitor, inhibited both events. RNase L mRNA was present in both virus-infected and uninfected cells. Messenger RNA for the interferon inducible enzyme 2′–5′ oligoadenylate synthetase (2′–5′ OAS), which polymerizes ATP into 2′–5′ oligo adenylate (2–5A, the activator of RNase L) in the presence of double-stranded RNA, was not detected following virus infection. 2′–5′ OAS mRNA was induced by treatment of the cells with interferon-β (IFN-β). IFN-β mRNA was marginally induced following infection. However, phosphorylated STAT 1, a key regulator of interferon-stimulated gene transcription was not detected in virus infected cells. STAT 1 phosphorylation in response to IFN treatment was lower in virus-infected cells, compared to uninfected cells treated with interferon, suggesting that 18f virus infection interferes with interferon signaling. The results suggest that 18f infection causes the induction of a 2–5A independent RNase L like activity. url: https://www.ncbi.nlm.nih.gov/pubmed/15451183/ doi: 10.1016/j.antiviral.2004.02.004 id: cord-307893-mvl0wrsj author: Goulter-Thorsen, R.M. title: Disciplines Associated with Food Safety: Food Virology date: 2014-01-13 words: 4993.0 sentences: 249.0 pages: flesch: 46.0 cache: ./cache/cord-307893-mvl0wrsj.txt txt: ./txt/cord-307893-mvl0wrsj.txt summary: Poliovirus was the first enteric virus to be widely recognized, causing foodborne disease outbreaks in the early 1900s associated with the consumption of contaminated raw milk. This method, as well as cultivation methods for the vaccine strain of poliovirus, eventually allowed for the quantification of infective virus plaque forming units and facilitated studies on detection and control of enteric viruses in water and foods, with a particular focus on molluscan shellfish. Although promising, the utility of these molecular amplification methods for virus detection in food and environmental samples was limited by low levels of contamination; high levels of matrix-associated inhibitory substances that interfered with nucleic acid amplification; and the lack of broadly reactive primers and probes for HuNoV. Recent epidemiological data continue to support the fact that viruses, particularly HuNoV, are the most common cause of foodborne disease of known etiology in USA. HEV is a positive-sense single-stranded RNA virus that is transmitted via the fecal-oral route, generally through the consumption of water and sometimes food that has become contaminated with human feces. abstract: Food virology is a relatively young but important field in food safety. Viruses in general and human noroviruses in particular, are the leading cause of foodborne disease of known etiology in developed countries. Hepatitis A virus is also important, as are a number of emerging viruses. This article identifies the relevant viruses, describes their structural characteristics and the diseases they cause, and what is known about their epidemiological significance. It also describes why their transmission is so difficult to control, their detection difficult to achieve, and future research needs that will facilitate their study by food safety scientists. url: https://www.sciencedirect.com/science/article/pii/B978012378612800024X doi: 10.1016/b978-0-12-378612-8.00024-x id: cord-336319-8068s9a3 author: Graci, Jason D. title: Mechanisms of action of ribavirin against distinct viruses date: 2005-11-15 words: 6460.0 sentences: 343.0 pages: flesch: 36.0 cache: ./cache/cord-336319-8068s9a3.txt txt: ./txt/cord-336319-8068s9a3.txt summary: Indirect mechanisms include reduction in cellular guanosine triphosphate (GTP) pools via inosine monophosphate dehydrogenase (IMPDH) inhibition, and an immunomodulatory effect in which a T-helper type 1 (antiviral) immune response is maintained. Direct mechanisms include inhibition of RNA capping activity, direct inhibition of viral polymerases, and increased mutation frequency via incorporation of ribavirin into newly synthesised genomes leading to error catastrophe. For all three compounds, a linear correlation was noted between GTP pool inhibition and antiviral activity as measured by viral RNA synthesis, as well as antiviral effect measured by reduction in CPE, suggesting that IMPDH inhibition is the primary mechanism of antiviral activity for all three compounds. Although direct biochemical evidence was not obtained, this finding suggested that ribavirin inhibits the capping of RNA genomes, either by interfering with the guanylyltransferase or methyltransferase activities (both of which are thought to be encoded by nsP1) or potentially by being incorporated as a cap analogue, which may impact translation of the RNA. abstract: The nucleoside analogue ribavirin has antiviral activity against many distinct viruses both in vitro and in vivo. Five distinct mechanisms have been proposed to explain the antiviral properties of ribavirin. These include both indirect mechanisms (inosine monophosphate dehydrogenase inhibition, immunomodulatory effects) and direct mechanisms (interference with RNA capping, polymerase inhibition, lethal mutagenesis). Recent concerns about bioterrorism have renewed interest in exploring the antiviral activity of ribavirin against unique viruses. In this paper, we review the proposed mechanisms of action with emphasis on recent discoveries, as well as the implications of ribavirin resistance. Evidence exists to support each of the five proposed mechanisms of action, and distinct virus/host combinations may preferentially favour one or more of these mechanisms during antiviral therapy. Copyright © 2005 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16287208/ doi: 10.1002/rmv.483 id: cord-287487-qeltdch7 author: Graepel, Kevin W. title: Proofreading-Deficient Coronaviruses Adapt for Increased Fitness over Long-Term Passage without Reversion of Exoribonuclease-Inactivating Mutations date: 2017-11-07 words: 7470.0 sentences: 467.0 pages: flesch: 49.0 cache: ./cache/cord-287487-qeltdch7.txt txt: ./txt/cord-287487-qeltdch7.txt summary: Alanine substitution of ExoN catalytic residues [ExoN(-)] in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and murine hepatitis virus (MHV) disrupts ExoN activity, yielding viable mutant viruses with defective replication, up to 20-fold-decreased fidelity, and increased susceptibility to nucleoside analogues. High-or low-fidelity variants are described for many RNA viruses infecting animals, including the coronaviruses (CoVs) murine hepatitis virus (MHV-A59) and severe acute respiratory syndrome-associated coronavirus (SARS-CoV) (13) (14) (15) (16) (17) , as well as foot-and-mouth disease virus (18) (19) (20) (21) (22) , poliovirus (23) (24) (25) (26) (27) (28) (29) , Chikungunya virus (30, 31) , influenza virus (32) , coxsackievirus B3 (33, 34) , and human enterovirus 71 (35) (36) (37) . The evolved mutations in MHV-ExoN(-) nsp14 and nsp12, which encodes the RdRp, accounted for only part of the increased nucleoside analogue resistance of MHV-ExoN(-) P250, implicating multiple replicase proteins in adaptation for viral fitness. abstract: The coronavirus (CoV) RNA genome is the largest among the single-stranded positive-sense RNA viruses. CoVs encode a proofreading 3′-to-5′ exoribonuclease within nonstructural protein 14 (nsp14-ExoN) that is responsible for CoV high-fidelity replication. Alanine substitution of ExoN catalytic residues [ExoN(-)] in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and murine hepatitis virus (MHV) disrupts ExoN activity, yielding viable mutant viruses with defective replication, up to 20-fold-decreased fidelity, and increased susceptibility to nucleoside analogues. To test the stability of the ExoN(-) genotype and phenotype, we passaged MHV-ExoN(-) 250 times in cultured cells (P250), in parallel with wild-type MHV (WT-MHV). Compared to MHV-ExoN(-) P3, MHV-ExoN(-) P250 demonstrated enhanced replication and increased competitive fitness without reversion at the ExoN(-) active site. Furthermore, MHV-ExoN(-) P250 was less susceptible than MHV-ExoN(-) P3 to multiple nucleoside analogues, suggesting that MHV-ExoN(-) was under selection for increased replication fidelity. We subsequently identified novel amino acid changes within the RNA-dependent RNA polymerase and nsp14 of MHV-ExoN(-) P250 that partially accounted for the reduced susceptibility to nucleoside analogues. Our results suggest that increased replication fidelity is selected in ExoN(-) CoVs and that there may be a significant barrier to ExoN(-) reversion. These results also support the hypothesis that high-fidelity replication is linked to CoV fitness and indicate that multiple replicase proteins could compensate for ExoN functions during replication. url: https://www.ncbi.nlm.nih.gov/pubmed/29114026/ doi: 10.1128/mbio.01503-17 id: cord-272702-7uc4ozjy author: Graham, T. G. W. title: Inexpensive, versatile and open-source methods for SARS-CoV-2 detection date: 2020-09-18 words: 8061.0 sentences: 483.0 pages: flesch: 59.0 cache: ./cache/cord-272702-7uc4ozjy.txt txt: ./txt/cord-272702-7uc4ozjy.txt summary: We therefore tested whether we could detect SARS-CoV-2 RNA by adding 1 μ l of each swab sample to 20 μ l TaqPath reactions containing the N1, N2, and RNase P (RP) probes ( Fig 2A) . Taken together, these results show that RT-qPCR with BEARmix can detect SARS-CoV-2 in clinical samples, either using purified RNA or by direct addition of swab samples, albeit with somewhat less sensitivity than commercial TaqPath master mix. To evaluate a complete protocol in which swab samples are collected into PK solution and then added directly to BEARmix RT-PCRs, we prepared contrived swab samples in which live virus was mixed with pathogenfree human nasal fluid prior to dilution into either DNA/RNA Shield, VCM containing 0.4 mg/ml proteinase K, or a solution of 0.4 mg/ml proteinase K in water (Fig 6) . Here we have developed simple, academic laboratory-derived methods for RNA extraction, direct sample addition, and RT-PCR detection that provide low-cost alternatives to the use of commercial kits (Fig 8) . abstract: Re-opening of communities in the midst of the ongoing COVID-19 pandemic has ignited a second wave of infections in many places around the world. Mitigating the risk of reopening will require widespread SARS-CoV-2 testing, which would be greatly facilitated by simple, rapid, and inexpensive testing methods. To this end, we evaluated several protocols for RNA extraction and RT-qPCR that are simpler and less expensive than prevailing methods. First, we show that isopropanol precipitation provides an effective means of RNA extraction from nasopharyngeal (NP) swab samples. Second, we evaluate direct addition of NP swab samples to RT-qPCR reactions without an RNA extraction step. We describe a simple, inexpensive swab collection solution suitable for direct addition, which we validate using contrived swab samples. Third, we describe an open-source master mix for RT-qPCR and show that it permits detection of viral RNA in NP swab samples. Lastly, we show that an end-point fluorescence measurement provides an accurate diagnostic readout without requiring a qPCR thermocycler. Adoption of these simple, inexpensive methods has the potential to significantly reduce the time and expense of COVID-19 testing. url: https://doi.org/10.1101/2020.09.16.20193466 doi: 10.1101/2020.09.16.20193466 id: cord-349011-kxhpdvri author: Grandvaux, Nathalie title: CSV2018: The 2nd Symposium of the Canadian Society for Virology date: 2019-01-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The 2nd Symposium of the Canadian Society for Virology (CSV2018) was held in June 2018 in Halifax, Nova Scotia, Canada, as a featured event marking the 200th anniversary of Dalhousie University. CSV2018 attracted 175 attendees from across Canada and around the world, more than double the number that attended the first CSV symposium two years earlier. CSV2018 provided a forum to discuss a wide range of topics in virology including human, veterinary, plant, and microbial pathogens. Invited keynote speakers included David Kelvin (Dalhousie University and Shantou University Medical College) who provided a historical perspective on influenza on the 100th anniversary of the 1918 pandemic; Sylvain Moineau (Université Laval) who described CRISPR-Cas systems and anti-CRISPR proteins in warfare between bacteriophages and their host microbes; and Kate O’Brien (then from Johns Hopkins University, now relocated to the World Health Organization where she is Director of Immunization, Vaccines and Biologicals), who discussed the underlying viral etiology for pneumonia in the developing world, and the evidence for respiratory syncytial virus (RSV) as a primary cause. Reflecting a strong commitment of Canadian virologists to science communication, CSV2018 featured the launch of Halifax’s first annual Soapbox Science event to enable public engagement with female scientists, and the live-taping of the 499th episode of the This Week in Virology (TWIV) podcast, hosted by Vincent Racaniello (Columbia University) and science writer Alan Dove. TWIV featured interviews of CSV co-founders Nathalie Grandvaux (Université de Montréal) and Craig McCormick (Dalhousie University), who discussed the origins and objectives of the new society; Ryan Noyce (University of Alberta), who discussed technical and ethical considerations of synthetic virology; and Kate O’Brien, who discussed vaccines and global health. Finally, because CSV seeks to provide a better future for the next generation of Canadian virologists, the symposium featured a large number of oral and poster presentations from trainees and closed with the awarding of presentation prizes to trainees, followed by a tour of the Halifax Citadel National Historic Site and an evening of entertainment at the historic Alexander Keith’s Brewery. url: https://doi.org/10.3390/v11010079 doi: 10.3390/v11010079 id: cord-304356-jyp9gjh9 author: Grant, Rogan A. title: Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells date: 2020-08-05 words: 7453.0 sentences: 427.0 pages: flesch: 44.0 cache: ./cache/cord-304356-jyp9gjh9.txt txt: ./txt/cord-304356-jyp9gjh9.txt summary: We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. b. Sankey diagram illustrating relationship between number of BAL samples from participants with COVID-19, other viral pneumonia, non-viral pneumonia (other pneumonia) and non-pneumonia controls 1) enrolled in the SCRIPT study (534 samples), 2) analyzed via flow cytometry (344 samples), 3) bulk RNA-seq on flow-sorted alveolar macrophages (243 samples) and 4) single-cell RNA-seq (6 samples). To define the immune cell profile over the course of severe SARS-CoV-2-induced pneumonia, we analyzed 116 samples from 61 patients with confirmed COVID-19 in our cohort. As our analysis of transcriptomic data from alveolar macrophages suggested that SARS-CoV-2 pneumonia is uniquely associated with the activation of pathways induced by interferons, we looked for the expression of type I interferons in our single cell dataset. abstract: Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS) [1]. Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia [2]. We collected bronchoalveolar lavage fluid samples from 86 patients with SARS-CoV-2-induced respiratory failure and 252 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection at the onset of mechanical ventilation, the alveolar space is persistently enriched in alveolar macrophages and T cells without neutrophilia. Bulk and single cell transcriptomic profiling suggest SARS-CoV-2 infects alveolar macrophages that respond by recruiting T cells. These T cells release interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell recruitment. Our results suggest SARS-CoV-2 causes a slowly unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 transcripts and T cells form a positive feedback loop that drives progressive alveolar inflammation. This manuscript is accompanied by an online resource: https://www.nupulmonary.org/covid-19/ One sentence summary SARS-CoV-2-infected alveolar macrophages form positive feedback loops with T cells in patients with severe COVID-19. url: https://doi.org/10.1101/2020.08.05.238188 doi: 10.1101/2020.08.05.238188 id: cord-102547-nxut8ov1 author: Grädel, C. title: Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing date: 2020-06-09 words: 6505.0 sentences: 349.0 pages: flesch: 53.0 cache: ./cache/cord-102547-nxut8ov1.txt txt: ./txt/cord-102547-nxut8ov1.txt summary: DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. Taxonomic classification of viral reads (Oxford Nanopore) and contigs (Illumina MiSeq) using MEGAN based on BLASTN matches against NCBI''s nucleotide (nt) database at the species and genotype levels. In order to confirm the genotype identification and to obtain a highly accurate whole genome sequence of the enterovirus genome, we subsequently subjected the sample E590 also to cDNA sequencing using Illumina MiSeq. In this case, the cDNA was produced using genotype-specific primers given that low number of reads was obtained by DRS and MiSeq . Illumina sequencing of the cDNA from sample E026 produced using oligo-dT primers and random hexamers showed similar distributions on the domain level: The majority of contigs belonged to bacterial species (98.6% and 98.9%, respectively for oligo-dT and random hexamer approaches), with a minority of reads mapping to eukaryotes (0.49%, 0.50%) and viruses (0.87%, 0.56%). abstract: Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, those viruses are identified by PCR based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. Results of the approach were complemented with those obtained by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. The identification of the enterovirus sequences in the sample was confirmed by the short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94-97%. Here we show that nanopore DRS can be used to correctly identify the genotypes of enteroviruses from patient stool samples with high viral load. url: http://medrxiv.org/cgi/content/short/2020.06.09.20126219v1?rss=1 doi: 10.1101/2020.06.09.20126219 id: cord-293852-r72c6584 author: Greco, S. title: Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era date: 2020-10-31 words: 8163.0 sentences: 468.0 pages: flesch: 40.0 cache: ./cache/cord-293852-r72c6584.txt txt: ./txt/cord-293852-r72c6584.txt summary: Different studies found that the values of cardiac Troponins were increased in COVID-19 patients with more severe disease [4, 5, [68] [69] [70] , indicating an association of SARS-CoV-2 with myocardial damage. Moreover, the single-cell RNA-sequencing (scRNAseq) approach has been used to profile the SARS-CoV-2 host-response in the PBMCs of COVID-19 patients, and to comprehensively characterize the immunological changes [124] [125] [126] [127] [128] [129] [130] . However, SARS-CoV-2 infection of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) induced cytotoxic effects and RNA-seq findings highlighted significant transcriptional changes in gene pathways related to cellular metabolism and immune response [131] [132] [133] . This analysis also revealed several host-derived lncRNAs differentially expressed in COVID-19 patient-derived lung tissue, and in SARS-CoV-2 infected epithelial cells, including MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) and NEAT1 (nuclear-enriched autosomal transcript 1) [151] (Fig. 5) . abstract: COronaVIrus Disease 19 (COVID-19) is caused by the infection of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2). Although the main clinical manifestations of COVID-19 are respiratory, many patients also display acute myocardial injury and chronic damage to the cardiovascular system. Understanding both direct and indirect damage caused to the heart and the vascular system by SARS-CoV-2 infection is necessary to identify optimal clinical care strategies. The homeostasis of the cardiovascular system requires a tight regulation of the gene expression, which is controlled by multiple types of RNA molecules, including RNA encoding proteins (messenger RNAs) (mRNAs) and those lacking protein-coding potential, the noncoding-RNAs. In the last few years, dysregulation of noncoding-RNAs has emerged as a crucial component in the pathophysiology of virtually all cardiovascular diseases. Here we will discuss the potential role of noncoding RNAs in COVID-19 disease mechanisms and their possible use as biomarkers of clinical use. url: https://www.ncbi.nlm.nih.gov/pubmed/33129318/ doi: 10.1186/s12967-020-02582-8 id: cord-281174-3c1vue0y author: Greene, Shermalyn R title: Evaluation of the NucliSens® Basic Kit assay for detection of Norwalk virus RNA in stool specimens date: 2003-01-16 words: 5250.0 sentences: 248.0 pages: flesch: 48.0 cache: ./cache/cord-281174-3c1vue0y.txt txt: ./txt/cord-281174-3c1vue0y.txt summary: The application of a rapid nucleic acid sequence-based amplification (NASBA) assay for the detection of NLV RNA in stool is described using the NucliSens® Basic Kit. Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate. Despite the specificity of the NASBA primer/probe sequences for NV, other representatives from both NLV genogroups I and II could be detected by the Basic Kit assay in outbreak stool specimens, although the results were inconsistent. In this study, we report the application of a rapid NASBA assay for the detection of NV RNA in stool using the NucliSens † Basic Kit. This assay was compared directly with RT-PCR and used for the detection of NV and other NLVs in fecal specimens obtained from human challenge studies and NLV outbreaks. abstract: Norwalk-like viruses (NLVs) are a genetically diverse group of human caliciviruses that are the most common cause of epidemic gastroenteritis and are detected typically in stool by reverse transcription (RT)-PCR or electron microscopy (EM). The application of a rapid nucleic acid sequence-based amplification (NASBA) assay for the detection of NLV RNA in stool is described using the NucliSens® Basic Kit. Primers and probes for the NLV Basic Kit assay were based on the RNA polymerase region of the prototype NLV, Norwalk virus (NV) genome and could consistently detect 10(4) RT-PCR detectable units of NV RNA in a stool filtrate. When compared directly with RT-PCR on a dilution series of NV stool filtrate, the NucliSens® Basic Kit assay was equally sensitive. Cross-reactivity studies with a representative panel of other enteric pathogens were negative. When applied to 15 stool specimens from NV-challenged volunteers, the NASBA Basic Kit application for NV detection yielded 100% sensitivity, 50% specificity, and 67% concordance, using RT-PCR as the ‘gold standard’. Despite the specificity of the NASBA primer/probe sequences for NV, other representatives from both NLV genogroups I and II could be detected by the Basic Kit assay in outbreak stool specimens, although the results were inconsistent. Our results suggest that the NucliSens® Basic Kit assay provides a rapid and sensitive alternative to RT-PCR for detecting NV RNA in stool specimens. However, improvements in test specificity and primer design will be needed before the assay can be used routinely in the clinical setting. url: https://www.sciencedirect.com/science/article/pii/S0166093402002860 doi: 10.1016/s0166-0934(02)00286-0 id: cord-304424-048xo7jn author: Greninger, Alexander L. title: A decade of RNA virus metagenomics is (not) enough date: 2018-01-15 words: 9606.0 sentences: 495.0 pages: flesch: 43.0 cache: ./cache/cord-304424-048xo7jn.txt txt: ./txt/cord-304424-048xo7jn.txt summary: That same year 36,789 colony sequences from DNase-treated RNA extracted from viral concentrates of human feces revealed a preponderance of pepper mild mottle virus and other plant viruses, but no new human viruses (Zhang et al., 2005) . While finding a new virus in the environment is not necessarily a problem in either DNA or RNA, the low fidelity of RNA polymerases and the sequence space they are capable of sampling, along with the possibility of recombination, lend themselves to new species and genera that are the trophies of metagenomic viral discovery. While metagenomics delivered on the promise of finding novel human viruses, viral discovery in humans has increasingly become a tragic story of patients interacting with the wrong squirrel or tick on the wrong day and most samples sequenced are frankly negative (Hoffmann et al., 2015; McMullan et al., 2012) . The greatest paradigm shifter in recent viral metagenomics work has been the sheer number and diversity of novel RNA viruses present in arthropods and invertebrates. abstract: It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found. url: https://www.ncbi.nlm.nih.gov/pubmed/29055712/ doi: 10.1016/j.virusres.2017.10.014 id: cord-022262-ck2lhojz author: Gromeier, Matthias title: Genetics, Pathogenesis and Evolution of Picornaviruses date: 2007-09-02 words: 28035.0 sentences: 1423.0 pages: flesch: 46.0 cache: ./cache/cord-022262-ck2lhojz.txt txt: ./txt/cord-022262-ck2lhojz.txt summary: The following viruses have been recognized as picornaviruses on the basis of their genome sequences and physico-chemical properties as well as the result of comparative sequence analyses (see the section on Evolution): equine rhinovirus types I and 2, Aichi virus, porcine enterovirus, avian encephalomyelitis virus, infectious flacherie virus of silkworm Clusters of enteroviruses refer to groups of enteroviruses arranged predominantly according to genotypic kinship (Hyypia et al., 1997) . Briefly, when expression vectors ( Figure 12 .6E) consisting of a gag gene (encoding p17-p24; 1161 nt) of human immunodeficiency virus that was fused to the N-terminus of the poliovirus polyprotein (Andino et al., 1994; Mueller and Wimmer, 1998) were analysed after transfection into HeLa cells, the genomes were not only found to be severely impaired in viral replication but they were also genetically unstable (Mueller and Wimmer, 1997) . abstract: The discovery of viruses heralded an exciting new era for research in the medical and biological sciences. It has been realized that the cellular receptor guiding a virus to a target cell cannot be the sole determinant of a virus's pathogenic potential. Comparative analyses of the structures of genomes and their products have placed the picornaviruses into a large “picorna-like” virus family, in which they occupy a prominent place. Most human picornavirus infections are self-limiting, yet the enormously high rate of picornavirus infections in the human population can lead to a significant incidence of disease complications that may be permanently debilitating or even fatal. Picornaviruses employ one of the simplest imaginable genetic systems: they consist of single-stranded RNA that encodes only a single multidomain polypeptide, the polyprotein. The RNA is packaged into a small, rigid, naked, and icosahedral virion whose proteins are unmodified except for a myristate at the N-termini of VP4. The RNA itself does not contain modified bases. The key to ultimately understanding picornaviruses may be to rationalize the huge amount of information about these viruses from the perspective of evolution. It is possible that the replicative apparatus of picornaviruses originated in the precellular world and was subsequently refined in the course of thousands of generations in a slowly evolving environment. Picornaviruses cultivated the art of adaptation, which has allowed them to “jump” into new niches offered in the biological world. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155501/ doi: 10.1016/b978-012220360-2/50013-1 id: cord-254596-wsmnlnlk author: Grädel, Carole title: Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing date: 2020-07-31 words: 6911.0 sentences: 334.0 pages: flesch: 51.0 cache: ./cache/cord-254596-wsmnlnlk.txt txt: ./txt/cord-254596-wsmnlnlk.txt summary: In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains. In order to confirm genotype identification obtained via DRS and to obtain a highly accurate whole-genome enterovirus sequence, we also subjected sample E590 to cDNA sequencing using Illumina MiSeq. MiSeq sequencing library preparation was performed with stool material and following the routine diagnostic pre-treatment (as opposed to chloroform/bead treatment) given that low amount of patient stool sample was available (Figure 1 ). abstract: Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains. url: https://doi.org/10.3390/v12080841 doi: 10.3390/v12080841 id: cord-260168-rb7j94dh author: Gu, Jiang title: H5N1 infection of the respiratory tract and beyond: a molecular pathology study date: 2007-09-27 words: 6291.0 sentences: 369.0 pages: flesch: 51.0 cache: ./cache/cord-260168-rb7j94dh.txt txt: ./txt/cord-260168-rb7j94dh.txt summary: Negative controls also included an unrelated antisense probe against the fragment of the polymerase gene (R1AB) of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV), 20 as well as H5N1 in-situ hybridisation probes to tissues (including lung and tracheal) obtained from seven adults who died from infectious lung diseases other than H5N1 infl uenza (four, SARS; one, purulent bronchitis; two, pneumonia), one adult who died from a non-infectious disease (gastric ulcer), one pregnant woman who died from an amniotic embolism, and one aborted fetus. Presence of viral sequences and antigens in the CNS is consistent with the recent isolation of H5N1 virus from cerebrospinal fl uid of a boy who died from encephalitis 6 with neurological symptoms commonly seen in patients with H5N1 infl uenza (Gao Zh, unpublished), including the two cases in this study. abstract: BACKGROUND: Human infection with avian influenza H5N1 is an emerging infectious disease characterised by respiratory symptoms and a high fatality rate. Previous studies have shown that the human infection with avian influenza H5N1 could also target organs apart from the lungs. METHODS: We studied post-mortem tissues of two adults (one man and one pregnant woman) infected with H5N1 influenza virus, and a fetus carried by the woman. In-situ hybridisation (with sense and antisense probes to haemagglutinin and nucleoprotein) and immunohistochemistry (with monoclonal antibodies to haemagglutinin and nucleoprotein) were done on selected tissues. Reverse-transcriptase (RT) PCR, real-time RT-PCR, strand-specific RT-PCR, and nucleic acid sequence-based amplification (NASBA) detection assays were also undertaken to detect viral RNA in organ tissue samples. FINDINGS: We detected viral genomic sequences and antigens in type II epithelial cells of the lungs, ciliated and non-ciliated epithelial cells of the trachea, T cells of the lymph node, neurons of the brain, and Hofbauer cells and cytotrophoblasts of the placenta. Viral genomic sequences (but no viral antigens) were detected in the intestinal mucosa. In the fetus, we found viral sequences and antigens in the lungs, circulating mononuclear cells, and macrophages of the liver. The presence of viral sequences in the organs and the fetus was also confirmed by RT-PCR, strand-specific RT-PCR, real-time RT-PCR, and NASBA. INTERPRETATION: In addition to the lungs, H5N1 influenza virus infects the trachea and disseminates to other organs including the brain. The virus could also be transmitted from mother to fetus across the placenta. url: https://www.sciencedirect.com/science/article/pii/S0140673607615153 doi: 10.1016/s0140-6736(07)61515-3 id: cord-267326-355q6k6k author: Gu, Xiaoqiong title: Geospatial distribution of viromes in tropical freshwater ecosystems date: 2018-06-15 words: 8426.0 sentences: 424.0 pages: flesch: 44.0 cache: ./cache/cord-267326-355q6k6k.txt txt: ./txt/cord-267326-355q6k6k.txt summary: This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. However, up till now, studies of land use impacts on the virome community in freshwater ecosystems are still limited as they mainly rely on traditional methodology (culture-based method or qPCR/RT-qPCR), which focuses on limited human virus targets without considering the whole picture of the viral community in the water environment (Corsi et al., 2014; Lenaker et al., 2017) . Thus, the objectives of this study were to: 1) investigate the overall virome distribution and diversity in diverse freshwater ecosystems (reservoirs/tributaries) in a tropical environment, 2) compare the virome community based on the different land use patterns, 3) assess the extent of human-related pathogenic viruses in surface waters, especially emerging zoonotic and human-related viruses, which may have been undetected before. abstract: This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588 < r < 0.879, p < 0.05). This study shows that spatial factors (e.g., reservoirs/tributaries, land use) are the main drivers of the viral community structure in tropical freshwater ecosystems. url: https://www.ncbi.nlm.nih.gov/pubmed/29550725/ doi: 10.1016/j.watres.2018.03.017 id: cord-328259-3g4klpyg author: Guajardo-Leiva, Sergio title: Metagenomic Insights into the Sewage RNA Virosphere of a Large City date: 2020-09-21 words: 7626.0 sentences: 370.0 pages: flesch: 47.0 cache: ./cache/cord-328259-3g4klpyg.txt txt: ./txt/cord-328259-3g4klpyg.txt summary: Despite the overrepresentation of dsRNA viruses, our results show that Santiago''s sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Viral sequences identified as Partitiviridae-like viruses included in the "unclassified RNA viruses ShiM-2016" category in the NCBI taxonomy (~25% abundance; Figure 2B ) and Totiviriade family were also highly abundant in treated and untreated sewage samples from the EU [5, 7] . Therefore, the abundance of these viruses in the Trebal metagenome can expand the known sequence space associated with this family (only 10 genomes are currently available in the NCBI database) and contribute to a better understanding of the bacteriophage biology related to RNA genomes. Taken together, our results show that metagenomic surveys of RNA viruses in sewage samples and the use of HMMs could uncover extraordinary viral diversity through the detection of remote homologs in these human-impacted environments. abstract: Sewage-associated viruses can cause several human and animal diseases, such as gastroenteritis, hepatitis, and respiratory infections. Therefore, their detection in wastewater can reflect current infections within the source population. To date, no viral study has been performed using the sewage of any large South American city. In this study, we used viral metagenomics to obtain a single sample snapshot of the RNA virosphere in the wastewater from Santiago de Chile, the seventh largest city in the Americas. Despite the overrepresentation of dsRNA viruses, our results show that Santiago’s sewage RNA virosphere was composed mostly of unknown sequences (88%), while known viral sequences were dominated by viruses that infect bacteria (60%), invertebrates (37%) and humans (2.4%). Interestingly, we discovered three novel genogroups within the Picobirnaviridae family that can fill major gaps in this taxa’s evolutionary history. We also demonstrated the dominance of emerging Rotavirus genotypes, such as G8 and G6, that have displaced other classical genotypes, which is consistent with recent clinical reports. This study supports the usefulness of sewage viral metagenomics for public health surveillance. Moreover, it demonstrates the need to monitor the viral component during the wastewater treatment and recycling process, where this virome can constitute a reservoir of human pathogens. url: https://doi.org/10.3390/v12091050 doi: 10.3390/v12091050 id: cord-273367-gl266pvt author: Gunawardana, M. title: Longitudinal COVID-19 Surveillance and Characterization in the Workplace with Public Health and Diagnostic Endpoints date: 2020-07-28 words: 5731.0 sentences: 417.0 pages: flesch: 59.0 cache: ./cache/cord-273367-gl266pvt.txt txt: ./txt/cord-273367-gl266pvt.txt summary: Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples collected at three timepoints. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic participants. Subject 557 18, a self-quarantined employee who had just recovered from suspected COVID-19 (based on 558 symptomology) at the start of the study, repeatedly tested negative for SARS-CoV-2 RNA, but 559 tested positive for IgM antibodies that rapidly declined (τ1/2 = 8.8 d, Fig. 4A) . abstract: Background The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the associated coronavirus disease 2019 (COVID-19) have precipitated a global pandemic heavily challenging our social behavior, economy, and healthcare infrastructure. Public health practices currently represent the primary interventions for managing the spread of the pandemic. We hypothesized that frequent, longitudinal workplace disease surveillance would represent an effective approach to controlling SARS-CoV-2 transmission among employees and their household members, reducing potential economic consequences and loss of productivity of standard isolation methods, while providing new insights into viral-host dynamics. Methodology and Findings On March 23, 2020 a clinical study (OCIS-05) was initiated at a small Southern California organization. Results from the first 3 months of the ongoing study are presented here. Study participants (27 employees and 27 household members) consented to provide frequent nasal or oral swab samples that were analyzed by RT-qPCR for SARS-CoV-2 RNA using CDC protocols. Only participants testing negative were allowed to enter the "safe zone" workplace facility. Optional blood samples were collected at baseline and throughout the 3-month study. Serum virus-specific antibody concentrations (IgG, IgM, and IgA) were measured using a selective, sensitive, and quantitative ELISA assay developed in house. A COVID-19 infection model, based on traditional SEIR compartmental models combined with Bayesian non-linear mixed models and modern machine learning, was used to predict the number of employees and household members who would have become infected in the absence of workplace surveillance. Two study participants were found to be infected by SARS-CoV-2 during the study. One subject, a household member, tested positive clinically by RT-qPCR prior to enrollment and experienced typical COVID-19 symptoms that did not require hospitalization. While on study, the participant was SARS-CoV-2 RNA positive for at least 71 days and had elevated virus-specific antibody concentrations (medians: IgM, 9.83 ug mL-1; IgG, 11.5 ug mL-1; IgA, 1.29 ug mL-1) in serum samples collected at three timepoints. A single, unrelated employee became positive for SARS-CoV-2 RNA over the course of the study, but remained asymptomatic with low associated viral RNA copy numbers. The participant did not have detectable serum IgM and IgG concentrations, and IgA concentrations decayed rapidly (half-life: 1.3 d). The employee was not allowed entry to the safe zone workplace until testing negative three consecutive times over 7 d. No other employees or household members contracted COVID-19 over the course of the study. Our model predicted that under the current prevalence in Los Angeles County without surveillance intervention, up to 7 employees (95% CI = 3-10) would have become infected with at most 1 of them requiring hospitalizations and 0 deaths. Conclusions Our clinical study met its primary objectives by using intense longitudinal testing to provide a safe work environment during the COVID-19 pandemic, and elucidating SARS-CoV-2 dynamics in recovering and asymptomatic participants. The surveillance plan outlined here is scalable and transferrable. The study represents a powerful example on how an innovative public health initiative can be dovetailed with scientific discovery. url: https://doi.org/10.1101/2020.07.25.20160812 doi: 10.1101/2020.07.25.20160812 id: cord-346697-ixho9t5g author: Guo, Hua title: Novel hepacivirus in Asian house shrew, China date: 2019-01-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/30701456/ doi: 10.1007/s11427-018-9435-7 id: cord-262318-qpztmdnw author: Guo, Jingxu title: In crystallo-screening for discovery of human norovirus 3C-like protease inhibitors date: 2020-07-16 words: 6348.0 sentences: 319.0 pages: flesch: 58.0 cache: ./cache/cord-262318-qpztmdnw.txt txt: ./txt/cord-262318-qpztmdnw.txt summary: In this work we have crystallised the protease in its native form with an unperturbed catalytic triad and have conducted crystal-based fragment screening of 844 compounds with the aim of discovering novel inhibitory functional groups which have the potential to be developed as therapeutic agents, either on their own or through chemical coupling. Interestingly, the β-hairpin formed by β9 and β10, which is involved in binding the N-terminal side of the substrate peptide, adopts an appreciably different conformation from that observed in an earlier inhibitor-complexed structure ( The SV3CP enzyme has approximately 90 % sequence identity with other GI noroviral 3C proteases and an identity of the order of 68 % with the enzyme from the GII genotype. The X-ray structure of the Southampton virus 3CL pro has been determined at 1.3 Å resolution in a crystal form that has allowed fragment-screening for novel inhibitors to be undertaken at similar resolutions. abstract: Outbreaks of human epidemic nonbacterial gastroenteritis are mainly caused by noroviruses. Viral replication requires a 3C-like cysteine protease (3CL(pro)) which processes the 200 kDa viral polyprotein into six functional proteins. The 3CL(pro) has attracted much interest due to its potential as a target for antiviral drugs. A system for growing high-quality crystals of native Southampton norovirus 3CL(pro) (SV3CP) has been established, allowing the ligand-free crystal structure to be determined to 1.3 Å in a tetrameric state. This also allowed crystal-based fragment screening to be performed with various compound libraries, ultimately to guide drug discovery for SV3CP. A total of 19 fragments were found to bind to the protease out of the 844 which were screened. Two of the hits were located at the active site of SV3CP and showed good inhibitory activity in kinetic assays. Another 5 were found at the enzyme’s putative RNA-binding site and a further 10 were located in the symmetric central cavity of the tetramer. url: https://api.elsevier.com/content/article/pii/S2590152420300131 doi: 10.1016/j.yjsbx.2020.100031 id: cord-021115-2fkghukw author: Guo, Yun title: Molecular dynamics simulation of RNA pseudoknot unfolding pathway date: 2013-03-12 words: 3271.0 sentences: 178.0 pages: flesch: 63.0 cache: ./cache/cord-021115-2fkghukw.txt txt: ./txt/cord-021115-2fkghukw.txt summary: It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (MMTV) RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynamics simulation method in this paper. To study the factors that affect the stability and the unfolding pathways of the pseudoknots, the MMTV RNA was studied by all-atom molecule dynamics simulation methods under different ion concentrations and temperatures. The structural features of MMTV RNA pseudoknot in different ion concentration, the unfolding process of RNA pseudoknot, and two hairpin helices that constituted the RNA pseudoknot were studied with all atom molecular dynamics simulation method in this paper. abstract: Many biological functions of RNA molecules are related to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus (MMTV) RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynamics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hairpin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after formation of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure’s unfolding process, which means that both are the unzipping process. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149040/ doi: 10.1007/s11859-013-0905-0 id: cord-276908-9jthjf24 author: Gupta, Akanksha title: COVID‐19: Emergence of Infectious Diseases, Nanotechnology Aspects, Challenges, and Future Perspectives date: 2020-07-06 words: 5174.0 sentences: 385.0 pages: flesch: 57.0 cache: ./cache/cord-276908-9jthjf24.txt txt: ./txt/cord-276908-9jthjf24.txt summary: In last two decades, entire world faced three major outbreaks of coronaviruses like Severe Acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and novel coronavirus disease i.e., COVID-19. Previously, CoV causes an epidemic of SARS in humans and infected thousands viruses belong to family Coronaviridae, which shows crown-like appearances under an electron microscope. A recent study published, relied on this approach, using the predicted structure of all SARS-CoV-2 proteins based on their homology with other known coronavirus protein structures, and identified several compounds with potential antiviral activity. [39, 77] A biological preparation provides active acquired immunity against particular infectious disease like COVID19 [51, 68] 5 Shenzhen, China SARS-CoV, NL63, HKU1 The organosulfur in the essential garlic oil inhibit the ACE2 (host-receptor site of the virus) and main protease of the virus as well as to treat the infection due to SARS-CoV-2. abstract: Wuhan, a city of China, is the epicenter for the pandemic outbreak of coronavirus disease‐2019 (COVID‐19). It has become a severe public health challenge to the world and established a public health emergency of international worry. This infectious disease has pulled down the economy of almost all top developed nations. The coronaviruses (CoVs) known for various epidemics caused time to time. Infectious diseases such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS), followed by COVID‐19, are all coronaviruses led outbreaks that scourged the history of mankind. CoVs evolved themselves to more infectious, transmissible, and more pandemic with time. To prevent the spread of the SARS‐CoV‐2, many countries have ordered the complete lockdown to combat the outbreak. This paper briefly discussed the historical background of CoVs and the evolution of human coronaviruses (HCoVs), the case studies and the development of their antiviral medications. The viral infection encountered with present‐day challenges and futuristic approaches with the help of nanotechnology to minimize the spread of infectious viruses. The antiviral drugs and their clinical advances, along with herbal medicines for viral inhibition and immunity boosters, are described. Elaboration of tables related to CoVs for the compilation of the literature has been adopted for the better understanding. url: https://www.ncbi.nlm.nih.gov/pubmed/32835089/ doi: 10.1002/slct.202001709 id: cord-016419-v1f6dx3e author: Gupta, Varsha title: Production of Recombinant Pharmaceutical Proteins date: 2016-10-23 words: 9648.0 sentences: 602.0 pages: flesch: 50.0 cache: ./cache/cord-016419-v1f6dx3e.txt txt: ./txt/cord-016419-v1f6dx3e.txt summary: Usage of recombinant DNA technology for large-scale production of proteins requires ample amount of time, labor, and resources, but it also offers many opportunities for economic growth. The recombinant proteins approved by FDA are obtained either from Escherichia coli or other prokaryotes; from Saccharomyces cerevisiae or other fungal species; from insect cells , mammalian cells , or human cells ; or from transgenic plants or animals. Their advantages are low cost, high mass production, scale-up, lack of human pathogens , and addition of eukaryotic PTMs. The fi rst recombinant protein obtained in 1986 from tobacco plants was human growth hormone . The vector can be modifi ed to express genes for insulin (tomato) or Hep-B surface antigen (HBsAg) for recombinant therapeutics providing a human glycosylation pattern have increased attention, and the efforts are being made for the development of novel glycoengineered cell lines for production of fully glycosylated protein therapeutic. abstract: The proteins produced in the body control and mediate the metabolic processes and help in its routine functioning. Any kind of impairment in protein production, such as production of mutated protein, or misfolded protein, leads to disruption of the pathway controlled by that protein. This may manifest in the form of the disease. However, these diseases can be treated, by supplying the protein from outside or exogenously. The supply of active exogenous protein requires its production on large scale to fulfill the growing demand. The process is complex, requiring higher protein expression, purification, and processing. Each product needs unique settings or standardizations for large-scale production and purification. As only large-scale production can fulfill the growing demand, thus it needs to be cost-effective. The tools of genetic engineering are utilized to produce the proteins of human origin in bacteria, fungi, insect, or mammalian host. Usage of recombinant DNA technology for large-scale production of proteins requires ample amount of time, labor, and resources, but it also offers many opportunities for economic growth. After reading this chapter, readers would be able to understand the basics about production of recombinant proteins in various hosts along with the advantages and limitations of each host system and properties and production of some of the important pharmaceutical compounds and growth factors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120688/ doi: 10.1007/978-981-10-0875-7_4 id: cord-293790-7hyelm88 author: Guévin, Carl title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection date: 2010-09-01 words: 5267.0 sentences: 290.0 pages: flesch: 54.0 cache: ./cache/cord-293790-7hyelm88.txt txt: ./txt/cord-293790-7hyelm88.txt summary: title: Autophagy protein ATG5 interacts transiently with the hepatitis C virus RNA polymerase (NS5B) early during infection To identify novel cellular factors that may play an essential role in HCV RNA replication, we have previously screened a human liver cDNA library for proteins interacting with the HCV NS5B RNAdependent RNA polymerase (RdRp). Here we report that ATG5, a protein required for the formation of DMV in embryonic stem cell (Mizushima et al., 2001) , specifically interacts with HCV NS5B. As a control, a panel of proteins (RAR-β, RAR-α, HCV core, and nonstructural protein: NS3 prot , NS3 hel , NS4A, and NS4B) cloned in the GAL4 DNA binding domain was tested for interaction with ATG5. A. Soluble yeast extracts containing NS5BΔ21 (N-terminal c-myc tag) and ATG5 (N-terminal HA tag) were incubated with different monoclonal antibodies and the immunoprecipitates were pulled down using protein A/G beads. abstract: Autophagy is an important cellular process by which ATG5 initiates the formation of double membrane vesicles (DMVs). Upon infection, DMVs have been shown to harbor the replicase complex of positive-strand RNA viruses such as MHV, poliovirus, and equine arteritis virus. Recently, it has been shown that autophagy proteins are proviral factors that favor initiation of hepatitis C virus (HCV) infection. Here, we identified ATG5 as an interacting protein for the HCV NS5B. ATG5/NS5B interaction was confirmed by co-IP and metabolic labeling studies. Furthermore, ATG5 protein colocalizes with NS4B, a constituent of the membranous web. Importantly, immunofluorescence staining demonstrated a strong colocalization of ATG5 and NS5B within perinuclear regions of infected cells at 2 days postinfection. However, colocalization was completely lacking at 5 DPI, suggesting that HCV utilizes ATG5 as a proviral factor during the onset of viral infection. Finally, inhibition of autophagy through ATG5 silencing blocks HCV replication. url: https://www.sciencedirect.com/science/article/pii/S0042682210003764 doi: 10.1016/j.virol.2010.05.032 id: cord-288390-p1q3v1ie author: Habjan, Matthias title: Cytoplasmic sensing of viral nucleic acids date: 2015-02-07 words: 4040.0 sentences: 252.0 pages: flesch: 48.0 cache: ./cache/cord-288390-p1q3v1ie.txt txt: ./txt/cord-288390-p1q3v1ie.txt summary: These sensors induce expression of cytokines, affect cellular functions required for virus replication and directly target viral nucleic acids through degradation or sequestration. These sensors induce expression of cytokines, affect cellular functions required for virus replication and directly target viral nucleic acids through degradation or sequestration. In this review we concentrate on intracellular nucleic acid sensors and effector proteins that evolved to mediate specialised tasks including, firstly, expression of cytokines such as type I interferons (IFN-a/b); secondly, modulation of cellular machineries required for virus replication and thirdly, direct inhibition of virus growth ( Figure 1 ). Among the best characterised cytoplasmic proteins involved in virus sensing are RIG-I-like receptors (RLRs), a family of DExD/H-box helicases which specifically identify viral RNAs and have the ability to stimulate expression of IFN-a/b and other cytokines (Figure 3 ) [4, 17] . Virus infection activates a restricted set of sensor and effector proteins that modulate cellular pathways and directly target viral nucleic acid, thereby shaping the innate immune response. abstract: Viruses are the most abundant pathogens on earth. A fine-tuned framework of intervening pathways is in place in mammalian cells to orchestrate the cellular defence against these pathogens. Key for this system is sensor proteins that recognise specific features associated with nucleic acids of incoming viruses. Here we review the current knowledge on cytoplasmic sensors for viral nucleic acids. These sensors induce expression of cytokines, affect cellular functions required for virus replication and directly target viral nucleic acids through degradation or sequestration. Their ability to respond to a given nucleic acid is based on both the differential specificity of the individual proteins and the downstream signalling or adaptor proteins. The cooperation of these multiple proteins and pathways plays a key role in inducing successful immunity against virus infections. url: https://api.elsevier.com/content/article/pii/S1879625715000140 doi: 10.1016/j.coviro.2015.01.012 id: cord-329366-xuszdrsa author: Hackbart, Matthew title: Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors date: 2020-04-07 words: 7187.0 sentences: 445.0 pages: flesch: 57.0 cache: ./cache/cord-329366-xuszdrsa.txt txt: ./txt/cord-329366-xuszdrsa.txt summary: In this study, we show that CoV EndoU activity limits the abundance and length of the polyuridine (polyU) extension on 5′-polyU-containing, negative-sense (PUN) RNAs for both the beta-CoV mouse hepatitis virus strain A59 (MHV-A59) and the alpha-CoV PEDV. Overall, we propose a mechanism for EndoU, which is to cleave polyU sequences from PUN RNAs, thus limiting the formation of a PAMP and impeding the ability of MDA5 to activate the innate immune response to infection. EndoU Activity Limits Abundance and Length of PUN RNAs. Previous studies showed that the 5′ end of the CoV negative-sense RNA contains polyU extensions (35) , and that EndoU cleaves at uridine residues (22, 25, (27) (28) (29) (30) . We found that the products generated from positive-sense RNA were similar between wild-type and EndoUmut viruses, consistent with our previous results indicating that the polyA tail is not cleaved by EndoU activity (Fig. 5C ). abstract: Coronaviruses (CoVs) are positive-sense RNA viruses that can emerge from endemic reservoirs and infect zoonotically, causing significant morbidity and mortality. CoVs encode an endoribonuclease designated EndoU that facilitates evasion of host pattern recognition receptor MDA5, but the target of EndoU activity was not known. Here, we report that EndoU cleaves the 5′-polyuridines from negative-sense viral RNA, termed PUN RNA, which is the product of polyA-templated RNA synthesis. Using a virus containing an EndoU catalytic-inactive mutation, we detected a higher abundance of PUN RNA in the cytoplasm compared to wild-type−infected cells. Furthermore, we found that transfecting PUN RNA into cells stimulates a robust, MDA5-dependent interferon response, and that removal of the polyuridine extension on the RNA dampens the response. Overall, the results of this study reveal the PUN RNA to be a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP). We also establish a mechanism for EndoU activity to cleave and limit the accumulation of this PAMP. Since EndoU activity is highly conserved in all CoVs, inhibiting this activity may serve as an approach for therapeutic interventions against existing and emerging CoV infections. url: https://doi.org/10.1073/pnas.1921485117 doi: 10.1073/pnas.1921485117 id: cord-310920-itqwhi6a author: Haddad, Christina title: Integrated Approaches to Reveal Mechanisms by which RNA Viruses Reprogram the Cellular Environment date: 2020-07-02 words: 3698.0 sentences: 205.0 pages: flesch: 44.0 cache: ./cache/cord-310920-itqwhi6a.txt txt: ./txt/cord-310920-itqwhi6a.txt summary: Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. Obtaining structural details of the UTRs and identifying functional binding sites of RBPs will be deeply insightful in elucidating how this virus replicates within host cells. Given the large number of RBPs known to interact with genomic and subgenomic viral RNAs to modulate translation, replication and the shift between these two stages, CLIP-seq can be employed to understand virology at the molecular level. Studying RNA structural interactions and the effects of viral-host RBPs on RNA structure and function are essential for understanding translation, replication, and transcription processes in order to better understand how viruses reprogram the cellular environment. abstract: RNA viruses are major threats to global society and mass outbreaks can cause long-lasting damage to international economies. RNA and related retro viruses represent a large and diverse family that contribute to the onset of human diseases such as AIDS; certain cancers like T cell lymphoma; severe acute respiratory illnesses as seen with COVID-19; and others. The hallmark of this viral family is the storage of genetic material in the form of RNA, and upon infecting host cells, their RNA genomes reprogram the cellular environment to favor productive viral replication. RNA is a multifunctional biomolecule that not only stores and transmits heritable information, but it also has the capacity to catalyze complex biochemical reactions. It is therefore no surprise that RNA viruses use this functional diversity to their advantage to sustain chronic or lifelong infections. Efforts to subvert RNA viruses therefore requires a deep understanding of the mechanisms by which these pathogens usurp cellular machinery. Here, we briefly summarize several experimental techniques that individually inform on key physicochemical features of viral RNA genomes and their interactions with proteins. Each of these techniques provide important vantage points to understand the complexities of virus-host interactions, but we attempt to make the case that by integrating these and similar methods, more vivid descriptions of how viruses reprogram the cellular environment emerges. These vivid descriptions should expedite the identification of novel therapeutic targets. url: https://api.elsevier.com/content/article/pii/S1046202320301249 doi: 10.1016/j.ymeth.2020.06.013 id: cord-353475-dtn7h1gj author: Haddad, Hazem title: miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East date: 2020-08-20 words: 1462.0 sentences: 103.0 pages: flesch: 64.0 cache: ./cache/cord-353475-dtn7h1gj.txt txt: ./txt/cord-353475-dtn7h1gj.txt summary: In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. To understand the early steps of COVID-19 infection, we predicted miRNAs sequences targeting the submitted 29903bp of viral ss-RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 complete genomic RNA sequence) from the isolate of Wuhan-Hu-J o u r n a l P r e -p r o o f 1. abstract: MicroRNAs (miRNAs) are non-coding RNAs that control many functions within the human cells by controlling protein levels through binding to messenger RNA (mRNA) translation process or mRNA abundance. Many pieces of evidence show that miRNAs affect the viral RNA replication and pathogenesis through direct binding to the RNA virus to mediate changes in the host transcriptome. Many previous studies have been studying the interaction between human cells' miRNA and viral RNA to predict many targets along the viral genome. In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. Our predicted miRNA targets of the ss-RNA of SARS-CoV-2 might destabilize the ss-RNA translation of SARS-CoV-2 that has been established by more than 80% of asymptomatic infected cases in Jordan due to host miRNA interactions. In respiratory epithelial cells, the high prediction scoring for miRNAs covers the RNA from 5′ to 3′ that explains successful antiviral defenses against ss-RNA of SARS-CoV-2 and might lead to new nucleotide deletion mechanisms. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92. url: https://www.ncbi.nlm.nih.gov/pubmed/32839745/ doi: 10.1016/j.ncrna.2020.08.002 id: cord-254210-3mi2aop5 author: Haddad, Rodrigo title: Silencing of HTLV-1 gag and env genes by small interfering RNAs in HEK 293 cells date: 2011-01-26 words: 4490.0 sentences: 281.0 pages: flesch: 57.0 cache: ./cache/cord-254210-3mi2aop5.txt txt: ./txt/cord-254210-3mi2aop5.txt summary: title: Silencing of HTLV-1 gag and env genes by small interfering RNAs in HEK 293 cells Three small interference RNAs (siRNAs) corresponding to gag and three corresponding to env were designed to analyze the effect of silencing by RNAi technology. In the present study, siRNAs were used for inhibition of the expression of the HTLV-1 structural genes gag and env. Forty-eight hours after transfection, the expression of EGFP-target (gag or env) fusion proteins was observed directly under an inverted fluorescence microscope. HEK 293 cells were observed 48 h posttransfection under a fluorescence microscope to determine the silencing effect of siRNAs on Gag and Env protein expression in cultured cells (Fig. 2B and C) . Based on the fluorescence data, flow cytometry and real time quantitative PCR, two siRNAs targeted to the HTLV-1 gag gene reduced efficiently gene expression by different amounts compared to the negative siRNA, scrambled siRNAs and controls without siRNA. abstract: Since the discovery of RNAi technology, several functional genomic and disease therapy studies have been conducted using this technique in the field of oncology and virology. RNAi-based antiviral therapies are being studied for the treatment of retroviruses such as HIV-1. These studies include the silencing of regulatory, infectivity and structural genes. The HTLV-1 structural genes are responsible for the synthesis of proteins involved in the entry, assembly and release of particles during viral infection. To examine the possibility of silencing HTLV-1 genes gag and env by RNA interference technology, these genes were cloned into reporter plasmids. These vectors expressed the target mRNAs fused to EGFP reporter genes. Three small interference RNAs (siRNAs) corresponding to gag and three corresponding to env were designed to analyze the effect of silencing by RNAi technology. The plasmids and siRNAs were co-transfected into HEK 293 cells. The results demonstrated that the expression of the HTLV-1 gag and env genes decreased significantly in vitro. Thus, siRNAs can be used to inhibit HTLV-1 structural genes in transformed cells, which could provide a tool for clarifying the roles of HTLV-1 structural genes, as well as a therapy for this infection. url: https://api.elsevier.com/content/article/pii/S0166093411000413 doi: 10.1016/j.jviromet.2011.01.012 id: cord-279691-v5kpmk0b author: Hagemeijer, Marne C. title: Biogenesis and Dynamics of the Coronavirus Replicative Structures date: 2012-11-21 words: 9036.0 sentences: 483.0 pages: flesch: 43.0 cache: ./cache/cord-279691-v5kpmk0b.txt txt: ./txt/cord-279691-v5kpmk0b.txt summary: Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. A distinctive common feature of +RNA viruses is the replication of their genomes in the cytoplasm of the host cell in association with rearranged cellular membranes that are remodeled into organelle-like membranous structures to which the viral replication-transcription complexes (RTCs) localize. The first detectable membrane rearrangements in CoV-infected cells are 200 to 350 nm organelle-like structures that have been described for both MHV [47, 62] and the SARS-CoV [5, 63] and consist of spherical vesicles containing double lipid bilayers, termed DMVs ( Figure 2 ). abstract: Coronaviruses are positive-strand RNA viruses that are important infectious agents of both animals and humans. A common feature among positive-strand RNA viruses is their assembly of replication-transcription complexes in association with cytoplasmic membranes. Upon infection, coronaviruses extensively rearrange cellular membranes into organelle-like replicative structures that consist of double-membrane vesicles and convoluted membranes to which the nonstructural proteins involved in RNA synthesis localize. Double-stranded RNA, presumably functioning as replicative intermediate during viral RNA synthesis, has been detected at the double-membrane vesicle interior. Recent studies have provided new insights into the assembly and functioning of the coronavirus replicative structures. This review will summarize the current knowledge on the biogenesis of the replicative structures, the membrane anchoring of the replication-transcription complexes, and the location of viral RNA synthesis, with particular focus on the dynamics of the coronavirus replicative structures and individual replication-associated proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/23202524/ doi: 10.3390/v4113245 id: cord-341541-3l6tjf3t author: Hajijafari Anaraki, Mozafar title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene date: 2020-05-26 words: 1276.0 sentences: 87.0 pages: flesch: 49.0 cache: ./cache/cord-341541-3l6tjf3t.txt txt: ./txt/cord-341541-3l6tjf3t.txt summary: title: Molecular characterization of infectious bronchitis virus based on RNA‐dependent RNA polymerase gene Extensive rate of variations in in spike glycoprotein subunit gene of infectious bronchitis virus (IBV) caused challenges for counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. The study aimed at investigating the possibility use of RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area. Using RdRp, as a genetic marker eliminates the challenges arise from the enormous variations that making difficult the discrimination between field and vaccine strains as well as affiliation of certain variants to various geographical areas. Based on the RT-PCR detection and sequence analysis of IBV RdRp gene, an overall prevalence of field strains estimated as 44.2%. abstract: Extensive rate of variations in in spike glycoprotein subunit gene of infectious bronchitis virus (IBV) caused challenges for counting variants for differentiation of infected from vaccinated birds and addressing the variants of unknown significance. The study aimed at investigating the possibility use of RNA‐dependent RNA polymerase gene (RdRp) as a target for molecular characterization of IBV strains in Iran. Samples collected from commercial broiler flocks (n= 52) showing respiratory syndrome. Specific polymerase chain reaction (PCR) primers were designed for a variable region locates in RdRp gene, flanked by highly conserved regions. Reverse transcriptase PCR (RT‐PCR) followed by sequencing and sequence analysis could identified 8 IBV variants in an overall prevalence of 44.2%. Deduced nucleotide and amino acid sequences were compared with published sequences for IBV strains. Due to the long‐distance similarities, the field samples could be discriminated from vaccine strains. Phylogenetic analysis of RdRp gene sequences resulted in clustering the IBV strains related to each area. Using RdRp, as a genetic marker eliminates the challenges arise from the enormous variations that making difficult the discrimination between field and vaccine strains as well as affiliation of certain variants to various geographical areas. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1111/1348-0421.12825 doi: 10.1111/1348-0421.12825 id: cord-292643-n6xp5mlz author: Hall, Richard J. title: Evaluation of rapid and simple techniques for the enrichment of viruses prior to metagenomic virus discovery date: 2013-09-13 words: 4803.0 sentences: 219.0 pages: flesch: 44.0 cache: ./cache/cord-292643-n6xp5mlz.txt txt: ./txt/cord-292643-n6xp5mlz.txt summary: The relative abundance of a virus (or viral nucleic acid) in a sample, compared to that of other organisms such as bacteria or host cells (or their genomes), is a critical factor for the discovery of viruses when using metagenomics. A study on human liver tissue compared enrichment techniques of freeze-thaw, centrifugation and nuclease-treatment for the detection of Hepatitis C Virus using both Roche 454 and Illumina high-throughput sequencing platforms (Daly et al., 2011) . After an initial 10 min reverse transcription step at 45 • C and 10 min denaturation Table 1 Virus enrichment process prior to sequencing in metagenomic studies on human and animal samples. This artificial sample represents a starting point to evaluate simple and rapid viral enrichment methods for use in virus metagenomics studies that seek to detect a virus that is causing disease in humans or animals. abstract: The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated. url: https://doi.org/10.1016/j.jviromet.2013.08.035 doi: 10.1016/j.jviromet.2013.08.035 id: cord-268206-ino9srb6 author: Hamed, Manal A. title: An overview on COVID-19: reality and expectation date: 2020-06-01 words: 6067.0 sentences: 330.0 pages: flesch: 46.0 cache: ./cache/cord-268206-ino9srb6.txt txt: ./txt/cord-268206-ino9srb6.txt summary: Recently, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), commonly known as coronavirus disease-2019 (COVID-19) has rapidly spread across China and around the world. In the current SARS-COV-2 pandemic, Wu and McGoogan (2020) showed that patients with chronic diseases, including diabetes, were at higher risk for severe COVID-19 infection and mortality. The former (S) is the wild type which is milder while the latter (L) is the novel one which resulted in high binding affinity between SARS-COV-2 virus with angiotensin-converting enzyme 2 receptor in human cells. The use of convalescent plasma was recommended before as an important treatment during outbreaks of Ebola virus, Middle East respiratory syndrome coronavirus, SARS-COV-1, H5N1 avian influenza, and H1N1 influenza (Zhou et al. In a study involving patients with pandemic influenza (H1N1) and SARS virus, treatment of severe infection with convalescent plasma was associated with reduced respiratory viral load, serum cytokine response, and mortality (Cheng et al. abstract: Recently, severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), commonly known as coronavirus disease-2019 (COVID-19) has rapidly spread across China and around the world. By the declaration of WHO, COVID-19 outbreak considered as a public health problem of international concern. The aim of this study is to provide a comprehensive view on COVID-19 and the future expectations to control virus progression. Patients with liver disease, diabetes, high blood pressure, and obesity are more susceptible to the incidence of COVID-19 infection. So, there is a rapid need for disease diagnosis, vaccine development, and drug discovery to detect, prevent, and treat this sudden and lethal virus. Real-time polymerase chain reaction (RT-PCR) is considered as a rapid, accurate, and specific tool for disease diagnosis. Under this emergency situation that the world facing against COVID-19, there are about 15 potential vaccine candidates tested globally based on messenger RNA, DNA-based, nanoparticle, synthetic, and modified virus-like particle. Certain drugs that are clinically approved for other diseases were tested against COVID-19 as chloroquine, hydroxychloroquine, ivermectin, favipiravir, ribavirin, and remdesivir. Convalescent plasma transfusion and traditional herbal medicine were also taken into consideration. Due to the absence of effective treatment or vaccines against COVID-19 so far, the precautionary measures according to WHO’s strategic objectives are the only way to confront this crisis. Governments should adopt national medical care programs to reduce the risk of exposure to any future viral outbreaks especially to patients with pre-existing medical conditions. url: https://doi.org/10.1186/s42269-020-00341-9 doi: 10.1186/s42269-020-00341-9 id: cord-325954-rhrkr97h author: Han, Mi Seon title: Viral RNA Load in Mildly Symptomatic and Asymptomatic Children with COVID-19, Seoul, South Korea date: 2020-10-17 words: 1423.0 sentences: 86.0 pages: flesch: 57.0 cache: ./cache/cord-325954-rhrkr97h.txt txt: ./txt/cord-325954-rhrkr97h.txt summary: Along with positive SARS-CoV-2 RNA in nasopharyngeal swabs, viral RNA was detectable at high concentration for >3 weeks in fecal samples from 12 mildly symptomatic and asymptomatic children with COVID-19 in Seoul, South Korea. For this study, we included all children <18 years of age who were confirmed to have COVID-19 by positive results for SARS-CoV-2 in combined nasopharyngeal and oropharyngeal swab specimens and who were hospitalized in Seoul Metropolitan Government-Seoul National University Boramae Medical Center during March 8-April 28, 2020. In comparison, the median initial fecal RNA load was 7.68 (range <4.10-10.27) log 10 copies/mL and Along with positive SARS-CoV-2 RNA in nasopharyngeal swabs, viral RNA was detectable at high concentration for >3 weeks in fecal samples from 12 mildly symptomatic and asymptomatic children with COVID-19 in Seoul, South Korea. In addition, the RNA load in feces remained steadily high, whereas that in nasopharyngeal swab specimens and saliva declined with time in both symptomatic and asymptomatic children. abstract: Along with positive SARS-CoV-2 RNA in nasopharyngeal swabs, viral RNA was detectable at high concentration for >3 weeks in fecal samples from 12 mildly symptomatic and asymptomatic children with COVID-19 in Seoul, South Korea. Saliva also tested positive during the early phase of infection. If proven infectious, feces and saliva could serve as transmission sources. url: https://doi.org/10.3201/eid2610.202449 doi: 10.3201/eid2610.202449 id: cord-301115-sedfbjlw author: Han, Mingfeng title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity date: 2020-08-28 words: 4577.0 sentences: 255.0 pages: flesch: 53.0 cache: ./cache/cord-301115-sedfbjlw.txt txt: ./txt/cord-301115-sedfbjlw.txt summary: title: Assessing SARS-CoV-2 RNA levels and lymphocyte/T cell counts in COVID-19 patients revealed initial immune status as a major determinant of disease severity The results of our analysis demonstrated that the initial SARS-CoV-2 RNA loads varied in patients, but were comparable in different patient groups stratified by age, gender, comorbidities and disease severity. We compared the measured SARS-CoV-2 RNA levels in sputum specimens from COVID-19 patients at admission among groups divided according to age, sex, underlying diseases and disease severity (Fig. 2a) . a, b The measured SARS-CoV-2 RNAs levels in sputum (a) and throat swab (b) specimens from COVID-19 patients at admission were compared according to the age, sex, comorbidity, and the disease severity. In this study, we analyzed the clinical features including SARS-CoV-2 RNA load and immunological characteristics of peripheral blood in a patient cohort with COVID-19 from Anhui Province, China. abstract: The magnitude of SARS-CoV-2 infection, the dynamic changes of immune parameters in patients with the novel coronavirus disease (COVID-19) and their correlation with the disease severity remain unclear. The clinical and laboratory results from 154 confirmed COVID-19 patients were collected. The SARS-CoV-2 RNA levels in patients were estimated using the Ct values of specific RT-PCR tests. The lymphocyte subsets and cytokine profiles in the peripheral blood were analyzed by flow cytometry and specific immunoassays. 154 confirmed COVID-19 patients were clinically examined up to 4 weeks after admission. The initial SARS-CoV-2 RNA Ct values at admission varied, but were comparable in the patient groups classified according to the age, gender, underlying diseases, and disease severity. Three days after admission, significant higher Ct values were found in severe cases. Significantly reduced counts of T cells and T cell subsets were found in patients with old age and underlying diseases at admission and were characteristic for the development of severe COVID-19. Severe COVID-19 developed preferentially in patients with underlying compromised immunity and was not associated with initial virus levels. Higher SARS-CoV-2 RNA levels in severe cases were apparently a result of impaired immune control associated with dysregulation of inflammation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00430-020-00693-z) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/32860073/ doi: 10.1007/s00430-020-00693-z id: cord-306948-wkisfz1m author: Han, Mingyuan title: Engineering the PRRS virus genome: Updates and perspectives date: 2014-12-05 words: 9514.0 sentences: 480.0 pages: flesch: 45.0 cache: ./cache/cord-306948-wkisfz1m.txt txt: ./txt/cord-306948-wkisfz1m.txt summary: Serologic marker candidates identified among B-cell linear epitopes of Nsp2 and structural proteins of a North American strain of porcine reproductive and respiratory syndrome virus A full-length cDNA infectious clone of North American type 1 porcine reproductive and respiratory syndrome virus: expression of green fluorescent protein in the Nsp2 region Identification of nonessential regions of the nsp2 replicase protein of porcine reproductive and respiratory syndrome virus strain VR-2332 for replication in cell culture Establishment of a DNA-launched infectious clone for a highly pneumovirulent strain of type 2 porcine reproductive and respiratory syndrome virus: identification and in vitro and in vivo characterization of a large spontaneous deletion in the nsp2 region Recovery of viable porcine reproductive and respiratory syndrome virus from an infectious clone containing a partial deletion within the Nsp2-encoding region Determination of the complete nucleotide sequence of a vaccine strain of porcine reproductive and respiratory syndrome virus and identification of the Nsp2 gene with a unique insertion abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is endemic in most pig producing countries worldwide and causes enormous economic losses to the pork industry. Infectious clones for PRRSV have been constructed, and so far at least 14 different infectious clones are available representing both genotypes I and II. Two strategies have been taken for progeny reconstitution: RNA transfection and DNA transfection. Mutations, insertions, deletions, and replacements of the viral genome have been employed to study the structure function relationship, foreign gene expression, functional complementation, and virulence determinants. Essential regions and non-essential regions for viral replication have been identified in both the coding regions and non-encoding regions. Foreign sequences have successfully been inserted into the nsp2 and N regions and in the space between ORF1b and ORF2a. Chimeras between member viruses in the family Arteriviridae have also been constructed and utilized to study cell tropism and functional complementation. This review discusses the advances and utilization of PRRSV reverse genetics and its potential for future research. url: https://doi.org/10.1016/j.vetmic.2014.10.007 doi: 10.1016/j.vetmic.2014.10.007 id: cord-354536-c9v9kbw8 author: Han, Yan-Jie title: Advances and challenges in the prevention and treatment of COVID-19 date: 2020-07-09 words: 5268.0 sentences: 330.0 pages: flesch: 48.0 cache: ./cache/cord-354536-c9v9kbw8.txt txt: ./txt/cord-354536-c9v9kbw8.txt summary: This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. 18 In view of the curative effect of ribavirin in the treatment of diseases caused by SARS-CoV and MERS-CoV, 21 it is expected to become one of the effective drugs to treat coronavirus. 16 The "Pneumonitis Diagnosis and Treatment Scheme for New Coronavirus Infection (Trial Version 7)" states that aerosolized interferon alpha can be used as a trial treatment against SARS-CoV-2 virus to improve the virus clearance effect of respiratory mucosa in patients. 64 It has been revealed that chlorpromazine is a broad-spectrum virus inhibitor that can inhibit HCV, alpha virus, and various coronaviruses including human coronavirus 229E, SARS-CoV and MERS-CoV in vitro. abstract: Since the end of 2019, a new type of coronavirus pneumonia (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been spreading rapidly throughout the world. Previously, there were two outbreaks of severe coronavirus caused by different coronaviruses worldwide, namely Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32714083/ doi: 10.7150/ijms.47836 id: cord-280795-wtrt13ij author: Han, Yu-Tsung title: Mutational analysis of a helicase motif-based RNA 5′-triphosphatase/NTPase from bamboo mosaic virus date: 2007-10-10 words: 5813.0 sentences: 300.0 pages: flesch: 52.0 cache: ./cache/cord-280795-wtrt13ij.txt txt: ./txt/cord-280795-wtrt13ij.txt summary: As a step toward better understanding the relationship between activities and structures of the helicase-like domain of BaMV replicase, we set out to investigate the importance of each signature motif to its NTPase and RNA 5′-triphosphatase activities by mutational and kinetic analyses. The apparent K i value of AMPPNP in inhibiting RNA 5′-triphosphatase activity The enzymatic activity was determined at 20°C by enzyme-coupled assay in 1 ml solution that contained 10 pmol enzyme, 0.1 to 3 mM NTP and other buffer components as described under Materials and methods except that the amounts of pyruvate kinase were increased up to 50, 75 and 300 U for GTPase, UTPase and CTPase assay, respectively, to assure the rate of NTP hydrolysis being the limiting step within the coupling reaction. The helicase-like domain of plant potexvirus replicase participates in formation of RNA 5′ cap structure by exhibiting RNA 5′-triphosphatase activity abstract: The helicase-like domain of BaMV replicase possesses NTPase and RNA 5′-triphosphatase activities. In this study, mutational effects of the helicase signature motifs and residue L543 on the two activities were investigated. Either activity was inactivated by K643A-S644A, D702A, D730A, R855A, or L543P mutations. On the other hand, Q826A, D858A and L543A had activities, in terms of k(cat)/K(m), reduced by 5- to 15-fold. AMPPNP, a nonhydrolyzable ATP analogue, competitively inhibited RNA 5′-triphosphatase activity. Analogies of mutational effects on the two activities and approximation of K(i(AMPPNP)) and K(m(ATP)) suggest that the catalytic sites of the activities are overlapped. Mutational effects on the viral accumulation in Chenopodium quinoa indicated that the activities manifested by the domain are required for BaMV survival. Results also suggest that Q826 in motif V plays an additional role in preventing tight binding to ATP, which would otherwise decrease further RNA 5′-triphosphatase, leading to demise of the virus in plant. url: https://api.elsevier.com/content/article/pii/S0042682207003492 doi: 10.1016/j.virol.2007.05.013 id: cord-013177-whd0znan author: Han, Zhenzhi title: The Husavirus Posa-Like Viruses in China, and a New Group of Picornavirales date: 2020-09-07 words: 5049.0 sentences: 265.0 pages: flesch: 44.0 cache: ./cache/cord-013177-whd0znan.txt txt: ./txt/cord-013177-whd0znan.txt summary: Novel posa-like viral genomes were first identified in swine fecal samples using metagenomics and were designated as unclassified viruses in the order Picornavirales. These posa-like viruses have undergone a complex evolutionary process, and have a wide geographic distribution, complex host spectrum, deep phylogenetic divergence, and diverse genomic organizations. Novel posa-like virus genomes were first identified in swine fecal samples using metagenomics and were assigned as unclassified viruses to the order Picornavirales [12] . Further reports of novel posaviruses with low amino acid sequence identity revealed novel genomic organization features and phylogenetic characteristics of posa-like viruses [15, 16] . Due to the low genomic sequence similarity between the husavirus and unclassified posa-like viruses in Picornavirales, it was difficult to perform a phylogenetic analysis at the full-length genome level. Posa-like viruses identified in previous reports and in the present study formed a single group and clustered with the genomes of family Marnaviridae (Figure 4) . abstract: Novel posa-like viral genomes were first identified in swine fecal samples using metagenomics and were designated as unclassified viruses in the order Picornavirales. In the present study, nine husavirus strains were identified in China. Their genomes share 94.1–99.9% similarity, and alignment of these nine husavirus strains identified 697 nucleotide polymorphism sites across their full-length genomes. These nine strains were directly clustered with the Husavirus 1 lineage, and their genomic arrangement showed similar characteristics. These posa-like viruses have undergone a complex evolutionary process, and have a wide geographic distribution, complex host spectrum, deep phylogenetic divergence, and diverse genomic organizations. The clade of posa-like viruses forms a single group, which is evolutionarily distinct from other known families and could represent a distinct family within the Picornavirales. The genomic arrangement of Picornavirales and the new posa-like viruses are different, whereas the posa-like viruses have genomic modules similar to the families Dicistroviridae and Marnaviridae. The present study provides valuable genetic evidence of husaviruses in China, and clarifies the phylogenetic dynamics and the evolutionary characteristics of Picornavirales. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551994/ doi: 10.3390/v12090995 id: cord-257569-36qx1sy9 author: Hanada, Kousuke title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes date: 2004-06-17 words: 3460.0 sentences: 156.0 pages: flesch: 43.0 cache: ./cache/cord-257569-36qx1sy9.txt txt: ./txt/cord-257569-36qx1sy9.txt summary: title: A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes. First, we estimated the rates of synonymous substitution for 46 different species of RNA viruses except Puumala virus, human T-lymphotropic virus 1 (HTLV-1) and GB virus C/hepatitis G virus (HGV), using the time-serial sample data. This indicated that the transmission mode affected the replication frequency and that differences in the replication frequencies contributed to the variation of the rate of synonymous substitution for RNA viruses. Moreover, in the present study, we proved that the variation in the synonymous substitution rates among RNA viruses was caused by variation of the replication frequency, and that differences in the infection and transmission modes affected the variation of replication frequencies. abstract: RNA viruses successfully adapt to various environments by repeatedly producing new mutants, often through generating a number of nucleotide substitutions. To estimate the degree of variation in mutation rates of RNA viruses and to understand the source of such variation, we studied the synonymous substitution rate because synonymous substitution is exempt from functional constraints at the protein level, and its rate reflects the mutation rate to a great extent. We estimated the synonymous substitution rates for a total of 49 different species of RNA viruses, and we found that the rates had tremendous variation by 5 orders of magnitude (from 1.3 × 10(−7) to 6.2 × 10(−2) /synonymous site/year). Comparing the synonymous substitution rates with the replication frequencies and replication error rates for the RNA viruses, we found that the main source of the rate variation was differences in the replication frequency because the rates of replication error were roughly constant over different RNA viruses. Moreover, we examined a relationship between viral life strategies and synonymous substitution rates to understand which viral life strategies affect replication frequencies. The results show that the variation of synonymous substitution rates has been influenced most by either the difference in the infection modes or the differences in the transmission modes. In conclusion, the variation of mutation rates for RNA viruses is caused by different replication frequencies, which are affected strongly by the infection and transmission modes. url: https://www.ncbi.nlm.nih.gov/pubmed/15014142/ doi: 10.1093/molbev/msh109 id: cord-007041-rloey02j author: Harel, Noam title: Direct sequencing of RNA with MinION Nanopore: detecting mutations based on associations date: 2019-12-16 words: 7126.0 sentences: 333.0 pages: flesch: 50.0 cache: ./cache/cord-007041-rloey02j.txt txt: ./txt/cord-007041-rloey02j.txt summary: We sequenced virus populations in parallel using both MinION and Illumina, allowing us to corroborate the inferences of AssociVar. This then allowed us to directly infer relationships between mutations and to deduce the entire genome sequences of viral strains in the population. We then determined the population frequency of each mutation at passage 1 and passage 15 through whole genome deep sequencing as described below, using Illumina and MinION. After applying AssociVar to the data, we were able to identify five out of the six mutations appearing at a frequency above 10% in the Illumina results in p15A, and all eight positions within the p15B sample (Figure 4 , Supplementary Table S2 ). We applied AssociVar to sequencing data from an evolved population of phages where Illumina sequencing was available, allowing us to corroborate whether mutations we found based on analysis of the MinION data alone were indeed real. abstract: One of the key challenges in the field of genetics is the inference of haplotypes from next generation sequencing data. The MinION Oxford Nanopore sequencer allows sequencing long reads, with the potential of sequencing complete genes, and even complete genomes of viruses, in individual reads. However, MinION suffers from high error rates, rendering the detection of true variants difficult. Here, we propose a new statistical approach named AssociVar, which differentiates between true mutations and sequencing errors from direct RNA/DNA sequencing using MinION. Our strategy relies on the assumption that sequencing errors will be dispersed randomly along sequencing reads, and hence will not be associated with each other, whereas real mutations will display a non-random pattern of association with other mutations. We demonstrate our approach using direct RNA sequencing data from evolved populations of the MS2 bacteriophage, whose small genome makes it ideal for MinION sequencing. AssociVar inferred several mutations in the phage genome, which were corroborated using parallel Illumina sequencing. This allowed us to reconstruct full genome viral haplotypes constituting different strains that were present in the sample. Our approach is applicable to long read sequencing data from any organism for accurate detection of bona fide mutations and inter-strain polymorphisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107797/ doi: 10.1093/nar/gkz907 id: cord-336012-8klkojpo author: Harilal, Divinlal title: SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission date: 2020-06-18 words: 3040.0 sentences: 144.0 pages: flesch: 45.0 cache: ./cache/cord-336012-8klkojpo.txt txt: ./txt/cord-336012-8klkojpo.txt summary: Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. Here we show that cWGS is cost-effective and is highly scalable when using a target enrichment sequencing method, and we also demonstrate its utility in tracking the origin of SARS-CoV-2 transmission. abstract: Background With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical and cost considerations of cWGS should be addressed before it can be widely implemented. Methods We performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences. Results We show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome compared to an average of 0.63% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains. Conclusions SARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic. url: https://doi.org/10.1101/2020.06.06.138339 doi: 10.1101/2020.06.06.138339 id: cord-007382-5kb16qb7 author: Hartmann, G. title: Nucleic Acid Immunity date: 2016-12-15 words: 16155.0 sentences: 915.0 pages: flesch: 47.0 cache: ./cache/cord-007382-5kb16qb7.txt txt: ./txt/cord-007382-5kb16qb7.txt summary: With the additions of RNAi and the CRISPR/Cas system, specific nucleases including the restriction-modification (R-M) systems, and antiviral effector proteins partially discovered only recently in the context of rare hereditary inflammatory diseases, the new concept of nucleic acid immunity evolves. While innate nucleic acid immune-sensing receptors elicit antiviral signaling pathways, a number of nucleic acid-detecting effector proteins (viral restriction factors, e.g., PKR, ADAR1, IFIT1) directly detect and restrict nucleic acid function and replication. Another member of the RIG-I-like helicase family of receptors is MDA5 which was found to be responsible for the long sought after type I IFN-inducing activity of cytosolic long double-stranded RNA including poly(I:C) . Extrinsic effects inside the same cell include degradation of the nucleic acid (e.g., RNase L activated by 2 0 -5 0 -OA generated by OAS1 upon binding of long double-stranded RNA). abstract: Organisms throughout biology need to maintain the integrity of their genome. From bacteria to vertebrates, life has established sophisticated mechanisms to detect and eliminate foreign genetic material or to restrict its function and replication. Tremendous progress has been made in the understanding of these mechanisms which keep foreign or unwanted nucleic acids from viruses or phages in check. Mechanisms reach from restriction-modification systems and CRISPR/Cas in bacteria and archaea to RNA interference and immune sensing of nucleic acids, altogether integral parts of a system which is now appreciated as nucleic acid immunity. With inherited receptors and acquired sequence information, nucleic acid immunity comprises innate and adaptive components. Effector functions include diverse nuclease systems, intrinsic activities to directly restrict the function of foreign nucleic acids (e.g., PKR, ADAR1, IFIT1), and extrinsic pathways to alert the immune system and to elicit cytotoxic immune responses. These effects act in concert to restrict viral replication and to eliminate virus-infected cells. The principles of nucleic acid immunity are highly relevant for human disease. Besides its essential contribution to antiviral defense and restriction of endogenous retroelements, dysregulation of nucleic acid immunity can also lead to erroneous detection and response to self nucleic acids then causing sterile inflammation and autoimmunity. Even mechanisms of nucleic acid immunity which are not established in vertebrates are relevant for human disease when they are present in pathogens such as bacteria, parasites, or helminths or in pathogen-transmitting organisms such as insects. This review aims to provide an overview of the diverse mechanisms of nucleic acid immunity which mostly have been looked at separately in the past and to integrate them under the framework nucleic acid immunity as a basic principle of life, the understanding of which has great potential to advance medicine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7112058/ doi: 10.1016/bs.ai.2016.11.001 id: cord-348204-365z3qxz author: Harun, Mohammad Syamsul Reza title: Transcriptional profiling of feline infectious peritonitis virus infection in CRFK cells and in PBMCs from FIP diagnosed cats date: 2013-11-09 words: 4691.0 sentences: 235.0 pages: flesch: 52.0 cache: ./cache/cord-348204-365z3qxz.txt txt: ./txt/cord-348204-365z3qxz.txt summary: Real time RT-qPCR developed focusing on 2 up-regulated genes (PD-L1 and A3H) together with an apoptosis associated gene PD-1 expressions in FIPV infected CRFK cells and in PBMCs from healthy and FIP diagnosed cats produced concordant results with transcriptome data. FIPV infected cells also showed high up-regulation of PD-1 expression at 3 h.p.i. and moderately up-regulated at 12 h.p.i but were being down-regulated at 6, 9, 24 and 48 h.p.i. Meanwhile, PD-L1 gene was consistently down-regulated from 3 hours to 48 h.p.i. Peripheral Blood Mononuclear Cells (PBMCs), obtained from cats with clinical signs associated with FIP (Table 4) , were purified and analysed with real-time PCR. The reference feline genome sequence assembly of transcriptome analysis of early infection (3 h.p.i.) of CRFK cells with FIPV 79-1146 showed that the expressions of 215 transcripts (0.8% of the trimmed annotated) were statistically significant, based on Kal''s Z test. abstract: BACKGROUND: Feline Infectious Peritonitis (FIP) is a lethal systemic disease, caused by the FIP Virus (FIPV); a virulent mutant of Feline Enteric Coronavirus (FECV). Currently, the viruses virulence determinants and host gene expressions during FIPV infection are not fully understood. METHODS: RNA sequencing of Crandell Rees Feline Kidney (CRFK) cells, infected with FIPV strain 79–1146 at 3 hours post infection (h.p.i), were sequenced using the Illumina next generation sequencing approach. Bioinformatic’s analysis, based on Felis catus 2X annotated shotgun reference genome, using CLC bio Genome Workbench mapped both control and infected cell reads to 18899 genes out of 19046 annotated genes. Kal’s Z test statistical analysis was used to analyse the differentially expressed genes from the infected CRFK cells. Real time RT-qPCR was developed for further transcriptional profiling of three genes (PD-1, PD-L1 and A3H) in infected CRFK cells and Peripheral Blood Mononuclear Cells (PBMCs) from healthy and FIP-diseased cats. RESULTS: Based on Kal’s Z-test, with False Discovery Rate (FDR) <0.05 and >1.99 fold change on gene expressions, a total of 61 genes were differentially expressed by both samples, where 44 genes were up-regulated and the remainder were down-regulated. Most genes were closely clustered together, suggesting a homogeneous expression. The majority of the genes that were significantly regulated, were those associated with monocytes-macrophage and Th1 cell functions, and the regulation of apoptosis. Real time RT-qPCR developed focusing on 2 up-regulated genes (PD-L1 and A3H) together with an apoptosis associated gene PD-1 expressions in FIPV infected CRFK cells and in PBMCs from healthy and FIP diagnosed cats produced concordant results with transcriptome data. CONCLUSION: The possible roles of these genes, and their importance in feline coronaviruses infection, are discussed. url: https://doi.org/10.1186/1743-422x-10-329 doi: 10.1186/1743-422x-10-329 id: cord-261417-4pf5nsw2 author: Harwig, Alex title: The Battle of RNA Synthesis: Virus versus Host date: 2017-10-21 words: 7864.0 sentences: 443.0 pages: flesch: 53.0 cache: ./cache/cord-261417-4pf5nsw2.txt txt: ./txt/cord-261417-4pf5nsw2.txt summary: Why the virus prefers to use these snRNAs as targets has yet to be experimentally established, but it has been proposed that the selective de-capping of U1 and U2 RNAs in combination with the binding of the viral NS1 protein to U6 snRNA may serve to inhibit host pre-mRNA splicing [66] . The folding of the TAR hairpin is key to the regulation of HIV-1 transcription [94] as it is used as a scaffold to recruit essential transcription factors, including the 86-101 amino acid (aa) viral trans-activator protein (Tat) [83] ( Figure 3C ). Interestingly, the human T-lymphotropic virus type 1 transcriptional activator Tax also utilizes P-TEFb for viral transcription and displaces P-TEFb from 7SK snRNP through binding CycT1 [101, 102] , suggesting that P-TEFb liberation from 7SK snRNP could be a common theme developed by different viruses to support their replication in host cells. abstract: Transcription control is the foundation of gene regulation. Whereas a cell is fully equipped for this task, viruses often depend on the host to supply tools for their transcription program. Over the course of evolution and adaptation, viruses have found diverse ways to optimally exploit cellular host processes such as transcription to their own benefit. Just as cells are increasingly understood to employ nascent RNAs in transcription regulation, recent discoveries are revealing how viruses use nascent RNAs to benefit their own gene expression. In this review, we first outline the two different transcription programs used by viruses, i.e., transcription (DNA-dependent) and RNA-dependent RNA synthesis. Subsequently, we use the distinct stages (initiation, elongation, termination) to describe the latest insights into nascent RNA-mediated regulation in the context of each relevant stage. url: https://www.ncbi.nlm.nih.gov/pubmed/29065472/ doi: 10.3390/v9100309 id: cord-278123-mq56em3z author: Hasan, Mohammad Rubayet title: Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA date: 2020-07-24 words: 3924.0 sentences: 259.0 pages: flesch: 58.0 cache: ./cache/cord-278123-mq56em3z.txt txt: ./txt/cord-278123-mq56em3z.txt summary: Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. Standard approach for detection of SARS-CoV-2 RNA from nasopharyngeal specimens in our laboratory involves extraction of total nucleic acids from specimens in an IVD-labeled, automated extraction platform followed by RT-qPCR, based on one of the assays (Table 1) suggested by World Health Organization (WHO) [11] . Based on these results, the optimal pre-treatment and reaction conditions for the direct approach were: i) transfer and dilute (4-fold) 10 μl of NPFS specimen in NFW; ii) incubate at 65˚C for 10 min; and iii) test 8 μl of heat lysed specimen in a 20 μl reaction using TaqPath™ 1-Step RT-qPCR Master Mix. The analytical sensitivity of the direct RT-qPCR assay using specimens prepared in this manner was determined by serially diluting a specimen positive for SARS-CoV-2 with a negative specimen as a diluent. abstract: To circumvent the limited availability of RNA extraction reagents, we aimed to develop a protocol for direct RT-qPCR to detect SARS-CoV-2 in nasopharyngeal swabs without RNA extraction. Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. The results were compared to that of standard approach that involves RNA extraction. Incubation of specimens at 65°C for 10 minutes along with the use of TaqPath(™) 1-Step RT-qPCR Master Mix provides higher analytical sensitivity for detection of SARS-CoV-2 RNA than many other conditions tested. The optimized direct RT-qPCR approach demonstrated a limit of detection of 6.6x10(3) copy/ml and high reproducibility (co-efficient of variation = 1.2%). In 132 nasopharyngeal specimens submitted for SARS-CoV-2 testing, the sensitivity, specificity and accuracy of our optimized approach were 95%, 99% and 98.5%, respectively, with reference to the standard approach. Also, the RT-qPCR C(T) values obtained by the two methods were positively correlated (Pearson correlation coefficient r = 0.6971, p = 0.0013). The rate of PCR inhibition by the direct approach was 8% compared to 9% by the standard approach. Our simple approach to detect SARS-CoV-2 RNA by direct RT-qPCR may help laboratories continue testing for the virus despite reagent shortages or expand their testing capacity in resource limited settings. url: https://doi.org/10.1371/journal.pone.0236564 doi: 10.1371/journal.pone.0236564 id: cord-333547-88dkh6xd author: Hasan, Shadi W. title: Detection and Quantification of SARS-CoV-2 RNA in Wastewater and Treated Effluents: Surveillance of COVID-19 Epidemic in the United Arab Emirates date: 2020-10-19 words: 3980.0 sentences: 220.0 pages: flesch: 54.0 cache: ./cache/cord-333547-88dkh6xd.txt txt: ./txt/cord-333547-88dkh6xd.txt summary: Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. A limited number of studies have shown that the shedding period of SARS-CoV-2 in stool samples varies considerably, and can still be detected up to 27.9 ± 10.7 days after infection in some cases [9, 11] . Consequently, the main objectives of this study were: (i) to detect the presence of SARS-CoV-2 virus in municipal (untreated) wastewater and treated effluents of wastewater treatment plants (WWTPs) in the UAE; (ii) to quantify the viral concentration in viral gene copies per liter; and (iii) to explore whether these measurements mirror infections in the population in order to comment on the utility of this method to track the epidemiology of the disease. abstract: Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. This study reports SARS-CoV-2 viral load in wastewater influents and treated effluents of 11 wastewater treatment plants (WWTPs), as well as untreated wastewater from 38 various locations, in the United Arab Emirates (UAE) in May and June 2020. Composite samples collected over twenty-four hours were thermally deactivated for safety, followed by viral concentration using ultrafiltration, RNA extraction using commercially available kits, and viral quantification using RT-qPCR. Furthermore, estimates of the prevalence of SARS-CoV-2 infection in different regions were simulated using Monte Carlo. Results showed that the viral load in wastewater influents from these WWTPs ranged from 7.50E+02 to over 3.40E+04 viral gene copies/L with some plants having no detectable viral RNA by RT-qPCR. The virus was also detected in 85% of untreated wastewater samples taken from different locations across the country, with viral loads in positive samples ranging between 2.86E+02 and over 2.90E+04 gene copies/L. It was also observed that the precautionary measures implemented by the UAE government correlated with a drop in the measured viral load in wastewater samples, which were in line with the reduction of COVID-19 cases reported in the population. Importantly, none of the 11 WWTPs’ effluents tested positive during the entire sampling period, indicating that the treatment technologies used in the UAE are efficient in degrading SARS-CoV-2, and confirming the safety of treated re-used water in the country. SARS-CoV-2 wastewater testing has the potential to aid in monitoring or predicting an outbreak location and can shed light on the extent viral spread at the community level. url: https://doi.org/10.1016/j.scitotenv.2020.142929 doi: 10.1016/j.scitotenv.2020.142929 id: cord-286232-jo24ia4s author: Hasebe, Rie title: Infectious entry of equine herpesvirus-1 into host cells through different endocytic pathways date: 2009-10-25 words: 6962.0 sentences: 364.0 pages: flesch: 51.0 cache: ./cache/cord-286232-jo24ia4s.txt txt: ./txt/cord-286232-jo24ia4s.txt summary: Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. In HeLa and receptor-expressing CHO cells, infectious entry of HSV requires trafficking of the virus to an acidic intracellular compartment, phosphatidylinositol 3-kinase activity, glycoprotein D (gD) receptors, as well as viral gB, gD, and gH-gL (Nicola et al., 2003; Nicola and Straus, 2004) . With the use of ultrastructural analysis, we have previously suggested that EHV-1 enters equine brain microvascular endothelial cells (EBMECs) via endocytosis (Hasebe et al., 2006) . Localization of EHV-1 and caveolae during viral internalization Caveolar endocytosis has emerged as a route of entry for several viruses including simian virus 40 (SV40) (Anderson et al., 1996) , mouse polyomavirus (Richterová et al., 2001; Gilbert et al., 2003; Gilbert and Benjamin, 2004) , echovirus (Marjomäki et al., 2002) , human papillomavirus type 31 (Bousarghin et al., 2003; Smith et al., 2007) , human polyomavirus BK (BKV) (Eash et al., 2004) , and species C human adenovirus (Colin et al., 2005) . abstract: We investigated the mechanism by which equine herpesvirus-1 (EHV-1) enters primary cultured equine brain microvascular endothelial cells (EBMECs) and equine dermis (E. Derm) cells. EHV-1 colocalized with caveolin in EBMECs and the infection was greatly reduced by the expression of a dominant negative form of equine caveolin-1 (ecavY14F), suggesting that EHV-1 enters EBMECs via caveolar endocytosis. EHV-1 entry into E. Derm cells was significantly reduced by ATP depletion and treatments with lysosomotropic agents. Enveloped virions were detected from E. Derm cells by infectious virus recovery assay after viral internalization, suggesting that EHV-1 enters E. Derm cells via energy- and pH-dependent endocytosis. These results suggest that EHV-1 utilizes multiple endocytic pathways in different cell types to establish productive infection. url: https://www.sciencedirect.com/science/article/pii/S004268220900470X doi: 10.1016/j.virol.2009.07.032 id: cord-354465-5nqrrnqr author: Haslinger, Christian title: RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties date: 1999 words: 10341.0 sentences: 756.0 pages: flesch: 67.0 cache: ./cache/cord-354465-5nqrrnqr.txt txt: ./txt/cord-354465-5nqrrnqr.txt summary: Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. In case of one particular class of biopolymers, the ribonucleic acid (RNA) molecules, decoding of information stored in the sequence can be properly decomposed into two steps: (i) formation of the secondary structure, that is, of the pattern of Watson-Crick (and GU) base pairs, and (ii) the embedding of the contact structure in three-dimensional space. On the other hand, an increasing number of experimental findings, as well as results from comparative sequence analysis, suggest that pseudo-knots are important structural elements in many RNA molecules (Westhof and Jaeger, 1992) . abstract: The secondary structures of nucleic acids form a particularly important class of contact structures. Many important RNA molecules, however, contain pseudo-knots, a structural feature that is excluded explicitly from the conventional definition of secondary structures. We propose here a generalization of secondary structures incorporating ‘non-nested’ pseudo-knots, which we call bi-secondary structures, and discuss measures for the complexity of more general contact structures based on their graph-theoretical properties. Bi-secondary structures are planar trivalent graphs that are characterized by special embedding properties. We derive exact upper bounds on their number (as a function of the chain length n) implying that there are fewer different structures than sequences. Computational results show that the number of bi-secondary structures grows approximately like 2.35(n). Numerical studies based on kinetic folding and a simple extension of the standard energy model show that the global features of the sequence-structure map of RNA do not change when pseudo-knots are introduced into the secondary structure picture. We find a large fraction of neutral mutations and, in particular, networks of sequences that fold into the same shape. These neutral networks percolate through the entire sequence space. url: https://www.ncbi.nlm.nih.gov/pubmed/17883226/ doi: 10.1006/bulm.1998.0085 id: cord-270594-62xotol3 author: He, Lei title: Identification and characterization of vp7 gene in Bombyx mori cytoplasmic polyhedrosis virus date: 2017-09-05 words: 4444.0 sentences: 266.0 pages: flesch: 55.0 cache: ./cache/cord-270594-62xotol3.txt txt: ./txt/cord-270594-62xotol3.txt summary: In this study, the viral structural protein 7 (VP7) polyclonal antibody was prepared with immunized mouse to explore the presence of small VP7 gene-encoded proteins in Bombyx mori cytoplasmic polyhedrosis virus. The replication of BmCPV genome in the cultured cells and midgut of silkworm was decreased by reducing the expression level of vp7 gene using RNA interference. In immunoprecipitation experiments, using a polyclonal antiserum directed against the VP7, one additional shorter band in BmCPV infected midguts was detected, and then the band was analyzed with mass spectrum (MS), the MS results showed thatone candidate interacted protein (VP7 voltage-dependent anion-selective channel-like isoform, VDAC) was identified from silkworm. A novel protein was detected from the overexpression of vp7 gene in the BmCPV infected cultured cells, with VP7 antibody. Total proteins from the BmCPV infected silkworm midguts (from the first day to the twelfth day) were also extracted, and detected with VP7 antibody. abstract: The genome of Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) contains 10 double stranded RNA segments (S1–S10). The segment 7 (S7) encodes 50 kDa protein which is considered as a structural protein. The expression pattern and function of p50 in the virus life cycle are still unclear. In this study, the viral structural protein 7 (VP7) polyclonal antibody was prepared with immunized mouse to explore the presence of small VP7 gene-encoded proteins in Bombyx mori cytoplasmic polyhedrosis virus. The expression pattern of vp7 gene was investigated by its overexpression in BmN cells. In addition to VP7, supplementary band was identified with western blotting technique. The virion, BmCPV infected cells and midguts were also examined using western blotting technique. 4, 2 and 5 bands were detected in the corresponding samples, respectively. The replication of BmCPV genome in the cultured cells and midgut of silkworm was decreased by reducing the expression level of vp7 gene using RNA interference. In immunoprecipitation experiments, using a polyclonal antiserum directed against the VP7, one additional shorter band in BmCPV infected midguts was detected, and then the band was analyzed with mass spectrum (MS), the MS results showed thatone candidate interacted protein (VP7 voltage-dependent anion-selective channel-like isoform, VDAC) was identified from silkworm. We concluded that the novel viral product was generated with a leaky scanning mechanism and the VDAC may be an interacted protein with VP7. url: https://api.elsevier.com/content/article/pii/S0378111917304985 doi: 10.1016/j.gene.2017.06.048 id: cord-277355-si3g5dih author: He, Yu title: The role of capsid in the flaviviral life cycle and perspectives for vaccine development date: 2020-09-17 words: 6885.0 sentences: 319.0 pages: flesch: 45.0 cache: ./cache/cord-277355-si3g5dih.txt txt: ./txt/cord-277355-si3g5dih.txt summary: Although current studies on flaviviruses have shown that the flaviviral assembly process does not exhibit a necessary step occurring in the cell nucleus, it has been well demonstrated that many mosquito-borne flavivirus CPs partially localize in the cell nucleus [44] [45] [46] [47] [48] ; in the cytoplasm, in addition to localizing in the ER, DENV CP and ZIKV CP have also been demonstrated to accumulate on LDs [13, 16] , but the link between the functional importance and the subcellular distribution of CPs is still unclear. Interestingly, a study showed that a CD61-71 mutant had abolished ZIKV infectious virion production that was then restored by adaptive mutations (prM-E21K and NS2B-E27G) only in BHK21 cells but not in other cell lines (indicate complex interactions that apparently occur between structural and non-structural proteins during virus replication and/or assembly), making this live virus function like a single-round infectious particle (SRIP) in vivo and safely inducing strong immunity protection against vertical transmission in mice [33] . abstract: The arthropod-borne flaviviruses cause a series of diseases in humans and pose a significant threat to global public health. In this review, we aimed to summarize the structure of the capsid protein (CP), its relevant multiple functions in the viral life cycle and innovative vaccines targeting CP. The flaviviral CP is the smallest structural protein and forms a homodimer by antiparallel α-helixes. Its primary function is to package the genomic RNA; however, both steps of assembly and dissociation of nucleocapsid complexes (NCs) have been obscure until now; in fact, flaviviral budding is NC-free, demonstrated by the subviral particles that generally exist in flavivirus infection. In infected cells, CPs associate with lipid droplets, which possibly store CPs prior to packaging. However, the function of nuclear localization of CPs remains unknown. Moreover, introducing deletions into CPs can be used to rationally design safe and effective live-attenuated vaccines or noninfectious replicon vaccines and single-round infectious particles, the latter two representing promising approaches for innovative flaviviral vaccine development. url: https://doi.org/10.1016/j.vaccine.2020.08.053 doi: 10.1016/j.vaccine.2020.08.053 id: cord-286298-pn9nwl64 author: Helmy, Yosra A. title: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control date: 2020-04-24 words: 9290.0 sentences: 516.0 pages: flesch: 51.0 cache: ./cache/cord-286298-pn9nwl64.txt txt: ./txt/cord-286298-pn9nwl64.txt summary: Another group of researchers reported that the virus originated from bats based on the genome sequence of SARS-CoV-2, which is 96% identical to bat coronavirus RaTG13. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. These factors include, but are not limited to: (1) travel to or contact with individuals who have recently visited Wuhan, China, or other places experiencing an outbreak; (2) close contact with persons who are diagnosed positive for the disease, such as healthcare workers caring for patients with SARS-CoV-2; (3) contact with droplets and secretions (produced by sneezing or coughing) from an infected person and eating or handling wild animals native to China such as bats. abstract: A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global increases in the number of cases daily. Therefore, the WHO has declared COVID-19 a pandemic. The disease is characterized by fever, dry cough, and chest pain with pneumonia in severe cases. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. To date, there are no available vaccines or specific therapeutic drugs to treat the virus. There are many knowledge gaps about the newly emerged SARS-CoV-2, leading to misinformation. Therefore, in this review, we provide recent information about the COVID-19 pandemic. This review also provides insights for the control of pathogenic infections in humans such as SARS-CoV-2 infection and future spillovers. url: https://www.ncbi.nlm.nih.gov/pubmed/32344679/ doi: 10.3390/jcm9041225 id: cord-006129-5rog0s98 author: Hemida, Maged Gomaa title: Exploiting the Therapeutic Potential of MicroRNAs in Viral Diseases: Expectations and Limitations date: 2012-08-16 words: 7443.0 sentences: 508.0 pages: flesch: 50.0 cache: ./cache/cord-006129-5rog0s98.txt txt: ./txt/cord-006129-5rog0s98.txt summary: [12] Answering back, certain host miRNAs alter the cell gene expression to defend the cells against the viral infection by interfering with viral proteins or other cellular factors as a type of immune response against these particular viruses. [40] These virus-encoded miRNAs play important roles in the establishment of latent infection, as well as the pathogenesis of virally induced diseases. According to the most recent studies, herpesviruses utilize their encoded miRNAs in a wide range of biologic functions, such as inhibition of apoptosis, immune evasion, control of cellular proliferation, and regulation of viral replication. [58] Downregulation of UL114 protein, using miR-UL112-1, results in inhibition of viral DNA replication and subsequently triggers the latent phase of infection, making the virus able to evade the host immune system. abstract: New therapeutic approaches are urgently needed for serious diseases, including cancer, cardiovascular diseases, viral infections, and others. A recent direction in drug development is the utilization of nucleic acidbased therapeutic molecules, such as antisense oligonucleotides, ribozymes, short interfering RNA (siRNA), and microRNA (miRNA). miRNAs are endogenous, short, non-coding RNA molecules. Some viruses encode their own miRNAs, which play pivotal roles in viral replication and immune evasion strategies. Conversely, viruses that do not encode miRNAs may manipulate host cell miRNAs for the benefits of their replication. miRNAs have therefore become attractive tools for the study of viral pathogenesis. Lately, novel therapeutic strategies based on miRNA technology for the treatment of viral diseases have been progressing rapidly. Although this new generation of molecular therapy is promising, there are still several challenges to face, such as targeting delivery to specific tissues, avoiding off-target effects of miRNAs, reducing the toxicity of the drugs, and overcoming mutations and drug resistance. In this article, we review the current knowledge of the role and therapeutic potential of miRNAs in viral diseases, and discuss the limitations of these therapies, as well as strategies to overcome them to provide safe and effective clinical applications of these new therapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7099301/ doi: 10.1007/bf03256383 id: cord-299560-np6nfvf2 author: Hendaus, Mohamed A. title: Remdesivir in the treatment of coronavirus disease 2019 (COVID-19): a simplified summary date: 2020-05-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The pandemic of COVID-19 (Coronavirus Disease-2019) is an extremely contagious respiratory illness due to a novel coronavirus, SARS-CoV-2. Certain drugs have several protein targets and many illnesses share overlapping molecular paths. In such cases, reusing drugs for more than one objective and finding their novice uses can considerably decrease the time in finding new cures for unforeseen diseases. Remdesivir has been recently a strong candidate for the treatment of Covid-19. In this commentary, we have portrayed the structure of the coronavirus in a simple way as well as the site where remdesivir acts. We have also displayed the ongoing clinical trials, as well as a published study that was conducted on compassionate base. The covid-19 pandemic might wean down by the end of summer 2020, but the risk of seasonality exists. Therefore, future disposal of agents such as remdesivir might be crucial for ensuring an efficient treatment, decrease mortality and allow early discharge. Communicated by Ramaswamy H. Sarma url: https://doi.org/10.1080/07391102.2020.1767691 doi: 10.1080/07391102.2020.1767691 id: cord-048327-xgwbl8em author: Henderson, Clark M. title: Antisense-induced ribosomal frameshifting date: 2006-08-18 words: 4337.0 sentences: 232.0 pages: flesch: 49.0 cache: ./cache/cord-048327-xgwbl8em.txt txt: ./txt/cord-048327-xgwbl8em.txt summary: The ability of cis-acting RNA structures or trans-acting 2 0 -O-Methyl antisense oligonucleotides to induce ribosomal frameshifting was determined by in vitro transcription and translation of a dual luciferase reporter vector, p2Luc. p2Luc contains the Renilla and firefly luciferase genes on either side of a multiple cloning site, and can be transcribed using the T7 promoter located upstream of the Renilla luciferase gene (45) . As the AZ1A antisense oligonucleotide was designed to anneal directly adjacent to the UGA codon of the shift site, it was of interest to determine whether the wild-type antizyme pseudoknot could induce À1 frameshifting when located in the equivalent position. The ability of spermidine to stimulate antisense oligonucleotide induced ribosome frameshifting to the +1 reading frame at the UCC UGA shift site in the absence of the natural 3 0 stimulator demonstrates that this cis-acting element is not required for polyamine responsiveness. abstract: Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1–ORF2 fusion protein. Such programmed frameshifting is commonly utilized as a gene expression mechanism in viruses that infect eukaryotic cells and in a subset of cellular genes. RNA secondary structures, consisting of pseudoknots or stem–loops, located downstream of the shift site often act as cis-stimulators of frameshifting. Here, we demonstrate for the first time that antisense oligonucleotides can functionally mimic these RNA structures to induce +1 ribosomal frameshifting when annealed downstream of the frameshift site, UCC UGA. Antisense-induced shifting of the ribosome into the +1 reading frame is highly efficient in both rabbit reticulocyte lysate translation reactions and in cultured mammalian cells. The efficiency of antisense-induced frameshifting at this site is responsive to the sequence context 5′ of the shift site and to polyamine levels. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1616946/ doi: 10.1093/nar/gkl531 id: cord-279070-cy049zbi author: Hewson, I. title: Description of viral assemblages associated with the Gorgonia ventalina holobiont date: 2011-12-29 words: 2569.0 sentences: 152.0 pages: flesch: 52.0 cache: ./cache/cord-279070-cy049zbi.txt txt: ./txt/cord-279070-cy049zbi.txt summary: DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Ten samples of sea fans (5 each of visually ''healthy'' and ''diseased'' tissues) were used to generate metagenomic libraries of the viral fraction following protocols for tissues in Thurber et al. Contigs [ 100 bp that did not match protein databases by BLASTx against nr at e-values \ 10 -5 were further characterized by tBLASTx analysis against all viral genomes in GenBank. The proportion of annotated sequence reads (BLASTx against nr databse) and contigs was highest for DNA virus libraries and least for the RNA viral reads (Fig. 1) . The majority of matches for both DNA and RNA viral contigs and reads were to bacterial and metazoan proteins. In contrast to the RNA metaviromes, DNA viruses were well annotated, where *50% of contigs [ 100 bp matched proteins in the nr database. abstract: The diversity and function of viruses in coral holobionts has only recently received attention. The non-reef building gorgonian octocoral, Gorgonia ventalina, is a major constituent of Caribbean reefs. We investigated viral communities associated with G. ventalina tissues to understand their role in gorgonian ecology. Pyrosequencing was used to prepare a total of 514,632 sequence reads of DNA- and RNA-based mixed-community viral genomes (metaviromes). RNA viral assemblages were comprised of primarily unidentifiable reads, with most matching host transcripts and other RNA metaviromes. DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Only ~5% of contigs matched viral proteins that were primarily cyanophage and viruses of Chlorella and Ostreococcus. Our results confirm that DNA and RNA viruses comprise a component of the gorgonian holobiont, suggesting that they may play a role in the ecology of G. ventalina. url: https://doi.org/10.1007/s00338-011-0864-x doi: 10.1007/s00338-011-0864-x id: cord-015606-h9bbvpzd author: Highfield, P.E. title: Translation of infectious bronchitis virus RNA date: 2006-03-27 words: 1125.0 sentences: 72.0 pages: flesch: 63.0 cache: ./cache/cord-015606-h9bbvpzd.txt txt: ./txt/cord-015606-h9bbvpzd.txt summary: When RNA extracted from IBV-infected and uninfected chick embryo kidney cells was added to the reticulocyte system there was a stimulation of methionine incorporation (Table 1 ) and a whole spectrum of polypeptides could be found in the product (Fig. la) . It has a molecular weight of 55 000, co-migrates with one of the bands formed by translation of the virion RNA and is also present in the IBV capsid. When the products formed in the wheat germ synthesis by IBV infected cellular RNA were compared with those formed by uninfected cellular RNA, two new bands could be identified, with molecular weights Lomniczi [4] have demonstrated that the RNA is infectious and that the virion does not contain any transcriptase activity (Lomniczi, unpublished results) . In the reticulocyte system one of the products formed by the virion RNA appears to have the same molecular weight as one of the virion proteins. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7110396/ doi: 10.1111/j.1574-6968.1978.tb01922.x id: cord-103925-i73ymrov author: Hill, Chris H. title: Structural and molecular basis for protein-stimulated ribosomal frameshifting in Theiler’s murine encephalomyelitis virus date: 2020-08-11 words: 11552.0 sentences: 550.0 pages: flesch: 53.0 cache: ./cache/cord-103925-i73ymrov.txt txt: ./txt/cord-103925-i73ymrov.txt summary: Finally, we use metabolic labelling and ribosome profiling to study 2A-mediated frameshifting and translation of the TMEV genome at sub-codon resolution in infected cells. A meta-analysis of the inferred P site positions of ribosomes relative to host mRNA start and stop codons reveals that RPFs map to coding sequences with a triplet periodicity reflective of the length of a codon ( Figure S3D ). Moving on to look specifically at the frameshift site, a single-nucleotide resolution plot of reads mapping to this region reveals a peak on the SS mutant genome corresponding to a ribosome paused with the GUU codon of the slippery sequence in the P site ( Figure 5G , Figure S4C ). These read lengths were selected for analysis as potential "disome-protected fragments", and their density plotted on the viral genome at the inferred P site position of the upstream, colliding ribosome ( Figure 6C and D). abstract: The 2A protein of Theiler’s murine encephalomyelitis virus (TMEV) is required for stimulating programmed −1 ribosomal frameshifting (PRF) during infection. However, the amino acid sequence of TMEV 2A shares only 27% identity with the 2A orthologue from the related cardiovirus encephalomyocarditis virus (EMCV) for which a structure has been recently determined. Here we present the X-ray crystal structure of TMEV 2A, revealing that, despite the low sequence identity, the overall beta-shell architecture is retained, and the location of previously described mutations on this structure suggests a common RNA binding mode. We determine the minimal stimulatory element in the viral RNA required for 2A binding and show that 2A binds to this element with 1:1 stoichiometry and nanomolar affinity. We also demonstrate a critical role for bases upstream of the originally predicted stem-loop, providing evidence that an alternative pseudoknot-like conformation recently demonstrated for EMCV is a conserved feature of cardiovirus stimulatory elements. We go on to examine frameshifting in infected cells by ribosome profiling and metabolic labelling. We observe PRF efficiencies of up to 85%, highlighting this as the most efficient example of −1 PRF in any natural system thus far characterised. Furthermore, we document a series of ribosomal pauses in and around the site of PRF with potential implications for our understanding of translational control in cardioviruses. url: https://doi.org/10.1101/2020.08.11.245068 doi: 10.1101/2020.08.11.245068 id: cord-328960-46zui1sl author: Hillen, Hauke S. title: Structure of replicating SARS-CoV-2 polymerase date: 2020-04-27 words: 4541.0 sentences: 285.0 pages: flesch: 62.0 cache: ./cache/cord-328960-46zui1sl.txt txt: ./txt/cord-328960-46zui1sl.txt summary: Particle classification yielded a 3D reconstruction at a nominal resolution of 2.9 Å and led to a refined structure of the RdRp-RNA complex (Extended Data Figures 1 and 2) . The structure resembles that of the free enzyme 16 , but also reveals large additional protein regions in nsp8 that became ordered upon RNA binding and interact with RNA far outside the core enzyme (Extended Data Figure 3a ). The supernatant containing nsp12 was filtered using a 5-μm syringe filter, followed by filtration with a 0.8-µm syringe filter (Millipore) and applied onto a HisTrap HP 5 mL (GE Healthcare), preequilibrated in lysis buffer (300 mM NaCl, 50 mM Na-HEPES pH 7.4, 10 % (v/v) glycerol, 30 mM imidazole pH 8.0, 3 mM MgCl2, 5 mM β-mercaptoethanol, 0.284 µg ml-1 leupeptin, 1.37 µg ml-1 pepstatin, 0.17 mg ml-1 PMSF, and 0.33 mg ml-1 benzamidine). abstract: The coronavirus SARS-CoV-2 uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes. Here we present the cryo-electron microscopic structure of the SARS-CoV-2 RdRp in its replicating form. The structure comprises the viral proteins nsp12, nsp8, and nsp7, and over two turns of RNA template-product duplex. The active site cleft of nsp12 binds the first turn of RNA and mediates RdRp activity with conserved residues. Two copies of nsp8 bind to opposite sides of the cleft and position the RNA duplex as it exits. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged ‘sliding poles’ that may enable processive replication of the long coronavirus genome. Our results will allow for a detailed analysis of the inhibitory mechanisms used by antivirals such as remdesivir, which is currently in clinical trials for the treatment of coronavirus disease 2019 (COVID-19). url: https://doi.org/10.1101/2020.04.27.063180 doi: 10.1101/2020.04.27.063180 id: cord-305871-w1quh4fx author: Hindawi, Salwa I. title: Inactivation of Middle East respiratory syndrome‐coronavirus in human plasma using amotosalen and ultraviolet A light date: 2017-12-14 words: 4522.0 sentences: 212.0 pages: flesch: 49.0 cache: ./cache/cord-305871-w1quh4fx.txt txt: ./txt/cord-305871-w1quh4fx.txt summary: Furthermore, inoculation of inactivated plasma on Vero E6 cells did not result in any cytopathic effect (CPE) even after 7 days of incubation and three consecutive passages, nor the detection of MERS RNA compared to pretreatment samples which showed complete CPE within 2 to 3 days postinoculation and log viral RNA titer ranging from 9.48 to 10.22 copies/ mL in all three passages. Furthermore, inoculation of inactivated plasma on Vero E6 cells did not result in any cytopathic effect (CPE) even after 7 days of incubation and three consecutive passages, nor the detection of MERS RNA compared to pretreatment samples which showed complete CPE within 2 to 3 days postinoculation and log viral RNA titer ranging from 9.48 to 10.22 copies/ mL in all three passages. Similar to SARS-CoV, there is no proven evidence so far of transfusion-transmitted MERS-CoV infections, 25 but the presence of viral RNA in plasma and serum of acute patients raises this concern especially in endemic areas like Saudi Arabia. abstract: BACKGROUND: Middle East respiratory syndrome‐coronavirus (MERS‐CoV) is a novel zoonotic pathogen. Although the potential for MERS‐CoV transmission through blood transfusion is not clear, MERS‐CoV was recognized as a pathogen of concern for the safety of the blood supply especially after its detection in whole blood, serum, and plasma of infected individuals. Here we investigated the efficacy of amotosalen and ultraviolet A light (UVA) to inactivate MERS‐CoV in fresh‐frozen plasma (FFP). STUDY DESIGN AND METHODS: Pooled FFP units were spiked with a recent clinical MERS‐CoV isolate. Infectious and genomic viral titers were determined in plasma before and after inactivation with amotosalen/UVA treatment by plaque assay and reverse transcription–quantitative polymerase chain reaction, respectively. In addition, residual replicating or live virus after inactivation was examined by passaging in the permissive Vero E6 cells. RESULTS: The mean MERS‐CoV infectious titer in pretreatment samples was 4.67 ± 0.25 log plaque‐forming units (pfu)/mL, which was reduced to undetectable levels after inactivation with amotosalen/UVA demonstrating a mean log reduction of more than 4.67 ± 0.25 pfu/mL. Furthermore, inoculation of inactivated plasma on Vero E6 cells did not result in any cytopathic effect (CPE) even after 7 days of incubation and three consecutive passages, nor the detection of MERS RNA compared to pretreatment samples which showed complete CPE within 2 to 3 days postinoculation and log viral RNA titer ranging from 9.48 to 10.22 copies/mL in all three passages. CONCLUSION: Our data show that amotosalen/UVA treatment is a potent and effective way to inactivate MERS‐CoV infectious particles in FFP to undetectable levels and to minimize the risk of any possible transfusion‐related MERS‐CoV transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/29239484/ doi: 10.1111/trf.14422 id: cord-342456-5gp3cry0 author: Hoagland, Daisy A. title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds date: 2020-07-13 words: 4511.0 sentences: 240.0 pages: flesch: 48.0 cache: ./cache/cord-342456-5gp3cry0.txt txt: ./txt/cord-342456-5gp3cry0.txt summary: Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. These signatures were then used as queries against the LINCS L1000 dataset, a collection of gene expression profiles generated following the administration of >20,000 bioactive compounds including >1,000 FDA-approved drugs to human cell lines at a variety of different times and concentrations (Subramanian et al., 2017) With L1000FWD , we could identify reciprocal transcriptional signatures generated between SARS-CoV-2 infection and a given compound. Overall, based on the L1000 data, these seven compounds influence the same pharmacological high-dimensional gene expression signature space and are predicted to disrupt key cellular processes that are modulated in response to SARS-CoV-2 infection. abstract: To interfere with the biology of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, we focused on restoring the transcriptional response induced by infection. Utilizing expression patterns of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures. Here we demonstrate the successful identification of compounds that display efficacy in blocking SARS-CoV-2 replication based on their ability to counteract the virus-induced transcriptional landscape. These compounds were found to potently reduce viral load despite having no impact on viral entry or modulation of the host antiviral response in the absence of virus. RNA-Seq profiling implicated the induction of the cholesterol biosynthesis pathway as the underlying mechanism of inhibition and suggested that targeting this aspect of host biology may significantly reduce SARS-CoV-2 viral load. url: https://doi.org/10.1101/2020.07.12.199687 doi: 10.1101/2020.07.12.199687 id: cord-325328-3l3jznkj author: Holbrook, Stephen R title: RNA structure: the long and the short of it date: 2005-05-16 words: 3711.0 sentences: 165.0 pages: flesch: 44.0 cache: ./cache/cord-325328-3l3jznkj.txt txt: ./txt/cord-325328-3l3jznkj.txt summary: Structural studies and comparative sequence analyses have suggested that biological RNAs are largely modular in nature, composed primarily of conserved structural building blocks or motifs [4] of secondary (helices, and internal, external and junction loops) and tertiary (coaxial stacks, kissing hairpin loops, ribose zippers, etc.) structure. Other structures include the specificity domains of both A[17] and B-type ribonuclease P [18 ] ; RNAs corresponding to a guanine-responsive riboswitch (xpt) complexed with guanine [19 ] or hypoxanthine [20] , and an adenosine-responsive riboswitch (add) complexed with adenosine [19 ] ; a highly conserved stem-loop motif found at the 3 0 end of the genome of SARS (severe acute respiratory syndrome) virus and other coronaviruses [21 ] ; the core encapsidation signal of MMLV [2 ] ; and complexes between a high-affinity RNA aptamer and the NF-kB p50 homodimer [22] , and between the archaeal RNAbinding protein L7Ae and an RNA K-turn derived from a H/ACA small RNA [23] . abstract: The database of RNA structure has grown tremendously since the crystal structure analyses of ribosomal subunits in 2000–2001. During the past year, the trend toward determining the structure of large, complex biological RNAs has accelerated, with the analysis of three intact group I introns, A- and B-type ribonuclease P RNAs, a riboswitch–substrate complex and other structures. The growing database of RNA structures, coupled with efforts directed at the standardization of nomenclature and classification of motifs, has resulted in the identification and characterization of numerous RNA secondary and tertiary structure motifs. Because a large proportion of RNA structure can now be shown to be composed of these recurring structural motifs, a view of RNA as a modular structure built from a combination of these building blocks and tertiary linkers is beginning to emerge. At the same time, however, more detailed analysis of water, metal, ligand and protein binding to RNA is revealing the effect of these moieties on folding and structure formation. The balance between the views of RNA structure either as strictly a construct of preformed building blocks linked in a limited number of ways or as a flexible polymer assuming a global fold influenced by its environment will be the focus of current and future RNA structural biology. url: https://api.elsevier.com/content/article/pii/S0959440X05000849 doi: 10.1016/j.sbi.2005.04.005 id: cord-346853-0c1qdjb5 author: Holmes, E. C. title: The Evolutionary Genetics of Viral Emergence date: 2007 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Despite the wealth of data describing the ecological factors that underpin viral emergence, little is known about the evolutionary processes that allow viruses to jump species barriers and establish productive infections in new hosts. Understanding the evolutionary basis to virus emergence is therefore a key research goal and many of the debates in this area can be considered within the rigorous theoretical framework established by evolutionary genetics. In particular, the respective roles played by natural selection and genetic drift in shaping genetic diversity are also of fundamental importance for understanding the nature of viral emergence. Herein, we discuss whether there are evolutionary rules to viral emergence, and especially whether certain types of virus, or those that infect a particular type of host species, are more likely to emerge than others. We stress the complex interplay between rates of viral evolution and the ability to recognize cell receptors from phylogenetically divergent host species. We also emphasize the current lack of convincing data as to whether viral emergence requires adaptation to the new host species during the early stages of infection, or whether it is largely a chance process involving the transmission of a viral strain with the necessary genetic characteristics. url: https://www.ncbi.nlm.nih.gov/pubmed/17848060/ doi: 10.1007/978-3-540-70962-6_3 id: cord-263987-ff6kor0c author: Holmes, Ian H. title: Solving the master equation for Indels date: 2017-05-12 words: 7131.0 sentences: 357.0 pages: flesch: 44.0 cache: ./cache/cord-263987-ff6kor0c.txt txt: ./txt/cord-263987-ff6kor0c.txt summary: BACKGROUND: Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. MAIN TEXT: This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees. CONCLUSIONS: While approximations that use finite-state machines (Pair HMMs and transducers) currently represent the most practical approach to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly with the matrix exponential of the underlying continuous-time Markov chain also show promise, especially in view of recent advances. abstract: BACKGROUND: Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. MAIN TEXT: This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees. CONCLUSIONS: While approximations that use finite-state machines (Pair HMMs and transducers) currently represent the most practical approach to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly with the matrix exponential of the underlying continuous-time Markov chain also show promise, especially in view of recent advances. url: https://www.ncbi.nlm.nih.gov/pubmed/28494756/ doi: 10.1186/s12859-017-1665-1 id: cord-263357-krvei97r author: Holmes, Kathryn V. title: The New Age of Virus Discovery: Genomic Analysis of a Novel Human Betacoronavirus Isolated from a Fatal Case of Pneumonia date: 2013-01-08 words: 2076.0 sentences: 83.0 pages: flesch: 43.0 cache: ./cache/cord-263357-krvei97r.txt txt: ./txt/cord-263357-krvei97r.txt summary: Sequencing and bioinformatic analysis of the viral genomic RNA showed that it is a novel virus not previously detected in any other species and that its closest relatives are two Asian bat coronaviruses. demonstrated how state-of-the-art sequencing technology and bioinformatic analysis can quickly provide critical insight into the viral genome sequence, phylogeny, replication strategy, and potential drug and vaccine targets and generate tools to evaluate the possible epidemic risk associated with this novel human virus. In June 2012, a novel coronavirus, tentatively named HCoV-EMC (for Erasmus Medical Center where the initial genome sequence was done), was isolated in a monkey kidney cell line from a sputum specimen from a 60-year-old man from the Kingdom of Saudi Arabia who died of acute severe pneumonia and renal failure. The genomic analysis suggests that HCoV-EMC may be a zoonotic virus that spilled over to infect the 9 laboratory confirmed patients, either directly or indirectly, from an unknown reservoir, possibly a bat. abstract: A new human betacoronavirus in lineage c, tentatively called HCoV-EMC, was isolated from a patient from the Kingdom of Saudi Arabia who died from acute severe pneumonia and renal failure. The viral RNA has been detected in eight additional cases. Sequencing and bioinformatic analysis of the viral genomic RNA showed that it is a novel virus not previously detected in any other species and that its closest relatives are two Asian bat coronaviruses. HCoV-EMC may represent a sporadic spillover to humans from an unknown animal reservoir. In a recent article, van Boheemen et al. demonstrated how state-of-the-art sequencing technology and bioinformatic analysis can quickly provide critical insight into the viral genome sequence, phylogeny, replication strategy, and potential drug and vaccine targets and generate tools to evaluate the possible epidemic risk associated with this novel human virus. url: https://www.ncbi.nlm.nih.gov/pubmed/23300251/ doi: 10.1128/mbio.00548-12 id: cord-287228-0qm939ve author: Hong, Ke title: Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness date: 2020-10-27 words: 3616.0 sentences: 192.0 pages: flesch: 51.0 cache: ./cache/cord-287228-0qm939ve.txt txt: ./txt/cord-287228-0qm939ve.txt summary: In one study including 70 patients with COVID-19, 21% clinically recovered patients with two consecutive negative results of nucleic acid detection experienced a later positive testing for SARS-CoV-2, and the longest duration of viral RNA positivity in this study was 45 days following infection [4] . A total of 2860 COVID-19 patients were hospitalized and followed in this hospital since the epidemic, and those with persistent or intermittent viral RNA positivity in respiratory samples (including the nasopharyngeal, oropharyngeal and sputum samples) for at least 4 weeks were included in our study, regardless of the age and their clinical status. However, in most of these studies, PCR testing was used as a marker to indicate the existence of virus, and patients with positive viral RNA was considered infectious though they have been infected for months without further clinical symptoms. abstract: Prolonged presence of viral nucleic acid was reported in certain patients with coronavirus disease 2019 (COVID-19), with unclear clinical and epidemiological significance. We here described the clinical and epidemiological characteristics of 37 recovered COVID-19 patients with prolonged presence of viral RNA in Wuhan, China. For those who had been discharged and re-admitted, their close contacts outside the hospital were traced and evaluated. The median age of the 37 patients was 62 years (IQR 50, 68), and 24 (64.9%) were men. They had common or severe COVID-19. With prolonged positive RT-PCR, most patients were clinically stable, 29 (78.4%) denied any symptoms. A total of 431 PCR tests were carried out, with each patient at a median of 8 time points. The median time of PCR positivity to April 18 was 78 days (IQR 67.7, 84.5), and the longest 120 days. 22 of 37 patients had been discharged at a median of 44 days (IQR 22.3, 50) from disease onset, and 9 had lived with their families without personal protections for a total of 258 person-days and no secondary infection was identified through epidemiological investigation, nucleic acid and antibody screening. Infectiousness in COVID-19 patients with prolonged presence of viral nucleic acid should not solely be evaluated by RT–PCR. Those patients who have clinically recovered and whose disease course has exceeded four weeks were associated with very limited infectiousness. Reconsideration of disease control in such patients is needed. url: https://www.ncbi.nlm.nih.gov/pubmed/32981485/ doi: 10.1080/22221751.2020.1827983 id: cord-286149-awhnjwyc author: Hoon‐Hanks, L.L. title: Metagenomic Investigation of Idiopathic Meningoencephalomyelitis in Dogs date: 2017-12-02 words: 5441.0 sentences: 289.0 pages: flesch: 51.0 cache: ./cache/cord-286149-awhnjwyc.txt txt: ./txt/cord-286149-awhnjwyc.txt summary: In previous investigations of MUO in dogs, only brain samples were tested for infectious agents; however, CSF is a common sample utilized in the clinical evaluation of neurologic disease for the detection of infectious agent nucleic acids, especially by PCR. Additionally, RNA was extracted from postmortem brain samples from a mule deer (Odocoileus hemionus), green tree python (Morelia viridis), American crow (Corvus brachyrhynchos), and American robin (Turdus migratorius), all of which had previously been tested by PCR, metagenomic sequencing, or both, and were found to be infected with specific known infectious agents. There are several possible biological and technical explanations for our study''s inability to identify a candidate etiologic agent for MUO, including the underlying pathogenesis of the disease, sample type and collection methods, case inclusion criteria, sensitivity of diagnostics, and database limitations. abstract: BACKGROUND: Meningoencephalomyelitis of unknown origin (MUO) is a common and life‐threatening neuroinflammatory disease in dogs. Features of the disease are suggestive of an underlying immune‐mediated process, but the association of this disease with a pathogen is still unknown. HYPOTHESIS/OBJECTIVES: To search for candidate etiologic agent associated with cases if MUO using next generation metagenomic sequencing. ANIMALS: Twenty‐two dogs diagnosed with either MUO (11/22; 10 CSF and 3 brain), or noninflammatory CNS diseases inconsistent with MUO (11/22; 11 CSF and 2 brain) that served as negative controls. METHODS: A case control study was performed by identifying MUO and non‐MUO cases. Samples were blindly processed and then unblinded for comparative analyses. Inclusion criteria for MUO cases included consistent MRI lesions and inflammatory CSF with a negative PCR panel for infectious agents or histopathologic diagnosis. Dogs with glucocorticoid therapy within 2 weeks of sample collection were excluded. Fresh‐frozen cerebrospinal fluid (CSF; 21) and brain (5) samples were collected and RNA and DNA were extracted separately for shotgun metagenomic sequencing. Known positive samples were used as controls to validate our sequencing and analysis pipelines and to establish limits of detection. Sequencing results were analyzed at a nucleotide and protein level for broad comparison to known infectious organisms. RESULTS: No candidate etiologic agents were identified in dogs with MUO. CONCLUSIONS AND CLINICAL IMPORTANCE: These results support but do not prove the hypothesis that MUO is not associated with infectious agents and might be an autoimmune disease. url: https://doi.org/10.1111/jvim.14877 doi: 10.1111/jvim.14877 id: cord-254250-l0v602x9 author: Hooper, Chantelle title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh date: 2020-10-02 words: 6440.0 sentences: 309.0 pages: flesch: 48.0 cache: ./cache/cord-254250-l0v602x9.txt txt: ./txt/cord-254250-l0v602x9.txt summary: title: A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. rnaSPAdes assembly of combined libraries produced 38,826 contigs; 23 contigs, of average length 4560 bp, had similarity in protein sequence to YHV or gill-associated virus (GAV), but when the trimmed reads were aligned against the YHV genome (accession number GCA_003972805.1), no alignment was seen. rosenbergii were negative: MrNV and XSV, the causative agents of white tail disease [9, 10] ; MrTV, a virus associated with mass larval mortalities in China [15] , Spiroplasma eriocheiris [8] , and WSSV-shown to be able to infect M. abstract: Mass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of Macrobrachium rosenbergii golda virus (MrGV) suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture. url: https://doi.org/10.3390/v12101120 doi: 10.3390/v12101120 id: cord-000979-cav9n18w author: Hoppe, Sebastian title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni date: 2013-05-29 words: 10056.0 sentences: 595.0 pages: flesch: 50.0 cache: ./cache/cord-000979-cav9n18w.txt txt: ./txt/cord-000979-cav9n18w.txt summary: title: Rapid Identification of Novel Immunodominant Proteins and Characterization of a Specific Linear Epitope of Campylobacter jejuni The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. Additionally, the structure and antigenicity of the proteins and epitopes were modelled to analyze the suitability of the identified sequences for future applications like diagnostic tools or vaccine development. For a summary of the predicted characteristics, see S9: Transmembrane and antigenic potential of three potential epitope sites for cj0920c.Further, specificity control assays revealed that these signals do not drop significantly when using antibodies to Salmonella enterica indicative of nonspecific binding to occur, see S10: Specific vs. jejuni and were able to determine the important residue involved in antibody binding as well as modelling the epitope''s accessibility within the full-length protein. abstract: Campylobacter jejuni remains one of the major gut pathogens of our time. Its zoonotic nature and wide-spread distribution in industrialized countries calls for a quick and reliable diagnostic tool. Antibody-based detection presents a suitable means to identify pathogenic bacteria. However, the knowledge about immunodominant targets is limited. Thus, an approach is presented, which allows for the rapid screening of numerous cDNA derived expression clones to identify novel antigens. The deeper understanding of immunodominant proteins assists in the design of diagnostic tools and furthers the insight into the bacterium’s pathogenicity as well as revealing potential candidates for vaccination. We have successfully screened 1536 clones of an expression library to identify 22 proteins that have not been described as immunodominant before. After subcloning the corresponding 22 genes and expression of full-length proteins, we investigated the immunodominant character by microarrays and ELISA. Subsequently, seven proteins were selected for epitope mapping. For cj0669 and cj0920c linear epitopes were identified. For cj0669, specificity assays revealed a specific linear epitope site. Consequently, an eleven amino acid residue sequence TLIKELKRLGI was analyzed via alanine scan, which revealed the glycine residue to be significant for binding of the antibody. The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. The findings of a specific linear epitope pave the way for a plethora of future research and the potential use in diagnostic applications such as serological screenings. Moreover, the current approach is easily adaptable to other highly relevant bacteria making it a formidable tool for the future discovery of antigens and potential biomarkers. Consequently, it is desirable to simplify the identification of structural epitopes, as this would extend the spectrum of novel epitopes to be detected. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667084/ doi: 10.1371/journal.pone.0065837 id: cord-002045-m44fic4g author: Horie, Masayuki title: An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus date: 2016-05-13 words: 4805.0 sentences: 312.0 pages: flesch: 59.0 cache: ./cache/cord-002045-m44fic4g.txt txt: ./txt/cord-002045-m44fic4g.txt summary: Endogenous bornavirus-like L (EBLL) elements are inheritable sequences derived from ancient bornavirus L genes that encode a viral RNA-dependent RNA polymerase (RdRp) in many eukaryotic genomes. Furthermore, we showed that the EBLLs evolved under purifying selection and still possess functional motifs conserved among the Mononegavirales RdRps. These results strongly suggest that the EBLL elements encode functional proteins that may be RdRps. ORF screening for these elements in several mammalian species and found an EBLL element in the bat species Eptesicus fuscus (designated efEBLL-1; accession number ALEH01013293). Notably, this element (eEBLL-1) contains a 1,718-amino acid ORF that was conserved for more than 11.8 MY and included almost all of the sequence motifs essential for the enzymatic activity of a RNA virus RdRp. To the best of our knowledge, eEBLL-1 is the first example of an RNA virus-derived RdRp encoded by the mammalian genome. abstract: Endogenous bornavirus-like L (EBLL) elements are inheritable sequences derived from ancient bornavirus L genes that encode a viral RNA-dependent RNA polymerase (RdRp) in many eukaryotic genomes. Here, we demonstrate that bats of the genus Eptesicus have preserved for more than 11.8 million years an EBLL element named eEBLL-1, which has an intact open reading frame of 1,718 codons. The eEBLL-1 coding sequence revealed that functional motifs essential for mononegaviral RdRp activity are well conserved in the EBLL-1 genes. Genetic analyses showed that natural selection operated on eEBLL-1 during the evolution of Eptesicus. Notably, we detected efficient transcription of eEBLL-1 in tissues from Eptesicus bats. To the best of our knowledge, this study is the first report showing that the eukaryotic genome has gained a riboviral polymerase gene from an ancient virus that has the potential to encode a functional RdRp. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865735/ doi: 10.1038/srep25873 id: cord-275225-fvq8hezk author: Hornyák, Ákos title: Detection of subgenomic mRNA of feline coronavirus by real-time polymerase chain reaction based on primer-probe energy transfer (P-sg-QPCR) date: 2012-02-18 words: 7138.0 sentences: 337.0 pages: flesch: 50.0 cache: ./cache/cord-275225-fvq8hezk.txt txt: ./txt/cord-275225-fvq8hezk.txt summary: The quantitative sg-mRNA detection method revealed more than 10-50,000 times increase of the M gene sg-mRNA in organ materials of feline infectious peritonitis cases, compared to those of the enteric FCoV variants present in the faeces of normal, healthy cats. The quantitative sg-mRNA detection method revealed more than 10-50,000 times increase of the M gene sg-mRNA in organ materials of feline infectious peritonitis cases, compared to those of the enteric FCoV variants present in the faeces of normal, healthy cats. These results indicate the applicability of the new P-sg-QPCR test as a powerful novel tool for the better detection and quantitation of FCoV and for the improved diagnosis of feline infectious peritonitis, this important disease of the Felidae, causing serious losses in the cat populations at a global scale. The detailed analysis of the feline infectious peritonitis positive cat samples by SYBR-Green QPCR method revealed that the following organs harbour FCoV most frequently: lungs 6/6 (100%), liver 6/6 (100%), kidney 10/11 (90.9%), mesenteric lymph node 18/20 (90%), spleen 16/20 (80%) and gut 15/10 (66.7%). abstract: Feline infectious peritonitis is one of the most severe devastating diseases of the Felidae. Upon the appearance of clinical signs, a cure for the infected animal is impossible. Therefore rapid and proper diagnosis for both the presence of the causative agent, feline coronavirus (FCoV) and the manifestation of feline infectious peritonitis is of paramount importance. In the present work, a novel real-time RT-PCR method is described which is able to detect FCoV and to determine simultaneously the quantity of the viral RNA. The new assay combines the M gene subgenomic messenger RNA (sg-mRNA) detection and the quantitation of the genome copies of FCoV. In order to detect the broadest spectrum of potential FCoV variants and to achieve the most accurate results in the detection ability the new assay is applying the primer-probe energy transfer (PriProET) principle. This technology was chosen since PriProET is very robust to tolerate the nucleotide substitutions in the target area. Therefore, this technology provides a very broad-range system, which is able to detect simultaneously many variants of the virus(es) even if the target genomic regions show large scale of variations. The detection specificity of the new assay was proven by positive amplification from a set of nine different FCoV strains and negative from the tested non-coronaviral targets. Examination of faecal samples of healthy young cats, organ samples of perished animals, which suffered from feline infectious peritonitis, and cat leukocytes from uncertain clinical cases were also subjected to the assay. The sensitivity of the P-sg-QPCR method was high, since as few as 10 genome copies of FCoV were detected. The quantitative sg-mRNA detection method revealed more than 10–50,000 times increase of the M gene sg-mRNA in organ materials of feline infectious peritonitis cases, compared to those of the enteric FCoV variants present in the faeces of normal, healthy cats. These results indicate the applicability of the new P-sg-QPCR test as a powerful novel tool for the better detection and quantitation of FCoV and for the improved diagnosis of feline infectious peritonitis, this important disease of the Felidae, causing serious losses in the cat populations at a global scale. url: https://www.sciencedirect.com/science/article/pii/S0166093412000365 doi: 10.1016/j.jviromet.2012.01.022 id: cord-298905-c2uuvfm5 author: Horzinek, M. C. title: Molecular pathogenesis of virus infections date: 1987 words: 3888.0 sentences: 193.0 pages: flesch: 40.0 cache: ./cache/cord-298905-c2uuvfm5.txt txt: ./txt/cord-298905-c2uuvfm5.txt summary: Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organor animal species-spectrum) can dramatically change. Parainfluenzaviruses, for example, attach to neuraminic acid-containing receptors; since glycolipids and glycoproteins containing neuraminic acid abound in vertebrate cell membranes the adsorption/penetration process lacks the specificity required to explain the restrictions in host range and tissue tropism of paramyxoviruses 29. Also in influenza virus infection cap structures are essential: these are cannibalized from host cell nuclear RNA precursor molecules and used as primers for viral RNA replication and synthesis 28. Autoimmune phenomena involving both the humoral and cellular limbs of the immune response have been identified in neurological conditions following infections with e.g. canine distemper virus3; invasion of brain tissue is supposed to cause changes in the molecular constitution of myelin and membrane components, making them recognizable as ''nonself''. abstract: Although a very wide range of viral diseases exists in vertebrates, certain generalizations can be made regarding pathogenetic pathways on the molecular level. The presentation will focus on interactions of virions and their components with target cells. Using coronaviruses as examples the changes in virulence have been traced back to single mutational events; recombination, however, is likely to be an alternative mechanism by which virus-host interactions (e.g. the cell-, organ- or animal species-spectrum) can dramatically change. Receptor molecules are essential for the early interactions during infection and some ot these have been identified. Events in the target cell and the host organism are discussed, and wherever possible, aspects of virus evolution and cooperation between infectious agents are highlighted. url: https://www.ncbi.nlm.nih.gov/pubmed/2826215/ doi: 10.1007/bf01945522 id: cord-292751-tk1oggi9 author: Hosseini, Elahe Seyed title: The novel coronavirus Disease-2019 (COVID-19): Mechanism of action, detection and recent therapeutic strategies date: 2020-09-24 words: 3784.0 sentences: 222.0 pages: flesch: 46.0 cache: ./cache/cord-292751-tk1oggi9.txt txt: ./txt/cord-292751-tk1oggi9.txt summary: Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. The previously reported viral zoonotic pathogens include SARS-CoV (severe acute respiratory syndrome coronavirus) and MERS (Middle East respiratory syndrome coronavirus) [3, 4] , that can cause severe respiratory disease in human [5, 6] . SARS-CoV-2, a novel coronavirus (which causes COVID19) , has fast spread like a pandemic since its outbreak in Wuhan, China, in December 2019 [7] . Nowadays, Griffithsin, as an inhibitor of SARS and MERS spike, Remdesivir, favipiravir and ribavirin (nucleoside analogues), lopinavir/ritonavir (protease enzyme inhibitors) [61] , oseltamivir (neuraminidase inhibitors), anti-inflammatory drugs and EK1 peptide [62] , the clinical potential to be applied against the 2019-nCoV infection [67, 68] . Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan abstract: Novel coronavirus SARS-CoV-2, designated as COVID-19 by the World Health Organization (WHO) on the February 11, 2020, is one of the highly pathogenic β‐coronaviruses which infects human. Early diagnosis of COVID-19 is the most critical step to treat infection. The diagnostic tools are generally molecular methods, serology and viral culture. Recently CRISPR-based method has been investigated to diagnose and treat coronavirus infection. The emergence of 2019-nCoV during the influenza season, has led to the extensive use of antibiotics and neuraminidase enzyme inhibitors, taken orally and intravenously. Currently, antiviral inhibitors of SARS and MERS spike proteins, neuraminidase inhibitors, anti-inflammatory drugs and EK1 peptide are the available therapeutic options for SARS-CoV-2 infected individuals. In addition, Chloroquine, which was previously used for malarial and autoimmune disease, has shown efficacy in the 2019-nCoV infection treatment. In severe hypoxaemia, a combination of antibiotics, α-interferon, lopinavir and mechanical ventilation can effectively mitigate the symptoms. Comprehensive knowledge on the innate and adaptive immune responses, will make it possible to propose potent antiviral drugs with their effective therapeutic measures for the prevention of viral infection. This therapeutic strategy will help patients worldwide to protect themselves against severe and fatal viral infections, that potentially can evolve and develop drug resistance, and to reduce mortality rates. url: https://doi.org/10.1016/j.virol.2020.08.011 doi: 10.1016/j.virol.2020.08.011 id: cord-001453-l1r416w7 author: Hou, Linlin title: Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome date: 2014-11-10 words: 8358.0 sentences: 420.0 pages: flesch: 54.0 cache: ./cache/cord-001453-l1r416w7.txt txt: ./txt/cord-001453-l1r416w7.txt summary: title: Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome Consistently, a fusion protein containing full-length Csl4 and NTD of DnaG led to enhanced degradation of A-rich RNA by the exosome. The RNase PH-domain containing subunits Rrp41 and Rrp42 are arranged in a catalytically active hexamer, on the top of which a trimeric cap composed of the RNA-binding proteins Rrp4 and Csl4 is bound ( Figure 1B ; 4, 5, [22] [23] [24] . The bacterial primase DnaG is composed of an NTD containing a Zn-finger motif involved in DNA binding, the central, catalytic TOPRIM domain and a CTD neces-sary for the interaction with the replicative helicase DnaB ( Figure 1A , refs. coli cell-free extract was easily detectable by pull-down assays with Strep-Tactin Sepharose beads (for an example see Figure 7A be-low), we conclude that the CTD of DnaG is important for the binding to the archaeal exosome. abstract: The archaeal exosome is a phosphorolytic 3′–5′ exoribonuclease complex. In a reverse reaction it synthesizes A-rich RNA tails. Its RNA-binding cap comprises the eukaryotic orthologs Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. In Sulfolobus solfataricus DnaG and Rrp4 but not Csl4 show preference for poly(rA). Archaeal DnaG contains N- and C-terminal domains (NTD and CTD) of unknown function flanking a TOPRIM domain. We found that the NT and TOPRIM domains have comparable, high conservation in all archaea, while the CTD conservation correlates with the presence of exosome. We show that the NTD is a novel RNA-binding domain with poly(rA)-preference cooperating with the TOPRIM domain in binding of RNA. Consistently, a fusion protein containing full-length Csl4 and NTD of DnaG led to enhanced degradation of A-rich RNA by the exosome. We also found that DnaG strongly binds native and in vitro transcribed rRNA and enables its polynucleotidylation by the exosome. Furthermore, rRNA-derived transcripts with heteropolymeric tails were degraded faster by the exosome than their non-tailed variants. Based on our data, we propose that archaeal DnaG is an RNA-binding protein, which, in the context of the exosome, is involved in targeting of stable RNA for degradation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227792/ doi: 10.1093/nar/gku969 id: cord-296309-i1mpov7k author: Houldcroft, Charlotte J. title: Clinical and biological insights from viral genome sequencing date: 2017-01-16 words: 9050.0 sentences: 389.0 pages: flesch: 35.0 cache: ./cache/cord-296309-i1mpov7k.txt txt: ./txt/cord-296309-i1mpov7k.txt summary: We will also explore two areas in which viral WGS has recently proven its clinical utility: metagenomic sequencing to identify viruses that cause encephalitis (BOX 1) ; and the role of WGS in molecular epidemiology and public health management of the Pan-American Zika virus outbreak (BOX 2) . However, the increasing number of resistance genes that are located across viral genomes, together with decreasing costs of sequencing and the use of sequence data for transmission studies, are driving a reappraisal of the need for WGS. The numerous phylogenetically informative variant sites that can be obtained from full-length or near full-length genomes removes the need for high-quality sequences, which enabled the robust linking of cases of Ebola virus infection and public health interventions in real time during the 2015 epidemic 39 . There are several methods that are available to achieve WGS of viruses from clinical samples; amplicon sequencing, target enrichment or metagenomics. abstract: Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the clinical application of viral WGS, this technique provides important insights into virus transmission, evolution and pathogenesis. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nrmicro.2016.182) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1038/nrmicro.2016.182 doi: 10.1038/nrmicro.2016.182 id: cord-340046-kgbvld0y author: Houspie, Lieselot title: Exhaled breath condensate sampling is not a new method for detection of respiratory viruses date: 2011-03-04 words: 4081.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-340046-kgbvld0y.txt txt: ./txt/cord-340046-kgbvld0y.txt summary: BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms (defined in Table 1 ), using a commercially available condenser (RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA). Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract. abstract: BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. METHODS: In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. CONCLUSION: Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections. url: https://www.ncbi.nlm.nih.gov/pubmed/21375748/ doi: 10.1186/1743-422x-8-98 id: cord-291916-5yqc3zcx author: Hozhabri, Hossein title: The Global Emergency of Novel Coronavirus (SARS-CoV-2): An Update of the Current Status and Forecasting date: 2020-08-05 words: 16737.0 sentences: 847.0 pages: flesch: 45.0 cache: ./cache/cord-291916-5yqc3zcx.txt txt: ./txt/cord-291916-5yqc3zcx.txt summary: abstract: Over the past two decades, there have been two major outbreaks where the crossover of animal Betacoronaviruses to humans has resulted in severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). In December 2019, a global public health concern started with the emergence of a new strain of coronavirus (SARS-CoV-2 or 2019 novel coronavirus, 2019-nCoV) which has rapidly spread all over the world from its origin in Wuhan, China. SARS-CoV-2 belongs to the Betacoronavirus genus, which includes human SARS-CoV, MERS and two other human coronaviruses (HCoVs), HCoV-OC43 and HCoV-HKU1. The fatality rate of SARS-CoV-2 is lower than the two previous coronavirus epidemics, but it is faster spreading and the large number of infected people with severe viral pneumonia and respiratory illness, showed SARS-CoV-2 to be highly contagious. Based on the current published evidence, herein we summarize the origin, genetics, epidemiology, clinical manifestations, preventions, diagnosis and up to date treatments of SARS-CoV-2 infections in comparison with those caused by SARS-CoV and MERS-CoV. Moreover, the possible impact of weather conditions on the transmission of SARS-CoV-2 is also discussed. Therefore, the aim of the present review is to reconsider the two previous pandemics and provide a reference for future studies as well as therapeutic approaches. url: https://doi.org/10.3390/ijerph17165648 doi: 10.3390/ijerph17165648 id: cord-274401-pjyvg53w author: Hrkach, Jeff title: From micro to nano: evolution and impact of drug delivery in treating disease date: 2020-05-08 words: 2055.0 sentences: 100.0 pages: flesch: 38.0 cache: ./cache/cord-274401-pjyvg53w.txt txt: ./txt/cord-274401-pjyvg53w.txt summary: An early wave featured injectable (i.e., intramuscular, subcutaneous) biodegradable polymeric microspheres to control drug release profiles for peptides and small molecules (e.g., Lupron Depot®, Risperdal Consta®). With these early successes for microspheres, research shifted to exploring systemic delivery by intravenous injection, which required smaller particle sizes and modified surface properties (e.g., PEGylation) to enable long circulation times. These new innovations resulted in the nanoparticle medicines Doxil® and Abraxane®, designed to improve the therapeutic index of cytotoxic cancer agents by decreasing systemic exposure and delivering more drug to tumors. In 2003, the FDA approved Risperdal Consta®, a controlled release form of risperidone encapsulated in PLG microspheres that enabled dosing once every 2 weeks by intramuscular injection. The many successes of controlled release microsphere-based medicines led innovators to explore the potential of drug delivery for systemic administration to reach specific sites of disease, with particular interest in targeting tumors for treating cancer. abstract: Over the past 50 years, drug delivery breakthroughs have enabled the approval of several important medicines. Often, this path starts with innovation from academic collaborations amongst biologists, chemists, and engineers, followed by the formation of a start-up company driving clinical translation and approval. An early wave featured injectable (i.e., intramuscular, subcutaneous) biodegradable polymeric microspheres to control drug release profiles for peptides and small molecules (e.g., Lupron Depot®, Risperdal Consta®). With these early successes for microspheres, research shifted to exploring systemic delivery by intravenous injection, which required smaller particle sizes and modified surface properties (e.g., PEGylation) to enable long circulation times. These new innovations resulted in the nanoparticle medicines Doxil® and Abraxane®, designed to improve the therapeutic index of cytotoxic cancer agents by decreasing systemic exposure and delivering more drug to tumors. Very recently, the first siRNA lipid nanoparticle medicine, Patisiran (Onpattro®), was approved for treating hereditary transthyretin-mediated amyloidosis. In this inspirational note, we will highlight the technological evolution of drug delivery from micro- to nano-, citing some of the approved medicines demonstrating the significant impact of the drug delivery field in treating many diseases. url: https://doi.org/10.1007/s13346-020-00769-6 doi: 10.1007/s13346-020-00769-6 id: cord-267533-nmgtan4e author: Hu, Zhigang title: Delayed hospital admission and high-dose corticosteroids potentially prolong SARS-CoV-2 RNA detection duration of patients with COVID-19 date: 2020-10-29 words: 3605.0 sentences: 214.0 pages: flesch: 46.0 cache: ./cache/cord-267533-nmgtan4e.txt txt: ./txt/cord-267533-nmgtan4e.txt summary: By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. The study of Xu and colleagues [5] estimated the risk factors of delayed viral shedding (≥ 15 days after illness onset) and found that male, delayed hospital admission, and invasive mechanical ventilation were positively associated with prolonged SARS-CoV-2 RNA detection duration. Delayed hospital admission, hypokalemia, and subpleural lesion were still the independent risk factors of long-term SARS-CoV-2 RNA detection in multivariate binomial logistic regression analysis with a generalized additive model. LASSO analysis with Cox regression model found six independent risk factors of prolonged SARS-CoV-2 RNA detection duration, including cough, dyspnea, delayed hospital admission, subpleural lesion, the use of methylprednisolone, and the use of thymosin. abstract: Coronavirus disease 2019 (COVID-19) with the infection of SARS-CoV-2 has become a serious pandemic worldwide. However, only few studies focused on risk factors of prolonged SARS-CoV-2 RNA detection among patients with COVID-19. We included 206 adult patients with laboratory-confirmed COVID-19 from two hospitals between 23 Jan and 1 April 2020. Least absolute shrinkage and selection operator (LASSO) analysis was used to screen out independent risk factors of SARS-CoV-2 RNA detection. By multivariate binomial logistic regression analysis and Cox regression analysis, we further determined the associations between SARS-CoV-2 RNA detection and potential risk factors. All patients had two negative SARS-CoV-2 tests with 33 days of median duration of SARS-CoV-2 RNA detection (interquartile range: 25.2–39 days). LASSO and binomial logistic regression analyses suggested that delayed hospital admission (adjusted OR = 3.70, 95% CI: 1.82–7.50), hypokalemia, and subpleural lesion (adjusted OR = 4.32, 95% CI: 1.10–16.97) were associated with prolonged SARS-CoV-2 RNA detection. By LASSO and multivariate Cox regression analyses, we observed that delayed hospital admission, subpleural lesion, and high-dose corticosteroid use were independent risk factors of prolonged SARS-CoV-2 RNA detection. Early hospital admission shortened 5.73 days of mean duration of SARS-CoV-2 RNA detection than delayed hospital admission after adjusting confounding factors. Our study demonstrated that delayed hospital admission and subpleural lesion were associated with prolonged SARS-CoV-2 RNA detection among patients with COVID-19. The use of high-dose corticosteroids should be interpreted with extreme caution in treating COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/33123934/ doi: 10.1007/s10096-020-04085-2 id: cord-002937-7xauocti author: Huang, Chung-Guei title: A pilot study on primary cultures of human respiratory tract epithelial cells to predict patients’ responses to H7N9 infection date: 2018-02-20 words: 6238.0 sentences: 293.0 pages: flesch: 46.0 cache: ./cache/cord-002937-7xauocti.txt txt: ./txt/cord-002937-7xauocti.txt summary: We aimed to investigate whether primary cultures of human respiratory tract epithelial cells are helpful to understand H7N9 virus pathogenesis and tissue tropism, and to evaluate how patient-related characteristics can affect the host''s response to infection. In this scenario, primary cultures of human respiratory tract epithelial cells would be invaluable to understand H7N9 virus tissue tropism and pathogenesis, as well as to evaluate how patient-related characteristics can modulate the host''s response to infection. With regard to virus tropism, viral RNA quantities were significantly higher in epithelial cells obtained from the upper anatomical locations than from the lower anatomical locations, without adjustment (P = 0.030); however, the difference lost significance after adjustment for age, sex, medical comorbidities, and obesity (P = 0.490; Figure 2B ). abstract: Avian influenza A(H7N9) virus infections frequently lead to acute respiratory distress syndrome and death in humans. We aimed to investigate whether primary cultures of human respiratory tract epithelial cells are helpful to understand H7N9 virus pathogenesis and tissue tropism, and to evaluate how patient-related characteristics can affect the host's response to infection. Normal human bronchial epithelial cells (isolated from two different donors) and primary epithelial cells (harvested from 27 patients undergoing airway surgery) were experimentally infected with H7N9 and/or H1N1pdm for 72 h. After virus infection, the culture media were collected for viral RNA quantitation and cytokine detection. Both H7N9 and H1N1pdm viruses replicated and induced a cytokine response differently for each donor in the normal human bronchial epithelial model. H7N9 replicated equivalently in epithelial cells harvested from the inferior turbinate and paranasal sinus, and those from the larynx and bronchus, at 72 h post-infection. Viral RNA quantity at 72 h was significantly higher in patients aged 21–64 years than in patients aged ≥ 65 years; however, no effects of sex, medical comorbidities, and obesity were noted. H7N9-infected cultured cells released multiple cytokines within 72 h. Levels of interleukin-1β, interleukin-6, interleukin-8, interferon-γ, and tumor necrosis factor-α were associated differently with patient-related characteristics (such as age, sex, obesity, and medical comorbidities). In the era of precision medicine, these findings illustrate the potential utility of this primary culture approach to predict a host's response to H7N9 infection or to future infection by newly emerging viral infections, and to dissect viral pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865685/ doi: 10.18632/oncotarget.24537 id: cord-330200-l6bnxi40 author: Huang, Jianping title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study date: 2020-04-27 words: 4472.0 sentences: 306.0 pages: flesch: 59.0 cache: ./cache/cord-330200-l6bnxi40.txt txt: ./txt/cord-330200-l6bnxi40.txt summary: title: Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. In this study, we investigated the profiles of viral RNA, IgM, and IgG in a group of patients with confirmed SARS-CoV-2 pneumonia over an 8-week period after symptom onset. Demographic data, symptom onset time, clinical features, radiological findings, routine laboratory results, and the results of SARS-CoV-2 viral RNA in throat swabs, sputum, and stool samples were recorded during hospitalization and follow-up. We investigated the serial viral load and dynamics of antibodies from patients infected with SARS-CoV-2 over an eight-week period following the onset of symptoms. abstract: ABSTRACT OBJECTIVE To investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period. DESIGN Retrospective, observational case series. SETTING Wenzhou Sixth Peoples Hospital PARTICIPANTS Thirty-three patients with laboratory confirmed SARS-CoV-2 pneumonia admitted to hospital. Data were collected from January 27 to April 10, 2020. MAIN OUTCOME MEASURES Throat swabs, sputum, stool, and blood samples were collected, and viral load was measured by reverse transcription PCR (RT-PCR). Specific IgM and IgG against spike protein (S), spike protein receptor binding domain (RBD), and nucleocapsid (N) were analyzed. RESULTS At the early stages of symptom onset, SARS-CoV-2 viral load is higher in throat swabs and sputum, but lower in stool. The median (IQR) time of undetectable viral RNA in throat swab, sputum, and stool was 18.5 (13.25-22) days, 22 (18.5-27.5) days, and 17 (11.5-32) days, respectively. In sputum, 17 patients (51.5%) had undetectable viral RNA within 22 days (short persistence), and 16 (48.5%) had persistent viral RNA more than 22 days (long persistence). Three patients (9.1%) had a detectable relapse of viral RNA in sputum within two weeks of their discharge from the hospital. One patient had persistent viral RNA for 59 days or longer. The median (IQR) seroconversion time of anti-S IgM, anti-RBD IgM, and anti-N IgM was 10.5 (7.75-15.5) days, 14 (9-24) days, and 10 (7-14) days, respectively. The median (IQR) seroconversion time of anti-S IgG, anti-RBD IgG, and anti-N IgG was 10 (7.25-16.5) days, 13 (9-17) days, and 10 (7-14) days, respectively. By week 8 after symptom onset, IgM were negative in many of the previously positive patients, and IgG levels remained less than 50% of the peak levels in more than 20% of the patients. In about 40% of the patients, anti-RBD IgG levels were 4-times higher in convalescence than in acute phase. SARS-CoV-2 RNA coexisted with antibodies for more than 50 days. Anti-RBD IgM and IgG levels, including anti-RBD IgM levels at presentation and peak time, were significantly higher in viral RNA short persistence patients than in long persistence patients. CONCLUSION This study adds important new information about the features of viral load and antibody dynamics of SARS-CoV-2. It is clear from these results that the viral RNA persists in sputum and stool specimens for a relatively long time in many patients. Anti-RBD may also serve as a potential protective antibody against SARS-CoV-2 infection, as viral persistence appears to be related to anti-RBD levels. Earlier treatment intervention also appears to be a factor in viral persistence. url: http://medrxiv.org/cgi/content/short/2020.04.22.20071258v1?rss=1 doi: 10.1101/2020.04.22.20071258 id: cord-344636-go5cw92q author: Huang, Wei E. title: RT‐LAMP for rapid diagnosis of coronavirus SARS‐CoV‐2 date: 2020-04-25 words: 4771.0 sentences: 253.0 pages: flesch: 61.0 cache: ./cache/cord-344636-go5cw92q.txt txt: ./txt/cord-344636-go5cw92q.txt summary: In this work, we developed a COVID-19 diagnosis kit for the rapid detection of SARS-CoV-2, using one-step reverse transcription and loop-mediated isothermal amplification (RT-LAMP). Positive amplification products were obtained even for 2 copies of the synthetic viral DNA fragment template in 30 min when using the S17 primers (lane 4 in Fig. 1D ), demonstrating that the LAMP reaction was rapid and sensitive. To assess the potential of RT-LAMP in detecting RNA virus of SARS-CoV-2, we then tested the performance of these primers with synthesized RNA fragments of the N gene, S gene and Orf1ab gene obtained from in vitro transcription (Appendix S1). The ultimate aim is to develop an enclosed device that integrates RNA extraction, purification, reverse transcription (RT) and loop-mediated isothermal amplification (LAMP) to detect the SARS-CoV-2 virus directly from a throat swab sample. abstract: The pandemic coronavirus SARS‐CoV‐2 in the world has caused a large infected population suffering from COVID‐19. To curb the spreading of the virus, WHO urgently demanded an extension of screening and testing; thus, a rapid and simple diagnostic method is needed. We applied a reverse transcription‐loop‐mediated isothermal amplification (RT‐LAMP) to achieve the detection of SARS‐CoV‐2 in 30 min. We designed four sets of LAMP primers (6 primers in each set), targeting the viral RNA of SARS‐CoV‐2 in the regions of orf1ab, S gene and N gene. A colorimetric change was used to report the results, which enables the outcome of viral RNA amplification to be read by the naked eye without the need of expensive or dedicated instrument. The sensitivity can be 80 copies of viral RNA per ml in a sample. We validated the RT‐LAMP method in a hospital in China, employing 16 clinic samples with 8 positives and 8 negatives. The testing results are consistent with the conventional RT‐qPCR. In addition, we also show that one‐step process without RNA extraction is feasible to achieve RNA amplification directly from a sample. This rapid, simple and sensitive RT‐LAMP method paves a way for a large screening at public domain and hospitals, particularly regional hospitals and medical centres in rural areas. url: https://www.ncbi.nlm.nih.gov/pubmed/32333644/ doi: 10.1111/1751-7915.13586 id: cord-287931-cxqzac4a author: Huang, Weiwei title: An easy operating pathogen microarray (EOPM) platform for rapid screening of vertebrate pathogens date: 2013-09-20 words: 5161.0 sentences: 256.0 pages: flesch: 45.0 cache: ./cache/cord-287931-cxqzac4a.txt txt: ./txt/cord-287931-cxqzac4a.txt summary: RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. To facilitate the application of EOPM in multiple surveillance sites for infectious diseases, we designed software with a user-friendly interface, which is supported by a statistical analysis method based on a comprehensive microbial sequence identification database. Analysis of the enrichment results at the genus level revealed Cardiovirus as the number one match, showing significant enrichment ( The microarray raw data of other symptom-causing pathogens, such as streptococcus and mycoplasma, identified by EOPM in peripheral blood in infectious patients, were also submitted to the GEO database. These microarray platforms use long oligonucleotide probes (60-70-mer) and random PCR amplification, and have successfully identified unexpected pathogens in infectious disease outbreaks, even discovering novel viruses with homology to known species [8, 11] . abstract: BACKGROUND: Infectious diseases emerge frequently in China, partly because of its large and highly mobile population. Therefore, a rapid and cost-effective pathogen screening method with broad coverage is required for prevention and control of infectious diseases. The availability of a large number of microbial genome sequences generated by conventional Sanger sequencing and next generation sequencing has enabled the development of a high-throughput high-density microarray platform for rapid large-scale screening of vertebrate pathogens. METHODS: An easy operating pathogen microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed, and further implemented in a user-friendly web-based interface. RESULTS: Using multiple probes designed to specifically detect a microbial genus or species, EOPM can correctly identify known pathogens at the species or genus level in blinded testing. Despite a lower sensitivity than PCR, EOPM is sufficiently sensitive to detect the predominant pathogens causing clinical symptoms. During application in two recent clinical infectious disease outbreaks in China, EOPM successfully identified the responsible pathogens. CONCLUSIONS: EOPM is an effective surveillance platform for infectious diseases, and can play an important role in infectious disease control. url: https://doi.org/10.1186/1471-2334-13-437 doi: 10.1186/1471-2334-13-437 id: cord-279623-ezax8c1u author: Huang, Yong title: Regulatory long non-coding RNA and its functions date: 2012-04-26 words: 3564.0 sentences: 201.0 pages: flesch: 47.0 cache: ./cache/cord-279623-ezax8c1u.txt txt: ./txt/cord-279623-ezax8c1u.txt summary: (CCND1) promoter can produce low-copy transcript lncRNAs in human cell lines which can be combined to the 5 ′end regulatory region of the CCND1 that are induced in response to DNA damage signals for the recruitment of the translocated-in-liposarcoma protein to the CCND1 promoter to cause gene-specific Fig. 1 Paradigms for functions of lncRNAs expression inhibiting the CREB-binding protein and p300 histone acetyltransferase activities [59] . The results directly implicate long non-coding RNAmediated transcriptional regulation of gene expression as a fundamental control mechanism for physiologic processes, such as vascular development [32] . To sum up, intense investigation of the lncRNA transcription will likely expand our understanding of both the cell biology and functions of lncRNAs. Non-coding RNAs revealed during identification of genes involved in chicken immune responses Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells abstract: The discovery of large numbers of long non-coding RNAs (lncRNAs) has been driven by genome-wide transcriptional analyses. Compared to small ncRNAs, lncRNAs have been shown to harbor biological activities, but the functions of the great majority of lncRNAs are not known. There is growing evidence that lncRNAs can regulate gene expression at epigenetic, transcription, and post-transcription levels and widely take part in various physiological and pathological processes, such as participating in cell development, immunity, oncogenesis, clinical disease processes, etc. Here, the current research efforts on the function of lncRNA in recent years were summarized. url: https://doi.org/10.1007/s13105-012-0166-y doi: 10.1007/s13105-012-0166-y id: cord-352664-heoj8ji8 author: Hubbard, Amelia title: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population date: 2015-02-25 words: 9181.0 sentences: 460.0 pages: flesch: 45.0 cache: ./cache/cord-352664-heoj8ji8.txt txt: ./txt/cord-352664-heoj8ji8.txt summary: In this study, we developed a robust and rapid ''field pathogenomics'' strategy, using transcriptome sequencing of PST-infected wheat leaves to gain insight into the population structure of an emerging pathogen. To characterize the genotypic diversity of PST at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the UK in the spring and summer of 2013 ( Figure 1a ; Table S1 in Additional file 1). To determine the relationship between the 2013 PST field isolates and previously prevalent PST populations, the genomes of 14 UK and 7 French purified PST isolates collected between 1978 and 2011 were sequenced using an Illumina whole-genome shotgun approach Figure 2 Identification of wheat varieties using transcriptome data generated directly from PST-infected field samples. We used multivariate discriminant analysis of principal components (DAPC) with the 34,764 biallelic SNP sites to define the population structure and identify groups of genetically related PST isolates. abstract: BACKGROUND: Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. RESULTS: To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. CONCLUSIONS: Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0590-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/25723868/ doi: 10.1186/s13059-015-0590-8 id: cord-048485-b8xb1f12 author: Hulst, Marcel title: Early transcriptional response in the jejunum of germ-free piglets after oral infection with virulent rotavirus date: 2008-06-04 words: 6269.0 sentences: 313.0 pages: flesch: 45.0 cache: ./cache/cord-048485-b8xb1f12.txt txt: ./txt/cord-048485-b8xb1f12.txt summary: RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. However, the fluorescence intensity was not higher than the background threshold for any of these probes, indicating that mRNA concentrations of these cytokines (including IFN-c) in infected and uninfected mucosal scrapings were too low to detect by microarray analysis, probably due to the relatively low percentage of cytokine-producing (immune) cells present in intestinal mucosa [6] . Using microarray analysis, we detected a set of genes that are differently expressed in rotavirus-infected jejunal mucosa compared to uninfected mucosa. Perhaps, enhanced expression of a PLA2-inh in our study may be a countermeasure of specific intestinal epithelial cells to normalize and/or inhibit PLA2 enzyme activity in response to extra-and intracellular changes in [Ca 2+ ] evoked by rotavirus replication, either to protect specific cells from extra-and intracellular membrane-damage or to negatively regulate A-acid production. abstract: Germ-free piglets were orally infected with virulent rotavirus to collect jejunal mucosal scrapings at 12 and 18 hours post infection (two piglets per time point). IFN-gamma mRNA expression was stimulated in the mucosa of all four infected piglets, indicating that they all responded to the rotavirus infection. RNA pools prepared from two infected piglets were used to compare whole mucosal gene expression at 12 and 18 hpi to expression in uninfected germ-free piglets (n = 3) using a porcine intestinal cDNA microarray. Microarray analysis identified 13 down-regulated and 17 up-regulated genes. Northern blot analysis of a selected group of genes confirmed the data of the microarray. Genes were functionally clustered in interferon-regulated genes, proliferation/differentiation genes, apoptosis genes, cytoskeleton genes, signal transduction genes, and enterocyte digestive, absorptive, and transport genes. Down-regulation of the transport gene cluster reflected in part the loss of rotavirus-infected enterocytes from the villous tips. Data mining suggested that several genes were regulated in lower- or mid-villus immature enterocytes and goblet cells, probably to support repair of the damaged epithelial cell layer at the villous tips. Furthermore, up-regulation was observed for IFN-γ induced guanylate binding protein 2, a protein that effectively inhibited VSV and EMCV replication in vitro (Arch Virol 150:1213–1220, 2005). This protein may play a role in the small intestine’s innate defense against enteric viruses like rotavirus. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-008-0118-6) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441536/ doi: 10.1007/s00705-008-0118-6 id: cord-304283-nv4ret1f author: Hung, Chuan-Fu title: A novel siRNA validation system for functional screening and identification of effective RNAi probes in mammalian cells date: 2006-08-04 words: 7080.0 sentences: 367.0 pages: flesch: 45.0 cache: ./cache/cord-304283-nv4ret1f.txt txt: ./txt/cord-304283-nv4ret1f.txt summary: Since only a readily available short synthetic DNA fragment is needed for constructing this novel reporter-based siRNA validation system, this system not only provides a powerful strategy for screening highly effective siRNAs but also implicates in the use of RNAi for studying novel gene function in mammals. Since only a readily available short synthetic DNA fragment is needed for constructing both the targeting reporter and triggering siRNA expression vectors, this novel system should not only greatly facilitate large-scale lossof-function genetic screens in mammalian cells but also provide the basis for an improved approach to screen and identify the most potent siRNA for the purpose of the therapeutics. As the results shown in Fig. 5A , the siLMP1-2 exhibited no inhibition effects on pEGFP-3UTR-siLMP1-2-induced EGFP and pLuc+-3UTR-siLMP1-2-induced firefly luciferase expression as compared with the two standard positive controls, siEGFP and siLuc, indicating that the selected RNAi targeting sequence siLMP1-2 was inactive and non-functional. abstract: Abstract Small interfering RNAs (siRNAs) have become the most powerful and widely used gene silencing reagents for reverse functional genomics and molecular therapeutics. The key challenge for achieving effective gene silencing in particular for the purpose of the therapeutics is primarily dependent on the effectiveness and specificity of the RNAi targeting sequence. However, only a limited number of siRNAs is capable of inducing highly effective and sequence-specific gene silencing by RNA interference (RNAi) mechanism. In addition, the efficacy of siRNA-induced gene silencing can only be experimentally measured based on inhibition of the target gene expression. Therefore, it is important to establish a fully robust and comparative validating system for determining the efficacy of designed siRNAs. In this study, we have developed a reliable and quantitative reporter-based siRNA validation system that consists of a short synthetic DNA fragment containing an RNAi targeting sequence of interest and two expression vectors for targeting reporter and triggering siRNA expression. The efficacy of the siRNAs is measured by their abilities to inhibit expression of the targeting reporter gene with easily quantified readouts including enhanced green fluorescence protein (EGFP) and firefly luciferase. Using fully analyzed siRNAs against human hepatitis B virus (HBV) surface antigen (HBsAg) and tumor suppressor protein p53, we have demonstrated that this system could effectively and faithfully report the efficacy of the corresponding siRNAs. In addition, we have further applied this system for screening and identification of the highly effective siRNAs that could specifically inhibit expression of mouse matrix metalloproteinase-7 (MMP-7), Epstein–Barr virus (EBV) latent membrane protein 1 (LMP1), and human serine/threonine kinase AKT1. Since only a readily available short synthetic DNA fragment is needed for constructing this novel reporter-based siRNA validation system, this system not only provides a powerful strategy for screening highly effective siRNAs but also implicates in the use of RNAi for studying novel gene function in mammals. url: https://www.ncbi.nlm.nih.gov/pubmed/16793020/ doi: 10.1016/j.bbrc.2006.05.164 id: cord-346930-gl573ip9 author: Hussain, Azhar title: Emerging Pharmaceutical Treatments of Novel COVID-19: A Review date: 2020-05-24 words: 4177.0 sentences: 207.0 pages: flesch: 45.0 cache: ./cache/cord-346930-gl573ip9.txt txt: ./txt/cord-346930-gl573ip9.txt summary: Although multiple drugs show promise in the treatment of COVID-19 via either inhibiting viral replication or preventing fusion of the virus to the ACE2 receptors, further investigation is still warranted and necessary before the admission of any type of pharmaceutical agent. This review explores various drugs and their mechanism of action which are either currently being used in clinical trials or may be used in the future for the treatment of COVID-19. Since the emergence of the virus in China in December of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread across the globe resulting in the current global pandemic. Arbidol (also known as Umifenovir) is a promising repurposed antiviral agent with a unique mechanism of action targeting the S protein/ACE2 interaction and inhibiting membrane fusion of the viral envelope to the host cell [7] . abstract: As a new decade began, COVID-19 quickly gained importance as it became the cause of the current global pandemic. Research has been focusing on studying the structure of SARS-CoV-2 and investigates possible pharmaceutical approaches. With the number of cases increasing every day, globally, multiple drugs are being researched as possible candidates. Although multiple drugs show promise in the treatment of COVID-19 via either inhibiting viral replication or preventing fusion of the virus to the ACE2 receptors, further investigation is still warranted and necessary before the admission of any type of pharmaceutical agent. Furthermore, several supplements have also been documented in being utilized as treatment of COVID-19. The exact mechanism and efficacy of current candidate drugs are still being explored through clinical trials. Despite the advancements in current research with emerging treatments, social distancing and engaging in preventative measures remains crucial to attempt to prevent the occurrence of more cases and deaths, worldwide. This review explores various drugs and their mechanism of action which are either currently being used in clinical trials or may be used in the future for the treatment of COVID-19. url: https://doi.org/10.7759/cureus.8260 doi: 10.7759/cureus.8260 id: cord-292353-z86rjwle author: Hussein, Islam T.M. title: Recent Advances in Hantavirus Molecular Biology and Disease date: 2011-04-01 words: 13579.0 sentences: 708.0 pages: flesch: 47.0 cache: ./cache/cord-292353-z86rjwle.txt txt: ./txt/cord-292353-z86rjwle.txt summary: Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). The sequences at both the 3 0 and 5 0 termini of each RNA segment are complementary forming ''''panhandle'''' structures that are specifically recognized by the N protein and were shown to be important for viral transcription and replication. Further studies revealed that cellular 5 0capped mRNA oligoribonucleotides are rescued by N in virus-infected cells and stored in P-bodies for the later use as primers by the viral RdRp during transcription initiation . The UTRs are encapsidated by nucleocapsid protein and associate with RdRp both in the host cells and in the virion, and only these nucleocapsids are believed to be functional templates for mRNA synthesis and RNA replication by the viral RdRp. c. abstract: Hantaviruses are emerging zoonotic pathogens that belong to the Bunyaviridae family. They have been classified as category A pathogens by CDC (centers for disease control and prevention). Hantaviruses pose a serious threat to human health because their infection causes two highly fatal diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). These pathogens are transmitted to humans through aerosolized excreta of their infected rodent hosts. Hantaviruses have a tripartite-segmented negative-sense RNA genome. The three genomic RNA segments, S, M, and L, encode a nucleocapsid protein (N), a precursor glycoprotein that is processed into two envelope glycoproteins (Gn and Gc) and the viral RNA-dependent RNA polymerase (RdRp), respectively. N protein is the major structural component of the virus, its main function is to protect and encapsidate the three genomic RNAs forming three viral ribonucleocapsids. Recent studies have proposed that N in conjunction with RdRp plays important roles in the transcription and replication of viral genome. In addition, N preferentially facilitates the translation of viral mRNA in cells. Glycoproteins, Gn and Gc, play major roles in viral attachment and entry to the host cells, virulence, and assembly and packaging of new virions in infected cells. RdRp functions as RNA replicase and transcriptase to replicate and transcribe the viral RNA and is also thought to have endonuclease activity. Currently, no antiviral therapy or vaccine is available for the treatment of hantavirus-associated diseases. Understanding the molecular details of hantavirus life cycle will help in the identification of targets for antiviral therapeutics and in the design of potential antiviral drug for the treatment of HFRS and HCPS. Due to the alarming fatality of hantavirus diseases, development of an effective vaccine against hantaviruses is a necessity. url: https://www.sciencedirect.com/science/article/pii/B9780123870223000069 doi: 10.1016/b978-0-12-387022-3.00006-9 id: cord-350762-rh4zbehk author: Hutcheson, Jessica M. title: Delayed Newcastle disease virus replication using RNA interference to target the nucleoprotein date: 2015-06-04 words: 4301.0 sentences: 229.0 pages: flesch: 52.0 cache: ./cache/cord-350762-rh4zbehk.txt txt: ./txt/cord-350762-rh4zbehk.txt summary: In this study, we utilize microRNA (miRNA)-expressing constructs (a type of RNA interference) in an attempt to target and knockdown five NDV structural RNAs for nucleoprotein (NP), phosphoprotein (P), matrix (M), fusion (F), and large (L) protein genes. Using pre-miRNA to activate the cellular RNAi pathway, a miRNA can be used to target the messenger RNA of NDV structural proteins, leading to the degradation of the transcripts and inhibiting viral replication [11] . In this study, we attempted to determine if constitutive expression of miRNA sequences targeting the mRNA of five of the structural NDV proteins in chicken embryo fibroblast cells (DF-1) would lead to decreased viral yield after infection, and/or resistance against NDV cytopathic effects. Inhibition of Newcastle disease virus replication by RNA interference targeting the matrix protein gene in chicken embryo fibroblasts abstract: Each year millions of chickens die from Newcastle disease virus (NDV) worldwide leading to severe economic and food losses. Current vaccination campaigns have limitations especially in developing countries, due to elevated costs, need of trained personnel for effective vaccine administration, and functional cold chain network to maintain vaccine viability. These problems have led to heightened interest in producing new antiviral strategies, such as RNA interference (RNAi). RNAi methodology is capable of substantially decreasing viral replication at a cellular level, both in vitro and in vivo. In this study, we utilize microRNA (miRNA)-expressing constructs (a type of RNA interference) in an attempt to target and knockdown five NDV structural RNAs for nucleoprotein (NP), phosphoprotein (P), matrix (M), fusion (F), and large (L) protein genes. Immortalized chicken embryo fibroblast cells (DF-1) that transiently expressed miRNA targeting NP mRNA, showed increased resistance to NDV-induced cytopathic effects, as determined by cell count, relative to the same cells expressing miRNA against alternative NDV proteins. Upon infection with NDV, DF-1 cells constitutively expressing the NP miRNA construct had improved cell survival up to 48 h post infection (h.p.i) and decreased viral yield up to 24 h.p.i. These results suggest that overexpression of the NP miRNA in cells and perhaps live animal may provide resistance to NDV. url: https://doi.org/10.1016/j.biologicals.2015.03.004 doi: 10.1016/j.biologicals.2015.03.004 id: cord-322206-roxa3ix6 author: I. Sardi, Silvia title: High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics date: 2020-07-21 words: 4199.0 sentences: 212.0 pages: flesch: 46.0 cache: ./cache/cord-322206-roxa3ix6.txt txt: ./txt/cord-322206-roxa3ix6.txt summary: Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. Here, we applied RNA-based metatranscriptomics associated with Ion Torrent deep sequencing and a newly developed Bioinformatics approach to the high-quality reconstitution of viral genomes. abstract: Arboviruses, including the Zika virus, have recently emerged as one of the most important threats to human health. The use of metagenomics-based approaches has already proven valuable to aid surveillance of arboviral infections, and the ability to reconstruct complete viral genomes from metatranscriptomics data is key to the development of new control strategies for these diseases. Herein, we used RNA-based metatranscriptomics associated with Ion Torrent deep sequencing to allow for the high-quality reconstitution of an outbreak-related Zika virus (ZIKV) genome (10,739 nt), with extended 5′-UTR and 3′-UTR regions, using a newly-implemented bioinformatics approach. Besides allowing for the assembly of one of the largest complete ZIKV genomes to date, our strategy also yielded high-quality complete genomes of two arthropod-infecting viruses co-infecting C6/36 cell lines, namely: Alphamesonivirus 1 strain Salvador (20,194 nt) and Aedes albopictus totivirus-like (4618 nt); the latter likely represents a new viral species. Altogether, our results demonstrate that our bioinformatics approach associated with Ion Torrent sequencing allows for the high-quality reconstruction of known and unknown viral genomes, overcoming the main limitation of RNA deep sequencing for virus identification. url: https://www.ncbi.nlm.nih.gov/pubmed/32708079/ doi: 10.3390/v12070782 id: cord-337285-t6qr41wc author: Ikeda, Masanori title: Modulation of host metabolism as a target of new antivirals() date: 2007-10-10 words: 8180.0 sentences: 466.0 pages: flesch: 46.0 cache: ./cache/cord-337285-t6qr41wc.txt txt: ./txt/cord-337285-t6qr41wc.txt summary: Using cell culture systems, several cellular proteins have been identified as effective molecules for HCV RNA replication (Table 1) . [66] reported that lovastatin (LOV), one of the HMG-CoA reductase inhibitors, inhibited HCV RNA replication in HCV replicon-harboring cells. Depletion of the GGPP by statins may inhibit the geranylgeranylation of cellular proteins such as FBL2 and cause the anti-HCV effect in the cells. During the development of IFN therapy for patients with CH-C, the lack of a robust method of HCV RNA replication in cell culture has hampered research into the HCV life cycle and the discovery of potent new anti-HCV reagents. VX-950, a novel hepatitis C virus (HCV) NS3-4A protease inhibitor, exhibits potent antiviral activities in HCV replicon cells Selectable subgenomic and genome-length dicistronic RNAs derived from an infectious molecular clone of the HCV-N strain of hepatitis C virus replicate efficiently in cultured Huh7 cells abstract: The therapy for chronic hepatitis C (CH–C) started with interferon (IFN) monotherapy in the early 1990s and this therapy was considered effective in about 10% of cases. The present standard therapy of pegylated IFN with ribavirin achieves a sustained virologic response in about 50% of patients. However, about half of the CH–C patients are still at risk of fatal liver cirrhosis and hepatocellular carcinoma. The other significant event in hepatitis C virus (HCV) research has been the development of a cell culture system. The subgenomic replicon system enables robust HCV RNA replication in hepatoma cells. And recently, the complete life cycle of HCV has been achieved using a genotype 2a strain, JFH1. These hallmarks have provided much information about the mechanisms of HCV replication, including information on the host molecules required for the replication. Anti-HCV reagents targeting HCV proteins have been developed, and some of them are now in clinical trials. However, the RNA-dependent RNA polymerase frequently causes mutations in the HCV genome, which lead to the emergence of drug-resistant HCV mutants. Some of the cellular proteins essential for HCV RNA replication have already been discovered using the HCV cell culture system. These host molecules are also candidate targets for antivirals. Here, we describe the recent progress regarding the anti-HCV reagents targeting host metabolism. url: https://www.sciencedirect.com/science/article/pii/S0169409X07001317 doi: 10.1016/j.addr.2007.03.021 id: cord-338727-1kodz527 author: Ilinskaya, O. N. title: Ribonucleases as antiviral agents date: 2014-10-11 words: 4605.0 sentences: 227.0 pages: flesch: 44.0 cache: ./cache/cord-338727-1kodz527.txt txt: ./txt/cord-338727-1kodz527.txt summary: Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. Therefore, the formation of RNA fragments enhanced by RNase L, followed by their interaction with RIG I and MDA5, activates transcription factor NF κB and triggers transcription of interferon β gene, which prevents virus replication and stimulates the growth of immune system cells [9] . Previously, onconase, an RNases from oocytes of the leopard frog Rana pipiens, efficiently suppresses the replication of HIV 1 due to the selective degrada tion of viral RNA, which exhibits no pronounced cytotoxic effect on infected human cells [22] . At the first stage, when binase meets the virus outside cell, its catalytic activity is not inhibited by the natural RNase and it may destroy viral RNA (Fig. 3, C) . Ribonucleases in HIV type 1 inhibition: Effect of recombinant RNases on infection of primary T cells and immune activation induced RNase gene and protein expression abstract: Many ribonucleases (RNases) are able to inhibit the reproduction of viruses in infected cell cultures and laboratory animals, but the molecular mechanisms of their antiviral activity remain unclear. The review discusses the well-known RNases that possess established antiviral effects, including both intracellular RNases (RNase L, MCPIP1 protein, and eosinophil-associated RNases) and exogenous RNases (RNase A, BS-RNase, onconase, binase, and synthetic RNases). Attention is paid to two important, but not always obligatory, aspects of molecules of RNases that have antiviral properties, i.e., catalytic activity and ability to dimerize. The hypothetic scheme of virus elimination by exogenous RNases that reflects possible types of interaction of viruses and RNases with a cell is proposed. The evidence for RNases as classical components of immune defense and thus perspective agents for the development of new antiviral therapeutics is proposed. url: https://doi.org/10.1134/s0026893314040050 doi: 10.1134/s0026893314040050 id: cord-048222-1pq6dkl5 author: Imbeaud, Sandrine title: Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces date: 2005-03-30 words: 7001.0 sentences: 313.0 pages: flesch: 47.0 cache: ./cache/cord-048222-1pq6dkl5.txt txt: ./txt/cord-048222-1pq6dkl5.txt summary: With that prospect in mind, and with the aim of anticipating future standards by pre-normative research, we identified and tested two software packages recently developed to gauge the integrity of RNA samples with a user-independent strategy: one open source, the degradometer software for calculation of the degradation factor and ''true'' 28S:18S ratio based on peak heights (24) and the freely available RIN algorithm of the Agilent 2100 expert software, based on computation of a ''RNA Integrity Number'' (RIN) (25) . A RIN number is computed for each RNA profile (see Supplementary Table 4 online) resulting in the classification of RNA samples in 10 numerically predefined categories of integrity. The values of the mean fold changes, calculated according to the 2 ÀDDCt quantification method (see Materials and Methods), were found lower than 1.0, corresponding to the expression level (1·) in the sample exhibiting the highest RNA quality (Table 2 and Figure 5 ). abstract: While it is universally accepted that intact RNA constitutes the best representation of the steady-state of transcription, there is no gold standard to define RNA quality prior to gene expression analysis. In this report, we evaluated the reliability of conventional methods for RNA quality assessment including UV spectroscopy and 28S:18S area ratios, and demonstrated their inconsistency. We then used two new freely available classifiers, the Degradometer and RIN systems, to produce user-independent RNA quality metrics, based on analysis of microcapillary electrophoresis traces. Both provided highly informative and valuable data and the results were found highly correlated, while the RIN system gave more reliable data. The relevance of the RNA quality metrics for assessment of gene expression differences was tested by Q-PCR, revealing a significant decline of the relative expression of genes in RNA samples of disparate quality, while samples of similar, even poor integrity were found highly comparable. We discuss the consequences of these observations to minimize artifactual detection of false positive and negative differential expression due to RNA integrity differences, and propose a scheme for the development of a standard operational procedure, with optional registration of RNA integrity metrics in public repositories of gene expression data. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1072807/ doi: 10.1093/nar/gni054 id: cord-290948-cuu78cvl author: Imbert, Isabelle title: The SARS-Coronavirus PLnc domain of nsp3 as a replication/transcription scaffolding protein date: 2008-02-05 words: 7091.0 sentences: 356.0 pages: flesch: 53.0 cache: ./cache/cord-290948-cuu78cvl.txt txt: ./txt/cord-290948-cuu78cvl.txt summary: Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. SARS-CoV nsp3 is a large multidomain protein of 1922 amino acids Thiel et al., 2003) that is thought to contain at least seven domains: (1) an N-terminal Glu-rich acidic domain (AD); (2) an X domain (XD) with poly(ADP-ribose) binding properties Saikatendu et al., 2005) ; (3) the SUD domain (for SARS-CoV Unique Domain, an insertion not found in any other coronavirus thus far) with a specific affinity for oligo(G)-strings (Tan et al., in press); (4) a papain-like protease (PLP2), recently shown to exhibit deubiquitinating activity (Barretto et al., 2005; Harcourt et al., 2004; Lindner et al., 2005; Ratia et al., 2006) ; (5) an unknown domain possibly extending the papain-like protease domain, termed PLnc for Papain-Like noncanonical (see below); (6) a transmembrane domain (Kanjanahaluethai et al., 2007) corresponding to the N-terminal of the Y domain; and (7) the remainder of the Y domain, the abbreviation "Y domain" will be used for this part in this study. abstract: Many genetic and mechanistic features distinguish the coronavirus replication machinery from that encoded by most other RNA viruses. The coronavirus replication/transcription complex is an assembly of viral and, most probably, cellular proteins that mediate the synthesis of both the unusually large (∼30 kb) RNA genome and an extensive set of subgenomic mRNAs. The viral components of the complex are encoded by the giant replicase gene, which is expressed in the form of two polyproteins (pp1a and pp1ab) that are processed into 16 cleavage products (nonstructural proteins 1–16). Using the combination of yeast two-hybrid screening and GST pull-down assays, we have now analyzed all potential interactions between SARS-Coronavirus nonstructural proteins, which may contribute to the structure and/or function of the viral replication/transcription complex. We demonstrate the existence of a complex network of interactions involving all 16 nonstructural proteins. Our results both confirmed previously described associations and identified novel heterodimerizations. The interaction map thus provides a sum of the interactions that may occur at some point during coronavirus RNA synthesis and provides a framework for future research. url: https://doi.org/10.1016/j.virusres.2007.11.017 doi: 10.1016/j.virusres.2007.11.017 id: cord-285262-690kpupt author: Imre, Gergely title: The involvement of regulated cell death forms in modulating the bacterial and viral pathogenesis date: 2020-01-27 words: 13203.0 sentences: 714.0 pages: flesch: 38.0 cache: ./cache/cord-285262-690kpupt.txt txt: ./txt/cord-285262-690kpupt.txt summary: Apoptosis, necroptosis and pyroptosis represent three distinct types of regulated cell death forms, which play significant roles in response to viral and bacterial infections. Abstract Apoptosis, necroptosis and pyroptosis represent three distinct types of regulated cell death forms, which play significant roles in response to viral and bacterial infections. In this chapter, based on the current advances in the research, we give a detailed description about the key cell death modalities, including apoptosis, necroptosis and pyroptosis emerging in response to pathogenic insults, and we discuss how bacterial and viral infections can modulate these signaling pathways. The components of the bacterial T3SS trigger inflammasome formation and pyroptotic cell death in Shigella infected macrophages through the activation of the NLR family CARD domain containing protein 4 (NLRC4) (Fig. 3) . Macrophage activation redirects yersinia-infected host cell death from apoptosis to caspase-1-dependent pyroptosis abstract: Apoptosis, necroptosis and pyroptosis represent three distinct types of regulated cell death forms, which play significant roles in response to viral and bacterial infections. Whereas apoptosis is characterized by cell shrinkage, nuclear condensation, bleb formation and retained membrane integrity, necroptosis and pyroptosis exhibit osmotic imbalance driven cytoplasmic swelling and early membrane damage. These three cell death forms exert distinct immune stimulatory potential. The caspase driven apoptotic cell demise is considered in many circumstances as anti-inflammatory, whereas the two lytic cell death modalities can efficiently trigger immune response by releasing damage associated molecular patterns to the extracellular space. The relevance of these cell death modalities in infections can be best demonstrated by the presence of viral proteins that directly interfere with cell death pathways. Conversely, some pathogens hijack the cell death signaling routes to initiate a targeted attack against the immune cells of the host, and extracellular bacteria can benefit from the destruction of intact extracellular barriers upon cell death induction. The complexity and the crosstalk between these cell death modalities reflect a continuous evolutionary race between pathogens and host. This chapter discusses the current advances in the research of cell death signaling with regard to viral and bacterial infections and describes the network of the cell death initiating molecular mechanisms that selectively recognize pathogen associated molecular patterns. url: https://api.elsevier.com/content/article/pii/S1937644819301273 doi: 10.1016/bs.ircmb.2019.12.008 id: cord-298036-2zurc60t author: Imre, Gergely title: Cell death signalling in virus infection date: 2020-09-12 words: 8002.0 sentences: 414.0 pages: flesch: 37.0 cache: ./cache/cord-298036-2zurc60t.txt txt: ./txt/cord-298036-2zurc60t.txt summary: Subsequently, granzyme-B induces mitochondrial apoptosis by performing cleavage of the BCL-2 homology domain-3 (BH3)-only protein, BH3 interacting domain death agonist (BID), which then leads to BAX/BAK-mediated MOMP and the initiation of the caspase-9-driven apoptotic pathway [16] . Still, the mechanism, by which IRF-3 triggers cell death signalling pathways is only partially understood and the studies indicate a strong cell type specificity in the apoptosis sensitivity in response to viral PAMPs Z-RNA and z-DNA fragments, which are distinct from the B-structure of eukaryotic RNA and DNA are recognized by z-DNA/RNA binding protein-1 (ZBP1; also: DAI). Necroptosis initiation takes place upon TNFR ligation, which, however, primarily leads to NFkB activation via the assembly of so called complex-I, including adaptor proteins TNFRSF1A associated via death domain (TRADD), TRAF2, cellular IAP (cIAP) and ubiquitinated receptor interacting serine/threonine kinase 1 (RIPK1) [10] . abstract: Apoptosis, necroptosis and pyroptosis represent three major regulated cell death modalities. Apoptosis features cell shrinkage, nuclear fragmentation and cytoplasm-blebbing. Necroptosis and pyroptosis exhibit osmotic imbalances in the cell accompanied by early membrane ruptures, which morphologically resembles necrosis. Importantly, these two lytic cell death forms facilitate the release of damage associated molecular patterns into the extracellular space leading to inflammatory response. Whereas, during apoptosis, the membrane integrity is preserved and the apoptotic cell is removed by neighbouring cells ensuring the avoidance of immune-stimulation. Viruses comprise a versatile group of intracellular pathogens, which elicit various strategies to infect and to propagate. Viruses are recognized by a myriad of pathogen recognition receptors in the human cells, which consequently lead to activation of the immune system and in certain circumstances cell-autonomous cell death. Importantly, the long-standing view that a cell death inducing capacity of a virus is equal to its pathogenic potential seems to be only partially valid. The altruistic cell death of an infected cell may serve the whole organism by ultimately curbing the way of virus manufacturing. In fact, several viruses express “anti-cell death” proteins to avoid this viral-defence mechanism. Conversely, some viruses hijack cell death pathways to selectively destroy cell populations in order to compromise the immune system of the host. This review discusses the pros and cons of virus induced cell death from the perspective of the host cells and attempts to provide a comprehensive overview of the complex network of cell death signalling in virus infection. url: https://api.elsevier.com/content/article/pii/S0898656820302497 doi: 10.1016/j.cellsig.2020.109772 id: cord-307860-iqk1yiw4 author: Ionescu, Mihaela Ileana title: An Overview of the Crystallized Structures of the SARS-CoV-2 date: 2020-10-24 words: 9856.0 sentences: 668.0 pages: flesch: 57.0 cache: ./cache/cord-307860-iqk1yiw4.txt txt: ./txt/cord-307860-iqk1yiw4.txt summary: Structures retrieved from PDB (August 12, 2020) were analyzed for relevant information on COVID-19 infection, synthesis of new inhibitors, SARS-CoV-2 interaction with host receptors, and the neutralizing antibodies interactions with spike glycoprotein. The first X-ray structure found (PDB ID 6LU7) belongs to the nonstructural protein 5 (3C-like protease) of the SARS-CoV-2 in complex with the Michael acceptor-based inhibitor N3 (PRD_002214). There is a cryo-EM crystal structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex (nsp12/nsp8/nsp7) with the antiviral drug remdesivir (PDB ID 7BV2) [37] . Previous studies on the crystal structures of SARS-CoV S glycoprotein mutants neutralized by 80R-specific antibodies have been considered a hope for the immunotherapeutic Fig. 8 The phylogenetic tree (cladogram) of the CoVs Spike (S) sequences of CoVs with different origin. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites abstract: Many research teams all over the world focus their research on the SARS-CoV-2, the new coronavirus that causes the so-called COVID-19 disease. Most of the studies identify the main protease or 3C-like protease (M(pro)/3CL(pro)) as a valid target for large-spectrum inhibitors. Also, the interaction of the human receptor angiotensin-converting enzyme 2 (ACE2) with the viral surface glycoprotein (S) is studied in depth. Structural studies tried to identify the residues responsible for enhancement/weaken virus-ACE2 interactions or the cross-reactivity of the neutralizing antibodies. Although the understanding of the immune system and the hyper-inflammatory process in COVID-19 are crucial for managing the immediate and the long-term consequences of the disease, not many X-ray/NMR/cryo-EM crystals are available. In addition to 3CL(pro), the crystal structures of other nonstructural proteins offer valuable information for elucidating some aspects of the SARS-CoV-2 infection. Thus, the structural analysis of the SARS-CoV-2 is currently mainly focused on three directions—finding M(pro)/3CL(pro) inhibitors, the virus-host cell invasion, and the virus-neutralizing antibody interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10930-020-09933-w) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/33098476/ doi: 10.1007/s10930-020-09933-w id: cord-325624-6anybxnk author: Ireland, Derek D. C. title: RNase L Mediated Protection from Virus Induced Demyelination date: 2009-10-02 words: 8082.0 sentences: 397.0 pages: flesch: 43.0 cache: ./cache/cord-325624-6anybxnk.txt txt: ./txt/cord-325624-6anybxnk.txt summary: The unique phenotype of infected RL(−/−) mice was rather manifested in earlier onset and increased severity of demyelination and axonal damage in brain stem and spinal cord without evidence for enhanced neuronal infection. RNase L specifically protected the brain stem from sustained infection and prevented spread of virus to microglia/macrophages located in spinal cord grey matter. The increased pathological changes in both brain stem and spinal cord thus correlated with the high mortality rates of RL 2/2 mice starting at day 9 p.i. The inability to directly link increased axonal damage with enhanced neuronal infection remains puzzling and supports dysregulation of oligodendrocyte function and/or neuroprotective functions of microglia as contributing factors to the severe pathological phenotype and clinical outcome. Numerous functions of RNase L, not directly associated with anti-viral activity, may contribute to the increased susceptibility of RL 2/2 mice to MHV-JHM infection. abstract: IFN-α/β plays a critical role in limiting viral spread, restricting viral tropism and protecting mice from neurotropic coronavirus infection. However, the IFN-α/β dependent mechanisms underlying innate anti-viral functions within the CNS are poorly understood. The role of RNase L in viral encephalomyelitis was explored based on its functions in inhibiting translation, inducing apoptosis, and propagating the IFN-α/β pathway through RNA degradation intermediates. Infection of RNase L deficient (RL(−/−)) mice with a sub-lethal, demyelinating mouse hepatitis virus variant revealed that the majority of mice succumbed to infection by day 12 p.i. However, RNase L deficiency did not affect overall control of infectious virus, or diminish IFN-α/β expression in the CNS. Furthermore, increased morbidity and mortality could not be attributed to altered proinflammatory signals or composition of cells infiltrating the CNS. The unique phenotype of infected RL(−/−) mice was rather manifested in earlier onset and increased severity of demyelination and axonal damage in brain stem and spinal cord without evidence for enhanced neuronal infection. Increased tissue damage coincided with sustained brain stem infection, foci of microglia infection in grey matter, and increased apoptotic cells. These data demonstrate a novel protective role for RNase L in viral induced CNS encephalomyelitis, which is not reflected in overall viral control or propagation of IFN-α/β mediated signals. Protective function is rather associated with cell type specific and regional restriction of viral replication in grey matter and ameliorated neurodegeneration and demyelination. url: https://www.ncbi.nlm.nih.gov/pubmed/19798426/ doi: 10.1371/journal.ppat.1000602 id: cord-318359-41h90h05 author: Irigoyen, Nerea title: Ribosome profiling of the retrovirus murine leukemia virus date: 2018-01-22 words: 4488.0 sentences: 238.0 pages: flesch: 54.0 cache: ./cache/cord-318359-41h90h05.txt txt: ./txt/cord-318359-41h90h05.txt summary: Here, we report the first high resolution analysis of retrovirus gene expression through tandem ribosome profiling (RiboSeq) and RNA sequencing (RNASeq) of MuLV-infected cells. Translation may proceed contiguously from this codon through the gag ORF; thus, presumably, giving rise to an alternative Glyco-Gag isoform which is N-terminally extended by a further 12 amino acids (MELTSSEHPAAT, assuming GUG is decoded by Met-tRNA i ) relative to the canonical Glyco-Gag. The GUG codon is present in some but not all MuLV strains, and is not well conserved among other gammaretroviral lineages for which sequence data are currently available (Additional file 1: Fig. S3-highlighted in green) , although some sequences have alternative nearby potential non-AUG initiation sites. Our data indicate the existence of new translation initiation sites, new translated short ORFs and the first measurement of the gag-pol stop codon readthrough efficiency in the context of the full-length virus genome during infection. abstract: BACKGROUND: The retrovirus murine leukemia virus (MuLV) has an 8.3 kb RNA genome with a simple 5′-gag-pol-env-3′ architecture. Translation of the pol gene is dependent upon readthrough of the gag UAG stop codon; whereas the env gene is translated from spliced mRNA transcripts. Here, we report the first high resolution analysis of retrovirus gene expression through tandem ribosome profiling (RiboSeq) and RNA sequencing (RNASeq) of MuLV-infected cells. RESULTS: Ribosome profiling of MuLV-infected cells was performed, using the translational inhibitors harringtonine and cycloheximide to distinguish initiating and elongating ribosomes, respectively. Meta-analyses of host cell gene expression demonstrated that the RiboSeq datasets specifically captured the footprints of translating ribosomes at high resolution. Direct measurement of ribosomal occupancy of the MuLV genomic RNA indicated that ~ 7% of ribosomes undergo gag stop codon readthrough to access the pol gene. Initiation of translation was found to occur at several additional sites within the 5′ leaders of the gag and env transcripts, upstream of their respective annotated start codons. CONCLUSIONS: These experiments reveal the existence of a number of previously uncharacterised, ribosomally occupied open reading frames within the MuLV genome, with possible regulatory consequences. In addition, we provide the first direct measurements of stop codon readthrough efficiency during cellular infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12977-018-0394-5) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/29357872/ doi: 10.1186/s12977-018-0394-5 id: cord-333473-c1lykari author: Irigoyen, Nerea title: High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling date: 2016-02-26 words: 18258.0 sentences: 844.0 pages: flesch: 56.0 cache: ./cache/cord-333473-c1lykari.txt txt: ./txt/cord-333473-c1lykari.txt summary: Also, it has been employed in the study of the replication of large DNA viruses; namely, human cytomegalovirus [17] [18] , Kaposi''s sarcoma-associated herpesvirus [19] , herpes simplex virus 1 [20] , vaccinia virus [21] , and bacteriophage lambda [22] , providing insights into the temporal regulation of gene expression in these viruses and identifying numerous previously unrecognized translated ORFs, including novel protein-coding ORFs and short regulatory uORFs. In this paper, we describe the first analysis of RNA virus replication and gene expression by ribosome profiling (and parallel RNASeq), using MHV as a model system. The latter are calculated on a per gene (rather than per transcript) basis, using RNASeq and RiboSeq reads contained entirely within annotated CDS regions (i.e. excluding 5 0 and 3 0 UTRs and also RPFs accumulating at or near to initiation or termination sites), and, like the virus values, are expressed relative to the mean levels for the cell (due to normalization by library size). abstract: Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global “snap-shot” of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal frameshift site. To our knowledge this is the first application of ribosome profiling to an RNA virus. url: https://www.ncbi.nlm.nih.gov/pubmed/26919232/ doi: 10.1371/journal.ppat.1005473 id: cord-335377-zrbn637z author: Ishimaru, Daniella title: RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus date: 2012-12-26 words: 7699.0 sentences: 376.0 pages: flesch: 52.0 cache: ./cache/cord-335377-zrbn637z.txt txt: ./txt/cord-335377-zrbn637z.txt summary: Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. We further show that kissing dimer formation plays a role in frameshift-stimulation and modulates the relative abundance of full-length and subgenomic viral RNAs. Plasmids containing wild-type pseudoknot as well as the ÁS3 pk mutant were described in Plant et al (1) . Our previous NMR analysis of exchangeable imino protons of the SARS-CoV pseudoknot ( Figure 1A , wild-type pk) provided unequivocal evidence for the existence of Stem 3 (1). Surprisingly, in the context of the SARS-CoV Stem 3 sequence, 5 0 -cuug-3 0 tetraloop-capped mutants readily formed extended duplex structures as revealed by native gel and NMR analysis. abstract: Messenger RNA encoded signals that are involved in programmed -1 ribosomal frameshifting (-1 PRF) are typically two-stemmed hairpin (H)-type pseudoknots (pks). We previously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (SARS) coronavirus (CoV) that stimulated -1 PRF. The conserved existence of a third stem–loop suggested an important hitherto unknown function. Here we present new information describing structure and function of the third stem of the SARS pseudoknot. We uncovered RNA dimerization through a palindromic sequence embedded in the SARS-CoV Stem 3. Further in vitro analysis revealed that SARS-CoV RNA dimers assemble through ‘kissing’ loop–loop interactions. We also show that loop–loop kissing complex formation becomes more efficient at physiological temperature and in the presence of magnesium. When the palindromic sequence was mutated, in vitro RNA dimerization was abolished, and frameshifting was reduced from 15 to 5.7%. Furthermore, the inability to dimerize caused by the silent codon change in Stem 3 of SARS-CoV changed the viral growth kinetics and affected the levels of genomic and subgenomic RNA in infected cells. These results suggest that the homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that loop–loop kissing interactions involving Stem 3 modulate -1 PRF and play a role in subgenomic and full-length RNA synthesis. url: https://www.ncbi.nlm.nih.gov/pubmed/23275571/ doi: 10.1093/nar/gks1361 id: cord-290801-dv6aak01 author: Ivanyi-Nagy, Roland title: Reprint of: Core protein-mediated 5′–3′ annealing of the West Nile virus genomic RNA in vitro() date: 2012-09-27 words: 6522.0 sentences: 296.0 pages: flesch: 49.0 cache: ./cache/cord-290801-dv6aak01.txt txt: ./txt/cord-290801-dv6aak01.txt summary: Since the core protein of flaviviruses is also endowed with potent RNA chaperone activities, we decided to examine the effect of West Nile virus (WNV) core on 5′–3′ genomic RNA annealing in vitro. These results indicate that core protein – besides its function in viral particle formation – might be involved in the regulation of flavivirus genomic RNA cyclization, and thus virus replication. In this study, we examined the effect of WNV core protein chaperoning on viral 5 -3 UTR annealing, using an in vitro model system with separate 5 and 3 RNAs. We found that core protein binding greatly increases the rate of 5 -3 complex formation, and is required for the interaction when full-length 3 UTR RNAs are used (Fig. 2) . abstract: Genome cyclization through conserved RNA sequences located in the 5′ and 3′ terminal regions of flavivirus genomic RNA is essential for virus replication. Although the role of various cis-acting RNA elements in panhandle formation is well characterized, almost nothing is known about the potential contribution of protein cofactors to viral RNA cyclization. Proteins with nucleic acid chaperone activities are encoded by many viruses (e.g., retroviruses, coronaviruses) to facilitate RNA structural rearrangements and RNA–RNA interactions during the viral replicative cycle. Since the core protein of flaviviruses is also endowed with potent RNA chaperone activities, we decided to examine the effect of West Nile virus (WNV) core on 5′–3′ genomic RNA annealing in vitro. Core protein binding resulted in a dramatic, dose-dependent increase in 5′–3′ complex formation. Mutations introduced in either the UAR (upstream AUG region) or CS (conserved sequence) elements of the viral RNA diminished core protein-dependent annealing, while compensatory mutations restored the 5′–3′ RNA interaction. The activity responsible for stimulating RNA annealing was mapped to the C-terminal RNA-binding region of WNV core protein. These results indicate that core protein – besides its function in viral particle formation – might be involved in the regulation of flavivirus genomic RNA cyclization, and thus virus replication. url: https://api.elsevier.com/content/article/pii/S0168170212003279 doi: 10.1016/j.virusres.2012.09.009 id: cord-018017-c8myq6bi author: Iversen, Patrick L. title: The Threat from Viruses date: 2018-09-30 words: 11563.0 sentences: 615.0 pages: flesch: 51.0 cache: ./cache/cord-018017-c8myq6bi.txt txt: ./txt/cord-018017-c8myq6bi.txt summary: Numerous emerging infections caused by viral agents have imposed high impact on human survival (Table 3 .3). The apparent success of these viruses is that as they move from reservoir hosts to humans and as humans become immune to the initial infection, the population of diverse genomes offers multiple chances to adapt by finding a "fit" genome version which can propagate until the next transition requiring adaption. Human T-cell Lymphotropic Virus (HTLV-1) HTLV-1 is a single-stranded RNA retrovirus, defined by their use of reverse transcriptase, a polymerase, that makes a DNA copy of the RNA 7 kb viral genome. If we combine cardiovascular events and neoplasia caused by infection, then infectious disease is the most significant threat to human life and qualifies as the area of greatest impact. Adeno-associated Virus (AAV) is a single stranded DNA virus that infects humans but are not known to cause disease. is a 5229 base double-stranded DNA virus infecting less than 5 percent of the human population. abstract: Infectious disease represent the most significant threat to human health. Significant geologic cataclysmic events have caused the extinction of countless species, but these “Wrath of God” events predate the emergence of Homo sapiens. Pandemic infections have accompanied the rise of human civilization frequently re-occurring leaving a lasting imprint on human history punctuated by profound loss of life. Emerging infections become endemic and are here to stay marking their presence with an annual death toll. Each decade brings a new onslaught of emerging infectious agents. We are surprised again and again but are never prepared. The long-term consequences often remain unrecognized and are always inconvenient including cancer, cardiovascular disease and immune associated diseases that threaten our health. Reliance on clusters of clinical symptoms in the face of diverse and non-descriptive viral infection symptoms is a foolhardy form of crisis management. Viral success is based on rapid replication resulting in large numbers. Single-stranded RNA viruses with their high replication error rate represent a paradigm for resilience. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122756/ doi: 10.1007/978-3-319-98164-2_3 id: cord-003792-v48xeqdz author: Izquierdo-Suzán, Mónica title: Natural Vertical Transmission of Zika Virus in Larval Aedes aegypti Populations, Morelos, Mexico date: 2019-08-17 words: 4017.0 sentences: 182.0 pages: flesch: 47.0 cache: ./cache/cord-003792-v48xeqdz.txt txt: ./txt/cord-003792-v48xeqdz.txt summary: We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Several studies carried out under laboratory conditions have demonstrated that Zika virus can infect many different Aedes mosquito species (3) ; still, the key species for the transmission of Zika virus to humans are Ae. aegypti and Ae. albopictus (4) (5) (6) . In this study, we sought to demonstrate natural vertical transmission in Ae. aegypti mosquitoes by detecting viral RNA and isolating infectious Zika virus from larvae hatched from field-collected eggs. In this work, we were also able to demonstrate the natural vertical transmission of Zika virus in Ae. aegypti mosquitoes by the successful isolation of infectious Zika virus (31N) from larvae raised from field-collected eggs. abstract: We characterized natural vertical transmission of Zika virus in pools of Aedes aegypti larvae hatched from eggs collected in Jojutla, Morelos, Mexico. Of the 151 pools analyzed, 17 tested positive for Zika virus RNA; infectious Zika virus was successfully isolated from 1 of the larvae pools (31N) in C6/36 cells. Real-time quantitative PCR and indirect immunofluorescence assays confirmed the identity of the isolate, named Zika virus isolate 31N; plaque assays in Vero cells demonstrated the isolate’s infectivity in a mammalian cell line. We obtained the complete genome of Zika virus isolate 31N by next-generation sequencing and identified 3 single-nucleotide variants specific to Zika virus isolate 31N using the meta-CATS tool. These results demonstrate the occurrence of natural vertical transmission of Zika virus in wild Ae. aegypti mosquitoes and suggest that this transmission mode could aid in the spread and maintenance of Zika virus in nature. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6649329/ doi: 10.3201/eid2508.181533 id: cord-322084-gkg1059v author: JEONG, YONG SEOK title: Coronavirus Transcription Mediated by Sequences Flanking the Transcription Consensus Sequence date: 1996-03-01 words: 6250.0 sentences: 302.0 pages: flesch: 52.0 cache: ./cache/cord-322084-gkg1059v.txt txt: ./txt/cord-322084-gkg1059v.txt summary: Abstract In our studies of murine coronavirus transcription, we continue to use defective interfering (DI) RNAs of mouse hepatitis virus (MHV) in which we insert a transcription consensus sequence in order to mimic subgenomic RNA synthesis from the nondefective genome. By using PCR-based sequences flanking the same intergenic region between site-directed mutagenesis, a 12-nucleotide-long segenes 6 and 7 do not affect the efficiency of subgenomic quence, TCTAATCTAAAC, was inserted into DI cDNA DI RNA transcription (Makino and Joo, 1993) . For all of the constructs used in Deletion analysis of those MHV DI RNAs that contain this study we sequenced the inserts that were derived the intergenic sequence from gene 6-7 with its naturally from PCR products to confirm the presence of specific occurring flanking sequences showed that reducing the mutations and the absence of extraneous mutations. abstract: Abstract In our studies of murine coronavirus transcription, we continue to use defective interfering (DI) RNAs of mouse hepatitis virus (MHV) in which we insert a transcription consensus sequence in order to mimic subgenomic RNA synthesis from the nondefective genome. Using our subgenomic DI system, we have studied the effects of sequences flanking the MHV transcription consensus sequence on subgenomic RNA transcription. We obtained the following results. (i) Insertion of a 12-nucleotide-long sequence including the UCUAAAC transcription consensus sequence at different locations of the DI RNA resulted in different efficiencies of subgenomic DI RNA synthesis. (ii) Differences in the amount of subgenomic DI RNA were defined by the sequences that flanked the 12-nucleotide-long sequence and were not affected by the location of the 12-nucleotide-long sequence on the DI RNA. (iii) Naturally occurring flanking sequences of intergenic sequences at gene 6–7, but not at genes 1–2 and 2–3, contained a transcription suppressive element(s). (iv) Each of three naturally occurring flanking sequences of an MHV genomic cryptic transcription consensus sequence from MHV gene 1 also contained a transcription suppressive element(s). These data showed that sequences flanking the transcription consensus sequence affected MHV transcription. url: https://www.sciencedirect.com/science/article/pii/S004268229690118X doi: 10.1006/viro.1996.0118 id: cord-004274-cot05vx7 author: Jackson, Nicholas A. C. title: The promise of mRNA vaccines: a biotech and industrial perspective date: 2020-02-04 words: 4253.0 sentences: 251.0 pages: flesch: 38.0 cache: ./cache/cord-004274-cot05vx7.txt txt: ./txt/cord-004274-cot05vx7.txt summary: "STATE-OF-THE-ART" mRNA CONSTRUCTS AND DELIVERY TECHNOLOGIES The core principle behind mRNA as a technology for vaccination is to deliver the transcript of interest, encoding one or more immunogen(s), into the host cell cytoplasm where expression generates translated protein(s) to be within the membrane, secreted or intracellularly located. Perspective #2: Translational sciences will inform preclinical and clinical studies to promote rapid downselection of constructs and formulations A key aspect of vaccine development efforts is the goal of making early informed decisions, based on objective data that favor or disfavor a particular candidate. 64 The current focus from a clinical perspective is to optimize the benefit (immunogenicity and efficacy) while reducing the risk (safety) profile of a candidate mRNA vaccine by optimizing the quality attributes that dictate expression and/or augmenting delivery. Thus, early-phase clinical trials need to be designed in a way to appropriately capture the inflammatory component intrinsic to all mRNA vaccines, given that several intracellular innate immune response sensors are activated by RNA. abstract: mRNA technologies have the potential to transform areas of medicine, including the prophylaxis of infectious diseases. The advantages for vaccines range from the acceleration of immunogen discovery to rapid response and multiple disease target manufacturing. A greater understanding of quality attributes that dictate translation efficiency, as well as a comprehensive appreciation of the importance of mRNA delivery, are influencing a new era of investment in development activities. The application of translational sciences and growing early-phase clinical experience continue to inform candidate vaccine selection. Here we review the state of the art for the prevention of infectious diseases by using mRNA and pertinent topics to the biotechnology and pharmaceutical industries. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000814/ doi: 10.1038/s41541-020-0159-8 id: cord-319842-4mnaicki author: Jackson, William T title: Subversion of Cellular Autophagosomal Machinery by RNA Viruses date: 2005-04-26 words: 6936.0 sentences: 320.0 pages: flesch: 39.0 cache: ./cache/cord-319842-4mnaicki.txt txt: ./txt/cord-319842-4mnaicki.txt summary: Infection of human cells with poliovirus induces the proliferation of double-membraned cytoplasmic vesicles whose surfaces are used as the sites of viral RNA replication and whose origin is unknown. Here, we explore the role of several constituents of autophagosome machinery in poliovirus-and rhinovirusinfected cells by monitoring: the presence of autophagosomal protein LC3 in virally induced vesicles, the acquisition of colocalization of LC3 and LAMP1 in virally infected cells, the viral induction of punctate structures that stain with monodansylcadaverine (MDC), and the effects of perturbing the autophagosomal pathway pharmacologically and via RNA interference on intracellular and extracellular virus yield. To determine whether the autophagosome-like membranes induced during poliovirus infection perform an antiviral function or facilitate viral replication, we tested the effect on poliovirus yield of pretreating H1-HeLa cells with either tamoxifen or rapamycin, known inducers of autophagy. abstract: Infection of human cells with poliovirus induces the proliferation of double-membraned cytoplasmic vesicles whose surfaces are used as the sites of viral RNA replication and whose origin is unknown. Here, we show that several hallmarks of cellular autophagosomes can be identified in poliovirus-induced vesicles, including colocalization of LAMP1 and LC3, the human homolog of Saccharomyces cerevisiae Atg8p, and staining with the fluorophore monodansylcadaverine followed by fixation. Colocalization of LC3 and LAMP1 was observed early in the poliovirus replicative cycle, in cells infected with rhinoviruses 2 and 14, and in cells that express poliovirus proteins 2BC and 3A, known to be sufficient to induce double-membraned vesicles. Stimulation of autophagy increased poliovirus yield, and inhibition of the autophagosomal pathway by 3-methyladenine or by RNA interference against mRNAs that encode two different proteins known to be required for autophagy decreased poliovirus yield. We propose that, for poliovirus and rhinovirus, components of the cellular machinery of autophagosome formation are subverted to promote viral replication. Although autophagy can serve in the innate immune response to microorganisms, our findings are inconsistent with a role for the induced autophagosome-like structures in clearance of poliovirus. Instead, we argue that these double-membraned structures provide membranous supports for viral RNA replication complexes, possibly enabling the nonlytic release of cytoplasmic contents, including progeny virions, from infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/15884975/ doi: 10.1371/journal.pbio.0030156 id: cord-298847-szezd2vb author: Jacomy, Hélène title: Vacuolating encephalitis in mice infected by human coronavirus OC43 date: 2003-10-10 words: 6882.0 sentences: 338.0 pages: flesch: 47.0 cache: ./cache/cord-298847-szezd2vb.txt txt: ./txt/cord-298847-szezd2vb.txt summary: Virus inoculation of 21-day postnatal C57BL/6 and BALB/c mice led to a generalized infection of the whole CNS, demonstrating HCoV-OC43 neuroinvasiveness and neurovirulence. Moreover, mice inoculated with supernatants from cell cultures infected with brain tissue from affected mice developed the same disease, demonstrating that the virus was responsible for pathology. Cells positive for viral antigens were first observed at HCoV-OC43-infected mice gained weight normally during the first 5 days after infection, after which they all lost weight during the acute phase of the disease. (A) 100% of brains from C57BL/6 mice inoculated ic with 10 TCID 50 of HCoV-OC43 were positive for viral RNA between 3 and 11 days postinfection. However, RT-PCR analysis revealed that viral RNA could not be detected after the second week postinfection, suggesting a nonpersistent infection of HCoV-OC43 virus in 21 DPN mice. Every 2 days postinfection, five animals from two groups of infected mice of each strain were sacrificed and processed for detection of viral RNA, viral proteins, and infectious virus. abstract: Involvement of viruses in human neurodegenerative diseases and the underlying pathologic mechanisms remain generally unclear. Human respiratory coronaviruses (HCoV) can infect neural cells, persist in human brain, and activate myelin-reactive T cells. As a means of understanding the human infection, we characterized in vivo the neurotropic and neuroinvasive properties of HCoV-OC43 through the development of an experimental animal model. Virus inoculation of 21-day postnatal C57BL/6 and BALB/c mice led to a generalized infection of the whole CNS, demonstrating HCoV-OC43 neuroinvasiveness and neurovirulence. This acute infection targeted neurons, which underwent vacuolation and degeneration while infected regions presented strong microglial reactivity and inflammatory reactions. Damage to the CNS was not immunologically mediated and microglial reactivity was instead a consequence of direct virus-mediated neuronal injury. Although this acute encephalitis appears generally similar to that induced by murine coronaviruses, an important difference rests in the prominent spongiform-like degeneration that could trigger neuropathology in surviving animals. url: https://www.ncbi.nlm.nih.gov/pubmed/14592756/ doi: 10.1016/s0042-6822(03)00323-4 id: cord-018798-yzxy9ogf author: Jain, Pradeep Kumar title: RNAi for Resistance Against Biotic Stresses in Crop Plants date: 2018-07-10 words: 12555.0 sentences: 711.0 pages: flesch: 47.0 cache: ./cache/cord-018798-yzxy9ogf.txt txt: ./txt/cord-018798-yzxy9ogf.txt summary: This chapter also reviews the rich history of RNAi research, gene regulation by small RNAs across different organisms, and application potential of RNAi for generating transgenic plants resistant to major pests(.) But, there are some limitations too which restrict wider applications of this technology to its full potential. Different delivery methods of dsRNA that have been used for successful RNAi in insects and nematodes include microinjection, feeding on either artificial diet (Table 4 .2), and/or host-mediated delivery through transgenic plants (Fig. 4.1) . RNAi mechanism partly occurs in the host itself and partly in nematodes feeding on the transgenic host plant expressing dsRNA for the target gene. despite the absence of Sid-1 and Sid-2 genes exhibit systemic RNAi when subjected to silencing technology indicating a presence of similar receptor-mediated endocytic process for dsRNA uptake as reported in insects ). abstract: RNA interference (RNAi)-based gene silencing has become one of the most successful strategies in not only identifying gene function but also in improving agronomical traits of crops by silencing genes of different pathogens/pests and also plant genes for improvement of desired trait. The conserved nature of RNAi pathway across different organisms increases its applicability in various basic and applied fields. Here we attempt to summarize the knowledge generated on the fundamental mechanisms of RNAi over the years, with emphasis on insects and plant-parasitic nematodes (PPNs). This chapter also reviews the rich history of RNAi research, gene regulation by small RNAs across different organisms, and application potential of RNAi for generating transgenic plants resistant to major pests(.) But, there are some limitations too which restrict wider applications of this technology to its full potential. Further refinement of this technology in terms of resolving these shortcomings constitutes one of the thrust areas in present RNAi research. Nevertheless, its application especially in breeding agricultural crops resistant against biotic stresses will certainly offer the possible solutions for some of the breeding objectives which are otherwise unattainable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123769/ doi: 10.1007/978-3-319-90650-8_4 id: cord-306288-w43wec48 author: Jang, Sungho title: RNA-based dynamic genetic controllers: development strategies and applications date: 2017-11-10 words: 4613.0 sentences: 285.0 pages: flesch: 36.0 cache: ./cache/cord-306288-w43wec48.txt txt: ./txt/cord-306288-w43wec48.txt summary: The aptamers and expression platforms were reassembled in a mix-and-match fashion to create chimeric riboswitches that retained their regulatory activities to turn off transcription upon ligand binding, and even combinations using artificial RNA aptamers were successful in regulating gene expression. Engineering of natural RNA-based regulation for dynamic control of gene expression requires detailed knowledge of each mechanism. Aptamers were placed upstream of IRES and several base-pairing sequences were designed to control the formation of critical structures (PK-III) depending on ligand binding (Figure 2b ). RNA molecules that regulate translation (IS10) or transcription (pT181) were combined with aptamers to control the formation of intramolecular structures depending on ligand binding [24] (Figure 2c ). Moreover, simultaneous utilization of high-throughput measurement of activity and next-generation sequencing analysis can not only screen and optimize dynamic RNA controllers, but also provide new design principles from sequence-structure-function relationships [14 ,15] . abstract: Dynamic regulation of gene expression in response to various molecules is crucial for both basic science and practical applications. RNA is considered an attractive material for creating dynamic genetic controllers because of its specific binding to ligands, structural flexibility, programmability, and small size. Here, we review recent advances in strategies for developing RNA-based dynamic controllers and applications. First, we describe studies that re-engineered natural riboswitches to generate new dynamic controllers. Next, we summarize RNA-based regulatory mechanisms that have been exploited to build novel artificial dynamic controllers. We also discuss computational methods and high-throughput selection approaches for de novo design of dynamic RNA controllers. Finally, we explain applications of dynamic RNA controllers for metabolic engineering and synthetic biology. url: https://www.ncbi.nlm.nih.gov/pubmed/29132120/ doi: 10.1016/j.copbio.2017.10.005 id: cord-256370-cz88t29n author: Jansen van Vuren, Petrus title: Isolation of a Novel Fusogenic Orthoreovirus from Eucampsipoda africana Bat Flies in South Africa date: 2016-02-29 words: 5529.0 sentences: 263.0 pages: flesch: 49.0 cache: ./cache/cord-256370-cz88t29n.txt txt: ./txt/cord-256370-cz88t29n.txt summary: This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. Maximum Likelihood trees were prepared using amino acid sequences of all open reading frames from all segments, showing the placement of Mahlapitsi virus (MAHLV) in the Orthoreovirus genus relative to other viruses in this genus for which sequence is available on Genbank. A Maximum Likelihood tree, constructed with nucleic acid sequence data for the RNA-dependent RNA polymerase (RdRp) encoding segments of representative viruses from the different genera within Reoviridae (Figure 7) shows the placement of both isolates amongst other orthoreoviruses in the family. Maximum Likelihood trees were prepared using the deduced amino acid sequences from the open reading frames (ORF''s) of all the virus'' segments and those of other viruses in the Orthoreovirus genus (Figures 8-10) . abstract: We report on the isolation of a novel fusogenic orthoreovirus from bat flies (Eucampsipoda africana) associated with Egyptian fruit bats (Rousettus aegyptiacus) collected in South Africa. Complete sequences of the ten dsRNA genome segments of the virus, tentatively named Mahlapitsi virus (MAHLV), were determined. Phylogenetic analysis places this virus into a distinct clade with Baboon orthoreovirus, Bush viper reovirus and the bat-associated Broome virus. All genome segments of MAHLV contain a 5' terminal sequence (5'-GGUCA) that is unique to all currently described viruses of the genus. The smallest genome segment is bicistronic encoding for a 14 kDa protein similar to p14 membrane fusion protein of Bush viper reovirus and an 18 kDa protein similar to p16 non-structural protein of Baboon orthoreovirus. This is the first report on isolation of an orthoreovirus from an arthropod host associated with bats, and phylogenetic and sequence data suggests that MAHLV constitutes a new species within the Orthoreovirus genus. url: https://doi.org/10.3390/v8030065 doi: 10.3390/v8030065 id: cord-276006-mjjnkqv6 author: Jarach, Natanel title: Polymers in the Medical Antiviral Front-Line date: 2020-07-31 words: 12573.0 sentences: 738.0 pages: flesch: 41.0 cache: ./cache/cord-276006-mjjnkqv6.txt txt: ./txt/cord-276006-mjjnkqv6.txt summary: Those anions show antiviral properties by affecting Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Larson studied modified PEI composed of N,N-Dodecylmethyl-PEI that exhibited antiviral effect on HSV-1 and HSV-2 viruses (see also Figure 6 ) [98] , influenza A virus [99] and on poliovirus and rotavirus [100] . Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. Xiao and Xue examined the antiviral effect of quaternary pyridinium containing co-polymers on several Influenza viruses (A, PR8, 8, 34) , as demonstrated in Figure 11 [35]. abstract: Antiviral polymers are part of a major campaign led by the scientific community in recent years. Facing this most demanding of campaigns, two main approaches have been undertaken by scientists. First, the classic approach involves the development of relatively small molecules having antiviral properties to serve as drugs. The other approach involves searching for polymers with antiviral properties to be used as prescription medications or viral spread prevention measures. This second approach took two distinct directions. The first, using polymers as antiviral drug-delivery systems, taking advantage of their biodegradable properties. The second, using polymers with antiviral properties for on-contact virus elimination, which will be the focus of this review. Anti-viral polymers are obtained by either the addition of small antiviral molecules (such as metal ions) to obtain ion-containing polymers with antiviral properties or the use of polymers composed of an organic backbone and electrically charged moieties like polyanions, such as carboxylate containing polymers, or polycations such as quaternary ammonium containing polymers. Other approaches include moieties hybridized by sulphates, carboxylic acids, or amines and/or combining repeating units with a similar chemical structure to common antiviral drugs. Furthermore, elevated temperatures appear to increase the anti-viral effect of ions and other functional moieties. url: https://doi.org/10.3390/polym12081727 doi: 10.3390/polym12081727 id: cord-346314-o9fjpqaj author: Jarboui, Mohamed Ali title: Nucleolar Protein Trafficking in Response to HIV-1 Tat: Rewiring the Nucleolus date: 2012-11-15 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The trans-activator Tat protein is a viral regulatory protein essential for HIV-1 replication. Tat trafficks to the nucleoplasm and the nucleolus. The nucleolus, a highly dynamic and structured membrane-less sub-nuclear compartment, is the site of rRNA and ribosome biogenesis and is involved in numerous cellular functions including transcriptional regulation, cell cycle control and viral infection. Importantly, transient nucleolar trafficking of both Tat and HIV-1 viral transcripts are critical in HIV-1 replication, however, the role(s) of the nucleolus in HIV-1 replication remains unclear. To better understand how the interaction of Tat with the nucleolar machinery contributes to HIV-1 pathogenesis, we investigated the quantitative changes in the composition of the nucleolar proteome of Jurkat T-cells stably expressing HIV-1 Tat fused to a TAP tag. Using an organellar proteomic approach based on mass spectrometry, coupled with Stable Isotope Labelling in Cell culture (SILAC), we quantified 520 proteins, including 49 proteins showing significant changes in abundance in Jurkat T-cell nucleolus upon Tat expression. Numerous proteins exhibiting a fold change were well characterised Tat interactors and/or known to be critical for HIV-1 replication. This suggests that the spatial control and subcellular compartimentaliation of these cellular cofactors by Tat provide an additional layer of control for regulating cellular machinery involved in HIV-1 pathogenesis. Pathway analysis and network reconstruction revealed that Tat expression specifically resulted in the nucleolar enrichment of proteins collectively participating in ribosomal biogenesis, protein homeostasis, metabolic pathways including glycolytic, pentose phosphate, nucleotides and amino acids biosynthetic pathways, stress response, T-cell signaling pathways and genome integrity. We present here the first differential profiling of the nucleolar proteome of T-cells expressing HIV-1 Tat. We discuss how these proteins collectively participate in interconnected networks converging to adapt the nucleolus dynamic activities, which favor host biosynthetic activities and may contribute to create a cellular environment supporting robust HIV-1 production. url: https://www.ncbi.nlm.nih.gov/pubmed/23166591/ doi: 10.1371/journal.pone.0048702 id: cord-002542-f7l4ty2j author: Jaworski, Elizabeth title: Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus date: 2017-05-05 words: 11789.0 sentences: 535.0 pages: flesch: 49.0 cache: ./cache/cord-002542-f7l4ty2j.txt txt: ./txt/cord-002542-f7l4ty2j.txt summary: Using a combination of longand short-read Next-Generation Sequencing, we have characterized the formation of DI-RNAs during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms of DI-RNA emergence and evolution. By combining these data, we aimed to determine the correlation of recombination events within single RNA virus genomes, characterize the distribution of defective RNA genomes, and determine the exact make-up of DI-RNAs during serial passaging of FHV in cell culture. This observation indicates the protection of cells from infection and/or CPE when supplied with a large dose of viral particles that contain a large proportion of DI-RNAs. In this manuscript, we sought to provide a thorough and comprehensive analysis of the frequency and identity of recombination events present during the serial passaging of Flock House virus in cell culture in order to elucidate the pathways and mechanism of DI-RNA emergence and evolution. abstract: Defective-Interfering RNAs (DI-RNAs) have long been known to play an important role in virus replication and transmission. DI-RNAs emerge during virus passaging in both cell-culture and their hosts as a result of non-homologous RNA recombination. However, the principles of DI-RNA emergence and their subsequent evolution have remained elusive. Using a combination of long- and short-read Next-Generation Sequencing, we have characterized the formation of DI-RNAs during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms of DI-RNA emergence and evolution. For short-read RNAseq, we employed ‘ClickSeq’ due to its ability to sensitively and confidently detect RNA recombination events with nucleotide resolution. In parallel, we used the Oxford Nanopore Technologies’s (ONT) MinION to resolve full-length defective and wild-type viral genomes. Together, these accurately resolve both rare and common RNA recombination events, determine the correlation between recombination events, and quantifies the relative abundance of different DI-RNAs throughout passaging. We observe the formation of a diverse pool of defective RNAs at each stage of viral passaging. However, many of these ‘intermediate’ species, while present in early stages of passaging, do not accumulate. After approximately 9 days of passaging we observe the rapid accumulation of DI-RNAs with a correlated reduction in specific infectivity and with the Nanopore data find that DI-RNAs are characterized by multiple RNA recombination events. This suggests that intermediate DI-RNA species are not competitive and that multiple recombination events interact epistatically to confer ‘mature’ DI-RNAs with their selective advantage allowing for their rapid accumulation. Alternatively, it is possible that mature DI-RNA species are generated in a single event involving multiple RNA rearrangements. These insights have important consequences for our understanding of the mechanisms, determinants and limitations in the emergence and evolution of DI-RNAs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5435362/ doi: 10.1371/journal.ppat.1006365 id: cord-300399-21xozruq author: Jayamohan, Harikrishnan title: SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations date: 2020-10-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification–, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting. url: https://www.ncbi.nlm.nih.gov/pubmed/33073312/ doi: 10.1007/s00216-020-02958-1 id: cord-276493-hoaxv5e0 author: Jeong, Gi Uk title: Therapeutic Strategies Against COVID-19 and Structural Characterization of SARS-CoV-2: A Review date: 2020-07-14 words: 5687.0 sentences: 363.0 pages: flesch: 56.0 cache: ./cache/cord-276493-hoaxv5e0.txt txt: ./txt/cord-276493-hoaxv5e0.txt summary: With increasing structural data of key proteins in both SARS-CoV-2 and the host, such as the spike glycoprotein (S), the main protease (M pro ), RNA-dependent RNA polymerase (RdRp), and human angiotensin-converting enzyme 2 (hACE2), the structure-based design of new drugs has emerged as the most promising antiviral strategy. Several structure-based drug discovery studies have investigated the interaction of inhibitors in the substrate-binding pockets of SARS-CoV-2 M pro ( Figure 3C ) (Dai et al., 2020; Jin et al., 2020; Zhang et al., 2020b) . Because most inhibitors occupy the substrate binding pocket of SARS-CoV-2 FIGURE 4 | CryoEM structure of RdRp in complex with cofactors (nsp7 and nsp8), RNA template, and remdesivir. In addition, we provided structural insights into the mechanism of action of well-characterized drugs targeting the interaction between hACE2 and the spike protein of SARS-CoV-2 for viral entry, as well as M pro and RdRp for viral replication. abstract: The novel coronavirus, SARS-CoV-2, or 2019-nCoV, which originated in Wuhan, Hubei province, China in December 2019, is a grave threat to public health worldwide. A total of 3,672,238 confirmed cases of coronavirus disease 2019 (COVID-19) and 254,045 deaths were reported globally up to May 7, 2020. However, approved antiviral agents for the treatment of patients with COVID-19 remain unavailable. Drug repurposing of approved antivirals against other viruses such as HIV or Ebola virus is one of the most practical strategies to develop effective antiviral agents against SARS-CoV-2. A combination of repurposed drugs can improve the efficacy of treatment, and structure-based drug design can be employed to specifically target SARS-CoV-2. This review discusses therapeutic strategies using promising antiviral agents against SARS-CoV-2. In addition, structural characterization of potentially therapeutic viral or host cellular targets associated with COVID-19 have been discussed to refine structure-based drug design strategies. url: https://doi.org/10.3389/fmicb.2020.01723 doi: 10.3389/fmicb.2020.01723 id: cord-285868-fz5utxss author: Jheng, Jia-Rong title: ER stress, autophagy, and RNA viruses date: 2014-08-05 words: 9345.0 sentences: 480.0 pages: flesch: 38.0 cache: ./cache/cord-285868-fz5utxss.txt txt: ./txt/cord-285868-fz5utxss.txt summary: In addition to regulation of cell death, it is reported that HCV induces the expression of CHOP at mRNA and protein levels and is correlated with autophagy induction; knockdown of CHOP not only increases HCV PAMP-mediated innate immune activation, but also elevates its inhibitory effect on virus replication (Ke and Chen, 2011) . Overexpression of HCV E1 and/or E2 induces the expression of CHOP in a PERK-dependent manner (Chan and Egan, 2005) ; while upon HCV infection, CHOP protein is upregulated by PERK, activating transcription factor (ATF6), and inositol-requiring transmembrane kinase/endonuclease 1 (IRE1) collectively. It was reported that rotavirus NSP4 viroporin initiates autophagy to transport viral proteins to sites of virus replication for assembly of mature particles, which involves an increase of cytoplasmic calcium and subsequent activation of the CaMKK-β-AMPK pathway. Regulated IRE1-dependent decay pathway is activated during Japanese encephalitis virus-induced unfolded protein response and benefits viral replication abstract: Endoplasmic reticulum (ER) stress is a general term for representing the pathway by which various stimuli affect ER functions. ER stress induces the evolutionarily conserved signaling pathways, called the unfolded protein response (UPR), which compromises the stimulus and then determines whether the cell survives or dies. In recent years, ongoing research has suggested that these pathways may be linked to the autophagic response, which plays a key role in the cell's response to various stressors. Autophagy performs a self-digestion function, and its activation protects cells against certain pathogens. However, the link between the UPR and autophagy may be more complicated. These two systems may act dependently, or the induction of one system may interfere with the other. Experimental studies have found that different viruses modulate these mechanisms to allow them to escape the host immune response or, worse, to exploit the host's defense to their advantage; thus, this topic is a critical area in antiviral research. In this review, we summarize the current knowledge about how RNA viruses, including influenza virus, poliovirus, coxsackievirus, enterovirus 71, Japanese encephalitis virus, hepatitis C virus, and dengue virus, regulate these processes. We also discuss recent discoveries and how these will produce novel strategies for antiviral treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/25140166/ doi: 10.3389/fmicb.2014.00388 id: cord-305591-ir3wz6nr author: Ji, Danyang title: Discovery of G-quadruplex-forming sequences in SARS-CoV-2 date: 2020-06-01 words: 5138.0 sentences: 315.0 pages: flesch: 55.0 cache: ./cache/cord-305591-ir3wz6nr.txt txt: ./txt/cord-305591-ir3wz6nr.txt summary: We have analyzed and identified 25 four contiguous GG runs (G(2)N(x)G(2)N(y)G(2)N(z)G(2)) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). We confirm Gquadruplex structure forming in the top-ranked PQSs by multiple spectroscopic assays in vitro and characterize the crosstalk between G-quadruplexes and viral helicase by microscale thermophoresis (MST) and molecular docking. Our analysis of Gquadruplex-forming sequences in SARS-CoV-2 provides insights into the design of anti-viral treatment by targeting the viral helicase and G-quadruplex structures. Interestingly, PQSs at positions 13385 and 24268 with the highest G-scores indicating high probability to adopt G-quadruplex structures only share high sequence similarity to the bat CoVs (see Supplementary Information S1 available online at https://academic.oup.com/bib and Table 2 ). In comparison, our G-quadruplex search across the genome of SARS-CoV-2 also identified a number of GG PQSs. PQS at position 13385 was confirmed to adopt G-quadruplex structures, which also contains a [GAAAG] sequence in the middle ( Table 1 ). abstract: The outbreak caused by the novel coronavirus SARS-CoV-2 has been declared a global health emergency. G-quadruplex structures in genomes have long been considered essential for regulating a number of biological processes in a plethora of organisms. We have analyzed and identified 25 four contiguous GG runs (G(2)N(x)G(2)N(y)G(2)N(z)G(2)) in the SARS-CoV-2 RNA genome, suggesting putative G-quadruplex-forming sequences (PQSs). Detailed analysis of SARS-CoV-2 PQSs revealed their locations in the open reading frames of ORF1 ab, spike (S), ORF3a, membrane (M) and nucleocapsid (N) genes. Identical PQSs were also found in the other members of the Coronaviridae family. The top-ranked PQSs at positions 13385 and 24268 were confirmed to form RNA G-quadruplex structures in vitro by multiple spectroscopic assays. Furthermore, their direct interactions with viral helicase (nsp13) were determined by microscale thermophoresis. Molecular docking model suggests that nsp13 distorts the G-quadruplex structure by allowing the guanine bases to be flipped away from the guanine quartet planes. Targeting viral helicase and G-quadruplex structure represents an attractive approach for potentially inhibiting the SARS-CoV-2 virus. url: https://doi.org/10.1093/bib/bbaa114 doi: 10.1093/bib/bbaa114 id: cord-293766-vpfda3pd author: Ji, Jingjing title: Glucocorticoid therapy does not delay viral clearance in COVID-19 patients date: 2020-09-21 words: 740.0 sentences: 54.0 pages: flesch: 63.0 cache: ./cache/cord-293766-vpfda3pd.txt txt: ./txt/cord-293766-vpfda3pd.txt summary: authors: Ji, Jingjing; Zhang, Jinxia; Shao, Ziyun; Xie, Qifeng; Zhong, Li; Liu, Zhifeng Patients were diagnosed as mild type, general type, severe type, and critical type according to the Chinese Recommendations for Diagnosis and Treatment of Novel Coronavirus (SARS-CoV-2) Infection (Trial 7th version) [4] . The current multicenter cohort study demonstrates that GC therapy does not change viral clearance and peripheral lymphocyte counts in COVID-19 patients. Low-dose corticosteroid therapy does not delay viral clearance in patients with COVID-19 Persistence and clearance of viral RNA in 2019 novel coronavirus disease rehabilitation patients Jinxia Zhang, Ziyun Shao, Qifeng Xie, and Li Zhong were responsible for collecting the data. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication. The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.Ethics approval and consent to participate abstract: nan url: https://doi.org/10.1186/s13054-020-03287-6 doi: 10.1186/s13054-020-03287-6 id: cord-259152-pwvcwlh8 author: Ji, Wei title: Cross‐species transmission of the newly identified coronavirus 2019‐nCoV date: 2020-02-19 words: 1674.0 sentences: 114.0 pages: flesch: 51.0 cache: ./cache/cord-259152-pwvcwlh8.txt txt: ./txt/cord-259152-pwvcwlh8.txt summary: The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019‐nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019‐nCoV sequence. 4 On 10 January, it was reported that a novel coronavirus designated 2019-nCoV by the World Health Organization (WHO) 5 was identified by high-throughput sequencing of the viral RNA genome, which was released through virological.org. Highthroughput sequencing of viral RNA from patients'' samples has identified a novel coronavirus designated 2019-nCoV by the World Health Organization. 10, 11 Results from our analysis suggest that 2019-nCoV has most similar genetic information with bat coronovirus and has most similar codon usage bias with snake. abstract: The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019‐nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019‐nCoV sequence. Results obtained from our analyses suggest that the 2019‐nCoV may appear to be a recombinant virus between the bat coronavirus and an origin‐unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019‐nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019‐nCoV cross‐species transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/31967321/ doi: 10.1002/jmv.25682 id: cord-324984-ojrpsdt9 author: Ji, Xingyue title: Medicinal chemistry strategies toward host targeting antiviral agents date: 2020-02-14 words: 16814.0 sentences: 825.0 pages: flesch: 43.0 cache: ./cache/cord-324984-ojrpsdt9.txt txt: ./txt/cord-324984-ojrpsdt9.txt summary: In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. 3 Altogether, targeting host factors is a very promising strategy with possibility to address the critical challenges faced with the DAAs. In this review, we summarize the recent advances made in HTAs from a medicinal chemistry standpoint, and the host targets are generally classified into three different categories based on the development stage of their corresponding inhibitors/modulators, namely the ones which reached Food and Drug Administration (FDA) approval, that have entered clinical trials and those in preclinical studies. abstract: Direct‐acting antiviral agents (DAAs) represent a class of drugs targeting viral proteins and have been demonstrated to be very successful in combating viral infections in clinic. However, DAAs suffer from several inherent limitations, including narrow‐spectrum antiviral profiles and liability to drug resistance, and hence there are still unmet needs in the treatment of viral infections. In comparison, host targeting antivirals (HTAs) target host factors for antiviral treatment. Since host proteins are probably broadly required for various viral infections, HTAs are not only perceived, but also demonstrated to exhibit broad‐spectrum antiviral activities. In addition, host proteins are not under the genetic control of viral genome, and hence HTAs possess much higher genetic barrier to drug resistance as compared with DAAs. In recent years, much progress has been made to the development of HTAs with the approval of chemokine receptor type 5 antagonist maraviroc for human immunodeficiency virus treatment and more in the pipeline for other viral infections. In this review, we summarize various host proteins as antiviral targets from a medicinal chemistry prospective. Challenges and issues associated with HTAs are also discussed. url: https://doi.org/10.1002/med.21664 doi: 10.1002/med.21664 id: cord-290218-dvyeg5fk author: Jiang, Yi title: RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19 date: 2020-09-04 words: 2249.0 sentences: 143.0 pages: flesch: 53.0 cache: ./cache/cord-290218-dvyeg5fk.txt txt: ./txt/cord-290218-dvyeg5fk.txt summary: Interestingly, the structure of complexed nsp12 is almost identical to nsp12 in apo RdRp, with an RMSD of 0.5 Å [17] , coinciding with the high processivity of the viral RNA polymerase, which does not need to consume extra energy for conformation changes in the active site during the replication cycle (Fig. 3B ). These "sliding poles" are stabilized by interactions formed between the positively charged residues at the extended N-terminal of nsp8 and bases in RNA backbones ( Fig. 3E ) and reported to account for the known processivity of the RdRp, which is required for replicating the long coronavirus genomes [39] . Although the sequence identity of nsp12 across the RNA viruses is low, the polymerase active site is structurally highly conserved, suggesting that RdRp inhibitors may serve as a potential J o u r n a l P r e -p r o o f broad-spectrum antiviral drug against RNA viruses. abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global pandemic. Although great efforts have been made to develop effective therapeutic interventions, only the nucleotide analog remdesivir was approved for emergency use against COVID-19. Remdesivir targets the RNA-dependent RNA polymerase (RdRp), an essential enzyme for viral RNA replication and a promising drug target for COVID-19. Recently, several structures of RdRp in complex with substrate RNA and remdesivir were reported, providing insights into the mechanisms of RNA recognition by RdRp. These structures also reveal the mechanism of RdRp inhibition by nucleotide inhibitors and offer a molecular template for the development of RdRp-targeting drugs. This review discusses the recognition mechanism of RNA and nucleotide inhibitor by RdRp, and its implication in drug discovery. url: https://api.elsevier.com/content/article/pii/S0006291X20317216 doi: 10.1016/j.bbrc.2020.08.116 id: cord-323737-6ajqy0ch author: Jiang, Yuanyuan title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2''-O-ribose methyltransferase of SARS-CoV-2 coronavirus date: 2020-10-04 words: 6799.0 sentences: 399.0 pages: flesch: 51.0 cache: ./cache/cord-323737-6ajqy0ch.txt txt: ./txt/cord-323737-6ajqy0ch.txt summary: title: Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2''-O-ribose methyltransferase of SARS-CoV-2 coronavirus In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify potential inhibitors targeting 2 0 -O-MTase of SARS-CoV-2. To identify inhibitors targeting nsp16, we first performed comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs. Supplementary Table 1 lists the detailed genome and protein information that were employed in this study. As seen from MM-PBSA results and docking studies, drugs including Hesperidin, Osi-027, Rimegepant, Sonedenoson, and Gs-9667 had higher binding affinities than SAM with the 2 0 -O-MTase of SARS-CoV-2. abstract: SARS-CoV-2, an emerging coronavirus, has spread rapidly around the world, resulting in over ten million cases and more than half a million deaths as of July 1, 2020. Effective treatments and vaccines for SARS-CoV-2 infection do not currently exist. Previous studies demonstrated that nonstructural protein 16 (nsp16) of coronavirus is an S-adenosyl methionine (SAM)-dependent 2’-O-methyltransferase (2’-O-MTase) that has an important role in viral replication and prevents recognition by the host innate immune system. In the present study, we employed structural analysis, virtual screening, and molecular simulation approaches to identify clinically investigated and approved drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. Comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs defined the key residues for nsp16 2-O’-MTase functions. Virtual screening and docking analysis ranked the potential inhibitors of nsp16 from more than 4,500 clinically investigated and approved drugs. Furthermore, molecular dynamics simulations were carried out on eight top candidates, including Hesperidin, Rimegepant, Gs-9667, and Sonedenoson, to calculate various structural parameters and understand the dynamic behavior of the drug-protein complexes. Our studies provided the foundation to further test and repurpose these candidate drugs experimentally and/or clinically for COVID-19 treatment. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/33016237/ doi: 10.1080/07391102.2020.1828172 id: cord-331607-2h56vb0n author: Jin, Xuejiao title: Three-Dimensional Architecture and Biogenesis of Membrane Structures Associated with Plant Virus Replication date: 2018-01-30 words: 10714.0 sentences: 488.0 pages: flesch: 39.0 cache: ./cache/cord-331607-2h56vb0n.txt txt: ./txt/cord-331607-2h56vb0n.txt summary: reported the first 3D architecture of the membrane-bound (+) RNA viral replication compartments in FHV-infected Drosophila cells (Kopek et al., 2007) , several 3D models of cellular remodeling during plant virus infection have been characterized. Confocal microscopy analysis showed that actin patches are closely associated with large p33-containing replication organelle-like structures in yeast cells and that such patches are present throughout the large replication compartments in plant cells, suggesting that actin plays a role in recruiting viral and cellular components (e.g., lipid) for VRC assembly (Nawaz-Ul-Rehman et al., 2016; Xu and Nagy, 2016) . The examples given above provide a good illustration of a common theme in membrane remodeling and the formation of spherules/vesicles: viral proteins, sometimes with the involvement of viral RNAs, recruit host factors that are diverted from their original functions and used to create virus replication factories (Diaz and Wang, 2014; Laliberté and Zheng, 2014; Wang, 2015; Nagy, 2016) . Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulumtargeted viral protein abstract: Positive-sense (+) RNA viruses represent the most abundant group of viruses and are dependent on the host cell machinery to replicate. One remarkable feature that occurs after (+) RNA virus entry into cells is the remodeling of host endomembranes, leading to the formation of viral replication factories. Recently, rapid progress in three-dimensional (3D) imaging technologies, such as electron tomography (ET) and focused ion beam-scanning electron microscopy (FIB-SEM), has enabled researchers to visualize the novel membrane structures induced by viruses at high resolution. These 3D imaging technologies provide new mechanistic insights into the viral infection cycle. In this review, we summarize the latest reports on the cellular remodeling that occurs during plant virus infection; in particular, we focus on studies that provide 3D architectural information on viral replication factories. We also outline the mechanisms underlying the formation of these membranous structures and discuss possible future research directions. url: https://doi.org/10.3389/fpls.2018.00057 doi: 10.3389/fpls.2018.00057 id: cord-341804-rnj3wtg4 author: Jin, Zhe title: Drug treatment of coronavirus disease 2019 (COVID-19) in China. date: 2020-06-27 words: 2048.0 sentences: 136.0 pages: flesch: 43.0 cache: ./cache/cord-341804-rnj3wtg4.txt txt: ./txt/cord-341804-rnj3wtg4.txt summary: This article reviewed the clinical use, mechanism and efficacy of the clinically approved drugs recommended in the Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (DTPNCP) released by National Health Commission of P.R.China, and the novel therapeutic agents now undergoing clinical trials approved by China National Medical Products Administration (NMPA) to evaluate experimental treatment for COVID-19. However, more evidence is needed either for 4 supporting or opposing the systemic therapeutic administration of glucocorticoids in 5 patients with SARS-CoV-2 infection (Qin et al., 2020 a variety of immune cells 20 and improves the immunity, while IFN-β takes effect by inhibiting the adsorption of certain 1 viruses, enhancing phagocytosis of natural killer cells and mononuclear macrophages Tocilizumab is a recombinant humanized anti-IL-6 receptor (IL-6R) monoclonal antibody, 21 13 which can specifically bind to soluble and membrane-bound IL-6 receptors and inhibit 1 signal transduction mediated by IL-6, thereby reducing inflammation and blocking cytokine 2 storm caused by COVID-19 (Scheinecker et al., 2009) . abstract: Since December 2019, the coronavirus disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread throughout China as well as other countries. More than 8,700,000 confirmed COVID-19 cases have been recorded worldwide so far, with much more cases popping up overseas than those inside. As the initial epicenter in the world, China has been combating the epidemic for a relatively longer period and accumulated valuable experience in prevention and control of COVID-19. This article reviewed the clinical use, mechanism and efficacy of the clinically approved drugs recommended in the Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (DTPNCP) released by National Health Commission of P.R.China, and the novel therapeutic agents now undergoing clinical trials approved by China National Medical Products Administration (NMPA) to evaluate experimental treatment for COVID-19. Reviewing the progress in drug development for the treatment against COVID-19 in China may provide insight into the epidemic control in other countries. url: https://www.sciencedirect.com/science/article/pii/S0014299920304180?v=s5 doi: 10.1016/j.ejphar.2020.173326 id: cord-291962-rp172ugk author: Jing, Huiyuan title: Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 date: 2019-07-15 words: 5726.0 sentences: 366.0 pages: flesch: 51.0 cache: ./cache/cord-291962-rp172ugk.txt txt: ./txt/cord-291962-rp172ugk.txt summary: title: Nucleotide-binding oligomerization domain-like receptor X1 restricts porcine reproductive and respiratory syndrome virus-2 replication by interacting with viral Nsp9 To test this, increasing dose of NLRX1 was transfected into Marc-145 cells followed by PRRSV infection, qPCR was then performed to test the total viral RNA levels. On the other hand, recent literature indicated that the interaction of Nsp9 with SUMO E2 conjugating enzyme Ubc9 and cellular protein interleukin-2 enhancer binding factor 2 (ILF2) through its RdRp domain resulted in a significantly decrease of virus titers, indicating that cells utilize host antiviral factors as defense mechanisms to limit PRRSV infection Wen et al., 2017) . An intracellularly expressed Nsp9-specific nanobody in MARC-145 cells inhibits porcine reproductive and respiratory syndrome virus replication Porcine reproductive and respiratory syndrome virus nucleocapsid protein interacts with Nsp9 and cellular DHX9 to regulate viral RNA synthesis The DEADbox RNA helicase 5 positively regulates the replication of porcine reproductive and respiratory syndrome virus by interacting with viral Nsp9 in vitro abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) causes one of the most economically important diseases of swine worldwide. Current antiviral strategies provide only limited protection. Nucleotide-binding oligomerization domain-like receptor (NLR) X1 is unique among NLR proteins in its functions as a pro-viral or antiviral factor to different viral infections. To date, the impact of NLRX1 on PRRSV infection remains unclear. In this study, we found that PRRSV infection promoted the expression of NLRX1 gene. In turn, ectopic expression of NLRX1 inhibited PRRSV replication in Marc-145 cells, whereas knockdown of NLRX1 enhanced PRRSV propagation in porcine alveolar macrophages (PAMs). Mechanistically, NLRX1 was revealed to impair intracellular viral subgenomic RNAs accumulation. Finally, Mutagenic analyses indicated that the LRR (leucine-rich repeats) domain of NLRX1 interacted with PRRSV Nonstructural Protein 9 (Nsp9) RdRp (RNA-dependent RNA Polymerase) domain and was necessary for antiviral activity. Thus, our study establishes the role of NLRX1 as a new host restriction factor in PRRSV infection. url: https://api.elsevier.com/content/article/pii/S0168170219302485 doi: 10.1016/j.virusres.2019.05.011 id: cord-318576-dc5n6ni4 author: Jitobaom, Kunlakanya title: Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation date: 2020-05-08 words: 6821.0 sentences: 345.0 pages: flesch: 53.0 cache: ./cache/cord-318576-dc5n6ni4.txt txt: ./txt/cord-318576-dc5n6ni4.txt summary: From the previous section, we demonstrated that human genes in the GO terms of the cell cycle and the regulation of the cell cycle process adopt codon usage patterns similar to those of þssRNA (subgroups 6, 7), -ssRNA (subgroup 4), retrovirus (HIV-1), and ambisense (subgroup 4) viruses. The lists of upregulated proteins upon viral infection were submitted to GO-TermFinder (Supplementary File 3) , and the enriched GO terms were compared to the enriched GO terms of human genes with codon usage patterns similar to RNA viruses from every subgroup. Several enriched GO terms of upregulated protein profiles during viral infections were found to be identical to the GO terms of human genes with codon usage patterns similar to RNA viruses ( Figure 4 ). Several GO terms of human genes with codon usage patterns similar to RNA viruses have been found by previous studies to be identical to the GO terms of upregulated protein profiles in viral infections. abstract: The codon usage pattern is a specific characteristic of each species; however, the codon usage of all of the genes in a genome is not uniform. Intriguingly, most viruses have codon usage patterns that are vastly different from the optimal codon usage of their hosts. How viral genes with different codon usage patterns are efficiently expressed during a viral infection is unclear. An analysis of the similarity between viral codon usage and the codon usage of the individual genes of a host genome has never been performed. In this study, we demonstrated that the codon usage of human RNA viruses is similar to that of some human genes, especially those involved in the cell cycle. This finding was substantiated by its concordance with previous reports of an upregulation at the protein level of some of these biological processes. It therefore suggests that some suboptimal viral codon usage patterns may actually be compatible with cellular translational machineries in infected conditions. url: https://www.ncbi.nlm.nih.gov/pubmed/32395662/ doi: 10.1016/j.heliyon.2020.e03915 id: cord-307904-lnagg1uw author: Johnson, Jennifer A title: Sequence elements controlling expression of Barley stripe mosaic virus subgenomic RNAs in vivo date: 2003-08-15 words: 10666.0 sentences: 536.0 pages: flesch: 58.0 cache: ./cache/cord-307904-lnagg1uw.txt txt: ./txt/cord-307904-lnagg1uw.txt summary: One RNA, ␥KpnI/HpaI, provided a source of the ␥a replicase protein and also contained a 350-nt deletion (from positions 2112 to 2461 on RNA␥) to remove the majority of the ␥b ORF, and a second derivative designed to assess promoter activity contained deletions engineered within the putative sgRNA␥ promoter ( Fig. 2A) . This result implies that competition between the two promoters has a major role in regulating the differential rates of synthesis of the two sgRNAs. To initially define sequences flanking the sgRNA␤2 promoter, two large deletions were generated in the ␤1Ϫ34/ ϩ14 clone that eliminated RNA␤ positions 1705 to 2109 and 2287 to 2434. Analysis of four deletions extending from position Ϫ179 to positions Ϫ110, Ϫ76, Ϫ52, and Ϫ28 relative to the transcription start site revealed that the mutant RNAs were able to replicate in protoplasts, but only mutants containing the deletions Ϫ179/Ϫ110 or Ϫ179/Ϫ76 were able to direct synthesis of sgRNA␤2 (Fig. 4A ). abstract: Barley stripe mosaic virus (BSMV) contains three positive-sense, single-stranded genomic RNAs, designated α, β, and γ, that encode seven major proteins and one minor translational readthrough protein. Three proteins (αa, βa, and γa) are translated directly from the genomic RNAs and the remaining proteins encoded on RNAβ and RNAγ are expressed via three subgenomic messenger RNAs (sgRNAs). sgRNAβ1 directs synthesis of the triple gene block 1 (TGB1) protein. The TGB2 protein, the TGB2′ minor translational readthrough protein, and the TGB3 protein are expressed from sgRNAβ2, which is present in considerably lower abundance than sgRNAβ1. A third sgRNA, sgRNAγ, is required for expression of the γb protein. We have used deletion analyses and site-specific mutations to define the boundaries of promoter regions that are critical for expression of the BSMV sgRNAs in infected protoplasts. The results reveal that the sgRNAβ1 promoter encompasses positions −29 to −2 relative to its transcription start site and is adjacent to a cis-acting element required for RNAβ replication that maps from −107 to −74 relative to the sgRNAβ1 start site. The core sgRNAβ2 promoter includes residues −32 to −17 relative to the sgRNAβ2 transcriptional start site, although maximal activity requires an upstream hexanucleotide sequence residing from positions −64 to −59. The sgRNAγ promoter maps from −21 to +2 relative to its transcription start site and therefore partially overlaps the γa gene. The sgRNAβ1, β2, and γ promoters also differ substantially in sequence, but have similarities to the putative homologous promoters of other Hordeiviruses. These differences are postulated to affect competition for the viral polymerase, coordination of the temporal expression and abundance of the TGB proteins, and constitutive expression of the γb protein. url: https://api.elsevier.com/content/article/pii/S004268220300285X doi: 10.1016/s0042-6822(03)00285-x id: cord-007474-ckqghr3b author: Johnson, Michael E. title: Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes date: 2002-11-13 words: 6487.0 sentences: 362.0 pages: flesch: 51.0 cache: ./cache/cord-007474-ckqghr3b.txt txt: ./txt/cord-007474-ckqghr3b.txt summary: Recombinant complementary DNA (cDNA) representing gene 9 (the gene encoding the neutralization antigens in VP7 glycoprotein) from OSU (porcine rotavirus serotype 1) and Gottfried (porcine rotavirus serotype 2) strains were used to determine the optimal hybridization conditions which allow specific detection of group A porcine rotaviruses. In the present study, a dot blot hybridization assay is described for the detection and serotypic differentiation of porcine rotavirus utilizing hybridization probes prepared from recombinant cDNA representing gene 9 from OSU and Gottfried strains (porcine rotavirus serotypes 1 and 2, respectively). Five subfragments of gene 9 from OSU and Gottfried (Table 1 ) were 32p-labeled and hybridized to heterologous rotavirus RNA under both high and low stringency conditions. They reported that rotavirus serotypes 2 and 3 could be differentiated with the gene 9 cDNA probe by using conditions of low stringency (56 ° C), and comparison with the results obtained with hybridization at 56°C, 13% formamide. abstract: A dot blot hybridization assay is described for the detection and differentiation of porcine rotavirus serotypes. Recombinant complementary DNA (cDNA) representing gene 9 (the gene encoding the neutralization antigens in VP7 glycoprotein) from OSU (porcine rotavirus serotype 1) and Gottfried (porcine rotavirus serotype 2) strains were used to determine the optimal hybridization conditions which allow specific detection of group A porcine rotaviruses. Probes were prepared by excision of the inserts from the recombinant plasmids and radiolabeling of cDNA with (32)P by the random primer extension method. Probes were hybridized at various stringencies with viral RNA from different rotavirus serotypes bound to nylon membranes. Hybridization at low stringency (26% base pair mismatch for stable hybrid formation) had high sensitivity but low specificity. Hybridization at high stringency (16% base pair mismatch for stable hybrid formation) produced high specificity but decreased the sensitivity observed at low stringency. Probes were specific for rotavirus at both stringencies and did not hybridize with nucleic acids from other porcine viruses. Subgenomic gene 9 fragments were then tested to provide more specific probes. A 322 bp fragment from OSU gene 9 between nucleotides 382 and 704 and a 266 bp fragment from Gottfried gene 9 between nucleotides 230 and 496 were found to be specific as hybridization probes. These studies demonstrated the feasibility of the dot blot hybridization assay using subgenomic fragments of gene 9 to detect and differentiate serotypes of porcine rotavirus. Additional studies are warranted to further evaluate the sensitivity and the capability of these probes to detect porcine field isolates of the same serotype. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117278/ doi: 10.1016/0378-1135(90)90180-4 id: cord-304876-txaoz7oh author: Jordan, Paul C title: Nucleosides for the treatment of respiratory RNA virus infections date: 2018-03-21 words: 10962.0 sentences: 654.0 pages: flesch: 46.0 cache: ./cache/cord-304876-txaoz7oh.txt txt: ./txt/cord-304876-txaoz7oh.txt summary: 42 Viral polymerase: An important molecular target for antiviral therapy Nucleoside analogs represent one of the dominant classes of antiviral agents due to their widespread use against the common chronic infections caused by human immunodeficiency virus (HIV), hepatitis B virus, and herpesviruses. 43 After being metabolized by host kinases to their triphosphate form, antiviral nucleotides compete with natural nucleoside triphosphates (NTPs) to bind to the active site of viral polymerases and alter DNA or RNA synthesis. 122 However, the results summarized here indicate that nucleoside analogs targeting the viral RNA polymerase of rhinovirus, EV71, and other enteroviruses have the potential to be efficacious in preclinical animal models, providing a rationale to conduct human studies with safer molecules sharing the same mode of action. Structure and functional analysis of the RNA-and viral phosphoprotein-binding domain of respiratory syncytial virus M2-1 protein abstract: Influenza virus, respiratory syncytial virus, human metapneumovirus, parainfluenza virus, coronaviruses, and rhinoviruses are among the most common viruses causing mild seasonal colds. These RNA viruses can also cause lower respiratory tract infections leading to bronchiolitis and pneumonia. Young children, the elderly, and patients with compromised cardiac, pulmonary, or immune systems are at greatest risk for serious disease associated with these RNA virus respiratory infections. In addition, swine and avian influenza viruses, together with severe acute respiratory syndrome-associated and Middle Eastern respiratory syndrome coronaviruses, represent significant pandemic threats to the general population. In this review, we describe the current medical need resulting from respiratory infections caused by RNA viruses, which justifies drug discovery efforts to identify new therapeutic agents. The RNA polymerase of respiratory viruses represents an attractive target for nucleoside and nucleotide analogs acting as inhibitors of RNA chain synthesis. Here, we present the molecular, biochemical, and structural fundamentals of the polymerase of the four major families of RNA respiratory viruses: Orthomyxoviridae, Pneumoviridae/Paramyxoviridae, Coronaviridae, and Picornaviridae. We summarize past and current efforts to develop nucleoside and nucleotide analogs as antiviral agents against respiratory virus infections. This includes molecules with very broad antiviral spectrum such as ribavirin and T-705 (favipiravir), and others targeting more specifically one or a few virus families. Recent advances in our understanding of the structure(s) and function(s) of respiratory virus polymerases will likely support the discovery and development of novel nucleoside analogs. url: https://www.ncbi.nlm.nih.gov/pubmed/29562753/ doi: 10.1177/2040206618764483 id: cord-335441-bj3me7p8 author: Jourdain, Elsa title: Influenza Virus in a Natural Host, the Mallard: Experimental Infection Data date: 2010-01-28 words: 6354.0 sentences: 311.0 pages: flesch: 52.0 cache: ./cache/cord-335441-bj3me7p8.txt txt: ./txt/cord-335441-bj3me7p8.txt summary: Five of the six ducks excreted viral RNA in their feces on the first day post-inoculation (PI) and all samples (feces, cloacal and oral swabs) from all birds were positive on the second day PI (Figures 4 and S1 ). Intermittent and moderate (high ct-values) viral RNA shedding was detected for all birds in water, fecal or cloacal samples between day 1 and 7 after H7N7 re-inoculation ( Figure 4 ). Active H5 infection was confirmed only in one duck, by expression of H5-specific antibodies and detection of viral RNA in the various sample types (feces, water, oral and cloacal swabs) with a pattern similar to the H5-inoculated control bird. Eight 3-month-old male wild-type mallards (Anas platyrhynchos) of approximately the same body mass and size (measurement of the left wing, the right tarsus length and the distance from bill tip to back of the skull) were selected from a Swedish duck farm known from previous successive sampling to be free from IAV infection. abstract: Wild waterfowl, particularly dabbling ducks such as mallards (Anas platyrhynchos), are considered the main reservoir of low-pathogenic avian influenza viruses (LPAIVs). They carry viruses that may evolve and become highly pathogenic for poultry or zoonotic. Understanding the ecology of LPAIVs in these natural hosts is therefore essential. We assessed the clinical response, viral shedding and antibody production of juvenile mallards after intra-esophageal inoculation of two LPAIV subtypes previously isolated from wild congeners. Six ducks, equipped with data loggers that continually monitored body temperature, heart rate and activity, were successively inoculated with an H7N7 LPAI isolate (day 0), the same H7N7 isolate again (day 21) and an H5N2 LPAI isolate (day 35). After the first H7N7 inoculation, the ducks remained alert with no modification of heart rate or activity. However, body temperature transiently increased in four individuals, suggesting that LPAIV strains may have minor clinical effects on their natural hosts. The excretion patterns observed after both re-inoculations differed strongly from those observed after the primary H7N7 inoculation, suggesting that not only homosubtypic but also heterosubtypic immunity exist. Our study suggests that LPAI infection has minor clinically measurable effects on mallards and that mallard ducks are able to mount immunological responses protective against heterologous infections. Because the transmission dynamics of LPAIVs in wild populations is greatly influenced by individual susceptibility and herd immunity, these findings are of high importance. Our study also shows the relevance of using telemetry to monitor disease in animals. url: https://doi.org/10.1371/journal.pone.0008935 doi: 10.1371/journal.pone.0008935 id: cord-355179-wmfwl2bh author: Jung, Eunhye title: Neutralization of Acidic Intracellular Vesicles by Niclosamide Inhibits Multiple Steps of the Dengue Virus Life Cycle In Vitro date: 2019-06-18 words: 5305.0 sentences: 271.0 pages: flesch: 44.0 cache: ./cache/cord-355179-wmfwl2bh.txt txt: ./txt/cord-355179-wmfwl2bh.txt summary: Overall, the data indicate that the antiviral activity of niclosamide during the early stage of the DENV life cycle correlates with the neutralization profile of the low-pH compartments, suggesting that blocking endosomal acidification results in the inhibition of viral genome replication and polyprotein processing, which further impedes viral protein expression and virus production. In this study, we found that neutralization of low-pH intracellular compartments by niclosamide not only inhibited the early stage of the DENV viral life cycle, such as viral RNA replication, independent of the entry step but also the late stage, specifically, the maturation of virus particles into infectious virions. Indeed, niclosamide treatment www.nature.com/scientificreports www.nature.com/scientificreports/ during the first 6 h of infection reduced DENV replication in BHK-21 cells harbouring dengue replicons to a level comparable to that of ribavirin, suggesting that the drug affects viral RNA replication and/or translation independent of its effect on entry, membrane fusion and genome release. abstract: Dengue fever is one of the most important mosquito-borne viral infections in large parts of tropical and subtropical countries and is a significant public health concern and socioeconomic burden. There is an urgent need to develop antivirals that can effectively reduce dengue virus (DENV) replication and decrease viral load. Niclosamide, an antiparasitic drug approved for human use, has been recently identified as an effective antiviral agent against a number of pH-dependent viruses, including flaviviruses. Here, we reveal that neutralization of low-pH intracellular compartments by niclosamide affects multiple steps of the DENV infectious cycle. Specifically, niclosamide-induced endosomal neutralization not only prevents viral RNA replication but also affects the maturation of DENV particles, rendering them non-infectious. We found that niclosamide-induced endosomal neutralization prevented E glycoprotein conformational changes on the virion surface of flaviviruses, resulting in the release of non-infectious immature virus particles with uncleaved pr peptide from host cells. Collectively, our findings support the potential application of niclosamide as an antiviral agent against flavivirus infection and highlight a previously uncharacterized mechanism of action of the drug. url: https://www.ncbi.nlm.nih.gov/pubmed/31213630/ doi: 10.1038/s41598-019-45095-1 id: cord-305859-vt8vwo3y author: Jung, Kwonil title: Calves are susceptible to infection with the newly emerged porcine deltacoronavirus, but not with the swine enteric alphacoronavirus, porcine epidemic diarrhea virus date: 2017-04-03 words: 3232.0 sentences: 167.0 pages: flesch: 56.0 cache: ./cache/cord-305859-vt8vwo3y.txt txt: ./txt/cord-305859-vt8vwo3y.txt summary: Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. Our study demonstrated that Gn calves orally inoculated with the PDCoV strain OH-FD22 (ICs of cell-culture grown PDCoV from infected Gn pigs) develop an acute infection with persistent fecal PDCoV RNA shedding and PDCoVspecific serum IgG antibody responses, but show no signs of significant intestinal lesions or clinical disease [8] . In our study, there were no detectable fecal viral RNA shedding, virus-specific serum IgG antibody responses, histological lesions, and clinical disease in Gn calves orally inoculated with the PEDV strain PC21A (ICs of wild-type PEDV-infected Gn pigs) [6] . abstract: Fecal virus shedding, seroconversion and histopathology were evaluated in 3-7-year-old gnotobiotic calves orally inoculated with porcine deltacoronavirus (PDCoV) (9.0-9.6 log(10) genomic equivalents [GE] of OH-FD22-P5; n=4) or porcine epidemic diarrhea virus (PEDV) (10.2-12.5 log(10) GE of PC21A; n=3). In PDCoV-inoculated calves, an acute but persisting fecal viral RNA shedding and PDCoV-specific serum IgG antibody responses were observed, but without lesions or clinical disease. However, no fecal shedding, seroconversion, histological lesions, and clinical disease were detected in PEDV-inoculated calves. Our data indicate that calves are susceptible to infection by the newly emerged PDCoV, but not by the swine coronavirus, PEDV. url: https://www.ncbi.nlm.nih.gov/pubmed/28374120/ doi: 10.1007/s00705-017-3351-z id: cord-351548-jvl63652 author: Juranic Lisnic, Vanda title: Dual Analysis of the Murine Cytomegalovirus and Host Cell Transcriptomes Reveal New Aspects of the Virus-Host Cell Interface date: 2013-09-26 words: 11978.0 sentences: 623.0 pages: flesch: 49.0 cache: ./cache/cord-351548-jvl63652.txt txt: ./txt/cord-351548-jvl63652.txt summary: Finally, a recent transcriptomic analysis of newly synthesized RNA in MCMV infected fibroblasts [15] applied RNA-Seq technology to study regulation of viral gene expression and identified a very early peak of viral gene transcriptional activity at 1-2 hours post infection followed by rapid cellular countermeasures but did not attempt to re-annotate MCMV genome. The MCMV transcripts identified through our classical cDNA cloning and sequencing (green arrows) and the RNA-Seq expression profiles (gray histograms), showed complementary results to each other but diverged dramatically from current annotations. Because cDNA cloning and RNA-Seq identified significant differences between the MCMV transcriptome and current annotations, we performed an in depth analysis of several genomic regions by northern analyses ( Figure 5 , Figures S2, S3 , S4, S5) using our cDNA clones to generate strand specific riboprobes ( Table 1) . abstract: Major gaps in our knowledge of pathogen genes and how these gene products interact with host gene products to cause disease represent a major obstacle to progress in vaccine and antiviral drug development for the herpesviruses. To begin to bridge these gaps, we conducted a dual analysis of Murine Cytomegalovirus (MCMV) and host cell transcriptomes during lytic infection. We analyzed the MCMV transcriptome during lytic infection using both classical cDNA cloning and sequencing of viral transcripts and next generation sequencing of transcripts (RNA-Seq). We also investigated the host transcriptome using RNA-Seq combined with differential gene expression analysis, biological pathway analysis, and gene ontology analysis. We identify numerous novel spliced and unspliced transcripts of MCMV. Unexpectedly, the most abundantly transcribed viral genes are of unknown function. We found that the most abundant viral transcript, recently identified as a noncoding RNA regulating cellular microRNAs, also codes for a novel protein. To our knowledge, this is the first viral transcript that functions both as a noncoding RNA and an mRNA. We also report that lytic infection elicits a profound cellular response in fibroblasts. Highly upregulated and induced host genes included those involved in inflammation and immunity, but also many unexpected transcription factors and host genes related to development and differentiation. Many top downregulated and repressed genes are associated with functions whose roles in infection are obscure, including host long intergenic noncoding RNAs, antisense RNAs or small nucleolar RNAs. Correspondingly, many differentially expressed genes cluster in biological pathways that may shed new light on cytomegalovirus pathogenesis. Together, these findings provide new insights into the molecular warfare at the virus-host interface and suggest new areas of research to advance the understanding and treatment of cytomegalovirus-associated diseases. url: https://doi.org/10.1371/journal.ppat.1003611 doi: 10.1371/journal.ppat.1003611 id: cord-026641-eemp6b5j author: Kabiljo, Julijan title: From threat to cure: understanding of virus-induced cell death leads to highly immunogenic oncolytic influenza viruses date: 2020-06-11 words: 6689.0 sentences: 373.0 pages: flesch: 37.0 cache: ./cache/cord-026641-eemp6b5j.txt txt: ./txt/cord-026641-eemp6b5j.txt summary: In the absence of NS1 apoptosis appears to be induced through the viral-RNA-mediated induction of retinoic acidinducible gene I (RIG-I) and interferon (IFN) signaling including protein kinase R (PKR) and eukaryotic initiation factor 2 alpha (eIF2α) activation and subsequent block of translation [39] [40] [41] . Another study screened a variety of wild-type influenza A viruses for their infectivity in pancreatic carcinoma cell lines and showed oncolytic effectiveness in a mouse model of human pancreatic cancer 67 . expressed a recombinant humanized cytotoxic T-lymphocyte-associated protein 4 (CTLA4) immune checkpoint inhibiting antibody from two different RNA fragments of the influenza A virus genome in order to enhance its anti-cancer effectiveness in a murine B16 melanoma model 96 . Further effects of oncolytic influenza A viruses on the cancer-immune microenvironment shown in murine models include activation of NK-cells and macrophage polarization towards immuno-stimulatory M1 phenotypes 66, 114 . abstract: Oncolytic viruses constitute an emerging strategy in immunomodulatory cancer treatment. The first oncolytic virus, Talimogene laherparepvec (T-VEC), based on herpes simplex virus 1 (HSV-1), was approved by the Food and Drug Administration (FDA) and European Medicines Agency (EMA) in 2015. The field of oncolytic virotherapy is still in its beginnings, since many promising viruses remain only superficially explored. Influenza A virus causes a highly immunogenic acute infection but never leads to a chronic disease. While oncolytic influenza A viruses are in preclinical development, they have not made the transition into clinical practice yet. Recent insights into different types of cell death caused by influenza A virus infection illuminate novel possibilities of enhancing its therapeutic effect. Genetic engineering and experience in influenza A virus vaccine development allow safe application of the virus in patients. In this review we give a summary of efforts undertaken to develop oncolytic influenza A viruses. We discuss strategies for targeting viral replication to cancerous lesions and arming them with immunogenic transgenes. We furthermore describe which modes of cell death are induced by influenza A virus infection and how these insights may be utilized to optimize influenza A virus-based oncolytic virus design. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288254/ doi: 10.1038/s41420-020-0284-1 id: cord-294800-akr4f5p8 author: Kabir, Md. Tanvir title: nCOVID-19 Pandemic: From Molecular Pathogenesis to Potential Investigational Therapeutics date: 2020-07-10 words: 14084.0 sentences: 700.0 pages: flesch: 44.0 cache: ./cache/cord-294800-akr4f5p8.txt txt: ./txt/cord-294800-akr4f5p8.txt summary: They also summarized that as viral load is quite high during the time of hospital admissions, use of potent antiviral agents at an early stage might prove Abbreviations: ACE2, angiotensin converting enzyme 2; AP, antigen presentation; APCs, antigen presentation cells; APN, aminopeptidase N, ARBs, angiotensin II receptor blockers; ARDS, acute respiratory distress syndrome; CDC, Centers for Disease Control; nCOVID-19, novel coronavirus disease 2019; CoVs, coronaviruses; DPP4, dipeptidyl peptidase 4; dsRNA, double-strand RNA; EC 50 , half maximal effective concentration; ED, emergency department; ELISA, enzymelinked immunosorbent assay; EUA, emergency use authorization; FDA, Food and Drug Administration; GGO, ground-glass opacity; HCV, hepatitis C virus; HIV, human immunodeficiency virus;, MHC, major histocompatibility complex; or HLA, human leukocyte antigen; ICU, intensive care unit; IL-6, interleukin 6; LPV/r, lopinavir/ritonavir; mAbs, monoclonal antibodies; MERS, Middle East respiratory syndrome; N7-MTase, N7-methyltransferase; NSAIDs, nonsteroidal anti-inflammatory drugs; PRRs, pattern recognition receptors; PUI, patient under investigation; RdRp, RNA-dependent RNA polymerase; RSV, respiratory syncytial virus; S protein, spike protein; SAM, S-adenosyl-methionine; SARS, severe acute respiratory syndrome; SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; WHO, World Health Organization. abstract: In December 2019, a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related epidemic was first observed in Wuhan, China. In 2020, owing to the highly infectious and deadly nature of the virus, this widespread novel coronavirus disease 2019 (nCOVID-19) became a worldwide pandemic. Studies have revealed that various environmental factors including temperature, humidity, and air pollution may also affect the transmission pattern of COVID-19. Unfortunately, still, there is no specific drug that has been validated in large-scale studies to treat patients with confirmed nCOVID-19. However, remdesivir, an inhibitor of RNA-dependent RNA polymerase (RdRp), has appeared as an auspicious antiviral drug. Currently, a large-scale study on remdesivir (i.e., 200 mg on first day, then 100 mg once/day) is ongoing to evaluate its clinical efficacy to treat nCOVID-19. Good antiviral activity against SARS-CoV-2 was not observed with the use of lopinavir/ritonavir (LPV/r). Nonetheless, the combination of umifenovir and LPV/r was found to have better antiviral activity. Furthermore, a combination of hydroxychloroquine (i.e., 200 mg 3 times/day) and azithromycin (i.e., 500 mg on first day, then 250 mg/day from day 2–5) also exhibited good activity. Currently, there are also ongoing studies to evaluate the efficacy of teicoplanin and monoclonal and polyclonal antibodies against SARS-CoV-2. Thus, in this article, we have analyzed the genetic diversity and molecular pathogenesis of nCOVID-19. We also present possible therapeutic options for nCOVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32754599/ doi: 10.3389/fcell.2020.00616 id: cord-333979-bx2xspbe author: Kalikiri, Mahesh K R title: High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads date: 2020-04-11 words: 2029.0 sentences: 102.0 pages: flesch: 52.0 cache: ./cache/cord-333979-bx2xspbe.txt txt: ./txt/cord-333979-bx2xspbe.txt summary: title: High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads We developed a method using a widely available lysis buffer coupled with solid-phase reverse immobilization (SPRI) beads to extract viral RNA from swabs collected in viral transport medium (VTM) which can be performed manually or on a Hamilton STAR liquid-handling robot. Retrospective, residual nasopharyngeal specimens that previously tested positive or negative for respiratory syncytial virus (RSV) using the Cepheid GeneXpert Flu/RSV kit or the Fast Track Diagnostics Respiratory Pathogens 21 PCR (FTD-RESP21) were extracted with our new approach on a Hamilton STAR liquid handling robot with 8 CO-RE channels. When applying these conditions to 204 clinical samples, we only observed a 2.5% inhibition of the RT-qPCR, indicating that our method is suitable for large-scale use in testing laboratories. In this manuscript, we demonstrate the feasibility of using reagents commonly available in molecular biology and next-generation sequencing laboratories for the extraction of SARS-CoV-2 viral RNA for the diagnosis of COVID-19. abstract: The ongoing pandemic of the novel coronavirus, SARS-CoV-2, has led to a global surge in laboratory testing for the virus. The gold standard approach to detecting an active viral infection is the use of RT-qPCR. This approach requires the isolation of viral RNA from respiratory specimens, such as nasopharyngeal swabs. We developed a method using a widely available lysis buffer coupled with solid-phase reverse immobilization (SPRI) beads to extract viral RNA from swabs collected in viral transport medium (VTM) which can be performed manually or on a Hamilton STAR liquid-handling robot. Using a WHO recommended, laboratory-developed RT-qPCR for SARS-CoV-2, we validated this method in a CAP-accredited laboratory, against the IVD-labelled bioMérieux NucliSENS easyMAG automated extraction platform. Our method demonstrates a comparable sensitivity and specificity, making it suitable for large-scale testing and monitoring of suspected COVID-19 cases and healthcare workers. This is especially important as the world faces critical shortages of viral RNA extraction reagents for the existing commercial extraction systems. url: https://doi.org/10.1101/2020.04.08.20055731 doi: 10.1101/2020.04.08.20055731 id: cord-270940-acwkh6ed author: Kallio-Kokko, Hannimari title: Viral zoonoses in Europe date: 2005-06-29 words: 14695.0 sentences: 733.0 pages: flesch: 46.0 cache: ./cache/cord-270940-acwkh6ed.txt txt: ./txt/cord-270940-acwkh6ed.txt summary: Recently, during an outbreak in Finland in 2002, the causative agent of Pogosta disease was isolated for the first time in Europe from skin biopsies and a blood sample of patients [115] ; the virus strains were most closely related to SINV strains isolated from mosquitoes in Sweden and Russia 20 years previously. The genus Nairovirus (family Bunyaviridae) is composed of 34 predominantly tick-borne viruses that have been divided into seven serogroups [154] including several associated with severe human and livestock diseases (especially Crimean-Congo hemorrhagic fever virus (CCHFV) and Nairobi sheep disease virus). Rift Valley fever virus (RVFV), which is the type species of the genus and is transmitted by mosquitoes, causing an influenza-like disease that affects domestic animals and humans. abstract: A number of new virus infections have emerged or re-emerged during the past 15 years. Some viruses are spreading to new areas along with climate and environmental changes. The majority of these infections are transmitted from animals to humans, and thus called zoonoses. Zoonotic viruses are, as compared to human-only viruses, much more difficult to eradicate. Infections by several of these viruses may lead to high mortality and also attract attention because they are potential bioweapons. This review will focus on zoonotic virus infections occurring in Europe. url: https://www.ncbi.nlm.nih.gov/pubmed/16024128/ doi: 10.1016/j.femsre.2005.04.012 id: cord-347351-emdj66vj author: Kampf, Günter title: Potential sources, modes of transmission and effectiveness of prevention measures against SARS-CoV-2 date: 2020-09-18 words: 10283.0 sentences: 592.0 pages: flesch: 50.0 cache: ./cache/cord-347351-emdj66vj.txt txt: ./txt/cord-347351-emdj66vj.txt summary: Originating from a single travel-associated primary case from China, the first documented chain of multiple human-to-human transmissions of SARS-CoV-2 outside of Asia allowed a detailed study of transmission events and identified several factors (e.g. cumulative face-toface contact, direct contact with secretions or body fluids of a patient, personal protective equipment) to classify contacts as low or high risk [32] . In the close surrounding of COVID-19 patients in hospitals SARS-CoV-2 RNA is detected more frequently compared to surfaces outside the patient rooms but samples were so far consistently negative for infectious virus. General disinfection of frequently touched surfaces in the public such as shopping carts or door handles is, however, unlikely to add any protective value because even in COVID-19 wards inanimate surfaces were mainly contaminated in the permanent and immediate surrounding of symptomatic patients (detection of viral RNA, not of infectious virus) and only rarely one room away [138] suggesting that the risk to find SARS-CoV-2 on frequently touched surfaces in the public is low. abstract: During the current SARS-CoV-2 pandemic new studies are emerging daily providing novel information about sources, transmission risks and possible prevention measures. In this review, we aimed to comprehensively summarize the current evidence on possible sources for SARS-CoV-2, including evaluation of transmission risks and effectiveness of applied prevention measures. Next to symptomatic patients, asymptomatic or pre-symptomatic carriers are a possible source with respiratory secretions as the most likely cause for viral transmission. Air and inanimate surfaces may be sources; however, viral RNA has been inconsistently detected. Similarly, even though SARS-CoV-2 RNA has been detected on or in personnel protective equipment, blood, urine, eyes, the gastrointestinal tract and pets, these sources are currently thought to play a negligible role for transmission. Finally, various prevention measures such as hand washing, hand disinfection, face masks, gloves, surface disinfection or physical distancing for the healthcare setting and public are analysed for their expected protective effect. url: https://doi.org/10.1016/j.jhin.2020.09.022 doi: 10.1016/j.jhin.2020.09.022 id: cord-304873-ppb9k3zu author: Kang, Hunseung title: Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1 date: 1998-04-01 words: 2497.0 sentences: 177.0 pages: flesch: 66.0 cache: ./cache/cord-304873-ppb9k3zu.txt txt: ./txt/cord-304873-ppb9k3zu.txt summary: Our S1, V1, and T1 endonuclease mappings, together with UV melting analysis, clearly indicate that this sequence element of the HIV-1 mRNA frameshift site forms a stem-loop structure, not a pseudoknot structure. The enhancer secondary RNA structure, either a stem-loop or a pseudoknot, downstream of the shift site induces pausing of the ribosome and stimulates w x slippage at the shift sequence 4-7 . Here, we determine the secondary structure of the HIV-1 mRNA frameshifting sequence elements including the shift site, the spacer, and the downstream enhancer sequence by using ultraviolet melting and enzymatic mapping analysis. Our results agree well with the mutational studies showing a simple stem-loop structure for the downstream enhancer sequence of the frameshifting region of the HIV-1 mRNA. Nucleotides A24-A27 were cleaved This cleavage pattern, as summarized in Fig. 4 , indicates that in the context of the frameshifting sequence elements of the HIV-1 RNA consisting of the spacer and the enhancer, the enhancer sequence adopts a stem-loop structure separated from the shift site by a spacer sequence. abstract: Abstract Programmed ribosomal frameshifting in viral messenger RNA occurs in response to neighboring sequence elements consisting of: a frameshift site, a spacer, and a downstream enhancer sequence. In human immunodeficiency virus type 1 (HIV-1) mRNA, this sequence element has a potential to form either a stem-loop or a pseudoknot structure. Based on many mutational studies, the stem-loop structure has been proposed for the downstream enhancer region of the HIV-1 mRNA. This stimulatory stem-loop structure is separated from the shift site by a spacer of seven nucleotides. In contrast, a recent report has proposed an alternative model in which the bases in the spacer sequence form a pseudoknot structure as the downstream enhancer sequence [Du et al., Biochemistry 35 (1996) 4187–4198.]. Using UV melting and enzymatic mapping analyses, we have investigated the conformation of the sequence region involved in ribosomal frameshifting in HIV-1. Our S1, V1, and T1 endonuclease mappings, together with UV melting analysis, clearly indicate that this sequence element of the HIV-1 mRNA frameshift site forms a stem-loop structure, not a pseudoknot structure. This finding further supports the stem-loop structure proposed by many mutational studies for the downstream enhancer sequence of the HIV-1 mRNA. url: https://www.sciencedirect.com/science/article/pii/S0167478198000049 doi: 10.1016/s0167-4781(98)00004-9 id: cord-324495-0pee1i3o author: Kang, Hyeonjeong title: Sasa quelpaertensis Nakai extract suppresses porcine reproductive and respiratory syndrome virus replication and modulates virus-induced cytokine production date: 2015-06-06 words: 6119.0 sentences: 300.0 pages: flesch: 49.0 cache: ./cache/cord-324495-0pee1i3o.txt txt: ./txt/cord-324495-0pee1i3o.txt summary: Therefore, the present study was conducted to determine whether Sasa quelpaertensis Nakai extract (SQE) inhibits PRRSV infection in cultured porcine alveolar macrophages (PAMs). Further experiments revealed that SQE suppresses post-entry steps in the replication cycle of PRRSV, including viral genomic and sg RNA synthesis, viral protein expression, and virus production. The presence of SQE notably altered expression of cytokine genes in PRRSV-infected PAM cells, suggesting that SQE activity is involved in the modulation of inflammatory responses during viral infection. As shown in Fig. 5 , SQE treatment resulted in a maximal reduction in the synthesis of PRRSV genomic RNA and sg mRNA of 90 % and 80 %, respectively, at a concentration of 5 mg/ ml, when compared with untreated infected cells. Treatment of cells with SQE resulted in significant inhibition of post-entry steps during the replication of PRRSV, as demonstrated by reduced progeny production, diminished viral protein expression, and reduced synthesis of genomic RNA and sg mRNA. abstract: Although Sasa quelpaertensis Nakai, a dwarf bamboo, is known to exert a variety of beneficial effects on health, its antiviral effect remains to be elucidated. Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most devastating viral pathogens of swine and has a substantial economic impact on the global pork industry. Therefore, the present study was conducted to determine whether Sasa quelpaertensis Nakai extract (SQE) inhibits PRRSV infection in cultured porcine alveolar macrophages (PAMs). Our results demonstrated that SQE treatment suppressed the replication of PRRSV in a dose-dependent manner. The antiviral activity of SQE on PRRSV replication was found to be primarily exerted at early times postinfection. Treatment with SQE resulted in marked reduction of viral genomic and subgenomic RNA synthesis, viral protein expression, and progeny virus production. Notably, pro-inflammatory cytokine production in PAM cells infected with PRRSV was shown to be modulated in the presence of SQE. Taken together, our data indicate that SQE has potential as a therapeutic agent against PRRSV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00705-015-2469-0) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/26047649/ doi: 10.1007/s00705-015-2469-0 id: cord-351377-xorj8tnz author: Kao, Chi-Fei title: The Characterization of Immunoprotection Induced by a cDNA Clone Derived from the Attenuated Taiwan Porcine Epidemic Diarrhea Virus Pintung 52 Strain date: 2018-10-04 words: 5936.0 sentences: 234.0 pages: flesch: 48.0 cache: ./cache/cord-351377-xorj8tnz.txt txt: ./txt/cord-351377-xorj8tnz.txt summary: Moreover, inoculation with iPEDVPT-P96 elicited comparable levels of anti-PEDV specific plasma IgG and fecal/salivary IgA, neutralizing antibody titers, and similar but less effective immunoprotection against the virulent PEDVPT-P5 challenge compared to the parental PEDVPT-P96. In the present study, an infectious cDNA clone of an attenuated G2b PEDV strain was successfully generated for the first time, and the in vitro and in vivo data indicate that iPEDVPT-P96 is further attenuated but remains immunogenic compared to its parental PEDVPT-P96 viral stock. While one piglet in the PEDVPT-P96 group showed intermittent loose diarrhea (score = 1) and viral shedding at 6 to 11 days post-inoculation (DPI) with the peak viral titer of 1.45 ± 3.24 log 10 RNA copies/mL at 8 DPI (Figure 4) , no evidence of PEDV-associated clinical signs and fecal viral shedding were demonstrated in both iPEDVPT-P96 and mock groups. abstract: The porcine epidemic diarrhea virus (PEDV) poses a great threat to the global swine industries and the unreliable protection induced by the currently available vaccines remains a major challenge. We previously generated a genogroup 2b (G2b) PEDV Taiwan Pintung 52 (PEDVPT) strain, PEDVPT-P96, and determined its promising host immune response against the virulent PEDVPT-P5 strain. To study the attenuation determinants of PEDVPT-P96 and establish a PEDVPT-P96-based recombinant vector as a vaccine platform for further antigenicity modification, iPEDVPT-P96, a full-length cDNA clone of PEDVPT-P96, was established. Comparing to the parental PEDVPT-P96 virus, the iPEDVPT-P96 virus showed efficient replication kinetics with a delayed decline of viral load and similar but much more uniform plaque sizes in Vero cells. In the 5-week-old piglet model, fecal viral shedding was observed in the PEDVPT-P96-inoculated piglets, whereas those inoculated with iPEDVPT-P96 showed neither detectable fecal viral shedding nor PEDV-associated clinical signs. Moreover, inoculation with iPEDVPT-P96 elicited comparable levels of anti-PEDV specific plasma IgG and fecal/salivary IgA, neutralizing antibody titers, and similar but less effective immunoprotection against the virulent PEDVPT-P5 challenge compared to the parental PEDVPT-P96. In the present study, an infectious cDNA clone of an attenuated G2b PEDV strain was successfully generated for the first time, and the in vitro and in vivo data indicate that iPEDVPT-P96 is further attenuated but remains immunogenic compared to its parental PEDVPT-P96 viral stock. The successful development of the iPEDVPT-P96 cDNA clone could allow for the manipulation of the viral genome to study viral pathogenesis and facilitate the rapid development of effective vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/30287770/ doi: 10.3390/v10100543 id: cord-259311-ccx61owl author: Kapitula, D. S. title: Performance & Quality Evaluation of Marketed COVID-19 RNA Detection Kits date: 2020-05-01 words: 3175.0 sentences: 187.0 pages: flesch: 53.0 cache: ./cache/cord-259311-ccx61owl.txt txt: ./txt/cord-259311-ccx61owl.txt summary: In order to provide better understanding of the Quality and performance of COVID-19 RNA detection kits on the market, we designed a system to evaluate the specificity (quantitation), sensitivity (LOD) and robustness of the kits using positive RNA and pseudovirus controls based on COVID-19 genomic sequence. At the time of submission, 23 diagnostic kits have been approved in China, of which 8 are based on quantitative Polymerase Chain Reaction (qPCR) using COVID-19 viral RNA sequence as templates and fluorescence detection. Our study aims at providing objective evaluation and comparison of the quality and performance characteristics of 8 of the currently marketed COVID-19 nucleic acid detection kits in China based on qPCR and fluorescence detection. Our study provides an elegant design to define the most important performance characteristics of the RNA detection kits for COVID-19, which are specificity (quantitative), sensitivity (LOD), and robustness. abstract: Compared to other coronaviruses, COVID-19 has a longer incubation period and features asymptomatic infection at a high rate (>25%). Therefore, early detection of infection is the key to early isolation and treatment. Direct detection of the virus itself has advantages over indirect detection. Currently, the most sensitive and commercially validated method for COVID-19 testing is RT-qPCR, designed to detect amplified virus-specific RNA. Reliable testing has proven to be a bottleneck in early diagnosis of virus infection in all countries dealing with the pandemic. Significant performance and quality issues with available testing kits have caused confusion and serious health risks. In order to provide better understanding of the Quality and performance of COVID-19 RNA detection kits on the market, we designed a system to evaluate the specificity (quantitation), sensitivity (LOD) and robustness of the kits using positive RNA and pseudovirus controls based on COVID-19 genomic sequence. We evaluated 8 Nucleic Acid qPCR Kits approved in China, some of which are also approved in the US and EU. Our study showed that half of these 8 kits lack 1:1 linear relationship for virus RNA copy: qPCR signal. Of the 4 with linear response, 2 demonstrated sensitivity at 1 Copy viral RNA/Reaction, suitable for early detection of virus infection. Furthermore, we established the best RNA extraction, handling and qPCR procedures allowing highly sensitive and consistent performance using BGI qPCR kits. Our study provides an effective method to assess and compare performance quality of all COVID-19 nucleic acid testing kits, globally. url: https://doi.org/10.1101/2020.04.25.20080002 doi: 10.1101/2020.04.25.20080002 id: cord-262347-ejhz9rra author: Kappes, Matthew A. title: PRRSV structure, replication and recombination: Origin of phenotype and genotype diversity date: 2015-03-07 words: 10170.0 sentences: 498.0 pages: flesch: 42.0 cache: ./cache/cord-262347-ejhz9rra.txt txt: ./txt/cord-262347-ejhz9rra.txt summary: The nidovirus order constitutes a group of singlestranded positive-sense RNA viruses which share a hallmark replication/transcription strategy, similar genomic organization, and a defining set of genetic elements, but differ in host species and range, disease phenotype, virion morphology, cellular tropism, genomic size and encoded content . It has been shown that the EAV replicase proteins (ORF1a/b) are sufficient to support viral replication (Molenkamp et al., 2000b) , but that infectivity is dependent on the presence of the structural genes encoded at the 3 0 -end of the arterivirus genome Molenkamp et al., 2000b; Verheije et al., 2002) . Leader-body junction sequence of the viral subgenomic mRNAs of porcine reproductive and respiratory syndrome virus isolated in Taiwan Molecular cloning and nucleotide sequencing of the 3 0 -terminal genomic RNA of the porcine reproductive and respiratory syndrome virus Comparison of the 5 0 leader sequences of North American isolates of reference and field strains of porcine reproductive and respiratory syndrome virus (PRRSV) abstract: Porcine reproductive and respiratory disease virus (PRRSV) has the intrinsic ability to adapt and evolve. After 25 years of study, this persistent pathogen has continued to frustrate efforts to eliminate infection of herds through vaccination or other elimination strategies. The purpose of this review is to summarize the research on the virion structure, replication and recombination properties of PRRSV that have led to the extraordinary phenotype and genotype diversity that exists worldwide. url: https://doi.org/10.1016/j.virol.2015.02.012 doi: 10.1016/j.virol.2015.02.012 id: cord-103377-j1mmx7k7 author: Karasik, Agnes title: Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences date: 2020-09-11 words: 11779.0 sentences: 646.0 pages: flesch: 58.0 cache: ./cache/cord-103377-j1mmx7k7.txt txt: ./txt/cord-103377-j1mmx7k7.txt summary: Since it was reported that RNase L activation increased translation of 3''UTR regions downstream of stop codons by interfering with factors that promote translation termination (eRF3) or ribosome recycling (ABCE1) (Le Roy et al., 2005) , we assessed the level of ribosome footprints in 3''UTRs. This level was assayed by computing the ratio of footprints in every 3''UTR relative to its respective main ORF within the coding sequence (density ratio, 3''UTR:ORF) for each transcript . The similarity in the effects suggests that translation of non-canonical regions occurs when RNase L is activated via naturally produced 2-5A from broad activation of the antiviral response by double-stranded RNAs. It should be noted that poly I:C treatment did result in slightly elevated 3''UTR ribosome footprints on some genes in a RNase L KO cell line (Supplemental Figure 4A ). abstract: Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5’ and 3’ UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L’s cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity. url: https://doi.org/10.1101/2020.09.10.291690 doi: 10.1101/2020.09.10.291690 id: cord-274097-11hvriqy author: Katz, Louis M. title: Is SARS‐CoV‐2 transfusion transmitted? date: 2020-06-16 words: 2023.0 sentences: 132.0 pages: flesch: 51.0 cache: ./cache/cord-274097-11hvriqy.txt txt: ./txt/cord-274097-11hvriqy.txt summary: The few studies of SARS-CoV-2 RNA in donors or of donors developing COVID-19 after giving blood are a mix of small series wherein prospectively test-positive units were quarantined and not transfused or involved units quarantined after donation to permit the donor time to get ill before units are distributed. In a lookback to recipients of 17 transfused components from seven South Korean donors who developed COVID-19 6 to 15 days after donation, there was no associated clinical morbidity in the recipients; however, archived samples tested by PCR after the donors reported their illnesses were negative. 21 Precise estimates of the prevalence of asymptomatic/presymptomatic infection and especially of whether RNA-emia or, more germane to this topic, viremia occur in the absence of illness (especially in healthy donors or the larger well population who might be qualified to donate) are among the key missing data needed to inform our debate about any risk of TTI and subsequent TTD. Severe acute respiratory syndrome coronavirus 2 RNA detected in blood donations abstract: See article on page 1119–1122, in this issue url: https://doi.org/10.1111/trf.15831 doi: 10.1111/trf.15831 id: cord-307603-uqr6r14u author: Kauppinen, S. title: Locked Nucleic Acid: High-Affinity Targeting of Complementary RNA for RNomics date: 2006 words: 5782.0 sentences: 298.0 pages: flesch: 47.0 cache: ./cache/cord-307603-uqr6r14u.txt txt: ./txt/cord-307603-uqr6r14u.txt summary: Several studies have demonstrated that LNA-modified oligonucleotides exhibit unprecedented thermal stability when hybridized with their DNA and RNA target molecules (Koshkin et al. 2005 ); (2) easy access-LNAs (fully modified or mixmers) are commercially available; (3) high-affinity and sequence-selective targeting of RNA molecules in vitro or in vivo Koshkin et al. Recently, it has been demonstrated that LNAzymes containing 3-4 LNA monomers at the ends of the binding arms cleave viral RNA structures that are resistant to hydrolysis by the corresponding unmodified DNAzyme, i.e., that efficient cleavage is correlated with improved binding affinity towards the target (Schubert et al. Efficient selection of polyadenylated mRNA from eukaryotic cells and tissues is an essential step for a wide selection of functional genomics applications, including full-length complementary (c)DNA library construction and sequencing, Northern and dot blot analyses, gene expression profiling by microarrays, and quantitative RT-PCR. LNA (locked nucleic acid): high affinity targeting of complementary RNA and DNA abstract: Locked nucleic acid (LNA) is a nucleic acid analog containing one or more LNA nucleotide monomers with a bicyclic furanose unit locked in an RNA-mimicking sugar conformation. This conformational restriction is translated into unprecedented hybridization affinity towards complementary single-stranded RNA molecules. That makes fully modified LNAs, LNA/DNA mixmers, or LNA/RNA mixmers uniquely suited for mimicking RNA structures and for RNA targeting in vitro or in vivo. The focus of this chapter is on LNA antisense, LNA-modified DNAzymes (LNAzymes), LNA-modified small interfering (si)RNA (siLNA), LNA-enhanced expression profiling by real-time RT-PCR and detection and analysis of microRNAs by LNA-modified probes. url: https://www.ncbi.nlm.nih.gov/pubmed/16594628/ doi: 10.1007/3-540-27262-3_21 id: cord-301285-p83ondy8 author: Kautz, Tiffany F title: Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy date: 2018-03-06 words: 8836.0 sentences: 472.0 pages: flesch: 53.0 cache: ./cache/cord-301285-p83ondy8.txt txt: ./txt/cord-301285-p83ondy8.txt summary: To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Due to the error-prone nature of the RNA-dependent RNApolymerase (RdRp), RNA virus replication is characterized by a high mutation rate that results in increased genetic diversity of progeny viruses (Domingo et al. When compared with unpassaged, wild-type (wt) viruses, fidelity mutants have similar growth kinetics in vitro, but are attenuated in vivo due to the alteration of diversity produced during replication, which hampers the ability of the virus to overcome bottlenecks in the host (Pfeiffer and Kirkegaard 2005; Vignuzzi et al. The 4x mutant, while exhibiting phenotypic similarities with other altered fidelity mutants, had no significant difference in virus diversity compared with the TC-83 parent after one cell culture passage. abstract: During RNA virus replication, there is the potential to incorporate mutations that affect virulence or pathogenesis. For live-attenuated vaccines, this has implications for stability, as replication may result in mutations that either restore the wild-type phenotype via reversion or compensate for the attenuating mutations by increasing virulence (pseudoreversion). Recent studies have demonstrated that altering the mutation rate of an RNA virus is an effective attenuation tool. To validate the safety of low-fidelity mutations to increase vaccine attenuation, several mutations in the RNA-dependent RNA-polymerase (RdRp) were tested in the live-attenuated Venezuelan equine encephalitis virus vaccine strain, TC-83. Next generation sequencing after passage in the presence of mutagens revealed a mutant containing three mutations in the RdRp, TC-83 3x, to have decreased replication fidelity, while a second mutant, TC-83 4x displayed no change in fidelity, but shared many phenotypic characteristics with TC-83 3x. Both mutants exhibited increased, albeit inconsistent attenuation in an infant mouse model, as well as increased immunogenicity and complete protection against lethal challenge of an adult murine model compared with the parent TC-83. During serial passaging in a highly permissive model, the mutants increased in virulence but remained less virulent than the parent TC-83. These results suggest that the incorporation of low-fidelity mutations into the RdRp of live-attenuated vaccines for RNA viruses can confer increased immunogenicity whilst showing some evidence of increased attenuation. However, while in theory such constructs may result in more effective vaccines, the instability of the vaccine phenotype decreases the likelihood of this being an effective vaccine strategy. url: https://www.ncbi.nlm.nih.gov/pubmed/29593882/ doi: 10.1093/ve/vey004 id: cord-331414-i0oxm5mr author: Kautz, Tiffany F. title: A Low Fidelity Virus Shows Increased Recombination during the Removal of an Alphavirus Reporter Gene date: 2020-06-19 words: 5064.0 sentences: 241.0 pages: flesch: 45.0 cache: ./cache/cord-331414-i0oxm5mr.txt txt: ./txt/cord-331414-i0oxm5mr.txt summary: To examine this, GFP was inserted into TC-83, a live-attenuated vaccine for the alphavirus Venezuelan equine encephalitis virus, as well as a low-fidelity variant of TC-83, and passaged until fluorescence was no longer observed. To examine reporter gene stability, three independent replicates of TC-83 GFP and low-fidelity TC-83 GFP were passaged 10 times on Vero cells using an approximate MOI of 0.5 ( Figure 1A ). All three TC-83 GFP replicates contained deletion variants present at a low frequency that were able to selectively remove the GFP reporter gene by passage 10 (Figure 2A) . To better understand the mechanisms underlying the conserved removal of the low-fidelity TC-83 GFP gene, M-fold was used to determine the RNA secondary structure of the virus genome ( Figure 4C-E) . To characterize the role of RNA structure of the virus genome in RNA recombination site selection, we modeled the three most common deletions that occurred at high levels during low-fidelity TC-83 GFP passaging. abstract: Reporter genes for RNA viruses are well-known to be unstable due to putative RNA recombination events that excise inserted nucleic acids. RNA recombination has been demonstrated to be co-regulated with replication fidelity in alphaviruses, but it is unknown how recombination events at the minority variant level act, which is important for vaccine and trans-gene delivery design. Therefore, we sought to characterize the removal of a reporter gene by a low-fidelity alphavirus mutant over multiple replication cycles. To examine this, GFP was inserted into TC-83, a live-attenuated vaccine for the alphavirus Venezuelan equine encephalitis virus, as well as a low-fidelity variant of TC-83, and passaged until fluorescence was no longer observed. Short-read RNA sequencing using ClickSeq was performed to determine which regions of the viral genome underwent recombination and how this changed over multiple replication cycles. A rapid removal of the GFP gene was observed, where minority variants in the virus population accumulated small deletions that increased in size over the course of passaging. Eventually, these small deletions merged to fully remove the GFP gene. The removal was significantly enhanced during the passaging of low-fidelity TC-83, suggesting that increased levels of recombination are a defining characteristic of this mutant. url: https://www.ncbi.nlm.nih.gov/pubmed/32575413/ doi: 10.3390/v12060660 id: cord-344749-omzhhr0k author: Kaya, Sariye Irem title: Electrochemical virus detections with nanobiosensors date: 2020-02-14 words: 8402.0 sentences: 508.0 pages: flesch: 37.0 cache: ./cache/cord-344749-omzhhr0k.txt txt: ./txt/cord-344749-omzhhr0k.txt summary: Cell culture-based virus isolation has been accepted as a "gold standard" in the detection and identification of viruses and is the technique by which all other test methods have been compared [35] . A novel method for dengue virus detection and antibody screening using a graphene-polymer based electrochemical biosensor Chitosan-carbon nanofiber modified single-use graphite electrodes developed for electrochemical detection of DNA hybridization related to hepatitis B virus A sensitive electrochemical biosensor for specific DNA sequence detection based on flower-like VS2, graphene and Au nanoparticles signal amplification Electrochemical DNA biosensor based on a tetrahedral nanostructure probe for the detection of avian influenza A (H7N9) virus Electrochemical DNA biosensor based on gold nanorods for detecting hepatitis B virus Electrochemical-DNA biosensor development based on a modified carbon electrode with gold nanoparticles for influenza a (H1N1) detection: effect of spacer Magnetic nanoparticle-based immunosensor for electrochemical detection of hepatitis B surface antigen abstract: Infectious diseases are caused from pathogens, which need a reliable and fast diagnosis. Today, expert personnel and centralized laboratories are needed to afford much time in diagnosing diseases caused from pathogens. Recent progress in electrochemical studies shows that biosensors are very simple, accurate, precise, and cheap at virus detection, for which researchers find great interest in this field. The clinical levels of these pathogens can be easily analyzed with proposed biosensors. Their working principle is based on affinity between antibody and antigen in body fluids. The progress still continues on these biosensors for accurate, rapid, reliable sensors in future. url: https://www.sciencedirect.com/science/article/pii/B9780128198704000177 doi: 10.1016/b978-0-12-819870-4.00017-7 id: cord-272268-8vrcwwll author: Kedersha, Nancy title: Chapter 4 Regulation of Translation by Stress Granules and Processing Bodies date: 2009-10-27 words: 8598.0 sentences: 456.0 pages: flesch: 45.0 cache: ./cache/cord-272268-8vrcwwll.txt txt: ./txt/cord-272268-8vrcwwll.txt summary: Cytoplasmic stress granules (SGs) and processing bodies (PBs) are dynamic structures that form in response to stress-induced translational arrest. Critical components of the ''''cell biology'''' of protein translation are mRNP granules known as processing bodies (PBs) and stress granules (SGs). These transient cytoplasmic ''''structures'''' are actively assembled from untranslated mRNA by a host of RNA-binding proteins, which determine whether specific transcripts will be reinitiated, degraded, or stored. In 1999, it was noted that stress-induced translational arrest causes untranslated mRNPs to assemble into large cytoplasmic ''''SGs,'''' whose formation is triggered by, and dependent upon, the phosphorylation of eIF2a. Virus infection also induces the assembly of SGs and PBs suggesting that RNA granules play a role in reprogramming mRNA translation/decay during viral infection. RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2a to the assembly of mammalian stress granules abstract: Stress necessitates rapid reprogramming of translation in order to facilitate an adaptive response and promote survival. Cytoplasmic stress granules (SGs) and processing bodies (PBs) are dynamic structures that form in response to stress-induced translational arrest. PBs are linked to mRNA silencing and decay, while SGs are more closely linked to translation and the sorting of specific mRNAs for different fates. While they share some components and can interact physically, SGs and PBs are regulated independently, house separate functions, and contain unique markers. SG formation is associated with numerous disease states, and the expanding list of SG-associated proteins integrates SG formation with other processes such as transcription, splicing, and survival. Growing evidence suggests that SG assembly is initiated by translational arrest, and mediates cross talk with many other signaling pathways. url: https://api.elsevier.com/content/article/pii/S1877117309900047 doi: 10.1016/s1877-1173(09)90004-7 id: cord-006049-sw1hki4r author: Keefe, Anthony D. title: Aptamers as therapeutics date: 2010 words: 9789.0 sentences: 510.0 pages: flesch: 42.0 cache: ./cache/cord-006049-sw1hki4r.txt txt: ./txt/cord-006049-sw1hki4r.txt summary: Nucleic acid aptamers can be selected from pools of random-sequence oligonucleotides to bind a wide range of biomedically relevant proteins with affinities and specificities that are comparable to antibodies. Although this is true for biological nucleic acids [1] [2] [3] [4] , it was only recently that a series of technological advances allowed the development of in vitro evolutionary methods for the discovery of additional, non-biological oligonucleotides that can bind to protein targets. Since the invention of the SELEX process around 1990 (REfS 5, 6) , researchers have identified high-affinity aptamers that target a broad cross-section of protein families including cytokines, proteases, kinases, cell-surface receptors and cell-adhesion molecules (TABLE 1) . In particular, the site-specific placement of functional groups for conjugation means that the modification of aptamers after the solid-phase step (for example with high molecular mass PEG 46 ) leads to products with discrete stoichiometries and defined chemical structures. Selection of a RNA aptamer that binds to human activated protein C and inhibits its protease function abstract: Nucleic acid aptamers can be selected from pools of random-sequence oligonucleotides to bind a wide range of biomedically relevant proteins with affinities and specificities that are comparable to antibodies. Aptamers exhibit significant advantages relative to protein therapeutics in terms of size, synthetic accessibility and modification by medicinal chemistry. Despite these properties, aptamers have been slow to reach the marketplace, with only one aptamer-based drug receiving approval so far. A series of aptamers currently in development may change how nucleic acid therapeutics are perceived. It is likely that in the future, aptamers will increasingly find use in concert with other therapeutic molecules and modalities. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097324/ doi: 10.1038/nrd3141 id: cord-000125-uvf5qzfd author: Kenworthy, Rachael title: Short-hairpin RNAs delivered by lentiviral vector transduction trigger RIG-I-mediated IFN activation date: 2009-09-03 words: 6633.0 sentences: 336.0 pages: flesch: 54.0 cache: ./cache/cord-000125-uvf5qzfd.txt txt: ./txt/cord-000125-uvf5qzfd.txt summary: The interaction between a PAMP and a PRR triggers activation of the interferon (IFN) pathway in mammalian cells, which significantly changes the gene-expression profile in the cells and contributes to the well-documented off-target effect of RNAi. IFN induction is especially problematic in antiviral studies employing RNAi, where the antiviral effect of IFN must be distinguished from that of RNAi. Typical IFN-inducing structure patterns include dsRNA of certain length, single-stranded RNA (ssRNA) containing 5 0 -triphosphates (5 0 -ppp), the dsRNA analogue polyinosinic-polycytidylic acid (poly I:C), and certain dsDNA molecules. Mammalian expression plasmids encoding each of these proteins, as well as the dominant negative (DN) mutants of RIG-I and MDA5, were transfected into 293FT cells with shRNAs and an IFN-b promoter reporter construct. abstract: Activation of the type I interferon (IFN) pathway by small interfering RNA (siRNA) is a major contributor to the off-target effects of RNA interference in mammalian cells. While IFN induction complicates gene function studies, immunostimulation by siRNAs may be beneficial in certain therapeutic settings. Various forms of siRNA, meeting different compositional and structural requirements, have been reported to trigger IFN activation. The consensus is that intracellularly expressed short-hairpin RNAs (shRNAs) are less prone to IFN activation because they are not detected by the cell-surface receptors. In particular, lentiviral vector-mediated transduction of shRNAs has been reported to avoid IFN response. Here we identify a shRNA that potently activates the IFN pathway in human cells in a sequence- and 5′-triphosphate-dependent manner. In addition to suppressing its intended mRNA target, expression of the shRNA results in dimerization of interferon regulatory factor-3, activation of IFN promoters and secretion of biologically active IFNs into the extracellular medium. Delivery by lentiviral vector transduction did not avoid IFN activation by this and another, unrelated shRNA. We also demonstrated that retinoic-acid-inducible gene I, and not melanoma differentiation associated gene 5 or toll-like receptor 3, is the cytoplasmic sensor for intracellularly expressed shRNAs that trigger IFN activation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770676/ doi: 10.1093/nar/gkp714 id: cord-291727-4wfhuvww author: Ketteler, Robin title: On programmed ribosomal frameshifting: the alternative proteomes date: 2012-11-19 words: 6681.0 sentences: 353.0 pages: flesch: 51.0 cache: ./cache/cord-291727-4wfhuvww.txt txt: ./txt/cord-291727-4wfhuvww.txt summary: There are two main mechanisms that produce out of frame peptides: changes in the genome sequence that result in insertions or deletions (indels) and programmed ribosomal frameshifting as a consequence of the ribosome either slipping back one nucleotide (−1 frameshifting) or skipping one nucleotide (+1 frameshifting) (Figure 1) . By contrast, programmed ribosomal frameshifting can result in dual-coding genes that produce alternative functional proteins, which form an integral part of the organism''s physiology. Although the slippery sequence and pseudoknot are the most common motifs for frameshifting identified thus far, there are alternative mechanisms that may result in the production of out-of-frame proteins. First, one has to identify in mRNAs the requirements for a productive frameshift peptide: One might argue that a slippery sequence and a pseudoknot are a good predictor of frameshifting events, but-as pointed out above-there are alternative mechanisms that result in frameshifting (see also Figure 2 ). searched the genome for slippery sequences and pseudoknot FIGURE 3 | Methods to detect frameshifting events and out-of-frame peptides. abstract: Frameshifting results from two main mechanisms: genomic insertions or deletions (indels) or programmed ribosomal frameshifting. Whereas indels can disrupt normal protein function, programmed ribosomal frameshifting can result in dual-coding genes, each of which can produce multiple functional products. Here, I summarize technical advances that have made it possible to identify programmed ribosomal frameshifting events in a systematic way. The results of these studies suggest that such frameshifting occurs in all genomes, and I will discuss methods that could help characterize the resulting alternative proteomes. url: https://www.ncbi.nlm.nih.gov/pubmed/23181069/ doi: 10.3389/fgene.2012.00242 id: cord-349358-leicos9j author: Ketzinel‐Gilad, Mali title: RNA interference for antiviral therapy date: 2006-06-16 words: 12734.0 sentences: 684.0 pages: flesch: 44.0 cache: ./cache/cord-349358-leicos9j.txt txt: ./txt/cord-349358-leicos9j.txt summary: During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Likewise, expression vectors of siRNAs specific for two different regions of the WNV genome protected 293T cells from WNV infection, and significantly reduced viral RNA replication and virus production [35] . From the reports on the use of siRNA against human viral pathogens causing acute disease, we could learn that for each specific pathogen infecting a specific cell lineage or tissue, we would probably need to perform an indepth assessment, with proper in vitro and in vivo models, and develop specific delivery systems. The most challenging part of RNAi approaches for chronic viral infections is to design the best delivery method that would facilitate the targeting of the specific organ/cells with the appropriate expression system, for durable intracellular levels of gene-silencing effect. abstract: Silencing gene expression through a process known as RNA interference (RNAi) has been known in the plant world for many years. In recent years, knowledge of the prevalence of RNAi and the mechanism of gene silencing through RNAi has started to unfold. It is now believed that RNAi serves in part as an innate response against invading viral pathogens and, indeed, counter silencing mechanisms aimed at neutralizing RNAi have been found in various viral pathogens. During the past few years, it has been demonstrated that RNAi, induced by specifically designed double‐stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Furthermore, it is now apparent that in in vitro and in some in vivo models, the prospects for this technology in developing therapeutic applications are robust. However, many key questions and obstacles in the translation of RNAi into a potential therapeutic platform still remain, including the specificity and longevity of the silencing effect, and, most importantly, the delivery of the dsRNA that induces the system. It is expected that for the specific examples in which the delivery issue could be circumvented or resolved, RNAi may hold promise for the development of gene‐specific therapeutics. Copyright © 2006 John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/16779870/ doi: 10.1002/jgm.929 id: cord-262511-96xp1v0r author: Khabar, Khalid S. A. title: Rapid transit in the immune cells: the role of mRNA turnover regulation date: 2007-03-30 words: 6542.0 sentences: 342.0 pages: flesch: 43.0 cache: ./cache/cord-262511-96xp1v0r.txt txt: ./txt/cord-262511-96xp1v0r.txt summary: Post-transcriptional regulation contributes significantly to this rapid transit by several mechanisms, including mRNA stability modulation and translational control; collectively, they aim to control the expression of key gene products involved in the immune response. The stabilization of cytokine mRNA and other immune response gene products can occur by the activity of mRNA stabilization-promoting proteins such as human antigen (HuR) protein or by inactivation of RNA decay-promoting proteins such as the zinc finger protein, tristetraprolin (TTP). Traditionally, post-transcriptional regulation in innate immunity has been studied in response to the bacterial endotoxin, LPS, which binds CD14 in a complex with TLR4 on the surface of neutrophils and macrophages and initiates a cascade of signals that causes cell activation, the inflammatory response, and phagocytosis [35] . With the coordinated kinetics model, stabilizing RNA-binding proteins such as HuR can occur initially following immune cell activation, allowing rapid and early response of cytokine production. abstract: There have been recent, significant advances about the role of mRNA turnover in controlling gene expression in immune cells. Post‐transcriptional regulation of gene expression contributes to the characteristics of many of the processes underlying the immune response by ensuring early, rapid, and transient action. The emphasis of this review is on current work that deals with the regulation of mRNA decay during innate immunity against microbes and T cell activation as a model of the adaptive response. url: https://www.ncbi.nlm.nih.gov/pubmed/17400611/ doi: 10.1189/jlb.0207109 id: cord-253862-jl1zhg13 author: Khalaf, Khalil title: SARS-CoV-2: Pathogenesis, and Advancements in Diagnostics and Treatment date: 2020-10-06 words: 14595.0 sentences: 760.0 pages: flesch: 45.0 cache: ./cache/cord-253862-jl1zhg13.txt txt: ./txt/cord-253862-jl1zhg13.txt summary: Although this novel virus is less severe than the first SARS-CoV outbreak, human-to-human transmission remains very high and the number of cases continues to rise exponentially in major urban areas, highlighting the urgent need to develop new containment, diagnostic, and treatment protocols. In the case of SARS-CoV-2, viral evasion of the innate immune system leads to an increase in cytokine production and late CD4+/CD8+ response, which then leads to pathogenic inflammation in patients with high viral loads. (ChiCTR2000029308), involving severe SARS-CoV-2 cases, compared lopinavir/ritonavir treatment with standard care alone, and they showed that the antivirals yielded no clinical benefits. In an open-label control study conducted by Cai et al., the antiviral activity of favipiravir + IFN-α was compared to that of lopinavir/ritonavir + IFN-α in patients with confirmed SARS-CoV-2 infection. abstract: The emergence and rapid spread of SARS-CoV-2 in December 2019 has brought the world to a standstill. While less pathogenic than the 2002–2003 SARS-CoV, this novel betacoronavirus presents a global threat due to its high transmission rate, ability to invade multiple tissues, and ability to trigger immunological hyperactivation. The identification of the animal reservoir and intermediate host were important steps toward slowing the spread of disease, and its genetic similarity to SARS-CoV has helped to determine pathogenesis and direct treatment strategies. The exponential increase in cases has necessitated fast and reliable testing procedures. Although RT-PCR remains the gold standard, it is a time-consuming procedure, paving the way for newer techniques such as serologic tests and enzyme immunoassays. Various clinical trials using broad antiviral agents in addition to novel medications have produced controversial results; however, the advancement of immunotherapy, particularly monoclonal antibodies and immune modulators is showing great promise in clinical trials. Non-orthodox medications such as anti-malarials have been tested in multiple institutions but definitive conclusions are yet to be made. Adjuvant therapies have also proven to be effective in decreasing mortality in the disease course. While no formal guidelines have been established, the multitude of ongoing clinical trials as a result of unprecedented access to research data brings us closer to halting the SARS-CoV-2 pandemic. url: https://doi.org/10.3389/fimmu.2020.570927 doi: 10.3389/fimmu.2020.570927 id: cord-350906-ew04zzh6 author: Khambhati, Khushal title: Current progress in CRISPR‐based diagnostic platforms date: 2018-10-26 words: 2266.0 sentences: 136.0 pages: flesch: 49.0 cache: ./cache/cord-350906-ew04zzh6.txt txt: ./txt/cord-350906-ew04zzh6.txt summary: 10 East-Seletsky et al 10 have taken the advantage and demonstrated the use of Cas13 for the detection of 0.01 nM of λRNA with high specificity, using the signals generated from fluorophore-quencher based reporter RNA molecule ( Figure 1 ). The resultant amplified DNA sequence is then subjected to in vitro T7 transcription, and produced RNA molecule is detected by Cas13-guided reporter assay. 11 For improved multiplexed detection, Cas12a has been used along with Cas13 RNAse. 11 F I G U R E 1 Schematic representation of CRISPR-based diagnostic tool, in the presence of the appropriate gRNA, Cas13 recognizes the target RNA sequence that is complementary. The produced RNA molecule can be recognized via fluorescence signals that are generated by the reporter molecule upon target recognition by the Cas13 RNAse. 4 The cleaved reporter molecule can also be detected in the form of bands through a lateral flow assay. abstract: The CRISPR‐Cas system is a key technology for genome editing and regulation in a wide range of organisms and cell types. Recently, CRISPR‐Cas–based diagnostic platform has shown idealistic properties for pathogen detection. Integrating the CRISPR‐Cas platform along with lateral flow system allows rapid, sensitive, specific, cheap, and reliable diagnostic. It has the potential to be in frontline for not only pathogen detection during the epidemic outbreak, but also cancer, and genetic diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/30362590/ doi: 10.1002/jcb.27690 id: cord-333524-a6p6ma8r author: Khan, Pavana title: Isothermal SARS-CoV-2 Diagnostics: Tools for Enabling Distributed Pandemic Testing as a Means of Supporting Safe Reopenings date: 2020-09-23 words: 8841.0 sentences: 603.0 pages: flesch: 50.0 cache: ./cache/cord-333524-a6p6ma8r.txt txt: ./txt/cord-333524-a6p6ma8r.txt summary: 19 The current most common diagnostic method used to identify SARS-CoV-2 infection is a molecular technique for detecting viral RNA through nucleic acid amplification, RT-PCR. Nucleic acid amplification tests (NAATs) are the most common diagnostic tests used to detect pathogens, and many of the current SARS-CoV-2 detection techniques are primarily based on NAATs. 21 NAATs involve nucleic acid amplification, a process that initiates with a small quantity of starting nucleic acids and uses primers that target specific, short nucleic acid sequences in conjunction with enzymes to amplify or increase the quantity of starting nucleic acids. 34 This test incorporates a nested nucleic acid amplification technique showing higher sensitivity of detection than LAMP alone and conventional RT-PCR for minimally processed SARS-CoV-2 samples. 55 The technique first uses RT-LAMP for reverse transcription and isothermal amplification of viral RNA, and then employs the Cas12a enzyme to identify sequences of SARS-CoV-2, allowing cleavage of a reporter molecule ( Figure 5 ). abstract: [Image: see text] The COVID-19 pandemic, caused by the SARS-CoV-2 virus, poses grave threats to both the global economy and health. The predominant diagnostic screens in use for SARS-CoV-2 detection are molecular techniques such as nucleic acid amplification tests. In this Review, we compare current and emerging isothermal diagnostic methods for COVID-19. We outline the molecular and serological techniques currently being used to detect SARS-CoV-2 infection, past or present, in patients. We also discuss ongoing research on isothermal techniques, CRISPR-mediated detection assays, and point-of-care diagnostics that have potential for use in SARS-CoV-2 detection. Large-scale viral testing during a global pandemic presents unique challenges, chief among them the simultaneous need for testing supplies, durable equipment, and personnel in many regions worldwide, with each of these regions possessing testing needs that vary as the pandemic progresses. The low-cost isothermal technologies described in this Review provide a promising means by which to address these needs and meet the global need for testing of symptomatic individuals as well as provide a possible means for routine testing of asymptomatic individuals, providing a potential means of safely enabling reopenings and early monitoring of outbreaks. url: https://www.ncbi.nlm.nih.gov/pubmed/32966744/ doi: 10.1021/acssynbio.0c00359 id: cord-260042-cs0wp99n author: Khan, Samiullah title: Genes involved in mitochondrial biogenesis and function may not show synchronised responses to mitochondria in shell gland of laying chickens under infectious bronchitis virus challenge date: 2019-04-01 words: 6931.0 sentences: 362.0 pages: flesch: 47.0 cache: ./cache/cord-260042-cs0wp99n.txt txt: ./txt/cord-260042-cs0wp99n.txt summary: The present study aimed to: a) determine mitochondrial counts in the cells of oviduct segments in laying hens at different time-points of egg formation in relation to the requirement of energy for egg production during IBV challenge; b) to determine the expression of nuclear DNA encoded genes in the shell gland to gain insights into their responses to IBV infection and time-points of egg-shell formation. Based on the lack of significant differences in mitochondrial count in the cells between the challenged and control groups for the magnum and isthmus, we focused further on shell gland tissue and studied the expression level of genes involved in mitochondrial density, biogenesis and fission. The lack of any significant difference in the relative expression levels of all of the genes except SDHA, between the control and IBV T challenged groups, may indicate that mitochondrial function may have been enhanced and thus overall egg quality may not have been affected by fewer mitochondria in the shell gland cells of IBV T infected hens. abstract: BACKGROUND: Egg formation takes place in the oviduct of laying hens over a 24 h period. Infectious bronchitis virus (IBV) causes pathological lesions in the chicken oviduct. In the current study, mitochondrial counts were determined in three different segments of the oviduct during egg formation in laying chickens challenged with IBV T strain. Nuclear DNA encoded genes that are involved in mitochondrial biogenesis, fission and function were studied in the shell gland of the oviduct undergoing virus multiplication. RESULTS: In the shell gland, the mitochondrial count was significantly lower (P < 0.05) in the challenged group, compared with the control group. However, it did not vary in response to IBV challenge in the isthmus and magnum regions of the oviduct. The gene succinate dehydrogenase complex, subunit A, flavoprotein variant (SDHA) was down-regulated in the shell gland by IBV challenge (P < 0.05), while other genes being studied did not show responses to the challenge (P > 0.05). Differential expression of the genes was observed at different time-points of egg-shell formation. The expression levels of citrate synthase (CS), cytochrome C, somatic (CYC, S) and sodium-potassium adenosine triphosphatase (Na(+)-K(+)ATPase) genes were significantly higher, while those of SDHA and dynamin related protein 1 (Drp1) genes were significantly lower, at 15 h compared with 5 h following oviposition of the previous egg. The expression level of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) did not show significant change at different time-points. CONCLUSIONS: It was concluded that IBV T strain infection in laying hens reduced mitochondrial counts only in the shell gland region of the oviduct. The genes involved in mitochondrial biogenesis or function may not show synchronised responses to that of mitochondria in the shell gland of chickens under T strain of IBV challenge. url: https://doi.org/10.1186/s12860-019-0190-7 doi: 10.1186/s12860-019-0190-7 id: cord-338680-wwlttymp author: Khonyongwa, K. title: Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence date: 2020-07-30 words: 4839.0 sentences: 288.0 pages: flesch: 53.0 cache: ./cache/cord-338680-wwlttymp.txt txt: ./txt/cord-338680-wwlttymp.txt summary: Due to the high prevalence of infection during the peak of the outbreak, one of the suggested strategies to prevent healthcare transmission was to screen all patients on admission by a single combined nose and throat swab assessed for SARS-CoV-2 RNA to allow segregation into COVID-19 positive and non COVID-19 cohort wards. The latter included assessment of the utility of a single combined throat and nose swab (CTNS) for patient placement, delayed RNA positivity, COVID-19 patients as sources of infection, self-reported COVID-19 sickness absence among hospital staff hospital bed occupancy, community incidence, and the incidence of other significant hospital-acquired infections. NHS England released its reporting criteria in May 2020 (written communication described in supplementary data) following which cases were also classified as per date of the SARS-CoV-2 RNA detection. Correlation between weekly incidence of HA-COVID-19 (including late indeterminate cases) and staff self-reported sickness absence, delayed RNA positive cases, community incidence and Trust COVID-19 bed occupancy is displayed in figure 3. abstract: Background: The sudden increase in COVID-19 admissions in hospitals during the SARS-CoV2 pandemic of 2020 has led to onward transmissions among vulnerable inpatients. Aims: This study was performed to evaluate the prevalence and clinical outcomes of Healthcare-associated COVID-19 infections (HA-COVID-19) during the 2020 epidemic and study factors which may promote or correlate with its incidence and transmission in a London Teaching Hospital Trust. Methods: Electronic laboratory, patient and staff self-reported sickness records were interrogated for the period 1st March to 18th April 2020. HA-COVID-19 was defined as symptom onset >14d of admission. Test performance of a single combined throat and nose swab (CTNS) for patient placement and the effect of delayed RNA positivity (DRP, defined as >48h delay) on patient outcomes was evaluated. The incidence of staff self-reported COVID-19 sickness absence, hospital bed occupancy, community incidence and DRP was compared HA-COVID-19. The incidence of other significant hospital-acquired bacterial infections (OHAI) was compared to previous years. Results: 58 HA-COVID-19 (7.1%) cases were identified. As compared to community-acquired cases, significant differences were observed in age (p=0.018), ethnicity (p<0.001) and comorbidity burden (p<0.001) but not in 30d mortality. CTNS negative predictive value was 60.3%. DRP was associated with greater mortality (p=0.034) and 34.5% HA-COVID-19 cases could be traced to delayed diagnosis in CA-COVID-19. Incidence of HA-COVID-19 correlated positively with DRP (R=0.7108) and staff sickness absence (R=0.7815). OHAI rates were similar to previous 2 years. Conclusion: Early diagnosis and isolation of COVID-19 would help reduce transmission. A single CTNS has limited value in segregating patients into positive and negative pathways. url: http://medrxiv.org/cgi/content/short/2020.07.24.20148262v1?rss=1 doi: 10.1101/2020.07.24.20148262 id: cord-328252-dk54w8z9 author: Kikkert, Marjolein title: Innate Immune Evasion by Human Respiratory RNA Viruses date: 2019-10-14 words: 11552.0 sentences: 550.0 pages: flesch: 43.0 cache: ./cache/cord-328252-dk54w8z9.txt txt: ./txt/cord-328252-dk54w8z9.txt summary: Whether PA-X also degrades viral dsRNA species to prevent recognition by cytosolic RNA sensors is not entirely clear, but mutant viruses in which this PA-X protein was expressed in significantly lower amounts elicited higher levels of innate immune response; for example, IFN-beta production was much higher in these infections [71] . This indeed suggests that PA-X, besides having a role in the degradation of cellular mRNAs, may also degrade viral RNA to prevent recognition by innate immune sensors and activation of innate immune responses, similar to what was shown for the CoVs. To my knowledge, an endoribonuclease has not been identified in the RSV genome, so this virus may use alternative innate immune evasion strategies, as discussed elsewhere in this review. [91] suggested that RSV specifically targets mRNA encoding surfactant protein A, an innate immune factor with an important role in the epithelial tissue of the lung, which directly binds to virus particles to cause their destruction by host defense mechanisms. abstract: The impact of respiratory virus infections on the health of children and adults can be very significant. Yet, in contrast to most other childhood infections as well as other viral and bacterial diseases, prophylactic vaccines or effective antiviral treatments against viral respiratory infections are either still not available, or provide only limited protection. Given the widespread prevalence, a general lack of natural sterilizing immunity, and/or high morbidity and lethality rates of diseases caused by influenza, respiratory syncytial virus, coronaviruses, and rhinoviruses, this difficult situation is a genuine societal challenge. A thorough understanding of the virus-host interactions during these respiratory infections will most probably be pivotal to ultimately meet these challenges. This review attempts to provide a comparative overview of the knowledge about an important part of the interaction between respiratory viruses and their host: the arms race between host innate immunity and viral innate immune evasion. Many, if not all, viruses, including the respiratory viruses listed above, suppress innate immune responses to gain a window of opportunity for efficient virus replication and setting-up of the infection. The consequences for the host's immune response are that it is often incomplete, delayed or diminished, or displays overly strong induction (after the delay) that may cause tissue damage. The affected innate immune response also impacts subsequent adaptive responses, and therefore viral innate immune evasion often undermines fully protective immunity. In this review, innate immune responses relevant for respiratory viruses with an RNA genome will briefly be summarized, and viral innate immune evasion based on shielding viral RNA species away from cellular innate immune sensors will be discussed from different angles. Subsequently, viral enzymatic activities that suppress innate immune responses will be discussed, including activities causing host shut-off and manipulation of stress granule formation. Furthermore, viral protease-mediated immune evasion and viral manipulation of the ubiquitin system will be addressed. Finally, perspectives for use of the reviewed knowledge for the development of novel antiviral strategies will be sketched. url: https://doi.org/10.1159/000503030 doi: 10.1159/000503030 id: cord-347128-6lyoz8nn author: Kim, Cheorl-Ho title: SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus–Host Interaction date: 2020-06-26 words: 15413.0 sentences: 988.0 pages: flesch: 53.0 cache: ./cache/cord-347128-6lyoz8nn.txt txt: ./txt/cord-347128-6lyoz8nn.txt summary: O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. In RNA viruses, the S glycoprotein (PDB: 6VSB) is the biggest protein, heavily glycosylated and its N-terminal domain (NTD) sequence binds to the host receptor to enter the ER of host cells. However, MERS-CoV does not have a similar enzyme and thus MER-CoV binding to SA receptors is mediated by energetically reversible interactions of the lipid rafts with increased SA receptors [75] , thus enhancing dipeptidyl peptidase 4 (DPP4) or carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) recognition power and viral entry [76] and membrane-associated 78-kDa glucose-regulated protein (GRP78) [77] . Entry of host cells needs binding of S glycoproteins to the CEACAM receptor, forming S-protein-mediated membrane fusion. For example, impairment of ACE2 receptor glycosylation does not influence S-glycoprotein-ACE2 interaction, however, SARS-CoV-2 virus entry into respiratory epithelial host cells was downregulated [133] . abstract: The recently emerged SARS-CoV-2 is the cause of the global health crisis of the coronavirus disease 2019 (COVID-19) pandemic. No evidence is yet available for CoV infection into hosts upon zoonotic disease outbreak, although the CoV epidemy resembles influenza viruses, which use sialic acid (SA). Currently, information on SARS-CoV-2 and its receptors is limited. O-acetylated SAs interact with the lectin-like spike glycoprotein of SARS CoV-2 for the initial attachment of viruses to enter into the host cells. SARS-CoV-2 hemagglutinin-esterase (HE) acts as the classical glycan-binding lectin and receptor-degrading enzyme. Most β-CoVs recognize 9-O-acetyl-SAs but switched to recognizing the 4-O-acetyl-SA form during evolution of CoVs. Type I HE is specific for the 9-O-Ac-SAs and type II HE is specific for 4-O-Ac-SAs. The SA-binding shift proceeds through quasi-synchronous adaptations of the SA-recognition sites of the lectin and esterase domains. The molecular switching of HE acquisition of 4-O-acetyl binding from 9-O-acetyl SA binding is caused by protein–carbohydrate interaction (PCI) or lectin–carbohydrate interaction (LCI). The HE gene was transmitted to a β-CoV lineage A progenitor by horizontal gene transfer from a 9-O-Ac-SA–specific HEF, as in influenza virus C/D. HE acquisition, and expansion takes place by cross-species transmission over HE evolution. This reflects viral evolutionary adaptation to host SA-containing glycans. Therefore, CoV HE receptor switching precedes virus evolution driven by the SA-glycan diversity of the hosts. The PCI or LCI stereochemistry potentiates the SA–ligand switch by a simple conformational shift of the lectin and esterase domains. Therefore, examination of new emerging viruses can lead to better understanding of virus evolution toward transitional host tropism. A clear example of HE gene transfer is found in the BCoV HE, which prefers 7,9-di-O-Ac-SAs, which is also known to be a target of the bovine torovirus HE. A more exciting case of such a switching event occurs in the murine CoVs, with the example of the β-CoV lineage A type binding with two different subtypes of the typical 9-O-Ac-SA (type I) and the exclusive 4-O-Ac-SA (type II) attachment factors. The protein structure data for type II HE also imply the virus switching to binding 4-O acetyl SA from 9-O acetyl SA. Principles of the protein–glycan interaction and PCI stereochemistry potentiate the SA–ligand switch via simple conformational shifts of the lectin and esterase domains. Thus, our understanding of natural adaptation can be specified to how carbohydrate/glycan-recognizing proteins/molecules contribute to virus evolution toward host tropism. Under the current circumstances where reliable antiviral therapeutics or vaccination tools are lacking, several trials are underway to examine viral agents. As expected, structural and non-structural proteins of SARS-CoV-2 are currently being targeted for viral therapeutic designation and development. However, the modern global society needs SARS-CoV-2 preventive and therapeutic drugs for infected patients. In this review, the structure and sialobiology of SARS-CoV-2 are discussed in order to encourage and activate public research on glycan-specific interaction-based drug creation in the near future. url: https://doi.org/10.3390/ijms21124549 doi: 10.3390/ijms21124549 id: cord-334463-nvu5tqxb author: Kim, Chonsaeng title: Echovirus 7 Entry into Polarized Intestinal Epithelial Cells Requires Clathrin and Rab7 date: 2012-04-10 words: 6207.0 sentences: 325.0 pages: flesch: 48.0 cache: ./cache/cord-334463-nvu5tqxb.txt txt: ./txt/cord-334463-nvu5tqxb.txt summary: We found that drugs, small interfering RNAs (siRNAs), and dominant negative mutants that target factors required for clathrin-mediated endocytosis, including clathrin and dynamin, inhibited both EV7 infection and internalization of virions from the cell surface. We previously (19) observed that, to infect polarized epithelium, CVB3 binds DAF on the cell surface, moves to the tight junction, and then enters the cell by an unusual mechanism that is independent of both dynamin and clathrin but which requires caveolin; contact with CAR in the tight junction leads to an essential conformational change in the CVB3 virion, but disruption of the capsid does not appear to occur until the virus has moved to an unidentified intracellular compartment. We had previously observed that CVB3 infection of Caco-2 cells occurs by a complex process that depends on caveolin but not dynamin-2, appears to be independent of clathrin-mediated endocytosis, and is inhibited by depletion of membrane cholesterol (19) . abstract: Enteroviruses invade the host by crossing the intestinal mucosa, which is lined by polarized epithelium. A number of enteroviruses, including echoviruses (EV) and group B coxsackieviruses (CVB), initiate infection by attaching to decay-accelerating factor (DAF), a molecule that is highly expressed on the apical surface of polarized epithelial cells. We previously observed that entry of DAF-binding CVB3 into polarized intestinal epithelial cells occurs by an unusual endocytic mechanism that requires caveolin but does not involve clathrin or dynamin. Here we examined the entry of a DAF-binding echovirus, EV7. We found that drugs, small interfering RNAs (siRNAs), and dominant negative mutants that target factors required for clathrin-mediated endocytosis, including clathrin and dynamin, inhibited both EV7 infection and internalization of virions from the cell surface. Once virus had entered the cell, it colocalized with markers of early endosomes (EEA1) and then late endosomes (LAMP-2). Inhibition of endosomal maturation—with siRNAs or dominant negative mutants targeting Rab5 and Rab7—inhibited infection and prevented release of viral RNA into the cell. These results indicate that EV7 is internalized by clathrin-mediated endocytosis and then moves to early and late endosomes before releasing its RNA. Trafficking through endosomes is known to be important for viruses that depend on low pH or endosomal cathepsin proteases to complete the entry process. However, we found that EV7 infection required neither low pH nor cathepsins. url: https://doi.org/10.1128/mbio.00304-11 doi: 10.1128/mbio.00304-11 id: cord-312517-b24zlaqt author: Kim, Denny title: The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines date: 2020-06-19 words: 1948.0 sentences: 98.0 pages: flesch: 44.0 cache: ./cache/cord-312517-b24zlaqt.txt txt: ./txt/cord-312517-b24zlaqt.txt summary: title: The Brighton collaboration standardized template for collection of key information for benefit-risk assessment of nucleic acid (RNA and DNA) vaccines The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) has prepared a standardized template to describe the key considerations for the benefit-risk assessment of nucleic acid vaccines. The Brighton Collaboration formed the Viral Vector Vaccines Safety Working Group (V3SWG) in October 2008 to improve the ability of key stakeholders to anticipate potential safety issues and meaningfully assess or interpret safety data, thereby facilitating greater public acceptance when viral vector vaccines are licensed [2] . When completing information on adverse effects in Section 8, please provide as many details as possible based on the Brighton Collaboration Guidelines for collection, analysis and presentation of vaccine safety data in pre-and post-licensure clinical studies [13] . abstract: Nucleic acid (DNA and RNA) vaccines are among the most advanced vaccines for COVID-19 under development. The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) has prepared a standardized template to describe the key considerations for the benefit-risk assessment of nucleic acid vaccines. This will facilitate the assessment by key stakeholders of potential safety issues and understanding of overall benefit-risk. The structured assessment provided by the template can also help improve communication and public acceptance of licensed nucleic acid vaccines. url: https://api.elsevier.com/content/article/pii/S0264410X20307891 doi: 10.1016/j.vaccine.2020.06.017 id: cord-302020-ypsh3rjv author: Kim, Dongwan title: The Architecture of SARS-CoV-2 Transcriptome date: 2020-04-23 words: 6092.0 sentences: 403.0 pages: flesch: 57.0 cache: ./cache/cord-302020-ypsh3rjv.txt txt: ./txt/cord-302020-ypsh3rjv.txt summary: In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2. (A) Read counts from nanopore direct RNA sequencing of total RNA from Vero cells infected with SARS-CoV-2. We further discovered RNA modification sites and measured the poly(A) tail length of gRNAs and sgRNAs. To delineate the SARS-CoV-2 transcriptome, we first performed DRS runs on a MinION nanopore sequencer with total RNA extracted from Vero cells infected with SARS-CoV-2 (Be-taCoV/Korea/KCDC03/2020). To unambiguously investigate the modifications, we generated negative control RNAs by in vitro transcription of the viral sequences and performed a DRS run on these unmodified controls ( Figure S4A ). abstract: SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 genome was reported recently, its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous discontinuous transcription events. In addition to the canonical genomic and 9 subgenomic RNAs, SARS-CoV-2 produces transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif, AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the modification and the 3′ tail. Functional investigation of the unknown transcripts and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32330414/ doi: 10.1016/j.cell.2020.04.011 id: cord-284933-flbibrcm author: Kim, Jong-Oh title: Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection date: 2017-01-13 words: 4259.0 sentences: 266.0 pages: flesch: 54.0 cache: ./cache/cord-284933-flbibrcm.txt txt: ./txt/cord-284933-flbibrcm.txt summary: title: Characterization of the Transcriptome and Gene Expression of Brain Tissue in Sevenband Grouper (Hyporthodus septemfasciatus) in Response to NNV Infection Ubiquitin-like protein 4a (UBL4a), C-C motif chemokine 2 (CCL2), lysozyme g (LYG_EPICO) and two novel genes (ID: SGU016297, SGU008676) were highly expressed in the NNV-infected group compared to that in the mock group. In this study, we performed a transcriptome analysis of the brain tissue of sevenband grouper infected with NNV compared to mock brain tissue using a RNA-Seq. The total number of unigenes and the average length of the unigenes were 104,348 and 845 bp, respectively. In this study, we performed a transcriptome analysis of the brain tissue of sevenband grouper infected with NNV compared to mock brain tissue using a RNA-Seq. The total number of unigenes and the average length of the unigenes were 104,348 and 845 bp, respectively. In this study, we identified innate immune response relevant genes of sevenband grouper involved in NNV infection. abstract: Grouper is one of the favorite sea food resources in Southeast Asia. However, the outbreaks of the viral nervous necrosis (VNN) disease due to nervous necrosis virus (NNV) infection have caused mass mortality of grouper larvae. Many aqua-farms have suffered substantial financial loss due to the occurrence of VNN. To better understand the infection mechanism of NNV, we performed the transcriptome analysis of sevenband grouper brain tissue, the main target of NNV infection. After artificial NNV challenge, transcriptome of brain tissues of sevenband grouper was subjected to next generation sequencing (NGS) using an Illumina Hi-seq 2500 system. Both mRNAs from pooled samples of mock and NNV-infected sevenband grouper brains were sequenced. Clean reads of mock and NNV-infected samples were de novo assembled and obtained 104,348 unigenes. In addition, 628 differentially expressed genes (DEGs) in response to NNV infection were identified. This result could provide critical information not only for the identification of genes involved in NNV infection, but for the understanding of the response of sevenband groupers to NNV infection. url: https://doi.org/10.3390/genes8010031 doi: 10.3390/genes8010031 id: cord-266464-wuf3s8m0 author: Kim, So Yeon title: Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection date: 2016-10-17 words: 1810.0 sentences: 100.0 pages: flesch: 50.0 cache: ./cache/cord-266464-wuf3s8m0.txt txt: ./txt/cord-266464-wuf3s8m0.txt summary: title: Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection We evaluated the diagnostic and clinical usefulness of blood specimens to detect Middle East respiratory syndrome coronavirus infection in 21 patients from the 2015 outbreak in South Korea. Respiratory specimens are preferred for viral RNA detection and confirmatory diagnosis of MERS-CoV infection in humans (5) . Our study aimed to evaluate the diagnostic utility of blood specimens for MERS-CoV infection by using large numbers of patients with a single viral origin and to determine the relationship between blood viral detection and clinical characteristics. Between the blood viral RNA-positive and -negative groups, we found no differences in age, duration from symptom onset to diagnosis of MERS-CoV infection, or an invasive procedure before the specimens were obtained (online Technical Appendix Table 3 ). Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission abstract: We evaluated the diagnostic and clinical usefulness of blood specimens to detect Middle East respiratory syndrome coronavirus infection in 21 patients from the 2015 outbreak in South Korea. Viral RNA was detected in blood from 33% of patients at initial diagnosis, and the detection preceded a worse clinical course. url: https://www.ncbi.nlm.nih.gov/pubmed/27479636/ doi: 10.3201/eid2210.160218 id: cord-280941-ds6x0yym author: Kim, Young-Seok title: Chaperna-Mediated Assembly of Ferritin-Based Middle East Respiratory Syndrome-Coronavirus Nanoparticles date: 2018-05-17 words: 9411.0 sentences: 491.0 pages: flesch: 51.0 cache: ./cache/cord-280941-ds6x0yym.txt txt: ./txt/cord-280941-ds6x0yym.txt summary: The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic "pace-keeping" role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections. Taken together, the results confirmed the immunologically relevant conformation of the MERS-CoV RBD displayed on the hybrid ferritin particles, and the crucial role of RNA in controlling the kinetic pathway for the assembly of viral antigen monomers into stable NPs. To evaluate the immunogenicity of ferritin-based NPs, BALB/c mice (n = 5) were immunized with RBD, RBD-FR, and RBD-[SSG]-FR NPs antigens. abstract: The folding of monomeric antigens and their subsequent assembly into higher ordered structures are crucial for robust and effective production of nanoparticle (NP) vaccines in a timely and reproducible manner. Despite significant advances in in silico design and structure-based assembly, most engineered NPs are refractory to soluble expression and fail to assemble as designed, presenting major challenges in the manufacturing process. The failure is due to a lack of understanding of the kinetic pathways and enabling technical platforms to ensure successful folding of the monomer antigens into regular assemblages. Capitalizing on a novel function of RNA as a molecular chaperone (chaperna: chaperone + RNA), we provide a robust protein-folding vehicle that may be implemented to NP assembly in bacterial hosts. The receptor-binding domain (RBD) of Middle East respiratory syndrome-coronavirus (MERS-CoV) was fused with the RNA-interaction domain (RID) and bacterioferritin, and expressed in Escherichia coli in a soluble form. Site-specific proteolytic removal of the RID prompted the assemblage of monomers into NPs, which was confirmed by electron microscopy and dynamic light scattering. The mutations that affected the RNA binding to RBD significantly increased the soluble aggregation into amorphous structures, reducing the overall yield of NPs of a defined size. This underscored the RNA-antigen interactions during NP assembly. The sera after mouse immunization effectively interfered with the binding of MERS-CoV RBD to the cellular receptor hDPP4. The results suggest that RNA-binding controls the overall kinetic network of the antigen folding pathway in favor of enhanced assemblage of NPs into highly regular and immunologically relevant conformations. The concentration of the ion Fe(2+), salt, and fusion linker also contributed to the assembly in vitro, and the stability of the NPs. The kinetic “pace-keeping” role of chaperna in the super molecular assembly of antigen monomers holds promise for the development and delivery of NPs and virus-like particles as recombinant vaccines and for serological detection of viral infections. url: https://doi.org/10.3389/fimmu.2018.01093 doi: 10.3389/fimmu.2018.01093 id: cord-335443-iv2gs3kg author: Kim, Youngchang title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2 date: 2020-06-28 words: 5464.0 sentences: 333.0 pages: flesch: 57.0 cache: ./cache/cord-335443-iv2gs3kg.txt txt: ./txt/cord-335443-iv2gs3kg.txt summary: Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme''s active site, providing basis for the uracil scaffold-based drug development. For SARS-CoV it was reported that Nsp15 cleaves highly conserved non-translated RNA on (+) sense strand showing that both RNA sequence and structure are important for cleavage 6, 7 . The enzyme cleaves efficiently eicosamer 5''GAACU¯CAU¯GGACCU¯U¯GGCAG3'' at all four uridine sites (Fig. 1) , as well as synthetic EndoU substrate ( 5′-6-FAM-dArU¯dAdA -6-TAMRA-3′ ) 8 in the presence of Mn 2+ and the reaction rate increases with metal ion concentration. SARS-CoV-2 Nsp15 protein was crystallized with 5''UMP, 3''UMP, 5''GpU and Tipiracil using methods described previously 8 and the structures were determined at 1.82 Å, 1.85 Å, 1.97 Å and 1.85 Å, respectively. In the crystal structure of Nsp15/5''GpU, the dinucleoside monophosphate binds to the active site with uracil interacting with Tyr343 and Ser294 (Fig. 4B ), as seen in the Nsp15/5''UMP complex. abstract: SARS-CoV-2 Nsp15 is a uridylate-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family. It degrades the polyuridine extensions in (−) sense strand of viral RNA and some non-translated RNA on (+) sense strand. This activity seems to be responsible for the interference with the innate immune response and evasion of host pattern recognition. Nsp15 is highly conserved in coronaviruses suggesting that its activity is important for virus replication. Here we report first structures with bound nucleotides and show that SARS-CoV-2 Nsp15 specifically recognizes U in a pattern previously predicted for EndoU. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. Inhibitors of Nsp15 have been reported but not actively pursued into therapeutics. The current COVID-19 pandemic brought to attention the repurposing of existing drugs and the rapid identification of new antiviral compounds. Tipiracil is an FDA approved drug that is used with trifluridine in the treatment of colorectal cancer. Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme’s active site, providing basis for the uracil scaffold-based drug development. url: https://doi.org/10.1101/2020.06.26.173872 doi: 10.1101/2020.06.26.173872 id: cord-272729-nbgdmavr author: Kim, Youngnam title: Ribavirin efficiently suppresses porcine nidovirus replication date: 2012-10-27 words: 6654.0 sentences: 296.0 pages: flesch: 44.0 cache: ./cache/cord-272729-nbgdmavr.txt txt: ./txt/cord-272729-nbgdmavr.txt summary: Investigations into the mechanism of action of ribavirin against PRRSV and PEDV revealed that the addition of guanosine to the ribavirin treatment significantly reversed the antiviral effects, suggesting that depletion of the intracellular GTP pool by inhibiting IMP dehydrogenase may be essential for ribavirin activity. Further experiments revealed that suppression of ribavirin affects post-entry steps of the replication cycle of PRRSV and PEDV, including viral genomic and sg RNA synthesis, viral protein expression, and virus production. Several mechanisms of action for the antiviral activity of ribavirin have been suggested, including a reduction in cellular GTP pools via inosine monophosphate dehydrogenase (IMPDH) inhibition and increased mutation frequency on the virus genome leading to error catastrophe (Graci and Cameron, 2006) . Treatment of cells with ribavirin resulted in significant attenuation of postentry steps during the replication of porcine nidovirus, as determined by lower progeny production, diminished viral protein expression, and decreased synthesis of genomic RNA and sg mRNA. abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) are porcine nidoviruses that represent emerging viral pathogens causing heavy economic impacts on the swine industry. Although ribavirin is a well-known antiviral drug against a broad range of both DNA and RNA viruses in vitro, its inhibitory effect and mechanism of action on porcine nidovirus replication remains to be elucidated. Therefore, the present study was conducted to determine whether ribavirin suppresses porcine nidovirus infection. Our results demonstrated that ribavirin treatment dose-dependently inhibited the replication of both nidoviruses. The antiviral activity of ribavirin on porcine nidovirus replication was found to be primarily exerted at early times post-infection. Treatment with ribavirin resulted in marked reduction of viral genomic and subgenomic RNA synthesis, viral protein expression, and progeny virus production in a dose-dependent manner. Investigations into the mechanism of action of ribavirin against PRRSV and PEDV revealed that the addition of guanosine to the ribavirin treatment significantly reversed the antiviral effects, suggesting that depletion of the intracellular GTP pool by inhibiting IMP dehydrogenase may be essential for ribavirin activity. Further sequencing analysis showed that the mutation frequency in ribavirin-treated cells was similar to that in untreated cells, indicating that ribavirin did not induce error-prone replication. Taken together, our data indicate that ribavirin might not only be a good therapeutic agent against porcine nidovirus, but also a potential candidate to be evaluated against other human and animal coronaviruses. url: https://www.sciencedirect.com/science/article/pii/S0168170212004078 doi: 10.1016/j.virusres.2012.10.018 id: cord-285935-5rsk6g7l author: Kinast, Volker title: Hepatitis E Virus Drug Development date: 2019-05-28 words: 6638.0 sentences: 364.0 pages: flesch: 46.0 cache: ./cache/cord-285935-5rsk6g7l.txt txt: ./txt/cord-285935-5rsk6g7l.txt summary: Cyclic peptides (CP) that had been developed to abrogate interaction of p6Gag and TSG101 and inhibited viral release of HIV Virus like particles (VLPs) [76] were tested for their activity against HEV [77] . The compounds RBV and mycophenolic acid (MPA), both of which target enzymes involved in nucleotide synthesis, are either already used as treatment against HEV or have been reported for their potential to inhibit the virus. So far, the antiviral activity against HEV of only four drugs (Sofosbuvir, pegIFN-α, Ribavirin and silvestrol) was approved in experimental settings beyond in vitro cell culture systems. Sofosbuvir Inhibits Hepatitis E Virus Replication In Vitro and Results in an Additive Effect When Combined With Ribavirin Sofosbuvir shows antiviral activity in a patient with chronic hepatitis E virus infection Zinc Salts Block Hepatitis E Virus Replication by Inhibiting the Activity of Viral RNA-Dependent RNA Polymerase The natural compound silvestrol inhibits hepatitis E virus (HEV) replication in vitro and in vivo abstract: Hepatitis E virus (HEV) is an underestimated disease, leading to estimated 20 million infections and up to 70,000 deaths annually. Infections are mostly asymptomatic but can reach mortality rates up to 25% in pregnant women or become chronic in immunocompromised patients. The current therapy options are limited to the unspecific antivirals Ribavirin (RBV) and pegylated Interferon-α (pegIFN-α). RBV leads to viral clearance in only 80% of patients treated, and is, similar to pegIFN-α, contraindicated in the major risk group of pregnant women, emphasizing the importance of new therapy options. In this review, we focus on the urgent need and current efforts in HEV drug development. We provide an overview of the current status of HEV antiviral research. Furthermore, we discuss strategies for drug development and the limitations of the approaches with respect to HEV. url: https://doi.org/10.3390/v11060485 doi: 10.3390/v11060485 id: cord-290744-m0vpizuh author: Kindler, E. title: Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response date: 2016-09-09 words: 7229.0 sentences: 399.0 pages: flesch: 52.0 cache: ./cache/cord-290744-m0vpizuh.txt txt: ./txt/cord-290744-m0vpizuh.txt summary: Here, we will summarize the insights gathered so far on an important aspect of virulence and host adaptation, the interactions of SARS-CoV and MERS-CoV with antiviral interferon (IFN) responses of human cells. The broad antiviral activity of IFNs occurs on several levels, namely virus entry, viral polymerase function, host cell translation, RNA availability, RNA stability, particle budding, apoptosis, or general boosting of innate and adaptive immune responses. Crystal structure of the middle east respiratory syndrome coronavirus (MERS-CoV) papain-like protease bound to ubiquitin facilitates targeted disruption of deubiquitinating activity to demonstrate its role in innate immune suppression Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses PACT-induced activation of RIG-I and MDA5 in the innate antiviral response abstract: Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are the most severe coronavirus (CoV)-associated diseases in humans. The causative agents, SARS-CoV and MERS-CoV, are of zoonotic origin but may be transmitted to humans, causing severe and often fatal respiratory disease in their new host. The two coronaviruses are thought to encode an unusually large number of factors that allow them to thrive and replicate in the presence of efficient host defense mechanisms, especially the antiviral interferon system. Here, we review the recent progress in our understanding of the strategies that highly pathogenic coronaviruses employ to escape, dampen, or block the antiviral interferon response in human cells. url: https://api.elsevier.com/content/article/pii/S0065352716300458 doi: 10.1016/bs.aivir.2016.08.006 id: cord-343221-e29of29o author: Kindler, Eveline title: Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication date: 2017-02-03 words: 7896.0 sentences: 423.0 pages: flesch: 51.0 cache: ./cache/cord-343221-e29of29o.txt txt: ./txt/cord-343221-e29of29o.txt summary: Specifically, we show that genetically engineered mutants of mouse hepatitis virus (MHV) and human coronavirus 229E (HCoV-229E), respectively, that encode an EndoU active-site substitution known to abolish nucleolytic activity, were severely attenuated and elicited an immediate and simultaneous activation of host cell dsRNA sensors. The severe attenuation of MHV H277A and HCoV-229E H250A replication in wild-type murine and human macrophages, respectively, precluded the use of primary macrophages to assess the sensitivity of EndoU-deficient coronaviruses to IFN-I pre-treatment. Our data suggest that direct restriction of replication of EndoU-deficient coronaviruses is mediated by RNase L-mediated RNA degradation and inhibition of host cell translation through activation of PKR. Notably, also in this case Xrn1 is required to further process the de-capped mRNAs. Our data show that early during coronavirus infection the EndoU activity conceptually fulfils the same task, namely the removal of dsRNA that would otherwise trigger host cell dsRNA responses, such as IFN-β expression and activation of PKR and OAS/RNase L. abstract: Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis–within the replicase complex—suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses. url: https://www.ncbi.nlm.nih.gov/pubmed/28158275/ doi: 10.1371/journal.ppat.1006195 id: cord-284609-1q75zw6b author: King, Andrew M.Q. title: Recombination in RNA date: 1982-07-31 words: 4067.0 sentences: 198.0 pages: flesch: 50.0 cache: ./cache/cord-284609-1q75zw6b.txt txt: ./txt/cord-284609-1q75zw6b.txt summary: RNAase Tl fingerprints of virus RNA, prepared from representatives of each recombinant type, confirmed the approximate crossover sites that had been deduced from the inheritance of proteins. The possibility of genetic recombination in such viruses was first suggested many years ago by Hirst (1962) and Ledinko (1963) , who showed that infection of cells with a mixture of inhibitor-sensitive variants of poliovirus resulted in an enhanced yield of resistant progeny that were genetically stable. Second, we have obtained biochemical evidence of genetic recombination by crossing temperature-sensitive mutants of aphthovirus that possess second-site mutations affecting polypeptide charge. This paper describes a cross between two subtype strains of aphthovirus that has provided the first biochemical demonstration of genetic recombination at the level of RNA. Several spontaneous temperature-sensitive mutants of subtype OS were isolated and screened by electrofocusing polypeptides induced in virus-infected cells. abstract: Abstract The aphthovirus genome consists of a single molecule of single-stranded RNA that encodes all the virus-induced proteins. We isolated recombinant aphthoviruses from cells simultaneously infected with temperature-sensitive mutants of two different subtype strains. Analysis of the proteins induced by 16 independently generated recombinants revealed two types of protein pattern, which were consistent with single genetic crossovers on the 5′ side and 3′ side, respectively, of the central P34-coding region. Recombinants invariably inherited all four coat proteins from the same parent, and novel recombinant proteins were not observed. RNAase T1 fingerprints of virus RNA, prepared from representatives of each recombinant type, confirmed the approximate crossover sites that had been deduced from the inheritance of proteins. These fingerprints provide molecular evidence of recombination at the level of RNA and demonstrate the potential of RNA recombination for producing genetic diversity among picornaviruses. url: https://api.elsevier.com/content/article/pii/0092867482904548 doi: 10.1016/0092-8674(82)90454-8 id: cord-319100-3gdawhfn author: Kirkland, P.D. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses date: 2020-06-10 words: 4624.0 sentences: 204.0 pages: flesch: 49.0 cache: ./cache/cord-319100-3gdawhfn.txt txt: ./txt/cord-319100-3gdawhfn.txt summary: authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses Also of concern are recommendations (3, 4) to include foetal bovine serum (fbs) as a source of protein to enhance the stabilising properties of VTMs. This report documents observations of the adverse impact of certain VTMs on real time reverse transcription PCR (qRT-PCR) assays for the detection of SARS-CoV-2 virus as well as on a Type A influenza virus and a herpesvirus and discuss the broader implications of the inclusion of foetal bovine serum as a protein supplement to VTMs. During the initial investigation, purified RNA from an Australian isolate (WMD DC1) of SARS-CoV-2 was supplied to the Elizabeth Macarthur Agriculture Institute (EMAI) by the Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales (NSW). abstract: During the 2020 SARS-Cov-2 pandemic, there has been an acute shortage of viral transport medium. Many different products have been used to meet the demands of large-scale diagnostic and surveillance testing. The stability of SARS-Cov-2 RNA was assessed in several commercially produced transport media and an in-house solution. Coronavirus RNA was rapidly destroyed in the commercial transport media though the deleterious effects on intact virus were limited. Similar results were obtained for a Type A influenza virus. There was reduced detection of both virus and nucleic acid when a herpesvirus sample and purified DNA were tested. Collectively these data showed that the commercial viral transport media contained nucleases or similar substances and may seriously compromise diagnostic and epidemiological investigations. Recommendations to include foetal bovine serum as a source of protein to enhance the stabilising properties of viral transport media are contraindicated. Almost all commercial batches of foetal bovine serum contain pestiviruses and at times other bovine viruses. In addition to the potential for there to be nucleases in the transport medium, the presence of these viruses and other extraneous nucleic acid in samples may compromise the interpretation of sequence data. The inclusion of foetal bovine serum presents a biosecurity risk for the movement of animal pathogens and renders these transport media unsuitable for animal disease diagnostic applications. While these transport media may be suitable for virus culture purposes, there could be misleading results if used for nucleic acid-based tests. Therefore, these products should be evaluated to ensure fitness for purpose. url: https://doi.org/10.1101/2020.06.09.142323 doi: 10.1101/2020.06.09.142323 id: cord-337508-nfzaw8gg author: Kirkland, P.D. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 date: 2020-10-05 words: 2708.0 sentences: 134.0 pages: flesch: 54.0 cache: ./cache/cord-337508-nfzaw8gg.txt txt: ./txt/cord-337508-nfzaw8gg.txt summary: authors: Kirkland, P.D.; Frost, M.J. title: The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 With the widespread introduction of molecular based diagnostic assays, especially real time PCR (qPCR), studies have been undertaken to evaluate the stability of viruses in VTMs, particularly in commercially prepared products, while being held at a range of temperatures. After becoming aware of concerns of variable results for the same samples in different assays, we initiated a study to compare the stability of SARS-CoV-2 RNA in several commercially manufactured VTMs and an in-house product. The results of these studies clearly indicate that the commercially prepared VTM solutions have had an adverse impact on the ability to detect both SARS-CoV-2 and influenza RNA. The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses abstract: nan url: https://www.sciencedirect.com/science/article/pii/S0031302520309405?v=s5 doi: 10.1016/j.pathol.2020.09.013 id: cord-336775-d4hi9myk author: Kirtipal, Nikhil title: From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses date: 2020-08-13 words: 8606.0 sentences: 442.0 pages: flesch: 46.0 cache: ./cache/cord-336775-d4hi9myk.txt txt: ./txt/cord-336775-d4hi9myk.txt summary: Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Hence, acute respiratory distress syndrome (ARDS) is caused by cytokine storm that triggers a destruction in host cells via immune system and subsequently results into multiple organs failure or death as stated in case of SARS-CoV-2 outbreak; similar observations were noted in case of SARS-CoV infection (Kumar et al., 2020) . When developing novel therapeutic strategies to check the immunoregulatory cytokines such as TNFβ and IL6, investigation should be considered on the viral strain and targeted organ specificity; for example, SARS-CoV-2 has more affinity to ACE2 which are scattering on different organs like lung and kidney while MERS-like CoV can even infect T-cells. Tumor necrosis factor-alpha convertase (ADAM17) mediates regulated ectodomain shedding of the severe-acute respiratory syndrome-coronavirus (SARS-CoV) receptor, angiotensin-converting enzyme-2 (ACE2) abstract: Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) – diseases termed as COVID-19. Current SARS-CoV-2 outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. In fact, evidence has now shown that coronaviruses undergoes repaid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target humoral immune system which further results in severe deterioration of the body such as by cytokine storm. This demands the understanding of phenotypic and genotypic classification, and pathogenesis of SARS-CoV-2 for the production of potential therapy. In lack of clear clinical evidences for the pathogenesis of COVID-19, comparative analysis of previous pandemic HCoVs associated immunological responses can provide insights into COVID-19 pathogenesis. In this Review, we summarize the possible origin and transmission mode of CoVs and the current understanding on the viral genome integrity of known pandemic virus against SARS-CoV-2. We also consider the host immune response and viral evasion based on available clinical evidences which would be helpful to remodel COVID-19 pathogenesis; and hence, development of therapeutic against broad spectrum of coronaviruses. url: https://doi.org/10.1016/j.meegid.2020.104502 doi: 10.1016/j.meegid.2020.104502 id: cord-002990-7flusgus author: Kitano, Mitsutaka title: Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro date: 2018-04-26 words: 7080.0 sentences: 313.0 pages: flesch: 50.0 cache: ./cache/cord-002990-7flusgus.txt txt: ./txt/cord-002990-7flusgus.txt summary: The application of a cell-based fluorescence resonance energy transfer (FRET) assay for protease activity demonstrated that these substitutions were involved in the enhanced resistance to rupintrivir. Furthermore, we validated the effect of these mutations using reverse genetics in murine norovirus (MNV), demonstrating that a recombinant MNV strain with a single I109V substitution in the protease also showed reduced susceptibility to rupintrivir. In the present study, we isolated replicon cells with reduced susceptibility to rupintrivir after several passages in the presence of rupintrivir and identified two amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease. To confirm the previously reported inhibitory effects of rupintrivir on human norovirus replication (10), we generated a human gastric adenocarcinoma cell line, HGT-NV, which stably maintained a Norwalk virus replicon encoding the neomycin resistance gene in place of the major capsid protein. abstract: Human norovirus (HuNoV) is a major cause of nonbacterial gastroenteritis worldwide, yet despite its impact on society, vaccines and antivirals are currently lacking. A HuNoV replicon system has been widely applied to the evaluation of antiviral compounds and has thus accelerated the process of drug discovery against HuNoV infection. Rupintrivir, an irreversible inhibitor of the human rhinovirus 3C protease, has been reported to inhibit the replication of the Norwalk virus replicon via the inhibition of the norovirus protease. Here we report, for the first time, the generation of rupintrivir-resistant human Norwalk virus replicon cells in vitro. Sequence analysis revealed that these replicon cells contained amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease NS6. The application of a cell-based fluorescence resonance energy transfer (FRET) assay for protease activity demonstrated that these substitutions were involved in the enhanced resistance to rupintrivir. Furthermore, we validated the effect of these mutations using reverse genetics in murine norovirus (MNV), demonstrating that a recombinant MNV strain with a single I109V substitution in the protease also showed reduced susceptibility to rupintrivir. In summary, using a combination of different approaches, we have demonstrated that, under the correct conditions, mutations in the norovirus protease that lead to the generation of resistant mutants can rapidly occur. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923142/ doi: 10.1128/aac.00201-18 id: cord-328042-e1is656g author: Klein, Steffen title: SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP date: 2020-08-07 words: 6328.0 sentences: 329.0 pages: flesch: 56.0 cache: ./cache/cord-328042-e1is656g.txt txt: ./txt/cord-328042-e1is656g.txt summary: The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Here, we show that the magnetic bead-based protocol yields RNA extracts comparable to the commercially available QIAcube viral RNA extraction kit, as determined by the commonly applied detection methods RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP) [16] . abstract: Rapid large-scale testing is essential for controlling the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. As a result of the large demand for testing, commercial RNA extraction kits may be limited and, alternatively, non-commercial protocols are needed. Here, we provide a magnetic bead RNA extraction protocol that is predominantly based on in-house made reagents and is performed in 96-well plates supporting large-scale testing. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Importantly, the presented diagnostic workflow can be quickly set up in a laboratory without access to an automated pipetting robot. url: https://doi.org/10.3390/v12080863 doi: 10.3390/v12080863 id: cord-002673-5a1rfi6k author: Knibb, Wayne title: Regional genetic diversity for NNV grouper viruses across the Indo-Asian region – implications for selecting virus resistance in farmed groupers date: 2017-09-06 words: 6692.0 sentences: 298.0 pages: flesch: 48.0 cache: ./cache/cord-002673-5a1rfi6k.txt txt: ./txt/cord-002673-5a1rfi6k.txt summary: This study uses statistical approaches and assessment of "characteristic attributes" (i.e. nucleotide positions that discriminate among strains) to assess whether published and new NNV RNA2 cds sequences show genetic differentiation over geography, host species and years. Within the red spotted grouper nervous necrosis virus (RGNNV) strain, to which all Asian grouper NNV belong, however, no one so far has reported evidence of genetic subgrouping by region, species or year in a formal statistical manner, especially when we restrict hosts just to Asian grouper. The goal of this report was to collate the most comprehensive data set to date on NNV RNA2 sequences for warm water Asian marine finfish, whether published and/or lodged in Genbank over the last 20 years, including some sequence data produced by our group for Vietnamese and Taiwanese grouper, to statistically test the data for evidence of NNV strain variation that associates with geography, host species and year and also to determine whether there are "characteristic attributes" that indicate regional (or host, year) specific differences among the strains. abstract: Grouper aquaculture around Asia is impacted by the nervous necrosis virus (NNV) and, in response, host resistance to this infection is being considered as a trait for selection. However efficient selection may be confounded if there are different genetic strains of NNV within and between regions and over years. This study uses statistical approaches and assessment of “characteristic attributes” (i.e. nucleotide positions that discriminate among strains) to assess whether published and new NNV RNA2 cds sequences show genetic differentiation over geography, host species and years. Rather clear evidence was found for regional strains of NNV. Interestingly, most of the geographic defining “characteristic attributes” were in codon position three, and not translated into differences for the protein capsid (i.e. they were synonymous variations), suggesting that while NNV strains were geographically isolated and had diverged in different regions for RNA sequences, selection had largely conserved the protein sequences among regions. The apparent selection constraint on the capsid protein may mitigate the risk that despite geographic subdivision, NNV strain variability will confound genetic selection for host resistance. The existence of regional Asian NNV strains may suggest that hatcheries are at risk from NNV not only from imported material but also from endemic reservoirs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587679/ doi: 10.1038/s41598-017-11263-4 id: cord-339172-210dwhgj author: Knoops, Kèvin title: SARS-Coronavirus Replication Is Supported by a Reticulovesicular Network of Modified Endoplasmic Reticulum date: 2008-09-16 words: 9930.0 sentences: 411.0 pages: flesch: 43.0 cache: ./cache/cord-339172-210dwhgj.txt txt: ./txt/cord-339172-210dwhgj.txt summary: Specific þRNA virus replicase subunits are targeted to the membranes of particular cell organelles that are subsequently modified into characteristic structures with which viral RNA synthesis is associated. We used electron microscopy and tomography for the three-dimensional imaging of the membrane alterations induced by severe acute respiratory syndrome (SARS)-coronavirus, a member of the virus group with the largest RNA genome known to date. The lumen of this unique membrane network contains numerous large (diameter 250-300 nm) ''''inner vesicles,'''' which were formerly thought to reside in isolated DMVs. Intriguingly, although the interior of these vesicles does not appear to be connected to the cytosol, it labels abundantly for double-stranded RNA, which presumably is present at the site of viral RNA synthesis. In some of our images, the SARS-CoV-induced CM appeared to be continuous with both DMV outer membranes ( Figure 2D ; inset) and ER cisternae, suggesting a link to the viral RTC also in coronaviruses. abstract: Positive-strand RNA viruses, a large group including human pathogens such as SARS-coronavirus (SARS-CoV), replicate in the cytoplasm of infected host cells. Their replication complexes are commonly associated with modified host cell membranes. Membrane structures supporting viral RNA synthesis range from distinct spherular membrane invaginations to more elaborate webs of packed membranes and vesicles. Generally, their ultrastructure, morphogenesis, and exact role in viral replication remain to be defined. Poorly characterized double-membrane vesicles (DMVs) were previously implicated in SARS-CoV RNA synthesis. We have now applied electron tomography of cryofixed infected cells for the three-dimensional imaging of coronavirus-induced membrane alterations at high resolution. Our analysis defines a unique reticulovesicular network of modified endoplasmic reticulum that integrates convoluted membranes, numerous interconnected DMVs (diameter 200–300 nm), and “vesicle packets” apparently arising from DMV merger. The convoluted membranes were most abundantly immunolabeled for viral replicase subunits. However, double-stranded RNA, presumably revealing the site of viral RNA synthesis, mainly localized to the DMV interior. Since we could not discern a connection between DMV interior and cytosol, our analysis raises several questions about the mechanism of DMV formation and the actual site of SARS-CoV RNA synthesis. Our data document the extensive virus-induced reorganization of host cell membranes into a network that is used to organize viral replication and possibly hide replicating RNA from antiviral defense mechanisms. Together with biochemical studies of the viral enzyme complex, our ultrastructural description of this “replication network” will aid to further dissect the early stages of the coronavirus life cycle and its virus-host interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/18798692/ doi: 10.1371/journal.pbio.0060226 id: cord-315069-xo4mbxei author: Knorr, D. A. title: De novo generation of defective interfering RNAs of tomato bushy stunt virus by high multiplicity passage date: 1991-03-31 words: 5134.0 sentences: 250.0 pages: flesch: 52.0 cache: ./cache/cord-315069-xo4mbxei.txt txt: ./txt/cord-315069-xo4mbxei.txt summary: Abstract Defective interfering (DI) RNAs were generated de novo in each of 12 independent isolates of tomato bushy stunt virus (TBSV) upon serial passage at high multiplicities of infection (m.o.i.) in plants, but not in any of 4 additional isolates after 11 serial passages at low m.o.i. The DI RNAs were detected in RNA isolated from virus particles and in 2.3 M LiCl-soluble RNA fractions isolated from inoculated leaves. On each host species, six isolates were passed at high m.o.i. and two control isolates were passed at low m.o.i. In these hosts, DI-free TBSV induces lethal necrosis within 7-l 0 days postinoculation (d.p.i.), except in the presence of DI RNAs which are associated with attenuation and the establishment of persistent infections (Hillman et a/., 1987) . The small RNAs which developed in each of the high m.o.i. isolates hybridized to both 5''-and 3''-proximal TBSV genomic sequences, but generally were larger (-600 bases) than the previously characterized DI 1 RNA species (-400 bases). abstract: Abstract Defective interfering (DI) RNAs were generated de novo in each of 12 independent isolates of tomato bushy stunt virus (TBSV) upon serial passage at high multiplicities of infection (m.o.i.) in plants, but not in any of 4 additional isolates after 11 serial passages at low m.o.i. The DI RNAs were detected in RNA isolated from virus particles and in 2.3 M LiCl-soluble RNA fractions isolated from inoculated leaves. Symptom attenuation leading to persistent infections was closely correlated with the passage in which DIs first developed. Comparisons of nucleotide sequences of 10 cDNA clones from 2 DI RNA populations and with a previously characterized TBSV DI RNA revealed the same four regions of sequence from the TBSV genome were strictly conserved in each of the DI RNAs: the virus 5′ leader sequence of 168 bases; a region of approximately 200–250 bases from the viral polymerase gene; approximately 70 bases from the 3′ terminus of the viral pl9 and p22 genes; and approximately 130 bases from the 3′terminal noncoding region. Conservation of the sequence motif present in all of the DIs suggests that there might be a common mechanism of DI formation as well as selection pressure to maintain sequences essential for replication and encapsidation. url: https://api.elsevier.com/content/article/pii/004268229190484S doi: 10.1016/0042-6822(91)90484-s id: cord-287748-co9j3uig author: Kobayashi, Tomoya title: Detection of bat hepatitis E virus RNA in microbats in Japan date: 2018-05-29 words: 1388.0 sentences: 70.0 pages: flesch: 55.0 cache: ./cache/cord-287748-co9j3uig.txt txt: ./txt/cord-287748-co9j3uig.txt summary: Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV). Here, we collected and screened 81 bat fecal samples from nine bat species in Japan to detect BatHEV RNA by RT-PCR using HEV-specific primers, and detected three positive samples. These data support the first detection of BatHEVs in Japanese microbats, indicating their wide geographical distribution among multiple bat species. BLAST analysis indicated that BtHEV-Ej1/-Ej2 showed the highest sequence identities to BatHEV/BS7, a German strain detected from the Serotine bat (Eptesicus serotinus), among strains previously reported in other countries. The closely related BatHEVs (BtHEV-Ej1/-Ej2 and Bat HEV/BS7) have been detected in different species of Eptesicus bats (E. PCR amplifications were performed using the KOD FX Neo (Toyobo) with consensus HEV primer sets (PanHEV F and R), which were designed in this study to amplify a 191-bp fragment of the RNA-dependent into Orthohepevirus D, in Japanese bats, suggesting wide geographical distribution of BatHEV among multiple bat species. abstract: Several recent studies have reported that various bat species harbor bat hepatitis E viruses (BatHEV) belonging to the family Hepeviridae, which also contains human hepatitis E virus (HEV). The distribution and ecology of BatHEV are not well known. Here, we collected and screened 81 bat fecal samples from nine bat species in Japan to detect BatHEV RNA by RT-PCR using HEV-specific primers, and detected three positive samples. Sequence and phylogenetic analyses indicated that these three viruses were BatHEVs belonging to genus Orthohepevirus D like other BatHEV strains reported earlier in various countries. These data support the first detection of BatHEVs in Japanese microbats, indicating their wide geographical distribution among multiple bat species. url: https://www.ncbi.nlm.nih.gov/pubmed/29845506/ doi: 10.1007/s11262-018-1577-9 id: cord-333636-h2sg6shp author: Kochan, G. title: Characterization of the RNA-binding activity of VP3, a major structural protein of Infectious bursal disease virus date: 2003 words: 5975.0 sentences: 334.0 pages: flesch: 53.0 cache: ./cache/cord-333636-h2sg6shp.txt txt: ./txt/cord-333636-h2sg6shp.txt summary: The histidine-tagged VP3 was affinity-purified and used to study its ability to bind RNA molecules using three complementary methods: (i) Northwestern blotting; (ii) binding of VP3 protein-RNA complexes to nitrocellulose membranes; and (iii) electrophoretic mobility shift assays. Briefly, increasing amounts (from 5 × 10 −2 mM to 5 × 10 −6 mM) of purified VP3 or BSA, used as a control for non-specific interaction, were mixed with 10 6 cpm of 32 P-labeled ssRNA probe B (5 × 10 −6 mM) in binding reaction buffer (50 mM Tris, 150 mM KCl, 150 mM NaCl 10% Glycerol, 0,01% Triton X 100), in 16 µl final volume, so the VP3/RNA molar ratio in these experiments varied from 10 4 to 1. Competition assays based on nitrocellulose binding were carried out using virus-derived radiolabeled ssRNA probes together with increasing concentrations of non-radioactive competitor RNA and DNA probes. abstract: Infectious bursal disease virus (IBDV) is the agent of an immune-depressive disease affecting the poultry industry worldwide. Infection of IBDV leads to expression of five mature virus-encoded proteins. Proteolytic processing of the virus-encoded polyprotein generates VP3 which coats the inner surface of the IBDV capsid. In this report, we describe the characterization of the RNA-binding activity of VP3. For these studies, the VP3 coding region was fused to a histidine tag and expressed in insect cells using a recombinant baculovirus. The histidine-tagged VP3 was affinity-purified and used to study its ability to bind RNA molecules using three complementary methods: (i) Northwestern blotting; (ii) binding of VP3 protein-RNA complexes to nitrocellulose membranes; and (iii) electrophoretic mobility shift assays. The results demonstrated that VP3 efficiently bound ssRNA and dsRNA. Under the experimental conditions used in this study, the formation of VP3-RNA complexes did not depend upon the presence of specific RNA sequences. A series of histidine-tagged VP3 deletion mutants spanning the whole VP3 coding region were generated. The use of these mutants revealed that the VP3 RNA-binding domain layed in a highly conserved 69 aa stretch close to the N-terminus of the protein. url: https://www.ncbi.nlm.nih.gov/pubmed/12664296/ doi: 10.1007/s00705-002-0949-5 id: cord-341171-s8vkgdhf author: Kojima, Mizuki title: Irradiation by a Combination of Different Peak-Wavelength Ultraviolet-Light Emitting Diodes Enhances the Inactivation of Influenza A Viruses date: 2020-07-08 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Influenza A viruses (IAVs) pose a serious global threat to humans and their livestock. This study aimed to determine the ideal irradiation by ultraviolet-light emitting diodes (UV-LEDs) for IAV disinfection. We irradiated the IAV H1N1 subtype with 4.8 mJ/cm(2) UV using eight UV-LEDs [peak wavelengths (WL) = 365, 310, 300, 290, 280, 270, and 260 nm)] or a mercury low pressure (LP)-UV lamp (Peak WL = 254 nm). Inactivation was evaluated by the infection ratio of Madin–Darby canine kidney (MDCK) cells or chicken embryonated eggs. Irradiation by the 260 nm UV-LED showed the highest inactivation among all treatments. Because the irradiation-induced inactivation effects strongly correlated with damage to viral RNA, we calculated the correlation coefficient (R(AE)) between the irradiant spectrum and absorption of viral RNA. The R(AE) scores strongly correlated with the inactivation by the UV-LEDs and LP-UV lamp. To increase the R(AE) score, we combined three different peak WL UV-LEDs (hybrid UV-LED). The hybrid UV-LED (R(AE) = 86.3) significantly inactivated both H1N1 and H6N2 subtypes to a greater extent than 260 nm (R(AE) = 68.6) or 270 nm (R(AE) = 42.2) UV-LEDs. The R(AE) score is an important factor for increasing the virucidal effects of UV-LED irradiation. url: https://doi.org/10.3390/microorganisms8071014 doi: 10.3390/microorganisms8071014 id: cord-287018-g4y5kjju author: Konstantinova, P title: Inhibition of human immunodeficiency virus type 1 by RNA interference using long-hairpin RNA date: 2006-05-18 words: 7164.0 sentences: 454.0 pages: flesch: 56.0 cache: ./cache/cord-287018-g4y5kjju.txt txt: ./txt/cord-287018-g4y5kjju.txt summary: In order to solve this durability problem, we tested DNA constructs encoding virus-specific long-hairpin RNAs (lhRNAs) for their ability to inhibit HIV-1 production. The lhRNA constructs were compared with in vitro diced double-stranded RNA and a DNA construct encoding an effective nef-specific shRNA for their ability to inhibit HIV-1 production in cells. For this reason, the DNA constructs encoding lhRNAs (a single-hairpin molecule) and long dsRNAs (two complementary molecules that form a duplex) were designed to target tat, rev and nef sequences as indicated in Figure 1 . 21 nef2 dsRNA induced a decrease in luciferase expression, but an even more pronounced level of inhibition was Figure 1 Scheme of the human immunodeficiency virus type 1 (HIV-1) pLAI proviral genome and target sequences used for the design of long-hairpin RNAs (lhRNAs). abstract: Inhibition of virus replication by means of RNA interference has been reported for several important human pathogens, including human immunodeficiency virus type 1 (HIV-1). RNA interference against these pathogens has been accomplished by introduction of virus-specific synthetic small interfering RNAs (siRNAs) or DNA constructs encoding short-hairpin RNAs (shRNAs). Their use as therapeutic antiviral against HIV-1 is limited, because of the emergence of viral escape mutants. In order to solve this durability problem, we tested DNA constructs encoding virus-specific long-hairpin RNAs (lhRNAs) for their ability to inhibit HIV-1 production. Expression of lhRNAs in mammalian cells may result in the synthesis of many siRNAs targeting different viral sequences, thus providing more potent inhibition and reducing the chance of viral escape. The lhRNA constructs were compared with in vitro diced double-stranded RNA and a DNA construct encoding an effective nef-specific shRNA for their ability to inhibit HIV-1 production in cells. Our results show that DNA constructs encoding virus-specific lhRNAs are capable of inhibiting HIV-1 production in a sequence-specific manner, without inducing the class I interferon genes. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/sj.gt.3302786) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/16708080/ doi: 10.1038/sj.gt.3302786 id: cord-303408-coesfldm author: Konstantinova, Pavlina title: Trans-inhibition of HIV-1 by a long hairpin RNA expressed within the viral genome date: 2007-03-01 words: 4886.0 sentences: 277.0 pages: flesch: 53.0 cache: ./cache/cord-303408-coesfldm.txt txt: ./txt/cord-303408-coesfldm.txt summary: BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) can be inhibited by means of RNA silencing or interference (RNAi) using synthetic short interfering RNAs (siRNAs) or gene constructs encoding short hairpin RNAs (shRNAs) or long hairpin RNAs (lhRNAs). Although these escape variants lost the ability to trans-inhibit HIV-1, they effectively outgrew the wild-type virus in competition experiments in SupT1 cells. In the current study, we constructed the HIV-lhNef variant, which contains a 300 bp extended hairpin structure at the 3'' genome position of the Nef gene of the otherwise wild-type HIV-1. HEK293T cells were transfected with the wild type HIV-1 construct or HIV-lhNef. We measured CA-p24 in the culture supernatant as a measure of virus production 2 days post-transfection. Compared to the effective HIV-lhNef inhibitor, all AS escape variants had lost the ability to actively inhibit wild-type virus production (Fig. 4B ). abstract: BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) can be inhibited by means of RNA silencing or interference (RNAi) using synthetic short interfering RNAs (siRNAs) or gene constructs encoding short hairpin RNAs (shRNAs) or long hairpin RNAs (lhRNAs). The use of siRNA and shRNA as antiviral therapeutic is limited because of the emergence of viral escape mutants. This problem is theoretically prevented by intracellular expression of lhRNAs generating multiple siRNAs that target the virus simultaneously, thus reducing the chance of viral escape. However, gene constructs encoding lhRNA molecules face problems with delivery to the right cells in an infected individual. In order to solve this problem, we constructed an HIV-1 variant with a 300 bp long hairpin structure in the 3' part of the genome corresponding to the Nef gene (HIV-lhNef). RESULTS: Intriguingly, HIV-lhNef potently inhibited wild-type HIV-1 production in trans. However, HIV-lhNef demonstrated a severe production and replication defect, which we were able to solve by selecting spontaneous virus variants with truncated hairpin structures. Although these escape variants lost the ability to trans-inhibit HIV-1, they effectively outgrew the wild-type virus in competition experiments in SupT1 cells. CONCLUSION: Expression of the lhNef hairpin within the HIV-1 genome results in potent trans-inhibition of wild-type HIV-1. Although the mechanism of trans-inhibition is currently unknown, it remains of interest to study the molecular details because the observed effect is extremely potent. This may have implications for the development of virus strains to be used as live-attenuated virus vaccines. url: https://www.ncbi.nlm.nih.gov/pubmed/17331227/ doi: 10.1186/1742-4690-4-15 id: cord-262923-kgzbd6w3 author: Koo, Bonhan title: CRISPR/dCas9-mediated biosensor for detection of tick-borne diseases date: 2018-11-10 words: 3628.0 sentences: 212.0 pages: flesch: 48.0 cache: ./cache/cord-262923-kgzbd6w3.txt txt: ./txt/cord-262923-kgzbd6w3.txt summary: Here, we report the development of an improved molecular diagnostics tool that utilizes CRISPR/dCas9-mediated biosensor that couples a nuclease inactivated Cas9 (dCas9) and single microring resonator biosensor, enables label-free and real-time detection of pathogenic DNA and RNA. In this study, we developed an improved diagnostic tool by combining a CRISPR/dCas9 and an isothermal diagnostic approach based on SMR biosensor for simultaneous nucleic acid (RNA and DNA) amplification and detection with speed as well as high sensitivity and specificity. For simultaneous amplification and detection of nucleic acid, sequence specific primer of target was immobilized to the surface of the SMR biosensor and dCas9 RNP was in reaction chamber with single temperature for isothermal reaction with RPA. To achieve sensitive detection with dCas9 RNP on SMR biosensor, we constructed guide RNAs (gRNAs) targeting two tick-borne pathogens that have substantially overlapping clinical presentations: Orientia tsutsugamushi, the causative agent of scrub typhus (ST), and bunyavirus, the causative agent of severe fever with thrombocytopenia syndrome (SFTS) (Fig. 1B) . abstract: Rapid and highly sensitive detection of biomolecules is greatly needed for pathogen diagnosis in clinical samples, but the method needs to be significantly improved in terms of sensitivity and specificity for actual use in clinical settings. Here, we report the development of an improved molecular diagnostics tool that utilizes CRISPR/dCas9-mediated biosensor that couples a nuclease inactivated Cas9 (dCas9) and single microring resonator biosensor, enables label-free and real-time detection of pathogenic DNA and RNA. We addressed the clinical utility of this CRISPR/dCas9-mediated biosensor in tick-borne illnesses including scrub typhus (ST) and severe fever with thrombocytopenia syndrome (SFTS), whose clinical presentations are too similar to be easily differentiated. By using CRISPR/dCas9-mediated biosensor, we achieved single molecule sensitivity for the detection of ST (0.54 aM) and SFTS (0.63 aM); this detection sensitivity is 100 times more sensitive than that of RT-PCR assay. Finally, CRISPR/dCas9-mediated biosensor was able to clearly distinguish between ST and SFTS in serum samples within 20 min. We believe that CRISPR/dCas9-mediated biosensor will be useful for rapid and accurate molecular diagnostic tool that is suitable for immediate clinical applications. url: https://doi.org/10.1016/j.snb.2018.06.069 doi: 10.1016/j.snb.2018.06.069 id: cord-310861-9kb0b6rq author: Koo, Bonhan title: An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections date: 2017-04-15 words: 5584.0 sentences: 295.0 pages: flesch: 58.0 cache: ./cache/cord-310861-9kb0b6rq.txt txt: ./txt/cord-310861-9kb0b6rq.txt summary: In this study, we report an isothermal and rapid one-step RNA amplification/detection (iROAD) assay to simultaneously amplify and detect the viral RNA in a label-free and real-time manner. Furthermore, we demonstrated the clinical utility of the iROAD assay by detecting respiratory viral RNAs extracted from the 63 nasopharyngeal samples with either IFN-A/B or HCoV-OC43/229E or RSV-A/B. Subsequently, the iROAD assay detected the respiratory viral targets from the clinical sample by measuring the resonance wavelength shift within 15-20 min (Fig. 1) . In case of the iROAD assay with label-free and real-time capabilities, the wavelength shift was sequentially increased based on the concentrations (2.5×10 1 to 10 5 copies/reaction) of IFN-B within 20 min, as compared to the negative control. In the case of the real-time RT-PCR assay, the fluorescent SYBR Green signal was observed in RNA samples diluted up to 2.5×10 2 copies/reaction and showed good linearity (R 2 =0.9795) for different concentrations of the target (Fig. 3C ). abstract: Recently, RNA viral infections caused by respiratory viruses, such as influenza, parainfluenza, respiratory syncytial virus, coronavirus, and Middle East respiratory syndrome-coronavirus (MERS-CoV), and Zika virus, are a major public health threats in the world. Although myriads of diagnostic methods based on RNA amplification have been developed in the last decades, they continue to lack speed, sensitivity, and specificity for clinical use. A rapid and accurate diagnostic method is needed for appropriate control, including isolation and treatment of the patients. Here, we report an isothermal, label-free, one-step RNA amplification and detection system, termed as iROAD, for the diagnosis of respiratory diseases. It couples a one-step isothermal RNA amplification method and a bio-optical sensor for simultaneous viral RNA amplification/detection in a label-free and real-time manner. The iROAD assay offers a one-step viral RNA amplification/detection example to rapid analysis (<20 min). The detection limit of iROAD assay was found to be 10-times more sensitive than that of real-time reverse transcription-PCR method. We confirmed the clinical utility of the iROAD assay by detecting viral RNAs obtained from 63 human respiratory samples. We envision that the iROAD assay will be useful and potentially adaptable for better diagnosis of emerging infectious diseases including respiratory diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/27894035/ doi: 10.1016/j.bios.2016.11.051 id: cord-264944-7xj27r98 author: Koopmans, Marion title: Optimization of extraction and PCR amplification of RNA extracts from paraffin-embedded tissue in different fixatives date: 1993-07-31 words: 5182.0 sentences: 255.0 pages: flesch: 54.0 cache: ./cache/cord-264944-7xj27r98.txt txt: ./txt/cord-264944-7xj27r98.txt summary: The method was compared to existing extraction techniques by studying the quality of the templates for reverse-transcriptase polymerase chain reaction amplification (RT-PCR), using virus-infected and mock-infected paraffin-embedded cell pellets as a model. The method was compared to existing extraction techniques by studying the quality of the templates for rcvcrsetranscriptase polymerase chain reaction amplification (RT-PCR), using virusinfected and mock-infected paraffin-embedded cell pellets as a model. In the work reported here we used paraffin-embedded torovirus-infected cell pellets to compare the effect of different fixatives and RNA extraction methods on RT-PCR amplification of tissue extracts. abstract: Abstract A method was developed for fast and efficient isolation of RNA from paraffin-embedded tissue sections for subsequent PCR analysis. This method is based on the binding of RNA to acid-treated glass beads in the presence of a high molarity of guanidinium salt. It can be completed within an hour, and obviates the need for dewaxing and phenol/chloroform extractions. The effect of various fixatives and fixation times was tested and the amplification of actin mRNA fragments ranging in length from 82 to 507 bp was used to demonstrate the presence of RNA in the extracts. The method was compared to existing extraction techniques by studying the quality of the templates for reverse-transcriptase polymerase chain reaction amplification (RT-PCR), using virus-infected and mock-infected paraffin-embedded cell pellets as a model. PCR amplification of cellular and viral RNA was successful for RNA isolated by use of all extraction techniques, although the glass bead method was preferred for its simplicity and rapidity. Specimens fixed with formalin were found to be suitable for PCR, but the best results were obtained with acetone-fixed paraffin-embedded material. Dewaxing of tissue sections had no effect on the yield and quality of RNA extractions, and further purification of the extracts using gel filtration did not improve the results. After the protocols were optimized, rotavirus-infected cell pellets were used to demonstrate that extraction and amplification of dsRNA was possible. The information obtained from the studies with the model system was used for extraction of toroviral and rotaviral RNA from archival intestinal material. These data indicate that paraffin-embedded archival tissue can be used for RT-PCR analysis, adding an important technique to diagnostic pathology and retrospective studies. url: https://www.ncbi.nlm.nih.gov/pubmed/8396155/ doi: 10.1016/0166-0934(93)90076-4 id: cord-349341-ap5n6ijl author: Kopek, Benjamin G title: Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle date: 2007-08-14 words: 8539.0 sentences: 431.0 pages: flesch: 44.0 cache: ./cache/cord-349341-ap5n6ijl.txt txt: ./txt/cord-349341-ap5n6ijl.txt summary: The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5''-triphosphate incorporation localized between inner and outer mitochondrial membranes inside ∼50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. To localize more precisely FHV RNA synthesis in relation to spherules, we incubated mitochondria isolated from uninfected and FHV-infected Drosophila cells with a nucleotide mix including 5-bromouridine 5''-triphosphate (BrUTP) and performed immunogold labeling EM with an antibody recognizing BrU incorporated into RNA, but not unincorporated BrUTP. To generate 3-D surface maps of the virus-induced membrane rearrangements associated with FHV RNA replication, we manually traced the inner and outer mitochondrial membranes (including spherules) over ;100 adjacent, 2.2nm-spaced virtual sections of selected tomographic reconstructions, and we used a computer-generated mesh overlay to join these tracings into continuous surfaces ( Figure 4 ). abstract: Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens. All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles. However, the exact sites of RNA synthesis and crucial topological relationships between relevant membranes, vesicle interiors, surrounding lumens, and cytoplasm generally are poorly defined. We applied electron microscope tomography and complementary approaches to flock house virus (FHV)–infected Drosophila cells to provide the first 3-D analysis of such replication complexes. The sole FHV RNA replication factor, protein A, and FHV-specific 5-bromouridine 5'-triphosphate incorporation localized between inner and outer mitochondrial membranes inside ∼50-nm vesicles (spherules), which thus are FHV-induced compartments for viral RNA synthesis. All such FHV spherules were outer mitochondrial membrane invaginations with interiors connected to the cytoplasm by a necked channel of ∼10-nm diameter, which is sufficient for ribonucleotide import and product RNA export. Tomographic, biochemical, and other results imply that FHV spherules contain, on average, three RNA replication intermediates and an interior shell of ∼100 membrane-spanning, self-interacting protein As. The results identify spherules as the site of protein A and nascent RNA accumulation and define spherule topology, dimensions, and stoichiometry to reveal the nature and many details of the organization and function of the FHV RNA replication complex. The resulting insights appear relevant to many other positive-strand RNA viruses and support recently proposed structural and likely evolutionary parallels with retrovirus and double-stranded RNA virus virions. url: https://www.ncbi.nlm.nih.gov/pubmed/17696647/ doi: 10.1371/journal.pbio.0050220 id: cord-325820-tnyzmrm8 author: Kovacikova, Kristina title: 6′-β-Fluoro-Homoaristeromycin and 6′-Fluoro-Homoneplanocin A Are Potent Inhibitors of Chikungunya Virus Replication through Their Direct Effect on Viral Nonstructural Protein 1 date: 2020-03-24 words: 9807.0 sentences: 519.0 pages: flesch: 55.0 cache: ./cache/cord-325820-tnyzmrm8.txt txt: ./txt/cord-325820-tnyzmrm8.txt summary: To discover new antiviral agents, we performed a compound screen in cell culture-based infection models and identified two carbocyclic adenosine analogues, 6′-β-fluoro-homoaristeromycin (FHA) and 6′-fluoro-homoneplanocin A (FHNA), that displayed potent activity against CHIKV and Semliki Forest virus (SFV) with 50% effective concentrations in the nanomolar range at nontoxic concentrations. Enzymatic assays with purified wild-type (wt) SFV nsP1 suggested that an oxidized (3′-keto) form, rather than FHNA itself, directly inhibited the MTase activity, while a mutant protein with the K231R and K299E substitutions was insensitive to the compound. Our combined data suggest that FHA and FHNA inhibit CHIKV and SFV replication by directly targeting the MTase activity of nsP1, rather than through an indirect effect on host SAH hydrolase. Since we also identified FHNA analogues that efficiently inhibit host SAH hydrolase in vitro without being active against CHIKV in cell-based assays (31), we reconsidered the possibility of a direct effect of the compound on nsP1 activity. abstract: Alphaviruses are arthropod-borne, positive-stranded RNA viruses capable of causing severe disease with high morbidity. Chikungunya virus (CHIKV) is an alphavirus that causes a febrile illness which can progress into chronic arthralgia. The current lack of vaccines and specific treatment for CHIKV infection underscores the need to develop new therapeutic interventions. To discover new antiviral agents, we performed a compound screen in cell culture-based infection models and identified two carbocyclic adenosine analogues, 6′-β-fluoro-homoaristeromycin (FHA) and 6′-fluoro-homoneplanocin A (FHNA), that displayed potent activity against CHIKV and Semliki Forest virus (SFV) with 50% effective concentrations in the nanomolar range at nontoxic concentrations. The compounds, designed as inhibitors of the host enzyme S-adenosylhomocysteine (SAH) hydrolase, impeded postentry steps in CHIKV and SFV replication. Selection of FHNA-resistant mutants and reverse genetics studies demonstrated that the combination of mutations G230R and K299E in CHIKV nonstructural protein 1 (nsP1) conferred resistance to the compounds. Enzymatic assays with purified wild-type (wt) SFV nsP1 suggested that an oxidized (3′-keto) form, rather than FHNA itself, directly inhibited the MTase activity, while a mutant protein with the K231R and K299E substitutions was insensitive to the compound. Both wt nsP1 and the resistant mutant were equally sensitive to the inhibitory effect of SAH. Our combined data suggest that FHA and FHNA inhibit CHIKV and SFV replication by directly targeting the MTase activity of nsP1, rather than through an indirect effect on host SAH hydrolase. The high potency and selectivity of these novel alphavirus mRNA capping inhibitors warrant further preclinical investigation of these compounds. url: https://www.ncbi.nlm.nih.gov/pubmed/31964798/ doi: 10.1128/aac.02532-19 id: cord-000578-jhetyd9t author: Kovalev, Nikolay title: A Co-Opted DEAD-Box RNA Helicase Enhances Tombusvirus Plus-Strand Synthesis date: 2012-02-16 words: 8793.0 sentences: 509.0 pages: flesch: 59.0 cache: ./cache/cord-000578-jhetyd9t.txt txt: ./txt/cord-000578-jhetyd9t.txt summary: In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV). In this paper, the authors show that the Ded1p DEAD-box helicase, which is an essential translation factor in yeast, is recruited by Tomato bushy stunt virus (TBSV) into its replicase complex. Interestingly, addition of purified Ded1p to the tombusvirus replicase assay containing the short RNA/DNA duplex ( Figure 7A Non-overlapping functions of Ded1p and GAPDH in promoting initiation by the tombusvirus replicase GAPDH (Tdh2p in yeast) RNA binding protein is also a host factor stimulating (+)RNA synthesis by the tombusvirus replicase [25, 50] . To test if Ded1p and GAPDH could play a complementary role during (+)RNA synthesis, we added the purified recombinant Ded1p and Tdh2p to the in vitro tombusvirus replicase assay based on the purified preparation ( Figure 8A ). abstract: Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV). To separate the role of Ded1p in viral protein translation from its putative replication function, we utilized a cell-free TBSV replication assay and recombinant Ded1p. The in vitro data show that Ded1p plays a role in enhancing plus-strand synthesis by the viral replicase. We also find that Ded1p is a component of the tombusvirus replicase complex and Ded1p binds to the 3′-end of the viral minus-stranded RNA. The data obtained with wt and ATPase deficient Ded1p mutants support the model that Ded1p unwinds local structures at the 3′-end of the TBSV (−)RNA, rendering the RNA compatible for initiation of (+)-strand synthesis. Interestingly, we find that Ded1p and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is another host factor for TBSV, play non-overlapping functions to enhance (+)-strand synthesis. Altogether, the two host factors enhance TBSV replication synergistically by interacting with the viral (−)RNA and the replication proteins. In addition, we have developed an in vitro assay for Flock house virus (FHV), a small RNA virus of insects, that also demonstrated positive effect on FHV replicase activity by the added Ded1p helicase. Thus, two small RNA viruses, which do not code for their own helicases, seems to recruit a host RNA helicase to aid their replication in infected cells. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280988/ doi: 10.1371/journal.ppat.1002537 id: cord-001257-t21l6i3f author: Kovalev, Nikolay title: The Expanding Functions of Cellular Helicases: The Tombusvirus RNA Replication Enhancer Co-opts the Plant eIF4AIII-Like AtRH2 and the DDX5-Like AtRH5 DEAD-Box RNA Helicases to Promote Viral Asymmetric RNA Replication date: 2014-04-17 words: 10621.0 sentences: 624.0 pages: flesch: 58.0 cache: ./cache/cord-001257-t21l6i3f.txt txt: ./txt/cord-001257-t21l6i3f.txt summary: Novel pro-viral function of AtRH2, AtRH5 and the yeast Dbp3p and Fal1p is to bind to the viral replication enhancer present in the tombusvirus minus-strand RNA To test if AtRH2, AtRH5 and the yeast Dbp3p and Fal1p play a comparable role with the previously analyzed yeast Ded1p (human DDX3-like) and Dbp2p (human p68-like) and the ortologous AtRH20 DEAD-box helicases [30, 49] , first we performed in vitro RNA binding experiments with affinity-purified recombinant helicase proteins. The replication process leads to the production of abundant (+)RNA progeny, while the (2)RNA templates are likely sequestered in dsRNA forms within the VRCs. The presented in vitro data based on the solubilized/purified tombusvirus replicase and the CFE assay containing the membrane-bound VRC indicate that the eIF4AIIIlike RNA helicases can mainly stimulate TBSV (+)-strand synthesis, while their effects on (2)RNA synthesis have not been observed (not shown). abstract: Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. Several of the co-opted host factors bind to the viral RNA, which plays multiple roles, including mRNA function, as an assembly platform for the viral replicase (VRC), template for RNA synthesis, and encapsidation during infection. It is likely that remodeling of the viral RNAs and RNA-protein complexes during the switch from one step to another requires RNA helicases. In this paper, we have discovered a second group of cellular RNA helicases, including the eIF4AIII-like yeast Fal1p and the DDX5-like Dbp3p and the orthologous plant AtRH2 and AtRH5 DEAD box helicases, which are co-opted by tombusviruses. Unlike the previously characterized DDX3-like AtRH20/Ded1p helicases that bind to the 3′ terminal promoter region in the viral minus-strand (−)RNA, the other class of eIF4AIII-like RNA helicases bind to a different cis-acting element, namely the 5′ proximal RIII(−) replication enhancer (REN) element in the TBSV (−)RNA. We show that the binding of AtRH2 and AtRH5 helicases to the TBSV (−)RNA could unwind the dsRNA structure within the RIII(−) REN. This unique characteristic allows the eIF4AIII-like helicases to perform novel pro-viral functions involving the RIII(−) REN in stimulation of plus-strand (+)RNA synthesis. We also show that AtRH2 and AtRH5 helicases are components of the tombusvirus VRCs based on co-purification experiments. We propose that eIF4AIII-like helicases destabilize dsRNA replication intermediate within the RIII(−) REN that promotes bringing the 5′ and 3′ terminal (−)RNA sequences in close vicinity via long-range RNA-RNA base pairing. This newly formed RNA structure promoted by eIF4AIII helicase together with AtRH20 helicase might facilitate the recycling of the viral replicases for multiple rounds of (+)-strand synthesis, thus resulting in asymmetrical viral replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990711/ doi: 10.1371/journal.ppat.1004051 id: cord-008556-oetrdm8g author: Kozak, Marilyn title: Regulation of Protein Synthesis in Virus-Infected Animal Cells date: 2008-03-01 words: 23945.0 sentences: 1270.0 pages: flesch: 51.0 cache: ./cache/cord-008556-oetrdm8g.txt txt: ./txt/cord-008556-oetrdm8g.txt summary: One consequence of the scanning mechanism is that deleting the "ribosome binding site" (i.e., the normal initiator codon and flanking sequences) will not abolish translation; ribosomes will simply use the next AUG codon downstream, which, in some cases, has been shown to direct the synthesis of a biologically active, truncated protein (Downey et al., 1984; Halpern and Smiley, 1984; Katinka and Yaniv, 1982) . The best evidence for this is the ability of both EMC and SFV 26 S mRNA to be translated in EMC virus-infected cells, in which host translation is drastically inhibited by a mechanism that has not been difined, but that clearly does not involve cap binding protein (Mosenkis et al., 1985) . In wild-type adenovirus-infected cells, in which host protein synthesis is drastically reduced, both adenovirus and influenza virus mRNAs are translated efficiently. abstract: This chapter summarizes the structural features that govern the translation of viral mRNAs: where the synthesis of a protein starts and ends, how many proteins can be produced from one mRNA, and how efficiently. It focuses on the interplay between viral and cellular mRNAs and the translational machinery. That interplay, together with the intrinsic structure of viral mRNAs, determines the patterns of translation in infected cells. It also points out some possibilities for translational regulation that can only be glimpsed at present, but are likely to come into focus in the future. The mechanism of selecting the initiation site for protein synthesis appears to follow a single formula. The translational machinery displays a certain flexibility that is exploited more frequently by viral than by cellular mRNAs. Although some of the parameters that determine efficiency have been identified, how efficiently a given mRNA will be translated cannot be predicted by summing the known parameters. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131717/ doi: 10.1016/s0065-3527(08)60265-1 id: cord-267475-6f4h3cck author: Kozak, Marilyn title: Pushing the limits of the scanning mechanism for initiation of translation date: 2002-10-16 words: 24538.0 sentences: 1234.0 pages: flesch: 50.0 cache: ./cache/cord-267475-6f4h3cck.txt txt: ./txt/cord-267475-6f4h3cck.txt summary: This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG(START) codon. (Whether the second AUG codon resides in a strong or weak context is not relevant; the ribosome reads the mRNA linearly and thus the decision to stop or to bypass the first AUG is not influenced by whether there is a better initiation site downstream.) The large number of genes that employ leaky scanning precludes discussion of the biological significance of the proteins thereby produced, but it merits noting that, for many of the viruses in Table 3 , replication requires production of both listed proteins. abstract: Selection of the translational initiation site in most eukaryotic mRNAs appears to occur via a scanning mechanism which predicts that proximity to the 5′ end plays a dominant role in identifying the start codon. This ‘position effect’ is seen in cases where a mutation creates an AUG codon upstream from the normal start site and translation shifts to the upstream site. The position effect is evident also in cases where a silent internal AUG codon is activated upon being relocated closer to the 5′ end. Two mechanisms for escaping the first-AUG rule – reinitiation and context-dependent leaky scanning – enable downstream AUG codons to be accessed in some mRNAs. Although these mechanisms are not new, many new examples of their use have emerged. Via these escape pathways, the scanning mechanism operates even in extreme cases, such as a plant virus mRNA in which translation initiates from three start sites over a distance of 900 nt. This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG(START) codon. The opposite problem occurs in the case of hereditary thrombocythemia: translational efficiency is increased by mutations that remove or restructure a small upstream open reading frame in thrombopoietin mRNA, and the resulting overproduction of the cytokine causes the disease. This and other examples support the idea that 5′ leader sequences are sometimes structured deliberately in a way that constrains scanning in order to prevent harmful overproduction of potent regulatory proteins. The accumulated evidence reveals how the scanning mechanism dictates the pattern of transcription – forcing production of monocistronic mRNAs – and the pattern of translation of eukaryotic cellular and viral genes. url: https://api.elsevier.com/content/article/pii/S0378111902010569 doi: 10.1016/s0378-1119(02)01056-9 id: cord-337879-liqhbqxl author: Kriesel, John D. title: Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain date: 2012-03-08 words: 5060.0 sentences: 296.0 pages: flesch: 54.0 cache: ./cache/cord-337879-liqhbqxl.txt txt: ./txt/cord-337879-liqhbqxl.txt summary: Sequences from GB virus C (GBV-C), a flavivirus not previously isolated from brain, were enriched in one of the MS samples. This study shows the feasibility of deep sequencing for the detection of occult viral infections in the brains of deceased persons with MS. Multiple sclerosis (MS) is a chronic demyelinating disease of unknown cause, which affects the brain and spinal cord of about 400,000 individuals in the U.S. A number of viral infections of the CNS can lead to demyelination, including distemper (dogs), measles (SSPE, humans), and influenza (humans). To enhance the detection of non-human sequences, RNA samples that passed the quality control step above were subjected to rRNA removal using the RiboMinus kit (Invitrogen Inc., Carlsbad, CA). One subject who died with primary-progressive MS had .1000 36 bp sequences detected that mapped to GBV-C virus (hepatitis G), a human flavivirus not known to cause any persistent disease and never before detected in human brain. abstract: Multiple sclerosis (MS) is a demyelinating disease of unknown origin that affects the central nervous system of an estimated 400,000 Americans. GBV-C or hepatitis G is a flavivirus that is found in the serum of 1–2% of blood donors. It was originally associated with hepatitis, but is now believed to be a relatively non-pathogenic lymphotropic virus. Fifty frozen specimens from the brains of deceased persons affected by MS were obtained along with 15 normal control brain specimens. RNA was extracted and ribosomal RNAs were depleted before sequencing on the Illumina GAII. These 36 bp reads were compared with a non-redundant database derived from the 600,000+ viral sequences in GenBank organized into 4080 taxa. An individual read successfully aligned to the viral database was considered to be a “hit”. Normalized MS specimen hit rates for each viral taxon were compared to the distribution of hits in the normal controls. Seventeen MS and 11 control brain extracts were sequenced, yielding 4–10 million sequences (“reads”) each. Over-representation of sequence from at least one of 12 viral taxa was observed in 7 of the 17 MS samples. Sequences resembling other viruses previously implicated in the pathogenesis of MS were not significantly enriched in any of the diseased brain specimens. Sequences from GB virus C (GBV-C), a flavivirus not previously isolated from brain, were enriched in one of the MS samples. GBV-C in this brain specimen was confirmed by specific amplification in this single MS brain specimen, but not in the 30 other MS brain samples available. The entire 9.4 kb sequence of this GBV-C isolate is reported here. This study shows the feasibility of deep sequencing for the detection of occult viral infections in the brains of deceased persons with MS. The first isolation of GBV-C from human brain is reported here. url: https://doi.org/10.1371/journal.pone.0031886 doi: 10.1371/journal.pone.0031886 id: cord-325113-sou8xyld author: Kuiper, Johannes W. P. title: Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification date: 2020-11-02 words: 4973.0 sentences: 241.0 pages: flesch: 51.0 cache: ./cache/cord-325113-sou8xyld.txt txt: ./txt/cord-325113-sou8xyld.txt summary: The use of unprocessed swap samples is enabled by employing a heat-stable RNAand DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. A RNA-and DNA-reading heat-stable polymerase reverse transcribes and amplifies viral RNA Evidence of an acute SARS-CoV-2 infection depends on the detection of viral RNA species in patient samples, which necessitates reverse transcription of RNA followed by PCR amplification of the resulting DNA. To evaluate the potential of the high-temperature RT-PCR protocol using Volvano3G for the detection of viral RNAs in patient material, we assessed the presence of SARS-CoV-2 in RNA isolated from a small cohort of COVID-19 suspected cases. Interestingly, for most positive samples detected by the high-temperature RT-PCR with Volcano3G, the cq-values were lower compared to the standard RT-PCR (Fig 3C and 3D) , indicating that the detection of SARS-CoV-2 from unprocessed patient material is not limited by the sensitivity of this direct approach. abstract: SARS-CoV-2 is spreading globally with unprecedented consequences for modern societies. The early detection of infected individuals is a pre-requisite to contain the virus. Currently, purification of RNA from patient samples followed by RT-PCR is the gold standard to assess the presence of this single-strand RNA virus. However, these procedures are time consuming, require continuous supply of specialized reagents, and are prohibitively expensive in resource-poor settings. Here, we report an improved nucleic-acid-based approach to detect SARS-CoV-2 with the ability to detect as little as five viral genome equivalents. The approach delivers results without the need to purify RNA, reduces handling steps, minimizes costs, and allows evaluation by non-specialized equipment. The use of unprocessed swap samples is enabled by employing a heat-stable RNA- and DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. As results are obtained within 2 hours and can be read-out by a hand-held LED-screen, this novel protocol will be of particular importance for large-scale virus surveillance in economically constrained settings. url: https://doi.org/10.1371/journal.pone.0241740 doi: 10.1371/journal.pone.0241740 id: cord-327855-txryqil7 author: Kulka, M. title: The cytopathic 18f strain of Hepatitis A virus induces RNA degradation in FrhK4 cells date: 2003 words: 8706.0 sentences: 394.0 pages: flesch: 50.0 cache: ./cache/cord-327855-txryqil7.txt txt: ./txt/cord-327855-txryqil7.txt summary: Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. In this study, we report that infection of FrhK4 cells with the HAV cp strain HM175/18f results in the degradation of ribosomal RNA (rRNA) and the reduction of several cellular mRNAs including β-actin and GAPDH. Degradation of rRNA is a feature of virus infection in interferon (IFN) treated cells and is believed to be due to the availability of double stranded RNA (dsRNA) during replication or transcription of the viral genome, resulting in the activation of the RNase L pathway [58, 59] . While the role of a viral protein in the activation of 2-5A/RNase L pathway in 18f or CBV1 infected FrhK4 cells cannot be ruled out, previous reports with EMC virus and the studies involving dsRNA clearly suggests a similar mechanism of rRNA degradation reported here. abstract: The mechanism responsible for the induction of apoptosis by the rapidly replicating HM175/18f strain of Hepatitis A virus (HAV) was investigated. Full length HAV RNA and viral capsid protein VP1 were detected in 18f infected cells at earlier times post-infection than in HM175/clone 1 infected cells. Analysis of total cellular RNA from HM175/18f infected FrhK4 cells by denaturing agarose gel electrophoresis and Northern blot hybridization revealed extensive degradation of both the 28S and 18S ribosomal RNA (rRNA) molecules. Similar degradation was observed when these cells were infected with Human coxsackievirus B1, a fast replicating enterovirus. In contrast, the parental strain of 18f, HM175/clone 1 did not induce RNA degradation. Inhibition of RNA degradation correlated with inhibition of virus replication. The pattern of rRNA degradation resembled degradation of rRNAs by RNase L, an enzyme activated in interferon-treated cells following infection with certain viruses. Ribosomal RNA degradation was accompanied by the reduction in the levels of several cellular RNAs including those for β-actin and glyceraldehyde-3-phosphate dehydrogenase, while the levels of c-myc and c-jun were higher. Interferon mRNAs could not be detected in either infected or mock-infected control cells, and STAT1, a key regulator of interferon action was not phosphorylated following virus infection. These results reveal a heretofore-undescribed pathway that involves the regulation of RNA degradation and apoptosis following HAV/18f replication in FrhK4 cells. url: https://www.ncbi.nlm.nih.gov/pubmed/12827461/ doi: 10.1007/s00705-003-0110-0 id: cord-283880-lrrkuist author: Kumar, Arvind title: Evolution of selective-sequencing approaches for virus discovery and virome analysis date: 2017-07-15 words: 5934.0 sentences: 286.0 pages: flesch: 38.0 cache: ./cache/cord-283880-lrrkuist.txt txt: ./txt/cord-283880-lrrkuist.txt summary: Use of sequence dependent (i.e; generic PCR assays and microarray) and sequence independent (i.e; single primer amplification (SISPA) and random priming) approaches for nucleic acid amplification combined with Sanger sequencing or HTS allowed the rapid identification of new viruses after 1980 (Bishop-Lilly et al., 2010; Chang et al., 1994; Day et al., 2010; Grard et al., 2012; Kapoor et al., 2015; Ladner et al., 2016; Linnen et al., 1996; Matsui et al., 1991; Mokili et al., 2012; Muerhoff et al., 1997; Nichol et al., 1993; Qin et al., 2014; Quan et al., 2010; Simons et al., 1995b) (Fig. 1) . For the virome analysis of clinical samples with an abundance of host cells, like blood or tissues, pre-extraction based enrichment is not appropriate as the virus genome itself can be present in its non-capsidated or transcribed form. In positive selection methods, samples are enriched for viral nucleic acids directly using probes targeting the viruses like in PCR assays, microarray or virus capture (in solution based hybridization) approaches. abstract: Abstract Recent advances in sequencing technologies have transformed the field of virus discovery and virome analysis. Once mostly confined to the traditional Sanger sequencing based individual virus discovery, is now entirely replaced by high throughput sequencing (HTS) based virus metagenomics that can be used to characterize the nature and composition of entire viromes. To better harness the potential of HTS for the study of viromes, sample preparation methodologies use different approaches to exclude amplification of non-viral components that can overshadow low-titer viruses. These virus-sequence enrichment approaches mostly focus on the sample preparation methods, like enzymatic digestion of non-viral nucleic acids and size exclusion of non-viral constituents by column filtration, ultrafiltration or density gradient centrifugation. However, recently a new approach of virus-sequence enrichment called virome-capture sequencing, focused on the amplification or HTS library preparation stage, was developed to increase the ability of virome characterization. This new approach has the potential to further transform the field of virus discovery and virome analysis, but its technical complexity and sequence-dependence warrants further improvements. In this review we discuss the different methods, their applications and evolution, for selective sequencing based virome analysis and also propose refinements needed to harness the full potential of HTS for virome analysis. url: https://www.sciencedirect.com/science/article/pii/S0168170216305986 doi: 10.1016/j.virusres.2017.06.005 id: cord-317037-1qydcc5e author: Kumar, Asit title: Extracellular Vesicles in Viral Replication and Pathogenesis and Their Potential Role in Therapeutic Intervention date: 2020-08-13 words: 9406.0 sentences: 511.0 pages: flesch: 37.0 cache: ./cache/cord-317037-1qydcc5e.txt txt: ./txt/cord-317037-1qydcc5e.txt summary: Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. HIV-infected U1 macrophages upon Cigarette smoke condensate (CSC) treatment enhanced the packaging of IL-6 in EVs; IL-8 served as a biomarker for HIV patients with altered immune function due to alcohol and tobacco abuse [20, 116, 117] Host protein APOBEC3G Inhibit replication of viral infectivity factor (vif) -deficient and wild-type HIV-1 in recipient cells [118] miRNA vmiR-88 and vmiR-99 Hepatocytes secreted exosomes participate in virus replication [142] Viral miRNAs HBV-miR-3 Represses viral protein production and HBV replication [143] HTLV-1 Viral proteins gp61, Tax, and HBZ Increase cell-to-cell contact and promote a potential increase in viral spread [144] Zika Viral genetic material and protein RNA and ZIKV-E EVs derived from Infected C6/36 cells promote infection and activation of monocytes with enhanced TNF-α mRNA expression. abstract: Extracellular vesicles (EVs) have shown their potential as a carrier of molecular information, and they have been involved in physiological functions and diseases caused by viral infections. Virus-infected cells secrete various lipid-bound vesicles, including endosome pathway-derived exosomes and microvesicles/microparticles that are released from the plasma membrane. They are released via a direct outward budding and fission of plasma membrane blebs into the extracellular space to either facilitate virus propagation or regulate the immune responses. Moreover, EVs generated by virus-infected cells can incorporate virulence factors including viral protein and viral genetic material, and thus can resemble noninfectious viruses. Interactions of EVs with recipient cells have been shown to activate signaling pathways that may contribute to a sustained cellular response towards viral infections. EVs, by utilizing a complex set of cargos, can play a regulatory role in viral infection, both by facilitating and suppressing the infection. EV-based antiviral and antiretroviral drug delivery approaches provide an opportunity for targeted drug delivery. In this review, we summarize the literature on EVs, their associated involvement in transmission in viral infections, and potential therapeutic implications. url: https://doi.org/10.3390/v12080887 doi: 10.3390/v12080887 id: cord-329710-vqorb6j7 author: Kumar, Krishna title: Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment date: 2020-05-27 words: 2477.0 sentences: 147.0 pages: flesch: 49.0 cache: ./cache/cord-329710-vqorb6j7.txt txt: ./txt/cord-329710-vqorb6j7.txt summary: We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. Many recent scientific reviews and essays have outlined vaccine efforts, as well as viral and host targets that are the focus of current campaigns aimed at redirecting clinically used compounds for COVID-19. The FDA-approved COVID-19 drug, remdesivir, is a nucleotide analog originally developed to treat Ebola infections (caused by another single-stranded RNA virus) and recently shown to inhibit the SARS-CoV-2 RdRP. HIV protease inhibitors lopinavir and ritonavir, included in the SOLIDARITY trial despite mixed reviews in the clinic, have been predicted to bind SARS-CoV-1 and CoV-2 3CL pro (96% sequence identity) based on computational studies. Using a recently solved crystal structure of the HR1 and HR2 domains of the SARS-CoV-2 S protein, lipidated peptide fusion inhibitors have been designed that inhibit pseudovirus infection of cells with IC 50 values in the single-digit nanomolar range. abstract: [Image: see text] Discovery and development of COVID-19 prophylactics and treatments remains a global imperative. This perspective provides an overview of important molecular pathways involved in the viral life cycle of SARS-CoV-2, the infectious agent of COVID-19. We highlight past and recent findings in essential coronavirus proteins, including RNA polymerase machinery, proteases, and fusion proteins, that offer opportunities for the design of novel inhibitors of SARS-CoV-2 infection. By discussing the current inventory of viral inhibitors, we identify molecular scaffolds that may be improved by medicinal chemistry efforts for effective therapeutics to treat current and future coronavirus-caused diseases. url: https://doi.org/10.1021/acsmedchemlett.0c00254 doi: 10.1021/acsmedchemlett.0c00254 id: cord-275565-xerr4vki author: Kumar, Manish title: Decay of SARS-CoV-2 RNA along the wastewater treatment outfitted with Upflow Anaerobic Sludge Blanket (UASB) system evaluated through two sample concentration techniques date: 2020-09-15 words: 3456.0 sentences: 230.0 pages: flesch: 58.0 cache: ./cache/cord-275565-xerr4vki.txt txt: ./txt/cord-275565-xerr4vki.txt summary: For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and filtration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. Thus, there still remains questions pertaining to: i) capability of conventional WWTPs to reduce the abundance of SARS-CoV-2 RNA, ii) better understanding of the protocol, virus J o u r n a l P r e -p r o o f Journal Pre-proof precipitation through PEG and filtration which one is better methods for concentrating the samples before RNA isolation. Appraising the genetic loading reduction through Upflow Anaerobic Sludge Blanket (UASB) systems, and iii) Comparing the performances between PEG and filtration as virus concentration methods in terms of SARS-CoV-2 RNA sensitivity and inhibition removal. abstract: For the first time, we present, i) an account of decay in the genetic material loading of SARS-CoV-2 during Upflow Anaerobic Sludge Blanket (UASB) treatment of wastewater, and ii) comparative evaluation of polyethylene glycol (PEG), and filtration as virus concentration methods from wastewater for the quantification of SARS-CoV-2 genes. The objectives were achieved through tracking of SARS-CoV-2 genetic loadings i.e. ORF1ab, N and S protein genes on 8th and 27th May 2020 along the wastewater treatment plant (106 million liters per day) equipped with UASB system in Ahmedabad, India. PEG method performed better in removing materials inhibiting RT-qPCR for SARS-CoV-2 gene detection from the samples, as evident from constant and lower CT values of control (MS2). Using the PEG method, we found a reduction >1.3 log10 in SARS-CoV-2 RNA abundance during UASB treatment, and the RNA was not detected at all in the final effluent. The study implies that i) conventional wastewater treatment systems is effective in SARS-CoV-2 RNA removal, and ii) UASB system significantly reduces SARS-CoV-2 genetic loadings. Finally, PEG method is recommended for better sensitivity and inhibition removal during SARS-CoV-2 RNA quantification in wastewater. url: https://api.elsevier.com/content/article/pii/S0048969720358587 doi: 10.1016/j.scitotenv.2020.142329 id: cord-292045-pnid9dmq author: Kumar, Manish title: First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2 date: 2020-07-28 words: 3037.0 sentences: 183.0 pages: flesch: 58.0 cache: ./cache/cord-292045-pnid9dmq.txt txt: ./txt/cord-292045-pnid9dmq.txt summary: While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic. Consistency between abundance of SARS-CoV-2 genetic materials and number of confirmed cases was observed in the previous reports in Australia, France, Italy, Spain and Japan Further, referring to the limitations of the present study owing to lockdown scenario, we recommend that although based MPC analysis, the efficiency of RNA extraction and RT-PCR is considered high for all the wastewater samples collected for this study, the efficiency of PEG method could have been better established. The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2 abstract: Abstract We made the first ever successful effort in India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of wastewater-based epidemiology (WBE) surveillance in India. Sampling was carried out on 8 and 27 May 2020 at the Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat that receives effluent from Civil Hospital treating COVID-19 patients. All three, i.e. ORF1ab, N and S genes of SARS-CoV-2, were found in the influent with no genes detected in effluent collected on 8 and 27 May 2020. Increase in SARS-CoV-2 genetic loading in the wastewater between 8 and 27 May 2020 samples concurred with corresponding increase in the number of active COVID-19 patients in the city. The number of gene copies was comparable to that reported in untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. However, temporal changes in SARS-CoV-2 RNA concentrations need to be substantiated further from the perspectives of daily and short-term changes of SARS-CoV-2 in wastewater through long-term monitoring. The study results SARS-CoV-2 will assist concerned authorities and policymakers to formulate and/or upgrade COVID-19 surveillance to have a more explicit picture of the pandemic curve. While infectivity of SARS-CoV-2 through the excreted viral genetic material in the aquatic environment is still being debated, the presence and detection of genes in wastewater systems makes a strong case for the environmental surveillance of the COVID-19 pandemic. url: https://doi.org/10.1016/j.scitotenv.2020.141326 doi: 10.1016/j.scitotenv.2020.141326 id: cord-320935-3n157yl4 author: Kumar, Manish title: Making Waves Perspectives of Modelling and Monitoring of SARS-CoV-2 in Aquatic Environment for COVID-19 Pandemic date: 2020-09-12 words: 6613.0 sentences: 346.0 pages: flesch: 44.0 cache: ./cache/cord-320935-3n157yl4.txt txt: ./txt/cord-320935-3n157yl4.txt summary: This paper aims to collate information on recent developments on WBE in monitoring the trend of community-scale SARS-CoV-2 prevalence as well as models to predict virus spread and transmission among populations. While several studies have identified the presence of SARS-CoV-2 in the faecal matter of corona-infected patients [35, 36] , there is a growing concern on the transmission of the virus through water treatment plants (WTPs) and WWTPs. Several studies also detected the genetic material of the virus in raw wastewater across the globe [22, 26, 27] . These studies provided enough excellent reasons for modelling the spread of 2019-nCoV with the external environmental conditions, assuming that the cases of infection will decrease through secondary infection routes due to the inactivation of the virus on different surfaces; however, the possibility of transmission via direct contact remains unchanged. abstract: Prevalence of SARS-CoV-2 in the aquatic environment pertaining to the COVID-19 pandemic has been a global concern. Though SARS-CoV-2 is known as a respiratory virus, its detection in faecal matter and wastewater demonstrates its enteric involvement resulting in vulnerable aquatic environment. Here, we provide the latest updates on wastewater-based epidemiology, which is gaining interest in the current situation as a unique tool of surveillance and monitoring of the disease. Transport pathways with its migration through wastewater to surface and subsurface waters, probability of infectivity and ways of inactivation of SARS-CoV-2 are discussed in detail. Epidemiological models, especially compartmental projections, have been explained with an emphasis on its limitation and the assumptions on which the future predictions of disease propagation are based. Besides, this review covers various predictive models to track and project disease spread in the future and gives an insight into the probability of a future outbreak of the disease. url: https://www.ncbi.nlm.nih.gov/pubmed/32953402/ doi: 10.1007/s40726-020-00161-5 id: cord-000556-uu1oz2ei author: Kumar, Ranjit title: RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336” date: 2012-01-20 words: 4407.0 sentences: 235.0 pages: flesch: 46.0 cache: ./cache/cord-000556-uu1oz2ei.txt txt: ./txt/cord-000556-uu1oz2ei.txt summary: Whole genome transcriptome analysis is a complementary method to identify "novel" genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. Therefore, genome structural annotation or the identification and demarcation of boundaries of functional elements in a genome (e.g., genes, non-coding RNAs, proteins, and regulatory elements) are critical elements in infectious disease systems biology. Whole genome transcriptome studies (such as whole genome tiling arrays [13, 14, 15] and high throughput sequencing [16, 17] ) are complementary experimental approaches for bacterial genome annotation and can identify ''''novel'''' genes, gene boundaries, regulatory regions, intergenic regions, and operon structures. We compared the RNA-Seq based transcriptome map with the available genome annotation to identify expressed, novel, and intergenic regions in the genome. The single nucleotide resolution map helped uncover the structure and complexity of this pathogen''s transcriptome and led to the identification of novel, small RNAs and protein coding genes as well as gene co-expression. abstract: Genome structural annotation, i.e., identification and demarcation of the boundaries for all the functional elements in a genome (e.g., genes, non-coding RNAs, proteins and regulatory elements), is a prerequisite for systems level analysis. Current genome annotation programs do not identify all of the functional elements of the genome, especially small non-coding RNAs (sRNAs). Whole genome transcriptome analysis is a complementary method to identify “novel” genes, small RNAs, regulatory regions, and operon structures, thus improving the structural annotation in bacteria. In particular, the identification of non-coding RNAs has revealed their widespread occurrence and functional importance in gene regulation, stress and virulence. However, very little is known about non-coding transcripts in Histophilus somni, one of the causative agents of Bovine Respiratory Disease (BRD) as well as bovine infertility, abortion, septicemia, arthritis, myocarditis, and thrombotic meningoencephalitis. In this study, we report a single nucleotide resolution transcriptome map of H. somni strain 2336 using RNA-Seq method. The RNA-Seq based transcriptome map identified 94 sRNAs in the H. somni genome of which 82 sRNAs were never predicted or reported in earlier studies. We also identified 38 novel potential protein coding open reading frames that were absent in the current genome annotation. The transcriptome map allowed the identification of 278 operon (total 730 genes) structures in the genome. When compared with the genome sequence of a non-virulent strain 129Pt, a disproportionate number of sRNAs (∼30%) were located in genomic region unique to strain 2336 (∼18% of the total genome). This observation suggests that a number of the newly identified sRNAs in strain 2336 may be involved in strain-specific adaptations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262788/ doi: 10.1371/journal.pone.0029435 id: cord-278099-ypov9ha3 author: Kumar, Surender title: Molecular characterization of a novel cryptic virus infecting pigeonpea plants date: 2017-08-03 words: 11403.0 sentences: 622.0 pages: flesch: 55.0 cache: ./cache/cord-278099-ypov9ha3.txt txt: ./txt/cord-278099-ypov9ha3.txt summary: The four dsRNAs eluted from the agarose gel were purified and have been used as templates for RT-PCR amplification employed in SISPA to generate fulllength cDNAs. It is of interest to examine if ArCV-1 RNA dependent RNA polymerase (RdRp) structurally resembles the known RdRp of the dsRNA bacteriophage Փ-6, reovirus, or with other viruses like calciviruses and picornaviruses [12] [13] [14] [15] [16] . We report here the results of elaborated computer-assisted analysis of ArCV-1 replicase which revealed the presence of conserved sequence motifs (A to G) present in the fingers and palm subdomains of the polymerase that are shared in most of the RdRps. Interestingly, ArCV-1 replicase has more structural resemblances with several members of ssRNA (+) mono-partite Picornaviruses (viral replication by primer-dependent initiation), than the de novo dsRNA bacteriophage Փ-6 and reovirus polymerases. Possible functions of the residues of the A to G motifs described for identical RdRps was conserved with respect to the ArCV-1 3Dpol structure and was discussed in structural analysis of ArCVTable 1 ) and the 3'' terminus contained the sequence "GCA CCCATATTC". abstract: A new member of the genus Deltapartitivirus was identified containing three dsRNAs with an estimated size of 1.71, 1.49 and 1.43 kb. The dsRNAs were extracted from symptomless pigeonpea [Cajanus cajan (L.) Millspaugh] plants cv. Erra Kandulu. This new virus with 4.64 kb genome was tentatively named Arhar cryptic virus-1 (ArCV-1). The genomic RNAs were amplified and characterized by sequence independent single primer amplification. The dsRNAs shared a highly conserved 16 nt 5’ non-coding region (5’-GATAATGATCCAAGGA-3’). The largest dsRNA (dsRNA-1) was identified as the viral RNA dependent RNA polymerase (replicase), predicted to encode a putative 55.34 kDa protein (P1). The two other smaller dsRNAs (dsRNA-2 and dsRNA-3) predicted to encode for putative capsid proteins of 38.50kDa (P2) and 38.51kDa (P3), respectively. Phylogenetic analysis indicated that ArCV-1 formed a clade together with Fragaria chiloensis cryptic virus, Rosa multiflora cryptic virus and Rose cryptic virus-1, indicating that ArCV-1 could be a new member of the genus Deltapartitivirus. ArCV-1 3D(pol) structure revealed several interesting features. The 3D(pol) in its full-length shares structural similarities with members of the family Caliciviridaeand family Picornaviridae. In addition, fourth dsRNA molecule (dsRNA-2A), not related to ArCV-1 genome, was found in the same plant tissue. The dsRNA-2A (1.6 kb) encodes a protein (P4), with a predicted size of 44.5 kDa. P4 shares similarity with coat protein genes of several cryptic viruses, in particular the bipartite cryptic viruses including Raphanus sativus cryptic virus-3. This is the first report of occurrence of a cryptic virus in pigeonpea plants. url: https://doi.org/10.1371/journal.pone.0181829 doi: 10.1371/journal.pone.0181829 id: cord-277841-7sp8ftbc author: Kumari, Pratibha title: Potential diagnostics and therapeutic approaches in COVID-19 date: 2020-08-12 words: 4873.0 sentences: 279.0 pages: flesch: 45.0 cache: ./cache/cord-277841-7sp8ftbc.txt txt: ./txt/cord-277841-7sp8ftbc.txt summary: Molecular diagnostic tests target the detection of any of the following markers such as the specific region of the viral genome, certain enzyme, RNA-dependent RNA polymerase, the structural proteins such as surface spike glycoprotein, nucleocapsid protein, envelope protein, or membrane protein of SARS-CoV-2. COVID-19 is a contagious disease, caused by a novel severe acute respiratory syndrome Coronavirus (SARS-CoV-2). In this article, we evaluated literature for reports informing various diagnostic methods, potential antiviral chemical therapeutics, and effective treatment strategies towards clinical management of COVID-19 patients. Molecular diagnostic methods target to detect either specific regions of the viral genome or RNA-dependent RNA polymerase (RdRP) and/or structural proteins of SARS-CoV-2 (Table 1) . Like most immunological diagnostic protocols, Enzyme-Linked Immunosorbent Assay (ELISA) for COVID-19 detection uses IgM and IgG antibody against nucleocapsid (N) and receptor binding domain spike proteins (S) of SARS-CoV-2. Table 2: Primers and probes for targeting SARS-Cov-2 genes in an RT-PCR test for COVID-19 diagnosis. abstract: Abstract The most important aspect of controlling COVID-19 is its timely diagnosis. Molecular diagnostic tests target the detection of any of the following markers such as the specific region of the viral genome, certain enzyme, RNA-dependent RNA polymerase, the structural proteins such as surface spike glycoprotein, nucleocapsid protein, envelope protein, or membrane protein of SARS-CoV-2. This review highlights the underlying mechanisms, advancements, and clinical limitations for each of the diagnostic techniques authorized by the Food and Drug Administration (USA). Significance of diagnosis triaging, information on specimen collection, safety considerations while handling, transport, and storage of samples have been highlighted to make medical and research community more informed so that better clinical strategies are developed. We have discussed here the clinical manifestations and hospital outcomes along with the underlying mechanisms for several drugs administered to COVID-19 prophylaxis. In addition to favourable clinical outcomes, the challenges, and the future directions of management of COVOD-19 are highlighted. Having a comprehensive knowledge of the diagnostic approaches of SARS-CoV-2, and its pathogenesis will be of great value in designing a long-term strategy to tackle COVID-19. url: https://www.sciencedirect.com/science/article/pii/S0009898120303958?v=s5 doi: 10.1016/j.cca.2020.08.013 id: cord-255619-5h3l6nh6 author: Kuo, Shu-Ming title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity date: 2013-03-23 words: 6329.0 sentences: 326.0 pages: flesch: 55.0 cache: ./cache/cord-255619-5h3l6nh6.txt txt: ./txt/cord-255619-5h3l6nh6.txt summary: title: Evolution of infectious bronchitis virus in Taiwan: Positively selected sites in the nucleocapsid protein and their effects on RNA-binding activity This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNAbinding capacity of the N protein. In this study, we showed that substituting either of the positively selected residues with the amino acid present in most CH IBVs dramatically reduced the binding capacity of the N protein for synthetic TRS repeats (Fig. 4) . abstract: RNA recombination has been shown to underlie the sporadic emergence of new variants of coronavirus, including the infectious bronchitis virus (IBV), a highly contagious avian pathogen. We have demonstrated that RNA recombination can give rise to a new viral population, supported by the finding that most isolated Taiwanese (TW) IBVs, similar to Chinese (CH) IBVs, exhibit a genetic rearrangement with the American (US) IBV at the 5’ end of the nucleocapsid (N) gene. Here, we further show that positive selection has occurred at two sites within the putative crossover region of the N-terminal domain (NTD) of the TW IBV N protein. Based on the crystal structure of the NTD, the stereographic positions of both predicted selected sites do not fall close to the RNA-binding groove. Surprisingly, converting either of the two residues to the amino acid present in most CH IBVs resulted in significantly reduced affinity of the N protein for the synthetic RNA repeats of the viral transcriptional regulatory sequence. These results suggest that modulating the amino acid residue at either selected site may alter the conformation of the N protein and affect the viral RNA–N interaction. This study illustrates that the N protein of the current TW IBV variant has been shaped by both RNA recombination and positive selection and that the latter may promote viral survival and fitness, potentially by increasing the RNA-binding capacity of the N protein. url: https://www.sciencedirect.com/science/article/pii/S0378113512005597 doi: 10.1016/j.vetmic.2012.10.020 id: cord-002720-lrkscs71 author: Kurosaki, Yohei title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification date: 2017-10-18 words: 4950.0 sentences: 251.0 pages: flesch: 55.0 cache: ./cache/cord-002720-lrkscs71.txt txt: ./txt/cord-002720-lrkscs71.txt summary: title: Development and evaluation of a rapid molecular diagnostic test for Zika virus infection by reverse transcription loop-mediated isothermal amplification The assay detected viral RNA at 14.5 TCID(50)/mL in virus-spiked serum or urine samples within 15 min, although it was slightly less sensitive than reference real time RT-PCR assay. We then evaluated the utility of this assay as a molecular diagnostic test using 90 plasma or serum samples and 99 urine samples collected from 120 suspected cases of arbovirus infection in the states of Paraíba and Pernambuco, Brazil in 2016. Therefore, it is difficult to detect ZIKV in blood samples from patients after the acute phase of infection, even with sensitive molecular diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) 14, 18, 19 . These results suggested that the RT-LAMP assay could be used as a rapid, sensitive diagnostic test for ZIKV, the Tp value (i.e., less than 15 min) can be used as an indicator of the number of RNA copies in each reaction. abstract: The recent outbreak of Zika virus (ZIKV) disease caused an enormous number of infections in Central and South America, and the unusual increase in the number of infants born with microcephaly associated with ZIKV infection aroused global concern. Here, we developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay using a portable device for the detection of ZIKV. The assay specifically detected ZIKV strains of both Asian and African genotypes without cross-reactivity with other arboviruses, including Dengue and Chikungunya viruses. The assay detected viral RNA at 14.5 TCID(50)/mL in virus-spiked serum or urine samples within 15 min, although it was slightly less sensitive than reference real time RT-PCR assay. We then evaluated the utility of this assay as a molecular diagnostic test using 90 plasma or serum samples and 99 urine samples collected from 120 suspected cases of arbovirus infection in the states of Paraíba and Pernambuco, Brazil in 2016. The results of this assay were consistent with those of the reference RT-PCR test. This portable RT-LAMP assay was highly specific for ZIKV, and enable rapid diagnosis of the virus infection. Our results provide new insights into ZIKV molecular diagnostics and may improve preparedness for future outbreaks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647432/ doi: 10.1038/s41598-017-13836-9 id: cord-348815-lthz75oc author: Kurreck, Jens title: RNA Interference: From Basic Research to Therapeutic Applications date: 2009-01-19 words: 14116.0 sentences: 846.0 pages: flesch: 56.0 cache: ./cache/cord-348815-lthz75oc.txt txt: ./txt/cord-348815-lthz75oc.txt summary: Successful applications in animal models have already led to the initiation of RNAi‐based clinical trials as a new therapeutic option.[Image: see text] Only ten years ago Andrew Fire and Craig Mello were able to show that double‐stranded RNA molecules could inhibit the expression of homologous genes in eukaryotes. This Review provides an overview of the molecular processes involved, with a particular focus on the posttranscriptional inhibition of gene expression in mammalian cells, the possible applications in research, and the results of the first clinical studies. Antisense and RNAi strategies have many things in common, such as the necessity to identify suitable binding sequences on the target RNA, the stabilization of the oligonucleotide by chemical modification, or the transport of the negatively charged polymer across the cell membrane. [19] There are, however, important differences between the two technologies: Antisense oligonucleotides are single-stranded (modified) DNA molecules, which primarily induce the cleavage of the target RNA in the cell nucleus by activation of RNase H. abstract: An efficient mechanism for the sequence‐specific inhibition of gene expression is RNA interference. In this process, double‐stranded RNA molecules induce cleavage of a selected target RNA (see picture). This technique has in recent years developed into a standard method of molecular biology. Successful applications in animal models have already led to the initiation of RNAi‐based clinical trials as a new therapeutic option.[Image: see text] Only ten years ago Andrew Fire and Craig Mello were able to show that double‐stranded RNA molecules could inhibit the expression of homologous genes in eukaryotes. This process, termed RNA interference, has developed into a standard method of molecular biology. This Review provides an overview of the molecular processes involved, with a particular focus on the posttranscriptional inhibition of gene expression in mammalian cells, the possible applications in research, and the results of the first clinical studies. url: https://www.ncbi.nlm.nih.gov/pubmed/19153977/ doi: 10.1002/anie.200802092 id: cord-353290-1wi1dhv6 author: Kustin, Talia title: Biased mutation and selection in RNA viruses date: 2020-09-28 words: 7611.0 sentences: 402.0 pages: flesch: 52.0 cache: ./cache/cord-353290-1wi1dhv6.txt txt: ./txt/cord-353290-1wi1dhv6.txt summary: We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses. Nevertheless, RNA viruses do share several common features that drive their evolution: (a) their ultimate dependence on the cell, (b) their high mutation rates, (c) strong purifying selection derived from constraints operating on a small and densely coding genome, and (d) sporadic but powerful positive selection driven by an evolutionary arms race with the host they infect. Two non-mutually exclusive hypotheses may be put forth to explain the consistent pattern of A-richness that we observe: there is selection for more A in viral sequences, and/or there is a mutational bias that leads to more A in genomes of viruses. abstract: RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and the recent COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based dataset spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases towards U rather than A in genomes of all viruses. In +ssRNA viruses we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In -ssRNA viruses the genomic mutational bias towards U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino-acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses. url: https://doi.org/10.1093/molbev/msaa247 doi: 10.1093/molbev/msaa247 id: cord-298078-uqrwq5qk author: Kwak, Hoyun title: Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus date: 2011-08-30 words: 5346.0 sentences: 318.0 pages: flesch: 56.0 cache: ./cache/cord-298078-uqrwq5qk.txt txt: ./txt/cord-298078-uqrwq5qk.txt summary: The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs. Ribosomal frameshifing is a recoding process of translation where a specific messenger RNA (mRNA)-mediated signal directs a ribosome to shift its reading frame and to continue in the new frame. To search for cellular proteins that directly interacted with IBV pseudoknot RNA, a RNA pull down assay was performed in the presence of cell extracts (Figure 2A ). Through the RNA-immunoprecipitation assay, we showed that ANXA2 specifically interacted with wild-type IBV pseudoknot RNA but not with mutant IBV RNA in LNCaP and HEK293T cells ( Figure 3C and 3D). To test how ANXA2 regulates the frameshifting efficiency of IBV pseudoknot RNA, we first overexpressed ANXA2 protein in the presence of the reporters and measured the luciferase activities. abstract: Annexin A2 (ANXA2) is a protein implicated in diverse cellular functions, including exocytosis, DNA synthesis and cell proliferation. It was recently proposed to be involved in RNA metabolism because it was shown to associate with some cellular mRNA. Here, we identified ANXA2 as a RNA binding protein (RBP) that binds IBV (Infectious Bronchitis Virus) pseudoknot RNA. We first confirmed the binding of ANXA2 to IBV pseudoknot RNA by ultraviolet crosslinking and showed its binding to RNA pseudoknot with ANXA2 protein in vitro and in the cells. Since the RNA pseudoknot located in the frameshifting region of IBV was used as bait for cellular RBPs, we tested whether ANXA2 could regulate the frameshfting of IBV pseudoknot RNA by dual luciferase assay. Overexpression of ANXA2 significantly reduced the frameshifting efficiency from IBV pseudoknot RNA and knockdown of the protein strikingly increased the frameshifting efficiency. The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs. url: https://doi.org/10.1371/journal.pone.0024067 doi: 10.1371/journal.pone.0024067 id: cord-269294-vx7xr80t author: Kwong, Ann D. title: Viral and cellular RNA helicases as antiviral targets date: 2005-09-23 words: 6378.0 sentences: 398.0 pages: flesch: 55.0 cache: ./cache/cord-269294-vx7xr80t.txt txt: ./txt/cord-269294-vx7xr80t.txt summary: Here, we discuss the role of these enzymes, factors affecting their potential as drug targets and progress in the development of agents that inhibit their activity using the hepatitis C virus-encoded helicase NS3 and the cellular helicase DDX3 adopted for use by HIV-1 as examples. The solution of the crystal structure of HCV helicase complexed with oligonucleotide, as well as mutagenesis studies, have identified key residues that are essential for enzyme activity or translocation of the RNA substrate 13, 72 . Theoretically, an unwinding assay should increase the odds of finding an inhibitor because inhibition of any of the potential mechanisms of action listed above, except those requiring a cellular environment (for example, turnover and replicase-complex formation), should result in ''hits'' (for example, low-potency chemical starting points for medicinal chemistry optimization). Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding abstract: Although there has been considerable progress in the development of antiviral agents in recent years, there is still a pressing need for new drugs both to improve on the properties of existing agents and to combat the problem of viral resistance. Helicases, both viral and human, have recently emerged as novel targets for the treatment of viral infections. Here, we discuss the role of these enzymes, factors affecting their potential as drug targets and progress in the development of agents that inhibit their activity using the hepatitis C virus-encoded helicase NS3 and the cellular helicase DDX3 adopted for use by HIV-1 as examples. url: https://www.ncbi.nlm.nih.gov/pubmed/16184083/ doi: 10.1038/nrd1853 id: cord-294056-7e477y1x author: La Monica, Nicola title: Coronavirus mRNA synthesis: Identification of novel transcription initiation signals which are differentially regulated by different leader sequences date: 1992-05-31 words: 3341.0 sentences: 173.0 pages: flesch: 58.0 cache: ./cache/cord-294056-7e477y1x.txt txt: ./txt/cord-294056-7e477y1x.txt summary: Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. To understand the mechanism of MHV mRNA transcription, we have attempted to determine whether the differential regulation of transcription initiation by leader RNA containing different UCUAA copy numbers is unique to mRNA 2-l. The analysis of several other recombinant viruses with different genome structures suggested that mRNA 3-l was synthesized only by viruses with a leader RNA containing three copies of UCUAA and gene 3 sequence derived from A59 but not JHM (10, 13). Using various primers representing sequences of different regions of gene 1 of the JHM strain of MHV (2) and a second primer representing the 5''-end of the leader RNA, we detected several PCR products which represented mRNAs initiated from various sites. abstract: Abstract The mRNA synthesis of mouse hepatitis virus (MHV) has been proposed to be the result of interaction between the leader RNA and the intergenic sites. Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. In this study, we have identified several sites which are regulated in the opposite way, namely, they are efficiently transcribed by the leader RNA with three UCUAA copies but not by those with two copies. These sites were characterized by primer extension and amplification by polymerase chain reaction. One of these sites is in the gene 3 region of a recombinant virus between A59 and JHM strains of MHV. Another is in the gene 2 region of MHV-1 strain. Both of these sites have a sequence similar to but different from the consensus transcription initiation signal (UCUAAUCUAUC and UUUAAUCUU, as opposed to UCUAAAC). These two novel intergenic sequences are not present in the genome of the JHM strain, consistent with the absence of these mRNAs in the JHM-infected cells. The discovery of this type of transcription initiation site provides additional evidence for the importance of the leader RNA in the transcription initiation of MHV mRNAs. url: https://www.ncbi.nlm.nih.gov/pubmed/1566582/ doi: 10.1016/0042-6822(92)90774-j id: cord-307934-84zfabti author: Lai, Chao-Kuen title: Nonstructural Protein 5A Is Incorporated into Hepatitis C Virus Low-Density Particle through Interaction with Core Protein and Microtubules during Intracellular Transport date: 2014-06-06 words: 8211.0 sentences: 465.0 pages: flesch: 55.0 cache: ./cache/cord-307934-84zfabti.txt txt: ./txt/cord-307934-84zfabti.txt summary: Further studies by cofractionation analysis and immunoelectron microscopy of the released particles showed that NS5A-Core complexes, but not NS4B, were present in the low-density fractions, but not in the high-density fractions, of the HCV RNA-containing virions and associated with the internal virion core. Overall, our results suggest that HCV NS5A is associated with the core of the low-density virus particles which exit the cell through a preexisting endosome/exosome pathway and may contribute to HCV natural infection. Both NS5A and Core proteins are found to be closely associated with and co-transported along the microtubules from the perinuclear region of cells via the LDs and endosomes to the plasma membrane. (A) The HCV-infected cells (at day 10 p.i.) were labeled with antibodies specific for Core protein (red) and NS5A (green) (upper row) or NS4B (green) (lower row). abstract: Nonstructural protein 5A (NS5A) of hepatitis C virus (HCV) serves dual functions in viral RNA replication and virus assembly. Here, we demonstrate that HCV replication complex along with NS5A and Core protein was transported to the lipid droplet (LD) through microtubules, and NS5A-Core complexes were then transported from LD through early-to-late endosomes to the plasma membrane via microtubules. Further studies by cofractionation analysis and immunoelectron microscopy of the released particles showed that NS5A-Core complexes, but not NS4B, were present in the low-density fractions, but not in the high-density fractions, of the HCV RNA-containing virions and associated with the internal virion core. Furthermore, exosomal markers CD63 and CD81 were also detected in the low-density fractions, but not in the high-density fractions. Overall, our results suggest that HCV NS5A is associated with the core of the low-density virus particles which exit the cell through a preexisting endosome/exosome pathway and may contribute to HCV natural infection. url: https://www.ncbi.nlm.nih.gov/pubmed/24905011/ doi: 10.1371/journal.pone.0099022 id: cord-001542-f089bs8r author: Lai, Kang Yiu title: Human Ebola virus infection in West Africa: a review of available therapeutic agents that target different steps of the life cycle of Ebola virus date: 2014-11-28 words: 11274.0 sentences: 604.0 pages: flesch: 42.0 cache: ./cache/cord-001542-f089bs8r.txt txt: ./txt/cord-001542-f089bs8r.txt summary: These may include monoclonal antibody (mAbs)-based therapies (e.g. ZMapp), anti-sense phosphorodiamidate morpholino oligomers (PMO AVI-6002), lipid nanoparticle small interfering RNA (LNP-siRNA: TKM-Ebola), and an EBOV glycoprotein-based vaccine using live-attenuated recombinant vesicular stomatitis virus (rVSV-EBOGP) or a chimpanzee adenovirus (rChAd-EBOGP)-based vector. The GP2 of the EBOV is able to counter the interferon (IFN)-inducible antiviral protein tetherin which restricts the VP40-dependent budding of the progeny viral particles from infected cells [16] [17] [18] . Currently available therapeutic agents that are effective in targeting the EBOV infection in cell or animal studies may include convalescent plasma, favipiravir, chloroquine, amiodarone, dronedarone, verapamil, clomiphene, toremifene, IFN-β, Na + /K + exchangers, Na + /K + -ATPase pump inhibitors, and antioxidants. The anti-EBOV activity of clomiphene and toremifene is dependent not on its estrogen receptor antagonistic action but upon the ability of both drugs to induce a Niemann-Pick C-like phenotype to inhibit viral entry at late endosome. abstract: The recent outbreak of the human Zaire ebolavirus (EBOV) epidemic is spiraling out of control in West Africa. Human EBOV hemorrhagic fever has a case fatality rate of up to 90%. The EBOV is classified as a biosafety level 4 pathogen and is considered a category A agent of bioterrorism by Centers for Disease Control and Prevention, with no approved therapies and vaccines available for its treatment apart from supportive care. Although several promising therapeutic agents and vaccines against EBOV are undergoing the Phase I human trial, the current epidemic might be outpacing the speed at which drugs and vaccines can be produced. Like all viruses, the EBOV largely relies on host cell factors and physiological processes for its entry, replication, and egress. We have reviewed currently available therapeutic agents that have been shown to be effective in suppressing the proliferation of the EBOV in cell cultures or animal studies. Most of the therapeutic agents in this review are directed against non-mutable targets of the host, which is independent of viral mutation. These medications are approved by the Food and Drug Administration (FDA) for the treatment of other diseases. They are available and stockpileable for immediate use. They may also have a complementary role to those therapeutic agents under development that are directed against the mutable targets of the EBOV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2049-9957-3-43) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334593/ doi: 10.1186/2049-9957-3-43 id: cord-352379-q5inrxcm author: Lai, Michael M. C. title: SARS virus: The beginning of the unraveling of a new coronavirus date: 2003-10-17 words: 7004.0 sentences: 376.0 pages: flesch: 49.0 cache: ./cache/cord-352379-q5inrxcm.txt txt: ./txt/cord-352379-q5inrxcm.txt summary: Nevertheless, the lack of a firm association of coronaviruses with any serious human illnesses had dampened the public''s interest in this virus family until the sudden emergence of the SARS coronavirus [24, 41, 62] , which caused the first new infectious disease of this millennium. In the SARS virus genome, the organization of gene la-lb, which accounts for more than two-thirds of the viral RNA, is very similar to that of the murine coronavirus MHV, except that it contains only one papain-like protease (PLpro-2) ( fig. Based on the predicted cleavage site specificity, the SARS virus gene la-lb is likely processed into thirteen final protein products. However, the published sequence analysis indicated that the entire SARS virus RNA resembled that of group II viruses; no evidence of recombination was noted [55, 66] . Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection abstract: Severe acute respiratory syndrome (SARS) virus caused a severe outbreak in several regions of the world in 2003. The virus is a novel coronavirus, which may have an origin in wild animals such as civet cats in southern China. Its genome structure, gene expression pattern and protein profiles are similar to those of other coronaviruses. However, distinct patterns of several open reading frames in the SARS virus genome may contribute to its severe virulence. The potential mutability of the coronavirus genome may pose problems in the control of future SARS outbreaks. The mechanism of SARS pathogenesis may involve both direct viral cytocidal effects on the target cells and immune-mediated mechanisms. The life cycle of the SARS virus is largely unknown; however, based on the analogy with other coronaviruses, several potential targets for antiviral development are identified. Vaccines offer an important preventive measure for possible future recurrences of SARS, but the prospect for their development is still unknown because of the uncertainty regarding the role of immune responses in SARS virus pathogenesis. The comparative studies of other coronaviruses offer insights into the understanding of SARS virus. url: https://www.ncbi.nlm.nih.gov/pubmed/14631105/ doi: 10.1007/bf02256318 id: cord-256444-grw5s2pf author: Lai, Michael M.C. title: The Molecular Biology of Coronaviruses date: 1997-12-31 words: 35222.0 sentences: 1753.0 pages: flesch: 51.0 cache: ./cache/cord-256444-grw5s2pf.txt txt: ./txt/cord-256444-grw5s2pf.txt summary: Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. This decade has seen the manipulation of these clones, and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs, to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The species and tissue specificity of a coronavirus infection is a t least partially dictated by the nature and distribution of cellular receptors and other related molecules that regulate virus entry, as evidenced by the viral replication that results when viral RNA is directly introduced into cell types of other animal species. abstract: Publisher Summary This chapter discusses the manipulation of clones of coronavirus and of complementary DNAs (cDNAs) of defective-interfering (DI) RNAs to study coronavirus RNA replication, transcription, recombination, processing and transport of proteins, virion assembly, identification of cell receptors for coronaviruses, and processing of the polymerase. The nature of the coronavirus genome is nonsegmented, single-stranded, and positive-sense RNA. Its size ranges from 27 to 32 kb, which is significantly larger when compared with other RNA viruses. The gene encoding the large surface glycoprotein is up to 4.4 kb, encoding an imposing trimeric, highly glycosylated protein. This soars some 20 nm above the virion envelope, giving the virus the appearance-with a little imagination-of a crown or coronet. Coronavirus research has contributed to the understanding of many aspects of molecular biology in general, such as the mechanism of RNA synthesis, translational control, and protein transport and processing. It remains a treasure capable of generating unexpected insights. url: https://api.elsevier.com/content/article/pii/S0065352708602869 doi: 10.1016/s0065-3527(08)60286-9 id: cord-332710-2s14knw6 author: Lai, Michael M.C. title: Recombination in large RNA viruses: Coronaviruses date: 1996-12-31 words: 4204.0 sentences: 236.0 pages: flesch: 42.0 cache: ./cache/cord-332710-2s14knw6.txt txt: ./txt/cord-332710-2s14knw6.txt summary: The capacity of coronaviruses to undergo recombination may be related to its mRNA transcription mechanism, which involves discontinuous RNA synthesis, suggesting the nonprocessive nature of the viral polymerase. The first coronavirus recombinant was isolated by coinfecting temperature-sensitive (ts) mutants of two mouse hepatitis virus (MHV) strains, A59 and JHM, and selecting progeny viruses which grew at the nonpermissive temperature. In contrast, clear-cut evidence of recombination has been obtained for natural isolates of avian infectious bronchitis virus (IBV), many of which have recombination between different strains in the spike protein gene or the 3''-end of viral RNA. 33 In this case, the viral RNA containing the sequence of the transfected RNA fragments was detected by reverse transcription-polymerase chain reaction (RT-PCR), although the actual recombinants could not be isolated because of lack of selection markers. abstract: Abstract Coronaviruses contain a very large RNA genome, which undergoes recombination at a very high frequency of nearly 25% for the entire genome. Recombination has been demonstrated to occur between viral genomes and between defective-interfering (DI) RNAs and viral RNA. It provides an evolutionary tool for both viral RNAs and DI RNA and may account for the diversity in the genomic structure of coronaviruses. The capacity of coronaviruses to undergo recombination may be related to its mRNA transcription mechanism, which involves discontinuous RNA synthesis, suggesting the nonprocessive nature of the viral polymerase. Recombination is used as a tool for the mutagenesis of viral genomic RNA. url: https://www.sciencedirect.com/science/article/pii/S1044577396900463 doi: 10.1006/smvy.1996.0046 id: cord-267036-llngs3v5 author: Lai, Ming‐Chih title: Functional interplay between viral and cellular SR proteins in control of post‐transcriptional gene regulation date: 2009-02-10 words: 4460.0 sentences: 263.0 pages: flesch: 44.0 cache: ./cache/cord-267036-llngs3v5.txt txt: ./txt/cord-267036-llngs3v5.txt summary: Numerous lines of evidence indicate that cellular SR proteins are important for regulation of viral RNA splicing and participate in other steps of post-transcriptional viral gene expression control. The E2 protein encoded by HPVs primarily regulates the transcription of early promoters by binding to a consensus element within the long control region of the viral genome, and also functions together with the E1 protein in viral DNA replication [16] . It has been shown that reduced activity of SR proteins resulting from viral infection can be recovered by overexpression of SR proteins or by their rephosphorylation in the host cells [74] , and that HIV expression can be greatly increased when SRp75 is phosphorylated by SRPK2 [69] . Cellular SR proteins and their cooperative or antagonistic factors may play a critical role in the life cycle control of viruses, which involves a series of alternative splicing events for expression of viral genome or proteins. HIV-1 infection induces changes in expression of cellular splicing factors that regulate alternative viral splcing and virus production in macrophages abstract: Viruses take advantage of cellular machineries to facilitate their gene expression in the host. SR proteins, a superfamily of cellular precursor mRNA splicing factors, contain a domain consisting of repetitive arginine/serine dipeptides, termed the RS domain. The authentic RS domain or variants can also be found in some virus‐encoded proteins. Viral proteins may act through their own RS domain or through interaction with cellular SR proteins to facilitate viral gene expression. Numerous lines of evidence indicate that cellular SR proteins are important for regulation of viral RNA splicing and participate in other steps of post‐transcriptional viral gene expression control. Moreover, viral infection may alter the expression levels or modify the phosphorylation status of cellular SR proteins and thus perturb cellular precursor mRNA splicing. We review our current understanding of the interplay between virus and host in post‐transcriptional regulation of gene expression via RS domain‐containing proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/19220464/ doi: 10.1111/j.1742-4658.2009.06894.x id: cord-305393-96mrxt8a author: Lai, Yvonne title: Viral Double-Strand RNA-Binding Proteins Can Enhance Innate Immune Signaling by Toll-Like Receptor 3 date: 2011-10-10 words: 9604.0 sentences: 587.0 pages: flesch: 60.0 cache: ./cache/cord-305393-96mrxt8a.txt txt: ./txt/cord-305393-96mrxt8a.txt summary: Recombinant 1b hepatitis C virus polymerase was found to enhance TLR3 signaling in the lung epithelial BEAS-2B cells when added to the media along with either poly(I:C) or viral dsRNAs. The polymerase from the genotype 2a JFH-1 HCV was a poor enhancer of TLR3 signaling until it was mutated to favor a conformation that could bind better to a partially duplexed RNA. These results demonstrate that several viral RNA-binding proteins can enhance the dsRNA-dependent innate immune response initiated by TLR3. Transfection of two plasmids, one containing an interferon stimulated response element (ISRE) promoter-driven firefly luciferase and a second encoding a constitutively expressed Renilla luciferase allow the analysis of TLR3 activation by different RNAs. HEK 293T cells expressing WT TLR3 responded to poly(I:C) (1-2 mg/ml), better than viral dsRNAs (1-2 mg/ml) purified from Reovirus and BPEV (Fig. 1B) . abstract: Toll-like Receptor 3 (TLR3) detects double-stranded (ds) RNAs to activate innate immune responses. While poly(I:C) is an excellent agonist for TLR3 in several cell lines and in human peripheral blood mononuclear cells, viral dsRNAs tend to be poor agonists, leading to the hypothesis that additional factor(s) are likely required to allow TLR3 to respond to viral dsRNAs. TLR3 signaling was examined in a lung epithelial cell line by quantifying cytokine production and in human embryonic kidney cells by quantifying luciferase reporter levels. Recombinant 1b hepatitis C virus polymerase was found to enhance TLR3 signaling in the lung epithelial BEAS-2B cells when added to the media along with either poly(I:C) or viral dsRNAs. The polymerase from the genotype 2a JFH-1 HCV was a poor enhancer of TLR3 signaling until it was mutated to favor a conformation that could bind better to a partially duplexed RNA. The 1b polymerase also co-localizes with TLR3 in endosomes. RNA-binding capsid proteins (CPs) from two positive-strand RNA viruses and the hepadenavirus hepatitis B virus (HBV) were also potent enhancers of TLR3 signaling by poly(I:C) or viral dsRNAs. A truncated version of the HBV CP that lacked an arginine-rich RNA-binding domain was unable to enhance TLR3 signaling. These results demonstrate that several viral RNA-binding proteins can enhance the dsRNA-dependent innate immune response initiated by TLR3. url: https://doi.org/10.1371/journal.pone.0025837 doi: 10.1371/journal.pone.0025837 id: cord-253616-7jyui5ca author: Lai, Zheng-Zong title: Harringtonine Inhibits Zika Virus Infection through Multiple Mechanisms date: 2020-09-07 words: 4969.0 sentences: 286.0 pages: flesch: 48.0 cache: ./cache/cord-253616-7jyui5ca.txt txt: ./txt/cord-253616-7jyui5ca.txt summary: To investigate the anti-ZIKV activity of harringtonine, we assessed the inhibition of virus infection in Vero cells with MOI = 0.01 under different concentrations of harringtonine for 48 h. Intracellular viral RNA levels, protein expression levels and virus progeny in supernatants were respectively determined by RT-qPCR, western blotting and fluorescent focus assay (FFA). The dose-dependent anti-ZIKV activities of harringtonine were observed to decrease viral RNA/protein production and progeny yield ( Figure 1B-D) , indicating that virus propagation was suppressed. Harringtonine (625 nM) was administered at different stages of ZIKV infection with MOI = 0.1, and then the levels of ZIKV RNA in cells, as well as virus titers in supernatants, were determined after 24 h treatment. Harringtonine (625 nM) was administered at different stages of ZIKV infection with MOI = 0.1, and then the levels of ZIKV RNA in cells, as well as virus titers in supernatants, were determined after 24 h treatment. abstract: Mosquito-borne Zika virus (ZIKV) is a Flavivirus that came under intense study from 2014 to 2016 for its well-known ability to cause congenital microcephaly in fetuses and neurological Guillain–Barré disease in adults. Substantial research on screening antiviral agents against ZIKV and preventing ZIKV infection are globally underway, but Food and Drug Administration (FDA)-approved treatments are not available yet. Compounds from Chinese medicinal herbs may offer an opportunity for potential therapies for anti-ZIKV infection. In this study, we evaluated the antiviral efficacy of harringtonine against ZIKV. Harringtonine possessed anti-ZIKV properties against the binding, entry, replication, and release stage through the virus life cycle. In addition, harringtonine have strong virucidal effects in ZIKV and exhibited prophylaxis antiviral ability prior ZIKV infection. The antiviral activity also observed in the treatment against Japanese encephalitis reporter virus (RP9-GFP strain). Overall, this study demonstrated that harringtonine would be a favorable potential candidate for the development of anti-ZIKV infection therapies. url: https://www.ncbi.nlm.nih.gov/pubmed/32906689/ doi: 10.3390/molecules25184082 id: cord-015673-rz74sh32 author: Lamers, Anne E. title: RNA Interference Mechanisms and Therapeutic Applications date: 2006 words: 2953.0 sentences: 177.0 pages: flesch: 54.0 cache: ./cache/cord-015673-rz74sh32.txt txt: ./txt/cord-015673-rz74sh32.txt summary: RNA interference (RNAi) is a technology developed after the recent discovery of well-conserved cellular processes that induce posttranscriptional gene silencing triggered by small fragments of double-stranded RNA. An ancient process for defense against viral infections and transposons, and in higher developed organisms an endogenous process that regulates gene expression, triggered by double-stranded RNA (dsRNA) was recently revealed (for reviews see Carrington and Ambros, 2003; Hammond et al., 2001; Sharp, 2001) . Furthermore, longer fragments seem to be more effective than short RNA particles, because they are more efficiently processed into more different siRNAs. The convenient method of introducing small dsRNA fragments into the cell by hairpin-expressing plasmids (Fig. 2) can overcome these disadvantages (Kawasaki and Taira, 2003; Yu et al., 2002) . Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells abstract: RNA interference (RNAi) is a technology developed after the recent discovery of well-conserved cellular processes that induce posttranscriptional gene silencing triggered by small fragments of double-stranded RNA. This technique is rapidly developing into a promising tool used for functional genetics and therapeutic applications. We focus here on the aspects concerning RNAi mechanism, applications in mammals, and construct design and delivery. We summarize some therapeutic applications in general and speculate on the relevance in cardiovascular medicine. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115010/ doi: 10.1007/0-387-23329-6_7 id: cord-329102-2y49kcwu author: Lan, Tammy C. T. title: Structure of the full SARS-CoV-2 RNA genome in infected cells date: 2020-06-30 words: 9315.0 sentences: 507.0 pages: flesch: 61.0 cache: ./cache/cord-329102-2y49kcwu.txt txt: ./txt/cord-329102-2y49kcwu.txt summary: We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1. abstract: SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs or vaccines with proven efficacy, and development of these treatments are hampered by our limited understanding of the molecular and structural biology of the virus. Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. Although genome and transcriptome data were recently reported, there is to date little experimental data on predicted RNA structures in SARS-CoV-2 and most putative regulatory sequences are uncharacterized. Here we report the secondary structure of the entire SARS-CoV-2 genome in infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq). Our results reveal previously undescribed structures within critical regulatory elements such as the genomic transcription-regulating sequences (TRSs). Contrary to previous studies, our in-cell data show that the structure of the frameshift element, which is a major drug target, is drastically different from prevailing in vitro models. The genomic structure detailed here lays the groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics. url: https://doi.org/10.1101/2020.06.29.178343 doi: 10.1101/2020.06.29.178343 id: cord-276541-u9ebql5a author: Lan, Yungang title: Inhibition of porcine hemagglutinating encephalomyelitis virus replication by short hairpin RNAs targeting of the nucleocapsid gene in a porcine kidney cell line date: 2011-11-25 words: 3067.0 sentences: 172.0 pages: flesch: 56.0 cache: ./cache/cord-276541-u9ebql5a.txt txt: ./txt/cord-276541-u9ebql5a.txt summary: title: Inhibition of porcine hemagglutinating encephalomyelitis virus replication by short hairpin RNAs targeting of the nucleocapsid gene in a porcine kidney cell line Here, we constructed a single short hairpin RNA (shRNA) plasmid expression system that targeted the N gene and investigated whether shRNAmediated RNA interference could inhibit PHEV replication in PK-15 cells. To study the inhibitory effects of RNA interference on PHEV replication, the level of viral antigen produced in the PK-15 cells after shRNA transfection and viral infection was examined 48 h post-infection by an indirect immunofluorescence assay (IFA) using anti-PHEV serum. To quantify the effect of shRNA on viral replication at 48 h postviral infection, the viral genome copy number was determined by real-time PCR, using the serially diluted plasmid pT-N as a standard. It is clear from this study that the DNA vector-based shRNA approach, that is, the use of RNAi expression plasmids directed against the PHEV N gene, could effectively block expression of the viral target gene and inhibit viral replication. abstract: Porcine hemagglutinating encephalomyelitis virus (PHEV), which causes porcine encephalomyelitis and is widespread among swine worldwide. RNA interference (RNAi) pathways have emerged as important regulators of virus–host cell interactions. In this study, two siRNA expression plasmids (shN1 and shN2) were generated to target two different coding regions of the nucleocapsid protein (N) of PHEV. The shRNAs were transiently transfected into a porcine kidney cell line, PK-15, to determine whether these constructs inhibited PHEV production. Our results revealed that both shRNAs were highly capable of inhibiting viral RNA genome replication, especially shN2. Next, stable transfection of shN2 was used to produce two siRNA stably expressing PK-15 cell clones (shN2-1 and shN2-2), and these two lines were infected with PHEV. The analysis of cytopathic effects (CPE) demonstrated that shN2-1 and shN2-2 were capable of protecting cells against PHEV infection with high specificity and efficiency. Furthermore, effective inhibition of viral replication persisted for up to 120 h by a TCID(50) assay. These results indicated that RNAi targeting of the N gene could facilitate studies of the specific function of viral genes associated with PHEV replication and may have potential therapeutic applications. url: https://api.elsevier.com/content/article/pii/S0166093411004447 doi: 10.1016/j.jviromet.2011.11.007 id: cord-000881-s90geszi author: Lang, Dorothy M. title: Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases date: 2012-12-25 words: 9703.0 sentences: 536.0 pages: flesch: 60.0 cache: ./cache/cord-000881-s90geszi.txt txt: ./txt/cord-000881-s90geszi.txt summary: In contrast to the relatively short lengths of previously described motifs, we found that most homomorphs are long, and each provides a structural connection between the template tunnel or NTP entry tunnel and the exterior of the protein. The structurally aligned sequences that comprised homomorph of Motif F (hmF) for RdRps and HIV are summarized in Figure 3A . Using T7 DNAP as a query (lowest segment of the figure) , only a small portion of the C-terminal edge of Motif D and a few species have similar structures. In the RdRps, the combined regions of structural homology represent $75% of the sequence from the start of homomorph of Motif G (hmG) through the end of hmE in each species ($375 residues). The tertiary position of each of the homomorphs includes at least one residue (and sometimes more) in contact with the exterior surface of the protein and one or more highly conserved functional residues located within or at the wall of the template tunnel. abstract: RNA-dependent RNA polymerase (RdRp) is essential to viral replication and is therefore one of the primary targets of countermeasures against these dangerous infectious agents. Development of broad-spectrum therapeutics targeting polymerases has been hampered by the extreme sequence variability of these sequences. RdRps range in length from 400–800 residues, yet contain only ∼20 residues that are conserved in most species. In this study, we made structure-based comparisons that are independent of sequence composition using a recently developed algorithm. We identified residue-to-residue correspondences of multiple protein structures and created (two-dimensional) structure-based alignment maps of 37 polymerase structures that provide both sequence and structure details. Using these maps, we determined that ∼75% of each polymerase species consists of seven protein segments, each of which has high structural similarity to segments in other species, though they are widely divergent in sequence composition and order. We define each of these segments as a ‘homomorph’, and each includes (though most are much larger than) the well-known conserved polymerase motifs. All homomorphs contact the template tunnel or nucleoside triphosphate (NTP) entry tunnel and the exterior of the protein, suggesting they constitute a structural and functional skeleton common among the polymerases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561941/ doi: 10.1093/nar/gks1251 id: cord-325958-1v1pg2z0 author: Lange, Clemens title: Expression of the COVID‐19 receptor ACE2 in the human conjunctiva date: 2020-05-06 words: 2672.0 sentences: 149.0 pages: flesch: 45.0 cache: ./cache/cord-325958-1v1pg2z0.txt txt: ./txt/cord-325958-1v1pg2z0.txt summary: In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high‐throughput RNA sequencing to assess mRNA expression of the SARS‐CoV‐2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. Since the outbreak, many studies described ACE2 expression across human tissues, including lung, stomach, ileum, colon, liver and kidney 8, 9 , supporting the clinical observation that SARS-CoV-2 can infect multiple organs. To obtain information on transcription of ACE2 and associated molecules required for cell entry by SARS-CoV-2, existing datasets of 38 conjunctival samples from 38 patients were included in this study. This study shows that ACE2, which is the main receptor for SARS-CoV-2 6 , is not significantly expressed in healthy and diseased human conjunctival samples. abstract: SARS‐CoV‐2 is assumed to use angiotensin‐converting enzyme 2 (ACE2) and other auxiliary proteins for cell entry. Recent studies have described conjunctival congestion in 0.8% of patients with laboratory‐confirmed SARS‐CoV‐2, and there has been speculation that SARS‐CoV‐2 can be transmitted through the conjunctiva. However, it is currently unclear whether conjunctival epithelial cells express ACE2 and its cofactors. In this study, a total of 38 conjunctival samples from 38 patients, including 12 healthy conjunctiva, 12 melanoma, 7 squamous cell carcinoma and 7 papilloma samples, were analyzed using high‐throughput RNA sequencing to assess mRNA expression of the SARS‐CoV‐2 receptor ACE2 and its cofactors including TMPRSS2, ANPEP, DPP4, and ENPEP. ACE2 protein expression was assessed in eight healthy conjunctival samples using immunohistochemistry. Our results show that the SARS‐CoV‐2 receptor ACE2 is not substantially expressed in conjunctival samples on the mRNA (median 0.0 transcripts per million (TPM), min 0.0 TPM, max 1.7 TPM) and protein levels. Similar results were obtained for the transcription of other auxiliary molecules. In conclusion, this study finds no evidence for a significant expression of ACE2 and its auxiliary mediators for cell entry in conjunctival samples, making conjunctival infection with SARS‐CoV‐2 via these mediators unlikely. This article is protected by copyright. All rights reserved. url: https://doi.org/10.1002/jmv.25981 doi: 10.1002/jmv.25981 id: cord-293747-ds8rhbkv author: Lani, Rafidah title: Antiviral activity of silymarin against chikungunya virus date: 2015-06-16 words: 5074.0 sentences: 254.0 pages: flesch: 51.0 cache: ./cache/cord-293747-ds8rhbkv.txt txt: ./txt/cord-293747-ds8rhbkv.txt summary: Three compounds: silymarin, quercetin and kaempferol were evaluated for their in vitro antiviral activities against CHIKV using a CHIKV replicon cell line and clinical isolate of CHIKV of Central/East African genotype. A cytopathic effect inhibition assay was used to determine their activities on CHIKV viral replication and quantitative reverse transcription PCR was used to calculate virus yield. Different non-cytotoxic concentrations of silymarin, kaempferol and quercetin were tested on CHIKV-infected Vero cells to find the effective compound. To confirm the post-entry antiviral activity of silymarin against CHIKV a virus yield assay using qRT-PCR was used. In contrast, dose-dependent reduction of amounts of nsP1, nsP3 and E2 proteins was observed (Fig. 6) indicating that silymarin limited CHIKV replication and virus-encoded protein synthesis within the treated cells. However, as in virus expression and replicon cell lines the synthesis of viral RNAs and proteins are coupled further study is necessary to evaluate the direct effect of silymarin on inhibition of newly synthesized CHIKV proteins. abstract: The mosquito-borne chikungunya virus (CHIKV) causes chikungunya fever, with clinical presentations such as severe back and small joint pain, and debilitating arthritis associated with crippling pains that persist for weeks and even years. Although there are several studies to evaluate the efficacy of drugs against CHIKV, the treatment for chikungunya fever is mainly symptom-based and no effective licensed vaccine or antiviral are available. Here, we investigated the antiviral activity of three types of flavonoids against CHIKV in vitro replication. Three compounds: silymarin, quercetin and kaempferol were evaluated for their in vitro antiviral activities against CHIKV using a CHIKV replicon cell line and clinical isolate of CHIKV of Central/East African genotype. A cytopathic effect inhibition assay was used to determine their activities on CHIKV viral replication and quantitative reverse transcription PCR was used to calculate virus yield. Antiviral activity of effective compound was further investigated by evaluation of CHIKV protein expression using western blotting for CHIKV nsP1, nsP3, and E2E1 proteins. Briefly, silymarin exhibited significant antiviral activity against CHIKV, reducing both CHIKV replication efficiency and down-regulating production of viral proteins involved in replication. This study may have important consequence for broaden the chance of getting the effective antiviral for CHIKV infection. url: https://doi.org/10.1038/srep11421 doi: 10.1038/srep11421 id: cord-263033-4790dhc5 author: Laptev, I. G. title: Posttranscriptional modification of messenger RNAs in eukaryotes date: 2015-12-11 words: 6792.0 sentences: 437.0 pages: flesch: 58.0 cache: ./cache/cord-263033-4790dhc5.txt txt: ./txt/cord-263033-4790dhc5.txt summary: The review considers posttranscriptional modification of eukaryotic mRNA, focusing on the major modified nucleotides, the role they play in the cell, the methods to detect them, and the enzymes responsible for modification. Regions distant from the mRNA ends may contain N6 methyladenosine (m 6 A), 5 methylcytidine (m 5 C), pseudouridine (Ψ), and inosine (I), which were believed to play only a minor role because their pro portion in cell RNA is extremely low as compared with the standard nucleotides. In the case of eukaryotic mRNAs, the method is suitable for probing the adenosine methylation status in a particular site of a particular RNA in various cell growth conditions. A method known as site specific cleavage and radioactive labeling followed by ligation assisted extrac tion and thin layer chromatography (SCARLET) [23] makes it possible to establish whether adenosine is methylated in a given position of a given molecule and to estimate the proportion of modified and unmodi fied nucleotides (Fig. 2) . abstract: Transcriptome-wide mapping of posttranscriptional modifications in eukaryotic RNA revealed tens of thousands of modification sites. Modified nucleotides include 6-methyladenosine, 5-methylcytidine, pseudouridine, inosine, etc. Many modification sites are conserved, and many are regulated. The function is known for a minor subset of modified nucleotides, while the role of their majority is still obscure. In view of the global character of mRNA modification, RNA epigenetics arose as a new field of molecular biology. The review considers posttranscriptional modification of eukaryotic mRNA, focusing on the major modified nucleotides, the role they play in the cell, the methods to detect them, and the enzymes responsible for modification. url: https://www.ncbi.nlm.nih.gov/pubmed/32214475/ doi: 10.1134/s002689331506014x id: cord-260708-l9w5jhsw author: Lasecka, Lidia title: The molecular biology of nairoviruses, an emerging group of tick-borne arboviruses date: 2013-12-11 words: 10690.0 sentences: 446.0 pages: flesch: 46.0 cache: ./cache/cord-260708-l9w5jhsw.txt txt: ./txt/cord-260708-l9w5jhsw.txt summary: The nairoviruses are a rapidly emerging group of tick-borne bunyaviruses that includes pathogens of humans (Crimean-Congo hemorrhagic fever virus [CCHFV]) and livestock (Nairobi sheep disease virus [NSDV], also known as Ganjam virus), as well as a large number of viruses for which the normal vertebrate host has not been established. As several potential cysteine-protease-like cleavage sites have been identified in the L protein sequence of nairoviruses [94] and some viral proteins containing an OTU-like protease domain have also been shown to undergo autoproteolytic cleavage to generate multiple mature proteins, e.g., the replicase of BlScV [98] , it has been suggested that the L proteins of nairoviruses may also be autoproteolytically cleaved into an active RNA polymerase and protein(s) with additional function [85] . Role of actin filaments in targeting of Crimean Congo hemorrhagic fever virus nucleocapsid protein to perinuclear regions of mammalian cells Structural analysis of a viral ovarian tumor domain protease from the Crimean-Congo hemorrhagic fever virus in complex with covalently bonded ubiquitin Induction of caspase activation and cleavage of the viral nucleocapsid protein in different cell types during Crimean-Congo hemorrhagic fever virus infection abstract: The nairoviruses are a rapidly emerging group of tick-borne bunyaviruses that includes pathogens of humans (Crimean-Congo hemorrhagic fever virus [CCHFV]) and livestock (Nairobi sheep disease virus [NSDV], also known as Ganjam virus), as well as a large number of viruses for which the normal vertebrate host has not been established. Studies on this group of viruses have been fairly limited, not least because CCHFV is a BSL4 human pathogen, restricting the number of labs able to study the live virus, while NSDV, although highly pathogenic in naive animals, is not seen as a threat in developed countries, making it a low priority. Nevertheless, recent years have seen significant progress in our understanding of the biology of these viruses, particularly that of CCHFV, and this article seeks to draw together our existing knowledge to generate an overall picture of their molecular biology, underlining areas of particular ignorance for future studies. url: https://www.ncbi.nlm.nih.gov/pubmed/24327094/ doi: 10.1007/s00705-013-1940-z id: cord-326017-qw4qynqv author: Laskar, Partha title: “Tomorrow Never Dies”: Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies date: 2020-08-06 words: 14797.0 sentences: 760.0 pages: flesch: 42.0 cache: ./cache/cord-326017-qw4qynqv.txt txt: ./txt/cord-326017-qw4qynqv.txt summary: Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Considering this, we have summarized diverse research areas covering the current known biological properties of SARS-CoV-2, diagnostic tools for detection, therapeutic measurements for possible treatment, and prevention techniques to stop further spreading of this pandemic. Overall, real-time RT-PCR based method enables developing a high-throughput testing for rapid, on-demand, low-cost, reliable, quantitative detection technique against COVID-19 in clinical settings [39] . Another newly developed method, SARS-CoV-2 DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), was found to perform simultaneous reverse transcription and isothermal amplification by (i) RT-LAMP for RNA extracted (for nasopharyngeal or oropharyngeal swabs), (ii) Cas12 detection of predefined coronavirus sequences, and (iii) cleavage of a reporter molecule confirms, which detects the virus [56] . abstract: The outbreak of novel coronavirus disease (2019-nCoV or COVID-19) is responsible for severe health emergency throughout the world. The attack of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is found to be responsible for COVID-19. The World Health Organization has declared the ongoing global public health emergency as a pandemic. The whole world fights against this invincible enemy in various capacities to restore economy, lifestyle, and safe life. Enormous amount of scientific research work(s), administrative strategies, and economic measurements are in place to create a successful step against COVID-19. Furthermore, differences in opinion, facts, and implementation methods laid additional layers of complexities in this battle against survival. Thus, a timely overview of the recent, important, and overall inclusive developments against this pandemic is a pressing need for better understanding and dealing with COVID-19. In this review, we have systematically summarized the epidemiological studies, clinical features, biological properties, diagnostic methods, treatment modalities, and preventive measurements related to COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32781617/ doi: 10.3390/diseases8030030 id: cord-000128-t74b5j2j author: Laufer, S.D title: Peptide-Mediated Cellular Delivery of Oligonucleotide-Based Therapeutics In Vitro: Quantitative Evaluation of Overall Efficacy Employing Easy to Handle Reporter Systems date: 2008-12-17 words: 11947.0 sentences: 681.0 pages: flesch: 41.0 cache: ./cache/cord-000128-t74b5j2j.txt txt: ./txt/cord-000128-t74b5j2j.txt summary: In this review, we will concentrate on peptide-mediated delivery of siRNAs and steric block oligonucleotides and discuss different methods for quantitative assessment of the amount of cargo taken up and how to correlate those numbers with biological effects by applying easy to handle reporter systems. The focus of this article is recent progress in the field of peptide-mediated cellular delivery of siRNA and steric block oligonucleotides in cell tissue culture as a starting point for further developments illustrated by own experimental data. In contrast to many noncovalent CPP-mediated siRNA delivery approaches, efficient splice correction was only achieved with conjugates of peptide and steric block oligonucleotide. As outlined above, our quantitative studies along with microscopic analyses of siRNAs and steric block oligonucleotides using either a peptide or a commercially availably cationic lipid as carrier clearly show that less than 0.1% -5% of molecules taken up are involved in a biological response, i.e. RNAimediated down regulation or splice correction-mediated up regulation of reporter gene activity. abstract: Cellular uptake of therapeutic oligonucleotides and subsequent intracellular trafficking to their target sites represents the major technical hurdle for the biological effectiveness of these potential drugs. Accordingly, laboratories worldwide focus on the development of suitable delivery systems. Among the different available non-viral systems like cationic polymers, cationic liposomes and polymeric nanoparticles, cell-penetrating peptides (CPPs) represent an attractive concept to bypass the problem of poor membrane permeability of these charged macromolecules. While uptake per se in most cases does not represent the main obstacle of nucleic acid delivery in vitro, it becomes increasingly apparent that intracellular trafficking is the bottleneck. As a consequence, in order to optimize a given delivery system, a side-by-side analysis of nucleic acid cargo internalized and the corresponding biological effect is required to determine the overall efficacy. In this review, we will concentrate on peptide-mediated delivery of siRNAs and steric block oligonucleotides and discuss different methods for quantitative assessment of the amount of cargo taken up and how to correlate those numbers with biological effects by applying easy to handle reporter systems. To illustrate current limitations of non-viral nucleic acid delivery systems, we present own data as an example and discuss options of how to enhance trafficking of molecules entrapped in cellular compartments. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778081/ doi: 10.2174/138161208786898806 id: cord-000937-8vk89i4h author: Law, John title: Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool date: 2013-04-17 words: 6644.0 sentences: 332.0 pages: flesch: 50.0 cache: ./cache/cord-000937-8vk89i4h.txt txt: ./txt/cord-000937-8vk89i4h.txt summary: RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Seven RNA libraries (aihP01, hbvP02, hcvP02, hcvP03, hcvP05, nshP01, norP01) and seven DNA libraries (aihP01D, hbvP02D, hcvP02D, hcvP03D, hcvP05D, nshP01D, norP01D) were constructed from patients with autoimmune hepatitis (AIH), hepatitis B virus (HBV) chronic infection, hepatitis C virus (HCV) chronic infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR). Plasma samples were obtained from patients with autoimmune hepatitis (AIH), chronic hepatitis B virus (HBV) infection, chronic hepatitis C virus (HCV) infection, non-alcoholic steatohepatitis (NASH), and healthy subjects (NOR); each RNA library was named by diagnosis (e.g. aihP01) and a suffix ''D'' was added for each DNA library (e.g. aihP01D). To a lesser extent (about one read per million), we also detected sequences resembling RNA viruses in our DNA libraries (Supplemental Tables S15-S28 ). Assembly of viral sequences was also possible for all viruses shown in Figure 2 as the most abundant virus in each library (data not shown). abstract: We conducted an unbiased metagenomics survey using plasma from patients with chronic hepatitis B, chronic hepatitis C, autoimmune hepatitis (AIH), non-alcoholic steatohepatitis (NASH), and patients without liver disease (control). RNA and DNA libraries were sequenced from plasma filtrates enriched in viral particles to catalog virus populations. Hepatitis viruses were readily detected at high coverage in patients with chronic viral hepatitis B and C, but only a limited number of sequences resembling other viruses were found. The exception was a library from a patient diagnosed with hepatitis C virus (HCV) infection that contained multiple sequences matching GB virus C (GBV-C). Abundant GBV-C reads were also found in plasma from patients with AIH, whereas Torque teno virus (TTV) was found at high frequency in samples from patients with AIH and NASH. After taxonomic classification of sequences by BLASTn, a substantial fraction in each library, ranging from 35% to 76%, remained unclassified. These unknown sequences were assembled into scaffolds along with virus, phage and endogenous retrovirus sequences and then analyzed by BLASTx against the non-redundant protein database. Nearly the full genome of a heretofore-unknown circovirus was assembled and many scaffolds that encoded proteins with similarity to plant, insect and mammalian viruses. The presence of this novel circovirus was confirmed by PCR. BLASTx also identified many polypeptides resembling nucleo-cytoplasmic large DNA viruses (NCLDV) proteins. We re-evaluated these alignments with a profile hidden Markov method, HHblits, and observed inconsistencies in the target proteins reported by the different algorithms. This suggests that sequence alignments are insufficient to identify NCLDV proteins, especially when these alignments are only to small portions of the target protein. Nevertheless, we have now established a reliable protocol for the identification of viruses in plasma that can also be adapted to other patient samples such as urine, bile, saliva and other body fluids. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629200/ doi: 10.1371/journal.pone.0060595 id: cord-008575-bbpmlo3c author: Lawton, Jeffrey A title: Mechanism of genome transcription in segmented dsRNA viruses date: 2004-01-07 words: 15879.0 sentences: 753.0 pages: flesch: 43.0 cache: ./cache/cord-008575-bbpmlo3c.txt txt: ./txt/cord-008575-bbpmlo3c.txt summary: Although no reconstitution system is yet available for any of the reoviruses, studies conducted using baculovirusexpressed recombinant rotavirus-like particles containing the viral RNA polymerase coexpressed with the inner capsid protein have begun to clarify the mechanism by which the dsRNA genome is synthesized from the mRNA templates in rotavirus Patton et al., 1996; Zeng et al., 1996) . One of the more interesting observations about the life cycle of dsRNA viruses is that genome transcription occurs only within structurally intact TCPs. In rotavirus, the transcriptionally competent form of the virus has a double-layered capsid consisting of the structural proteins VP2 and VP6 surrounding the dsRNA genome segments and the enzymatic machinery in the core. Although observation of the actively transcribing rotavirus particle by electron cryomicroscopy has not provided a clear definition of the pathway of mRNA translocation through the inner capsid layer, atomic resolution structural studies of the bluetongue virus TCP have suggested a possible route (Grimes et al., 1998) . abstract: This chapter discusses the mechanism of genome transcription in segmented double-stranded RNA (dsRNA) viruses. Genome transcription is a critical stage in the life cycle of a virus, as this is the process by which the viral genetic information is presented to the host cell protein-synthesis machinery for the production of the viral proteins needed for genome replication and progeny virion assembly. Viruses with dsRNA genomes face a particular challenge in that host cells do not produce proteins that can transcribe from a dsRNA template. One of the more striking observations about genome transcription in dsRNA viruses is that this process occurs efficiently only when the transcriptionally competent particle is fully intact. This observation suggests that all of the components of the transcriptionally competent particle, including the viral genome, the transcription enzymes, and the viral capsid, function together to produce and release messenger RNA transcripts and that each component has a specific and critical role to play in promoting the efficiency of this process. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7131957/ doi: 10.1016/s0065-3527(00)55004-0 id: cord-278186-t3izmz6n author: Le Naour, Julie title: Trial watch: TLR3 agonists in cancer therapy date: 2020-06-02 words: 7615.0 sentences: 473.0 pages: flesch: 40.0 cache: ./cache/cord-278186-t3izmz6n.txt txt: ./txt/cord-278186-t3izmz6n.txt summary: ABBREVIATIONS: cDC, conventional dendritic cell; CMT, cytokine modulating treatment; CRC, colorectal carcinoma; CTL, cytotoxic T lymphocyte; DC, dendritic cell; dsRNA, double-stranded RNA; FLT3LG, fms-related receptor tyrosine kinase 3 ligand; HNSCC, head and neck squamous cell carcinoma; IFN, interferon; IL, interleukin; ISV, in situ vaccine; MUC1, mucin 1, cell surface associated; PD-1, programmed cell death 1; PD-L1, programmed death-ligand 1; polyA:U, polyadenylic:polyuridylic acid; polyI:C, polyriboinosinic:polyribocytidylic acid; TLR, Toll-like receptor Alongside, a pilot study on patients with metastatic HNSCC and melanoma who received intratumoral or intramuscular Hiltonol™ reported clinical benefits for at least one of the 8 individuals enrolled in this trial, coupled to moderate side effects (such as inflammation at the injection site and fatigue) as well as increased levels of CD4, CD8, PD-1, and PD-L1 in tumors, confirming the activation of systemic immunity. abstract: Toll-like receptor 3 (TLR3) is a pattern recognition receptor that senses exogenous (viral) as well as endogenous (mammalian) double-stranded RNA in endosomes. On activation, TLR3 initiates a signal transduction pathway that culminates with the secretion of pro-inflammatory cytokines including type I interferon (IFN). The latter is essential not only for innate immune responses to infection but also for the initiation of antigen-specific immunity against viruses and malignant cells. These aspects of TLR3 biology have supported the development of various agonists for use as stand-alone agents or combined with other therapeutic modalities in cancer patients. Here, we review recent preclinical and clinical advances in the development of TLR3 agonists for oncological disorders. ABBREVIATIONS: cDC, conventional dendritic cell; CMT, cytokine modulating treatment; CRC, colorectal carcinoma; CTL, cytotoxic T lymphocyte; DC, dendritic cell; dsRNA, double-stranded RNA; FLT3LG, fms-related receptor tyrosine kinase 3 ligand; HNSCC, head and neck squamous cell carcinoma; IFN, interferon; IL, interleukin; ISV, in situ vaccine; MUC1, mucin 1, cell surface associated; PD-1, programmed cell death 1; PD-L1, programmed death-ligand 1; polyA:U, polyadenylic:polyuridylic acid; polyI:C, polyriboinosinic:polyribocytidylic acid; TLR, Toll-like receptor url: https://doi.org/10.1080/2162402x.2020.1771143 doi: 10.1080/2162402x.2020.1771143 id: cord-002439-wesyiymn author: Le, My-Tra title: Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch date: 2017-02-13 words: 12389.0 sentences: 589.0 pages: flesch: 60.0 cache: ./cache/cord-002439-wesyiymn.txt txt: ./txt/cord-002439-wesyiymn.txt summary: For this current report, optical tweezers (OT), a type of single molecule force spectroscopy, and steered molecular dynamic simulations (SMD) were used to examine the folding/unfolding pathways of the TSS. One possibility for why the TSS-only fragment was not stable was the omission of the upstream 5A, as it was subsequently shown that adjacent doublet mutations in 5A (positions 8 and 9 in Figure 1A ) or single mutations disrupting É 3 caused identical enhancements in flexibility of residues throughout the 5A/H4a/É 3 region as assayed Hairpins H4a, H4b and H5 and tertiary interactions É 2 and É 3 comprise the TSS. Initial explicit solvent SMD simulations performed on fragment TSS108 (C 5 through A 112 ) at pulling speeds of 1.0 Å /ps and 0.5 Å /ps terminated with H5 and H4b helices remaining partly basepaired, indicating that the RNA chain was ahead of its approximate equilibrium state. abstract: Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3’UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ(3) required five upstream adenylates, and H4a/Ψ(3) was necessary for cooperative association of two other hairpins (H5/H4b) in Mg(2+). SMD recapitulated the TSS unfolding order in the absence of Mg(2+), showed dependence of the resistance to pulling on the 3D orientation and gave structural insights into the measured contour lengths of the TSS structure elements. Adenylate mutations eliminated one-site RdRp binding to the 3’UTR, suggesting that RdRp binding to the adenylates disrupts H4a/Ψ(3), leading to loss of H5/H4b interaction and promoting a conformational switch interrupting translation and promoting replication. DOI: http://dx.doi.org/10.7554/eLife.22883.001 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5336357/ doi: 10.7554/elife.22883 id: cord-267027-diwm1940 author: Le, Shu-Yun title: Conserved tertiary structure elements in the 5′ untranslated region of human enteroviruses and rhinoviruses date: 1992-12-31 words: 4348.0 sentences: 270.0 pages: flesch: 59.0 cache: ./cache/cord-267027-diwm1940.txt txt: ./txt/cord-267027-diwm1940.txt summary: Abstract A combination of comparative sequence analysis and thermodynamic methods reveals the conservation of tertiary structure elements in the 5′ untranslated region (UTR) of human enteroviruses and rhinoviruses. Base pairings between highly conserved 17-nucleotide (nt) and 21-nt sequences in the 5′ UTR of human enteroviruses and rhinoviruses constitute a predicted pseudoknot that is significantly more stable than those that can be formed from a large set of randomly shuffled sequences. The predicted pseudoknots, K2 (tertiary interactions: between the region 497-501 and 550-554) and K3 (579-581 and 600-602) in the RLP of PV2L were found to be totally conserved in all 22 human enteroviruses and rhinoviruses. Based on the common RNA secondary structures (Le and Zuker, 1990 ) of the 5'' UTR in 18 human enteroviruses and rhinoviruses, two sequences complementary to the highly conserved polypyrimidine sequence in all picornaviruses were identified in human 18 S rRNA . abstract: Abstract A combination of comparative sequence analysis and thermodynamic methods reveals the conservation of tertiary structure elements in the 5′ untranslated region (UTR) of human enteroviruses and rhinoviruses. The predicted common structural elements occur in the 3′ end of a segment that is critical for internal ribosome binding, termed “ribosome landing pad” (RLP), of polioviruses. Base pairings between highly conserved 17-nucleotide (nt) and 21-nt sequences in the 5′ UTR of human enteroviruses and rhinoviruses constitute a predicted pseudoknot that is significantly more stable than those that can be formed from a large set of randomly shuffled sequences. A conserved single-stranded polypyrimidine tract is located between two conserved tertiary elements. R. Nicholson, J. Pelletier, S.-Y. Le, and N. Sonenberg (1991, J. Virol. 65, 5886–5894) demonstrated that the point mutations of 3-nt UUU out of an essential 4-nt pyrimidine stretch sequence UUUC abolished translation. Structural analysis of the mutant sequence indicates that small point mutations within the short polypyrimidine sequence would destroy the tertiary interaction in the predicted, highly ordered structure. The proposed common tertiary structure can offer experimentalists a model upon which to extend the interpretations for currently available data. Based on these structural features possible base-pairing models between human enteroviruses and 18 S rRNA and between human rhinoviruses and 18 S rRNA are proposed. The proposed common structure implicates a biological function for these sequences in translational initiation. url: https://www.sciencedirect.com/science/article/pii/004268229290261M doi: 10.1016/0042-6822(92)90261-m id: cord-013412-gj443yei author: Lebedeva, Natalya Sh. title: The Application of Porphyrins and Their Analogues for Inactivation of Viruses date: 2020-09-23 words: 13428.0 sentences: 626.0 pages: flesch: 46.0 cache: ./cache/cord-013412-gj443yei.txt txt: ./txt/cord-013412-gj443yei.txt summary: The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. A cationic substituent is necessary to increase the solubility of porphyrins and their analogues in aqueous media, and three nitro groups provide linking of the gp120 protein with the glycoprotein ( Figure 3 ) and thereby inhibit fusion between the virus and the cell membrane. abstract: The problem of treating viral infections is extremely relevant due to both the emergence of new viral diseases and to the low effectiveness of existing approaches to the treatment of known viral infections. This review focuses on the application of porphyrin, chlorin, and phthalocyanine series for combating viral infections by chemical and photochemical inactivation methods. The purpose of this review paper is to summarize the main approaches developed to date in the chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogues and to analyze and discuss the information on viral targets and antiviral activity of porphyrins, chlorins, of their conjugates with organic/inorganic compounds obtained in the last 10–15 years in order to identify the most promising areas. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7583985/ doi: 10.3390/molecules25194368 id: cord-288669-46tkedw7 author: Lee, Changhee title: The small envelope protein of porcine reproductive and respiratory syndrome virus possesses ion channel protein-like properties date: 2006-11-10 words: 9258.0 sentences: 455.0 pages: flesch: 51.0 cache: ./cache/cord-288669-46tkedw7.txt txt: ./txt/cord-288669-46tkedw7.txt summary: P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Our study suggests that the PRRSV E protein may function as a viroporin in the virion envelope that facilitates uncoating of the virus in order to release the genomic RNA into the cytoplasm for subsequent replication. At 24 h postinoculation, Marc-145 cells were fixed, and virus infection was examined by immunofluorescent staining with N-specific MAb. Marc-145 cells inoculated with a culture fluid from cells cotransfected with P129-ΔE and E gene showed bright N-specific fluorescent signal, indicating that the P129-ΔE replication may be rescued by trans-complementation of the E protein (Fig. 2C ). Strand-specific RT-PCR experiments were carried out and demonstrated that PRRSV-infected Marc-145 cells produced reduced levels of positive-sense genomic RNA at 2 days post-infection in the presence of the drugs chloroquine, amantadine and verapamil (Fig. 5A, upper panel) . abstract: The small envelope (E) protein of porcine reproductive and respiratory syndrome virus (PRRSV) is a hydrophobic 73 amino acid protein encoded in the internal open reading frame (ORF) of the bicistronic mRNA2. As a first step towards understanding the biological role of E protein during PRRSV replication, E gene expression was blocked in a full-length infectious clone by mutating the ATG translational initiation to GTG, such that the full-length mutant genomic clone was unable to synthesize the E protein. DNA transfection of PRRSV-susceptible cells with the E gene knocked-out genomic clone showed the absence of virus infectivity. P129-ΔE-transfected cells however produced virion particles in the culture supernatant, and these particles contained viral genomic RNA, demonstrating that the E protein is essential for PRRSV infection but dispensable for virion assembly. Electron microscopy suggests that the P129-ΔE virions assembled in the absence of E had a similar appearance to the wild-type particles. Strand-specific RT-PCR demonstrated that the E protein-negative, non-infectious P129-ΔE virus particles were able to enter cells but further steps of replication were interrupted. The entry of PRRSV has been suggested to be via receptor-mediated endocytosis, and lysomotropic basic compounds and known ion-channel blocking agents both inhibited PRRSV replication effectively during the uncoating process. The expression of E protein in Escherichia coli-mediated cell growth arrests and increased the membrane permeability. Cross-linking experiments in cells infected with PRRSV or transfected with E gene showed that the E protein was able to form homo-oligomers. Taken together, our data suggest that the PRRSV E protein is likely an ion-channel protein embedded in the viral envelope and facilitates uncoating of virus and release of the genome in the cytoplasm. url: https://api.elsevier.com/content/article/pii/S0042682206004521 doi: 10.1016/j.virol.2006.07.013 id: cord-328737-6mcefqn5 author: Lee, Eun Yeong title: A novel nucleic acid amplification system based on nano-gap embedded active disk resonators date: 2020-05-26 words: 4147.0 sentences: 181.0 pages: flesch: 45.0 cache: ./cache/cord-328737-6mcefqn5.txt txt: ./txt/cord-328737-6mcefqn5.txt summary: We here describe for the first time a novel nucleic acid amplification system based on nano-gap active resonators that can be used for in various molecular diagnostic applications, which requires a label-free and real-time detection with rapidity and high sensitivity. First, SRSN active disk resonators were used as photoluminescence sensors for the PL peaks J o u r n a l P r e -p r o o f generated by the direct amplification of nucleic acids on the sensor surface in a label-free and real-time manner. These complexes bind to the target nucleic acids and enable the strand exchange which will begin the amplification process both on the surface of disk resonator (solid) and solution simultaneously ( Fig. 1-rectangle) , with the temperature maintained at isothermal conditions (38°C or 43°C for DNA or RNA, respectively). This photoluminescence sensor enables label-free and real-time amplification and direct detection of either bacterial DNA or viral RNA on the resonator surface. abstract: Recent advances in nucleic acid based testing using bio-optical sensor approaches have been introduced but most are based on hybridization between the optical sensor and the bio-molecule and not on an amplification mechanism. Direct nucleic acid amplification on an optical sensor has several technical limitations, such as the sensitivity of the temperature sensor, instrument complexity, and high background signal. We here describe a novel nucleic acid amplification method based on a whispering gallery mode active resonator and discuss its potential molecular diagnostic application. By implanting nanoclusters as active compounds, this active resonator operates without tapered fiber coupling and emits a strong photoluminescence signal with low background in the wavelength of low absorption in an aqueous environment that is typical of biosensors. Our method also offers an extremely low detection threshold down to a single copy within 10 min due to the strong light-matter interaction in a nano-gap structure. We envision that this active resonator provides a high refractive index contrast for tight mode confinement with simple alignment as well as the possibility of reducing the device size so that a point-of-care system with low-cost, high-sensitivity and simplicity. url: https://www.ncbi.nlm.nih.gov/pubmed/32501366/ doi: 10.1016/j.snb.2020.128351 id: cord-345630-bam3pa70 author: Lee, Han-Jung title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase date: 1991-02-28 words: 5973.0 sentences: 418.0 pages: flesch: 65.0 cache: ./cache/cord-345630-bam3pa70.txt txt: ./txt/cord-345630-bam3pa70.txt summary: authors: Lee, Han-Jung; Shieh, Chien-Kou; Gorbalenya, Alexander E.; Koonin, Eugene V.; La Monica, Nicola; Tuler, Jeremy; Bagdzhadzhyan, Anush; Lai, Michael M.C. title: The complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase Third, the 3''-half of the gene 1 sequences of IBV and MHV-A59 contains the sequence motifs for RNA polymerase and helicase, which are the activities expected to be involved in RNA synthesis Gorbalenya et a/., 198913; Bredenbeek et a/., 1990) . The alignment of amino acids in ORF la of MHV-JHM and IBV showed that there are four possible stretches of moderate homology which are separated by highly diverged sequences (Fig. 8) . Although ORF la is highly diverged between MHV-JHM and IBV, common functional domains could be identified in this ORF of both viruses by detailed amino acid sequence analysis (see Materials and Methods) (Fig. 9 ). abstract: Abstract The 5′-most gene, gene 1, of the genome of murine coronavirus, mouse hepatitis virus (MHV), is presumed to encode the viral RNA-dependent RNA polymerase. We have determined the complete sequence of this gene of the JHM strain by cDNA cloning and sequencing. The total length of this gene is 21,798 nucleotides long, which includes two overlapping, large open reading frames. The first open reading frame, ORF 1 a, is 4488 amino acids long. The second open reading frame, ORF 1 b, overlaps ORF 1 a for 75 nucleotides, and is 2731 amino acids long. The overlapping region may fold into a pseudoknot RNA structure, similar to the corresponding region of the RNA of avian coronavirus, infectious bronchitis virus (IBV). The in vitro transcription and translation studies of this region indicated that these two ORFs were most likely translated into one polyprotein by a ribosomal frameshifting mechanism. Thus, the predicted molecular weight of the gene 1 product is more than 800,000 Da. The sequence of ORF 1 b is very similar to the corresponding ORF of IBV. In contrast, the ORF 1 a of these two viruses differ in size and have a high degree of divergence. The amino acid sequence analysis suggested that ORF 1 a contains several functional domains, including two hydrophobic, membrane-anchoring domains, and three cysteine-rich domains. It also contains a picornaviral 3C-like protease domain and two papain-like protease domains. The presence of these protease domains suggests that the polyprotein is most likely processed into multiple protein products. In contrast, the ORF 1b contains polymerase, helicase, and zinc-finger motifs. These sequence studies suggested that the MHV gene 1 product is involved in RNA synthesis, and that this product is processed autoproteolytically after translation. This study completes the sequence of the MHV genome, which is 31 kb long, and constitutes the largest viral RNA known. url: https://api.elsevier.com/content/article/pii/004268229190071I doi: 10.1016/0042-6822(91)90071-i id: cord-306754-qohrnpgq author: Lee, Justin S. title: Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species date: 2017-05-23 words: 7158.0 sentences: 335.0 pages: flesch: 48.0 cache: ./cache/cord-306754-qohrnpgq.txt txt: ./txt/cord-306754-qohrnpgq.txt summary: Our report provides advances in investigating several important aspects of TGC assay design, including (i) the range of fold enrichment possible for targeted nucleic acids, (ii) comparison of TGC pathogen detection with traditional methods currently used by diagnostic laboratories, (iii) documentation that a single assay design can be applied to more than one host species, (iv) the applicability of TGC to characterize pathogens in the context of veterinary medicine, and (v) the ability of TGC-NGS to characterize intrahost genetic diversity of viral pathogens (4) (5) (6) . Mean enrichment values of 250,000-fold and 9,100,000-fold with the DNA and RNA probes, respectively, and 147,000-fold for FIV contained in tissues clearly demonstrate the ability of the targeted capture probes to dramatically alter the relative abundance of specific nucleic acids across a range of sample types and diverse pathogen taxa. abstract: Traditional diagnostic assays often lack sensitivity and can be difficult to multiplex across many pathogens. Next-generation sequencing (NGS) can overcome some of these problems but has limited application in the detection of low-copy-number pathogens in complex samples. Targeted genome capture (TGC) utilizes oligonucleotide probes to enrich specific nucleic acids in heterogeneous extracts and can therefore increase the proportion of NGS reads for low-abundance targets. While earlier studies have demonstrated the utility of this technology for detection of novel pathogens in human clinical samples, the capacity and practicality of TGC-NGS in a veterinary diagnostic setting have not yet been evaluated. Here we report the use of TGC-NGS assays for the detection and characterization of diverse feline pathogen taxa. We detected 31 pathogens comprising nine pathogen taxa in 28 felid samples analyzed. This included 20 pathogens detected via traditional PCR and 11 additional pathogens that had not been previously detected in the same samples. Most of the pathogens detected were sequenced at sufficient breadth and depth to confidently classify them at the species or subspecies level. Target nucleic acids were enriched from a low of 58-fold to 56 million-fold relative to host nucleic acids. Despite the promising performance of these assays, a number of pathogens detected by conventional PCR or serology were not isolated by TGC-NGS, suggesting that further validation is required before this technology can be used in lieu of quality-controlled standard assays. We conclude that TGC-NGS offers great potential as a broad multiplex pathogen characterization assay in veterinary diagnostic and research settings. url: https://www.ncbi.nlm.nih.gov/pubmed/28330894/ doi: 10.1128/jcm.01463-16 id: cord-341502-jlzufa28 author: Lee, Sungyul title: The SARS-CoV-2 RNA interactome date: 2020-11-02 words: 5845.0 sentences: 362.0 pages: flesch: 51.0 cache: ./cache/cord-341502-jlzufa28.txt txt: ./txt/cord-341502-jlzufa28.txt summary: The second pool of 275 oligos ("Probe II") covers the remaining region (21563:29872, NC_045512.2) which is shared by both the gRNA and sgRNAs. To first check whether our method specifically captures the viral RNP complexes, we compared the resulting purification from Vero cells infected with SARS-CoV-2 (BetaCoV/Korea/KCDC03/2020) at MOI 0.1 for 24 hours (Kim et al., 2020b ) by either Probe I or Probe II. In combination, we define these 109 proteins as the "SARS-CoV-2 RNA interactome." 37 host proteins such as CSDE1 (Unr), EIF4H, FUBP3, G3BP2, PABPC1, ZC3HAV1 were enriched in both the Probe I and Probe II RNP capture experiments on infected cells ( Figure 1F ), thus identifying a robust set of the "core SARS-CoV-2 RNA interactome." Gene ontology (GO) term enrichment analysis revealed that these host factors are involved in RNA stability control, mRNA function, and viral process ( Figure S1F ). To measure the impact of these host proteins on coronavirus RNAs, we conducted knockdown experiments and infected Calu-3 cells with SARS-CoV-2 ( Figure 5A and 5B). abstract: SARS-CoV-2 is an RNA virus whose success as a pathogen relies on its ability to repurpose host RNA-binding proteins (RBPs) to form its own RNA interactome. Here, we developed and applied a robust ribonucleoprotein capture protocol to uncover the SARS-CoV-2 RNA interactome. We report 109 host factors that directly bind to SARS-CoV-2 RNAs including general antiviral factors such as ZC3HAV1, TRIM25, and PARP12. Applying RNP capture on another coronavirus HCoV-OC43 revealed evolutionarily conserved interactions between viral RNAs and host proteins. Network and transcriptome analyses delineated antiviral RBPs stimulated by JAK-STAT signaling and proviral RBPs responsible for hijacking multiple steps of the mRNA life cycle. By knockdown experiments, we further found that these viral-RNA-interacting RBPs act against or in favor of SARS-CoV-2. Overall, this study provides a comprehensive list of RBPs regulating coronaviral replication and opens new avenues for therapeutic interventions. url: https://doi.org/10.1101/2020.11.02.364497 doi: 10.1101/2020.11.02.364497 id: cord-317720-gbi11oxx author: Lefferts, Joel A. title: Implementation of an Emergency Use Authorization Test During an Impending National Crisis date: 2020-05-14 words: 2148.0 sentences: 80.0 pages: flesch: 39.0 cache: ./cache/cord-317720-gbi11oxx.txt txt: ./txt/cord-317720-gbi11oxx.txt summary: Concerned that the efforts of state laboratories would be further impacted by lack of resources, we began to identify sources -including the WHO, the CDC, and commercial vendors -of the required primers and probes for the reverse transcriptase polymerase chain reaction (RT-PCR) detection of the virus and placed orders for test reagents from potential suppliers. The document provided guidance for high complexity testing laboratories developing SARS-CoV-2 tests for submission for Emergency Use Authorization (EUA) status with respect to required validation experiments and reporting to the FDA. Initially laboratories were required to spike RNA transcripts into previously extracted nucleic acid from negative samples for the CDC assay to determine the limit of detection but this had its own challenges of not representing extraction of true clinical samples and issues with degradation were identified. Our plan included the production of enough contrived clinical specimens and control material to proceed with validation or verification of the multiple (laboratory-developed and CDC EUA) tests that we were evaluating. abstract: Abstract The laboratory response to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic may be termed heroic. From the identification of the novel coronavirus to implementation of routine laboratory testing around the world to the development of potential vaccines, laboratories have played a critical role in the efforts to curtail this pandemic. In this brief report, we review our own effort at a mid-sized, rural, academic medical center to implement a molecular test for the virus; and, we share insights and lessons learned from that process which might be helpful in similar situations in the future. url: https://www.sciencedirect.com/science/article/pii/S1525157820303251?v=s5 doi: 10.1016/j.jmoldx.2020.05.001 id: cord-289965-qcezqpze author: Lehmann, Kathleen C. title: Arterivirus nsp12 versus the coronavirus nsp16 2′-O-methyltransferase: comparison of the C-terminal cleavage products of two nidovirus pp1ab polyproteins date: 2015-09-01 words: 6580.0 sentences: 356.0 pages: flesch: 50.0 cache: ./cache/cord-289965-qcezqpze.txt txt: ./txt/cord-289965-qcezqpze.txt summary: The 39-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 29-O-methyltransferase (29-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 59 cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 59 cap although no candidate MTases have been identified thus far. The 39-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 29-O-methyltransferase (29-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 59 cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 59 cap although no candidate MTases have been identified thus far. abstract: The 3′-terminal domain of the most conserved ORF1b in three of the four families of the order Nidovirales (except for the family Arteriviridae) encodes a (putative) 2′-O-methyltransferase (2′-O-MTase), known as non structural protein (nsp) 16 in the family Coronaviridae and implicated in methylation of the 5′ cap structure of nidoviral mRNAs. As with coronavirus transcripts, arterivirus mRNAs are assumed to possess a 5′ cap although no candidate MTases have been identified thus far. To address this knowledge gap, we analysed the uncharacterized nsp12 of arteriviruses, which occupies the ORF1b position equivalent to that of the nidovirus 2′-O-MTase (coronavirus nsp16). In our in-depth bioinformatics analysis of nsp12, the protein was confirmed to be family specific whilst having diverged much further than other nidovirus ORF1b-encoded proteins, including those of the family Coronaviridae. Only one invariant and several partially conserved, predominantly aromatic residues were identified in nsp12, which may adopt a structure with alternating α-helices and β-strands, an organization also found in known MTases. However, no statistically significant similarity was found between nsp12 and the twofold larger coronavirus nsp16, nor could we detect MTase activity in biochemical assays using recombinant equine arteritis virus (EAV) nsp12. Our further analysis established that this subunit is essential for replication of this prototypic arterivirus. Using reverse genetics, we assessed the impact of 25 substitutions at 14 positions, yielding virus phenotypes ranging from WT-like to non-viable. Notably, replacement of the invariant phenylalanine 109 with tyrosine was lethal. We concluded that nsp12 plays an essential role during EAV replication, possibly by acting as a co-factor for another enzyme. url: https://www.ncbi.nlm.nih.gov/pubmed/26041874/ doi: 10.1099/vir.0.000209 id: cord-284707-72vx11aq author: Leibowitz, Julian L. title: Synthesis of virus-specific RNA in permeabilized murine coronavirus-infected cells date: 1988-09-30 words: 5498.0 sentences: 316.0 pages: flesch: 53.0 cache: ./cache/cord-284707-72vx11aq.txt txt: ./txt/cord-284707-72vx11aq.txt summary: For mouse hepatitis virus (MHV), one of the most extensively studied coronaviruses, there are seven species of MHV-specific mRNA present in infected cells, the largest of which is indistinguishable from virion RNA (Leibowitz et a/., 1981; Lai et a/., 1981; Spaan et a/., 1981) . In this paper we report the characteristics of a permeabilized cell system and demonstrate that it incorporates ribonucle-otide triphosphates into RNA molecules which appear identical to the virus-specific mRNAs synthesized in MHV-infected cells. Protease inhibitors and RNase inhibitors have both been reported to increase the RNA-dependent RNA polymerase activity present in extracts of West Nile virus-infected cells (Grun and Brinton, 1986) . The kinetics of the development of the MHV-specific RNA polymerase activity over the course of infection was determined in permeabilized cells. In this work we report the development and characterization of a permeabilized cell system for assaying MHV-specific RNA polymerase activity. abstract: Abstract We have developed a permeabilized cell system for assaying mouse hepatitis virus-specific RNA polymerase activity. This activity was characterized as to its requirements for mono- and divalent cations, requirements for an exogenous energy source, and pH optimum. This system faithfully reflects MHV-specific RNA synthesis in the intact cell, with regard to both its time of appearance during the course of infection and the products synthesized. The system is efficient and the RNA products were identical to those observed in intact MHV-infected cells as judged by agarose gel electrophoresis and hybridization. Permeabilized cells appear to be an ideal system for studying coronavirus RNA synthesis since they closely mimic in vivo conditions while allowing much of the experimental flexibility of truly cell-free systems. url: https://api.elsevier.com/content/article/pii/004268228890147X doi: 10.1016/0042-6822(88)90147-x id: cord-308835-999kewdw author: Leibowitz, Julian L. title: The virus-specific intracellular RNA species of two murine coronaviruses: MHV-A59 and MHV-JHM date: 1981-10-15 words: 6447.0 sentences: 404.0 pages: flesch: 56.0 cache: ./cache/cord-308835-999kewdw.txt txt: ./txt/cord-308835-999kewdw.txt summary: Abstract Seven virus-specific, polyadenylated RNA species have been identified in mouse cells infected with the murine coronaviruses MHV-A59 (A59V) or MHV-JHM (JHMV). MHV-infected 17CL·1 cells were labeled with [32P]orthophosphate in the presence of actinomycin D and the cytoplasmic RNA was extracted and analyzed by agarose gel electrophoresis. The largest intracellular RNA species is identical to RNA isolated from purified virions, as determined by agarose gel electrophoresis and oligonucleotide fingerprint studies of ribonuclease T1 digests. Oligonucleotide fingerprints of the six subgenomic RNAS show that the sequences they contain are present in virion RNA, confirming their virus-specific nature. Identification of MHV-Specific RNA Species A59V, JHMV, and mock-infected cells were labeled with [32P]orthophosphate from 4 to 8 hpi in the presence of actinomycin D. To determine if there is temporal regulation of MHV-specific RNA synthesis, replicate cultures of A59V, JHMV, or mock-infected cells were pulse labeled for 1 hr at hourly intervals and the intracellular RNA was extracted and analyzed by gel electrophoresis. abstract: Abstract Seven virus-specific, polyadenylated RNA species have been identified in mouse cells infected with the murine coronaviruses MHV-A59 (A59V) or MHV-JHM (JHMV). MHV-infected 17CL·1 cells were labeled with [32P]orthophosphate in the presence of actinomycin D and the cytoplasmic RNA was extracted and analyzed by agarose gel electrophoresis. These RNA species range in size from 6.3 × 105 to 6.1 × 106 daltons. The A59V and JHMV-specific RNAs have identical molecular weights and comigrate in agarose gels. The largest intracellular RNA species is identical to RNA isolated from purified virions, as determined by agarose gel electrophoresis and oligonucleotide fingerprint studies of ribonuclease T1 digests. Oligonucleotide fingerprints of the six subgenomic RNAS show that the sequences they contain are present in virion RNA, confirming their virus-specific nature. The fingerprinting studies also demonstrate that the six subgenomic RNA species make up a nested set. The sequences present in each RNA species are also present in all larger RNA species. These larger RNAs also contain additional sequences consistent with their greater size. The subgenomic RNAs fulfull many of the criteria for mRNAs. Possible mechanisms for generating these RNAs are discussed. url: https://www.sciencedirect.com/science/article/pii/0042682281902506 doi: 10.1016/0042-6822(81)90250-6 id: cord-324928-cpryxa6p author: Lello, Laura Sandra title: Cross-utilisation of template RNAs by alphavirus replicases date: 2020-09-04 words: 13762.0 sentences: 646.0 pages: flesch: 50.0 cache: ./cache/cord-324928-cpryxa6p.txt txt: ./txt/cord-324928-cpryxa6p.txt summary: The differences between outgroup viruses and those belonging to the SFV complex had an impact on the design of the template RNAs. The 5'' region of the CHIKV genome contains seven SL structures that affect genome replication in mammalian and/or mosquito cells [33] . Cross-utilisation of template RNAs by alphavirus replicases structures can be predicted for RNAs of other members of the SFV complex (S1 Fig), the 5'' ends of the template RNAs of SFV, MAYV, RRV and ONNV had an identical design to that of the previously constructed CHIKV template, i.e. the 5'' UTR was followed by 231nt encoding the N-terminus of nsP1 [43] . The levels of Fluc and Gluc expression in human cells, transfected with plasmids expressing template RNA and corresponding polymerase negative control replicase (P1234 GAA ), were similar for trans-replicases derived from different viruses and the same was observed for Ae albopictus cells. abstract: Most alphaviruses (family Togaviridae) including Sindbis virus (SINV) and other human pathogens, are transmitted by arthropods. The first open reading frame in their positive strand RNA genome encodes for the non-structural polyprotein, a precursor to four separate subunits of the replicase. The replicase interacts with cis-acting elements located near the intergenic region and at the ends of the viral RNA genome. A trans-replication assay was developed and used to analyse the template requirements for nine alphavirus replicases. Replicases of alphaviruses of the Semliki Forest virus complex were able to cross-utilize each other’s templates as well as those of outgroup alphaviruses. Templates of outgroup alphaviruses, including SINV and the mosquito-specific Eilat virus, were promiscuous; in contrast, their replicases displayed a limited capacity to use heterologous templates, especially in mosquito cells. The determinants important for efficient replication of template RNA were mapped to the 5' region of the genome. For SINV these include the extreme 5'- end of the genome and sequences corresponding to the first stem-loop structure in the 5' untranslated region. Mutations introduced in these elements drastically reduced infectivity of recombinant SINV genomes. The trans-replicase tools and approaches developed here can be instrumental in studying alphavirus recombination and evolution, but can also be applied to study other viruses such as picornaviruses, flaviviruses and coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32886709/ doi: 10.1371/journal.ppat.1008825 id: cord-315909-vwugf0wp author: Letko, Michael title: Studying Evolutionary Adaptation of MERS-CoV date: 2019-09-14 words: 1236.0 sentences: 100.0 pages: flesch: 52.0 cache: ./cache/cord-315909-vwugf0wp.txt txt: ./txt/cord-315909-vwugf0wp.txt summary: Here, we describe methods for in vitro serial passaging of Middle East respiratory syndrome coronavirus (MERS-CoV) to select for mutations which increase replication on semi-permissive cell lines as described in Letko et al., Cell Rep 24, 1730–1737, 2018. Forced adaptation experiments have been used to determine viral mutations that facilitate escape from drugs [4] [5] [6] , monoclonal antibodies [7, 8] , host restriction factors [9] [10] [11] , and species variation in host receptors [12] [13] [14] and to elucidate various viral mechanisms of infection and replication [15] [16] [17] . Below is the method employed to adapt MERS-CoV to a semi-permissive host receptor, Desmodus rotundus DPP4. To increase selective pressures on a viral population which is beginning to show signs of adaptation, one can apply a population bottleneck in the subsequent passage by reducing the amount of viral Evolution of MERS-CoV supernatant passaged to the next cell culture. abstract: Forced viral adaptation is a powerful technique employed to study the ways viruses may overcome various selective pressures that reduce viral replication. Here, we describe methods for in vitro serial passaging of Middle East respiratory syndrome coronavirus (MERS-CoV) to select for mutations which increase replication on semi-permissive cell lines as described in Letko et al., Cell Rep 24, 1730–1737, 2018. url: https://www.ncbi.nlm.nih.gov/pubmed/31883083/ doi: 10.1007/978-1-0716-0211-9_1 id: cord-266520-n439dwcx author: Levanova, Alesia A. title: Enzymatically synthesized 2''-fluoro-modified Dicer-substrate siRNA swarms against herpes simplex virus demonstrate enhanced antiviral efficacy and low cytotoxicity date: 2020-08-13 words: 3615.0 sentences: 251.0 pages: flesch: 54.0 cache: ./cache/cord-266520-n439dwcx.txt txt: ./txt/cord-266520-n439dwcx.txt summary: The antiviral efficacy of the 2''-F-siRNA swarms and the elicited cellular innate responses did not correlate suggesting that innate immunity pathways do not significantly contribute to the observed enhanced antiviral activity of the modified siRNAs. The results support further applications of enzymatically produced siRNA molecules with incorporated adenosine nucleotides, carrying fluoro-modification on ribose C2'' position, for further antiviral studies in vitro and in vivo. We have previously generated three antiviral siRNA swarms against herpes simplex virus type 1 (HSV-1) mRNAs encoding essential viral proteins, including glycoprotein B (UL27), the infected cell protein 8 (ICP8; UL29), and ICP27 (UL54) (Romanovskaya et al., 2012; Paavilainen et al., 2016) . The siRNA swarm targeting mRNA of HSV single-stranded DNA binding protein ICP8, encoded by the UL29 gene, harbors a most pronounced antiviral effect (Paavilainen et al., 2016) and induces only minimal non-specific cellular responses (Romanovskaya et al., 2012) . abstract: Chemical modifications of small interfering (si)RNAs are used to enhance their stability and potency, and to reduce possible off-target effects, including immunogenicity. We have earlier introduced highly effective antiviral siRNA swarms against herpes simplex virus (HSV), targeting 653 bp of the essential UL29 viral gene. Here, we report a method for enzymatic production and antiviral use of 2’-fluoro-modified siRNA swarms. Utilizing the RNA-dependent RNA polymerase from bacteriophage phi6, we produced 2’-F-siRNA swarms containing either all or a fraction of modified adenosine, cytidine or uridine residues in the antisense strand of the UL29 target. The siRNA containing modified pyrimidines demonstrated high resistance to RNase A and the antiviral potency of all the UL29-specific 2’-F-siRNA swarms was 100-fold in comparison with the unmodified counterpart, without additional cytotoxicity. Modest stimulation of innate immunity signaling, including induced expression of both type I and type III interferons, as well as interferon-stimulated gene 54, by 2’-F-cytidine and 2’-F-uridine modified siRNA swarms occurred at early time points after transfection while the 2’-F-adenosine-containing siRNA was similar to the unmodified antiviral siRNA swarm in this respect. The antiviral efficacy of the 2’-F-siRNA swarms and the elicited cellular innate responses did not correlate suggesting that innate immunity pathways do not significantly contribute to the observed enhanced antiviral activity of the modified siRNAs. The results support further applications of enzymatically produced siRNA molecules with incorporated adenosine nucleotides, carrying fluoro-modification on ribose C2’ position, for further antiviral studies in vitro and in vivo. url: https://www.ncbi.nlm.nih.gov/pubmed/32798603/ doi: 10.1016/j.antiviral.2020.104916 id: cord-017968-17d37a2z author: Lewinski, Martin title: Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana date: 2018-08-30 words: 6560.0 sentences: 389.0 pages: flesch: 50.0 cache: ./cache/cord-017968-17d37a2z.txt txt: ./txt/cord-017968-17d37a2z.txt summary: Here, we discuss recent progress to obtain a systems-level understanding of in vivo RNA–protein interactions in the reference plant Arabidopsis thaliana using protein-centric and RNA-centric methods as well as combined protein binding site and structure probing. Among the RBPs present in the Arabidopsis genome are 197 proteins with an RNA recognition motif (RRM), the most abundant type of RNA-binding domain, and 28 K homology (KH) domain proteins first identified in mammalian heterogeneous nuclear protein hnRNP K (Silverman et al. Functional characterization of a glycine-rich RNA-binding protein 2 in Arabidopsis thaliana under abiotic stress conditions Glycine-rich RNA-binding proteins are functionally conserved in Arabidopsis thaliana and Oryza sativa during cold adaptation process The circadian clock regulated RNA-binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre-mRNA An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with target transcripts in Arabidopsis thaliana abstract: Proteins that specifically interact with mRNAs orchestrate mRNA processing steps all the way from transcription to decay. Thus, these RNA-binding proteins represent an important control mechanism to double check which proportion of nascent pre-mRNAs is ultimately available for translation into distinct proteins. Here, we discuss recent progress to obtain a systems-level understanding of in vivo RNA–protein interactions in the reference plant Arabidopsis thaliana using protein-centric and RNA-centric methods as well as combined protein binding site and structure probing. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122672/ doi: 10.1007/978-3-319-92967-5_5 id: cord-263334-wwkdum94 author: Li, Chen title: Cellular DDX3 regulates Japanese encephalitis virus replication by interacting with viral un-translated regions date: 2014-01-20 words: 7683.0 sentences: 423.0 pages: flesch: 54.0 cache: ./cache/cord-263334-wwkdum94.txt txt: ./txt/cord-263334-wwkdum94.txt summary: BHK-21 cells transfected with the DDX3 shRNA were infected with JEV (MOI¼ 0.01) for 48 h, Viral titers determined by plaque formation assay at 48 hpi. (F) BHK-21 cells transfected with different amounts of DDX3 shRNA plasmid were infected with JEV (MOI ¼0.01), 48 h later, the amount of virus released into the medium was determined by plaque formation assay. In order to determine whether cellular DDX3 is involved in virus assembly or release, the BHK-21 cells were transfected with DDX3 shRNA plasmid before being infected with JEV (MOI ¼0.01). The virus titers were detected 2 days later by plaque formation assay, the results showed that overexpression of DDX3r-K230E, DDX3r-S382L and the control plasmid pcDNA3.1 after DDX3 knockdown resulted in the reduction of JEV replication for 13-fold (p o0.01), 12-fold (p o0.01) and 15-fold (p o0.01). The DEAD-box RNA helicase DDX5 acts as a positive regulator of Japanese encephalitis virus replication by binding to viral 3′ UTR abstract: Japanese encephalitis virus is one of the most common causes for epidemic viral encephalitis in humans and animals. Herein we demonstrated that cellular helicase DDX3 is involved in JEV replication. DDX3 knockdown inhibits JEV replication. The helicase activity of DDX3 is crucial for JEV replication. GST-pulldown and co-immunoprecipitation experiments demonstrated that DDX3 could interact with JEV non-structural proteins 3 and 5. Co-immunoprecipitation and confocal microscopy analysis confirmed that DDX3 interacts and colocalizes with these viral proteins and viral RNA during the infection. We determined that DDX3 binds to JEV 5′ and 3′ un-translated regions. We used a JEV-replicon system to demonstrate that DDX3 positively regulates viral RNA translation, which might affect viral RNA replication at the late stage of virus infection. Collectively, we identified that DDX3 is necessary for JEV infection, suggesting that DDX3 might be a novel target to design new antiviral agents against JEV or other flavivirus infections. url: https://doi.org/10.1016/j.virol.2013.11.008 doi: 10.1016/j.virol.2013.11.008 id: cord-002687-ql6zo8ka author: Li, Dan title: A potent human neutralizing antibody Fc-dependently reduces established HBV infections date: 2017-09-26 words: 14698.0 sentences: 772.0 pages: flesch: 55.0 cache: ./cache/cord-002687-ql6zo8ka.txt txt: ./txt/cord-002687-ql6zo8ka.txt summary: Neutralizing antibodies (nAbs), in addition to their capacity to specifically block viral entry via Fab (fragment of antigen binding) recognition of virus, have been found to exert a variety of immunological ''effector'' functions, including clearance of circulatory viruses as well as by mediating cytotoxic killing or phagocytosis of infected cells (DiLillo et al., 2014; Corti et al., 2011; Bournazos et al., 2014; Bruel et al., 2016; Lu et al., 2016; Hessell et al., 2007) , or even possibly triggering sustained host immune responses in vivo Pelegrin et al., 2015) . In the present study, we took advantage of a large non-immune phage display human antibody library and our human NTCP-enabled HBV cell culture system (Yan et al., 2012; Sun et al., 2016) to identify a panel of nAbs that specifically target the preS1 domain. abstract: Hepatitis B virus (HBV) infection is a major global health problem. Currently-available therapies are ineffective in curing chronic HBV infection. HBV and its satellite hepatitis D virus (HDV) infect hepatocytes via binding of the preS1 domain of its large envelope protein to sodium taurocholate cotransporting polypeptide (NTCP). Here, we developed novel human monoclonal antibodies that block the engagement of preS1 with NTCP and neutralize HBV and HDV with high potency. One antibody, 2H5-A14, functions at picomolar level and exhibited neutralization-activity-mediated prophylactic effects. It also acts therapeutically by eliciting antibody-Fc-dependent immunological effector functions that impose durable suppression of viral infection in HBV-infected mice, resulting in reductions in the levels of the small envelope antigen and viral DNA, with no emergence of escape mutants. Our results illustrate a novel antibody-Fc-dependent approach for HBV treatment and suggest 2H5-A14 as a novel clinical candidate for HBV prevention and treatment of chronic HBV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5614562/ doi: 10.7554/elife.26738 id: cord-278250-dwok857k author: Li, Heng title: The altered gut virome community in rhesus monkeys is correlated with the gut bacterial microbiome and associated metabolites date: 2019-08-19 words: 7452.0 sentences: 379.0 pages: flesch: 44.0 cache: ./cache/cord-278250-dwok857k.txt txt: ./txt/cord-278250-dwok857k.txt summary: We performed metagenomic sequencing of fecal samples to detect the bacterial microbiome and virome composition of healthy one-year-old rhesus monkeys housed at the IMBCAMS (Fig. 1) . We comprehensively analyzed the interactions among the gut virome, bacterial microbiome and metabolomes based on the above results there were noticeable differences in bacterial β-diversity between control and experimental animals, as determined using principal component analysis (PCA), and the results showed good repeatability within a single group (Additional file 2: Figure S2F ). Briefly, the fecal virome composition was noticeably altered after depletion of the bacterial microbiome, and the abundances of many DNA viruses, bacteriophages and RNA viruses in the gut were clearly decreased. As expected, the whole gut bacterial microbiome, including gram-positive and gram-negative bacteria (Additional file 2: Figure S2E ), was depleted after treatment with the antibiotic cocktail, except for Escherichia-Shigella species belonging to Proteobacteria, which were resistant to the cocktail. abstract: BACKGROUND: The gut microbiome is closely associated with the health of the host; although the interaction between the bacterial microbiome and the whole virome has rarely been studied, it is likely of medical importance. Examination of the interactions between the gut bacterial microbiome and virome of rhesus monkey would significantly contribute to revealing the gut microbiome composition. METHODS: Here, we conducted a metagenomic analysis of the gut microbiome of rhesus monkeys in a longitudinal cohort treated with an antibiotic cocktail, and we documented the interactions between the bacterial microbiome and virome. The depletion of viral populations was confirmed at the species level by real-time PCR. We also detected changes in the gut metabolome by GC-MS and LC-MS. RESULTS: A majority of bacteria were depleted after treatment with antibiotics, and the Shannon diversity index decreased from 2.95 to 0.22. Furthermore, the abundance-based coverage estimator (ACE) decreased from 104.47 to 33.84, and the abundance of eukaryotic viruses also changed substantially. In the annotation, 6 families of DNA viruses and 1 bacteriophage family were present in the normal monkeys but absent after gut bacterial microbiome depletion. Intriguingly, we discovered that changes in the gut bacterial microbiome composition may promote changes in the gut virome composition, and tryptophan, arginine, and quinone may play roles in the interaction between the bacterial microbiome and virome. CONCLUSION: Our results indicated that the clearly altered composition of the virome was correlated with depletion in the bacterial community and that metabolites produced by bacteria possibly play important roles in the interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-019-1211-z) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-019-1211-z doi: 10.1186/s12985-019-1211-z id: cord-338901-1kzy7rts author: Li, Heng title: Overview of therapeutic drug research for COVID-19 in China date: 2020-06-17 words: 5098.0 sentences: 253.0 pages: flesch: 48.0 cache: ./cache/cord-338901-1kzy7rts.txt txt: ./txt/cord-338901-1kzy7rts.txt summary: According to the information that we have collected so far, this article provides an overview of potential therapeutic drugs and compounds with much attention, including favipiravir and hydroxychloroquine, as well as traditional Chinese medicine, which have been reported with good clinical treatment effects. In these 155 pooled clinical trials, a number of approved chemical and biomacromolecule drugs have been used in COVID-19 treatment clinical trials for drug repurposing, most of which are nucleotide analogs and protease inhibitors against other viral pathogens, including influenza virus, HIV and HCV. In vitro studies have shown that lopinavir/ritonavir can inhibit the replication of MERS-CoV and SARS-CoV and exert antiviral effects [22] [23] [24] [25] . In the latest "Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia", it is recommended to use ribavirin at a dose of 500 mg each time for adults and in combination with interferon or lopinavir/ritonavir, with 2-3 intravenous infusions daily. In vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) abstract: Since the outbreak of novel coronavirus pneumonia (COVID-19) in December 2019, more than 2,500,000 people worldwide have been diagnosed with SARS-CoV-2 as of April 22. In response to this epidemic, China has issued seven trial versions of diagnosis and treatment protocol for COVID-19. According to the information that we have collected so far, this article provides an overview of potential therapeutic drugs and compounds with much attention, including favipiravir and hydroxychloroquine, as well as traditional Chinese medicine, which have been reported with good clinical treatment effects. Moreover, with further understanding of SARS-CoV-2 virus, new drugs targeting specific SARS-CoV-2 viral components arise and investigations on these novel anti-SARS-CoV-2 agents are also reviewed. url: https://doi.org/10.1038/s41401-020-0438-y doi: 10.1038/s41401-020-0438-y id: cord-305336-wxiazglk author: Li, Ji Lian title: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera date: 2014-01-21 words: 6907.0 sentences: 319.0 pages: flesch: 50.0 cache: ./cache/cord-305336-wxiazglk.txt txt: ./txt/cord-305336-wxiazglk.txt summary: In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV. abstract: Emerging and reemerging diseases that result from pathogen host shifts are a threat to the health of humans and their domesticates. RNA viruses have extremely high mutation rates and thus represent a significant source of these infectious diseases. In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. Additionally, we showed that TRSV-infected individuals were continually present in some monitored colonies. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Furthermore, we showed that TRSV was also found in ectoparasitic Varroa mites that feed on bee hemolymph, but in those instances the virus was restricted to the gastric cecum of Varroa mites, suggesting that Varroa mites may facilitate the spread of TRSV in bees but do not experience systemic invasion. Finally, our phylogenetic analysis revealed that TRSV isolates from bees, bee pollen, and Varroa mites clustered together, forming a monophyletic clade. The tree topology indicated that the TRSVs from arthropod hosts shared a common ancestor with those from plant hosts and subsequently evolved as a distinct lineage after transkingdom host alteration. This study represents a unique example of viruses with host ranges spanning both the plant and animal kingdoms. url: https://www.ncbi.nlm.nih.gov/pubmed/24449751/ doi: 10.1128/mbio.00898-13 id: cord-016755-ye37z5h9 author: Li, Jiandong title: The Discovery Process of SFTS in China date: 2019-10-12 words: 2310.0 sentences: 116.0 pages: flesch: 52.0 cache: ./cache/cord-016755-ye37z5h9.txt txt: ./txt/cord-016755-ye37z5h9.txt summary: Sequence from a novel species of phlebovirus was identified by sequence independent single primer amplification (SISPA) from the serum of a patient with SFTS. The virus was isolated in Vero cell culture and its complete genome sequence was determined, only distantly related to other known phleboviruses. Phylogenetic trees based on complete viral genomic sequence of L, M and S segments from strains (HB29, HN6, AN12, LN2, JS3 and SD4) from 6 provinces in China in comparison with other known phleboviruses showed that SFTS virus was related to prototypic viruses of Phlebovirus. The novel phlebovirus was isolated in cultured Vero cells inoculated with acute-phase serum of patient HB29 from Shuizhou area, Hubei province. Specificity, sensitivity and cross reactivity of the methods were verified with serum samples collected from patients with SFTS confirmed by RT-PCR and sera collected from healthy donors from the areas without reported SFTS cases. abstract: Heightened surveillance of acute febrile illness in China since 2004 led to the identification of a severe fever with thrombocytopenia syndrome (SFTS) with unknown etiology. Sporadic patients hospitalized with SFTS in 2009 and 2010 were identified and serum samples were collected. Sequence from a novel species of phlebovirus was identified by sequence independent single primer amplification (SISPA) from the serum of a patient with SFTS. The virus was isolated in Vero cell culture and its complete genome sequence was determined, only distantly related to other known phleboviruses. Electron microscopic analysis revealed a virion morphologically characteristic of phleboviruses. The virus was named as SFTS virus. The viral RNA and/or specific antibodies were detected from the blood of patients with SFTS. Serological assays demonstrated a virus-specific immune response in pairs of sera collected from patients at acute and convalescent phases. The pathogenic mechanisms of thrombocytopenia in human SFTS disease was resembled in a mouse model. The results had been collected to demonstrate that SFTS virus was etiologically associated with an acute and novel infectious disease, SFTS in humans. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121134/ doi: 10.1007/978-981-13-9562-8_2 id: cord-349042-u9svz7pf author: Li, Jifen title: The successes and future prospects of the linear antisense RNA amplification methodology date: 2018-03-29 words: 5015.0 sentences: 253.0 pages: flesch: 42.0 cache: ./cache/cord-349042-u9svz7pf.txt txt: ./txt/cord-349042-u9svz7pf.txt summary: The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. Examination of expression profiles of single live cells has shown that linear aRNA amplification neither results in occurs after synthesis of double-stranded cDNA, when T7 RNA polymerase is added and aRNA is transcribed from the cDNA template. 45 developed a method to facilitate aRNA detection of antibody-antigen interactions by covalently attaching a double-stranded cDNA that contains a T7 RNA polymerase promoter in front of a reporter sequence to a specific antibody. abstract: It has been over a quarter of a century since the introduction of the linear RNA amplification methodology known as antisense RNA (aRNA) amplification. Whereas most molecular biology techniques are rapidly replaced owing to the fast-moving nature of development in the field, the aRNA procedure has become a base that can be built upon through varied uses of the technology. The technique was originally developed to assess RNA populations from small amounts of starting material, including single cells, but over time its use has evolved to include the detection of various cellular entities such as proteins, RNA-binding-protein-associated cargoes, and genomic DNA. In this Perspective we detail the linear aRNA amplification procedure and its use in assessing various components of a cell's chemical phenotype. This procedure is particularly useful in efforts to multiplex the simultaneous detection of various cellular processes. These efforts are necessary to identify the quantitative chemical phenotype of cells that underlies cellular function. url: https://doi.org/10.1038/nprot.2018.011 doi: 10.1038/nprot.2018.011 id: cord-262841-nr42rs8f author: Li, Lanjuan title: SARS-coronavirus replicates in mononuclear cells of peripheral blood (PBMCs) from SARS patients date: 2003-12-31 words: 2124.0 sentences: 107.0 pages: flesch: 58.0 cache: ./cache/cord-262841-nr42rs8f.txt txt: ./txt/cord-262841-nr42rs8f.txt summary: Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, "replicative intermediates") and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR). Although the virus has been identified Abbreviations: BNIBernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany; BSL3biosafety level 3; CoVcoronavirus; MHVmouse hepatitis virus; PCRpolymerase chain reaction; minus -RNAreplicative negative-stranded RNA; plus -RNApositive-stranded genomic RNA; RTreverse transcription; SARSsevere acute respiratory syndrome; SCAsodium citrate anticoagulant. In order to evaluate (i) whether SARS-CoV can infect peripheral blood mononuclear cells (PBMCs) of infected persons, (ii) whether the virus can replicate in their PBMCs, and (iii) to reveal any dynamic changes to the virus during the course of the disease, we carried out follow-up investigations on the plusand minus-RNA forms in SARS patients. abstract: Abstract Background: The etiologic agent of severe acute respiratory syndrome (SARS) is a recently identified, positive single-stranded RNA (ssRNA) coronavirus (SARS-CoV). Little is known about the dynamic changes of the viral replicative form in SARS cases. Objectives: Evaluate whether SARS-CoV can infect and replicate in peripheral blood mononuclear cells (PBMCs) of infected persons and reveal any dynamic changes to the virus during the course of the disease. Study design: Peripheral blood mononuclear cells collected from SARS cases infected by the same infectious source were tested for both negative-stranded RNA (minus-RNA, “replicative intermediates”) and positive-stranded RNA (genomic RNA) of SARS-CoV during the course of hospitalization by reverse transcription-polymerase chain reaction (RT-PCR). Results: SARS-CoV minus-RNA was detected in PBMCs from SARS patients. The viral replicative forms in PBMCs were detectable during a period of 6 days post-onset of the disease, while the plus-RNA were detectable for a longer period (8–12 days post-onset). Conclusions: SARS-coronavirus can infect and replicate within PBMCs of SARS patients, but viral replication in PBMCs seems subject to self-limitation. url: https://api.elsevier.com/content/article/pii/S1386653203001951 doi: 10.1016/s1386-6532(03)00195-1 id: cord-254192-86ksgl5t author: Li, Liang title: IFN-Lambda 3 Mediates Antiviral Protection Against Porcine Epidemic Diarrhea Virus by Inducing a Distinct Antiviral Transcript Profile in Porcine Intestinal Epithelia date: 2019-10-17 words: 7233.0 sentences: 324.0 pages: flesch: 50.0 cache: ./cache/cord-254192-86ksgl5t.txt txt: ./txt/cord-254192-86ksgl5t.txt summary: Here, to resolve the mechanism responsible for the disparity between IFN-λ3 and type I IFN in anti-mucosal virus infection, we compared the transcription profiles induced by the two IFNs in porcine intestinal epithelial (IPEC-J2) cells by RNA-Seq. Our results showed that the pretreatment of IPEC-J2 cells with IFN-λ3 resulted in the differential expression of 983 genes. Here, to resolve the mechanism responsible for the disparity between IFN-λ3 and type I IFN in anti-mucosal virus infection, we compared the transcription profiles induced by the two IFNs in porcine intestinal epithelial (IPEC-J2) cells by RNA-Seq. Our results showed that the pretreatment of IPEC-J2 cells with IFN-λ3 resulted in the differential expression of 983 genes. In this study, we comprehensively compared the transcriptional profiling of IFN-λ3-and IFN-α-induced genes in a porcine intestinal epithelial cell line (IPEC-J2) and verified the RNA-Seq results by reverse transcriptase quantitative PCR (RT-qPCR) in vitro, and further confirmed the transcriptional profile difference in crypt-derived porcine enteroids. abstract: Type III interferon-lambda (IFN-λ) plays a critical role against infection, particularly in mucosal infection in the respiratory and gastrointestinal tract. Our study and other previous studies have shown that porcine IFN-λ more efficiently curtails the infection of porcine epidemic diarrhea virus (PEDV) in the intestine epithelia than type I IFN, whereas IFN-λ3 exerts a more potent effect than IFN-λ1. However, the underlying mechanism remains elusive, and in particular, the transcriptional profile induced by IFN-λ3 has not been reported. Here, to resolve the mechanism responsible for the disparity between IFN-λ3 and type I IFN in anti-mucosal virus infection, we compared the transcription profiles induced by the two IFNs in porcine intestinal epithelial (IPEC-J2) cells by RNA-Seq. Our results showed that the pretreatment of IPEC-J2 cells with IFN-λ3 resulted in the differential expression of 983 genes. In contrast, IFN-α only modified the expression of 134 genes, and 110 of these genes were also observed in the response to IFN-λ3. A transcriptional enrichment analysis indicated that IFN-λ3 or IFN-α regulates multiple cellular processes and that IFN-λ3 activates more robust signaling pathways, particularly the antiviral Jak-STAT signaling pathway, than IFN-α. Furthermore, we verified the RNA-Seq results through an RT-qPCR analysis of IPEC-J2 cells and porcine enteroids. Moreover, transient expression of the porcine rsad2 and mx2 genes among the top 10 genes induced by IFN-λ3 significantly inhibited PEDV infection. Collectively, the data showed that IFN-λ3 induces a unique transcriptional profile that does not completely overlap with that induced by IFN-α and strongly elicits a set of genes responsible for the antiviral activity of IFN-λ3. These findings provide important knowledge regarding the elicited ISGs of type I and III IFNs in restricting porcine intestinal viral infection. url: https://doi.org/10.3389/fimmu.2019.02394 doi: 10.3389/fimmu.2019.02394 id: cord-273609-whm2ce4u author: Li, Qingdi Quentin title: Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment date: 2012-06-29 words: 8166.0 sentences: 373.0 pages: flesch: 47.0 cache: ./cache/cord-273609-whm2ce4u.txt txt: ./txt/cord-273609-whm2ce4u.txt summary: title: Evaluation of reference genes for real-time quantitative PCR studies in Candida glabrata following azole treatment BACKGROUND: The selection of stable and suitable reference genes for real-time quantitative PCR (RT-qPCR) is a crucial prerequisite for reliable gene expression analysis under different experimental conditions. The most commonly used reference genes, including β-actin, cyclophilin, GAPDH, tubulin, and 18S and 28S ribosomal RNAs, have shown variable expression levels in different cells and tissues under different conditions, and therefore they are unsuitable for normalization purposes owing to large measurement error [6, . As seen in Table 7 , normalization of the RT-qPCR data against the reference genes suggested as optimal by the four software packages (hkgFinder, geNorm, BestKeeper, and NormFinder) or the 2 -ΔΔCT method, gave comparable relative expression levels of the target genes under fluconazole treatment in C. abstract: BACKGROUND: The selection of stable and suitable reference genes for real-time quantitative PCR (RT-qPCR) is a crucial prerequisite for reliable gene expression analysis under different experimental conditions. The present study aimed to identify reference genes as internal controls for gene expression studies by RT-qPCR in azole-stimulated Candida glabrata. RESULTS: The expression stability of 16 reference genes under fluconazole stress was evaluated using fold change and standard deviation computations with the hkgFinder tool. Our data revealed that the mRNA expression levels of three ribosomal RNAs (RDN5.8, RDN18, and RDN25) remained stable in response to fluconazole, while PGK1, UBC7, and UBC13 mRNAs showed only approximately 2.9-, 3.0-, and 2.5-fold induction by azole, respectively. By contrast, mRNA levels of the other 10 reference genes (ACT1, EF1α, GAPDH, PPIA, RPL2A, RPL10, RPL13A, SDHA, TUB1, and UBC4) were dramatically increased in C. glabrata following antifungal treatment, exhibiting changes ranging from 4.5- to 32.7-fold. We also assessed the expression stability of these reference genes using the 2(-ΔΔCT) method and three other software packages. The stability rankings of the reference genes by geNorm and the 2(-ΔΔCT) method were identical to those by hkgFinder, whereas the stability rankings by BestKeeper and NormFinder were notably different. We then validated the suitability of six candidate reference genes (ACT1, PGK1, RDN5.8, RDN18, UBC7, and UBC13) as internal controls for ten target genes in this system using the comparative C(T) method. Our validation experiments passed for all six reference genes analyzed except RDN18, where the amplification efficiency of RDN18 was different from that of the ten target genes. Finally, we demonstrated that the relative quantification of target gene expression varied according to the endogenous control used, highlighting the importance of the choice of internal controls in such experiments. CONCLUSIONS: We recommend the use of RDN5.8, UBC13, and PGK1 alone or the combination of RDN5.8 plus UBC13 or PGK1 as reference genes for RT-qPCR analysis of gene expression in C. glabrata following azole treatment. In contrast, we show that ACT1 and other commonly used reference genes (GAPDH, PPIA, RPL13A, TUB1, etc.) were not validated as good internal controls in the current model. url: https://www.ncbi.nlm.nih.gov/pubmed/22747760/ doi: 10.1186/1471-2199-13-22 id: cord-327000-oyg3oyx1 author: Li, Shasha title: Porcine Epidemic Diarrhea Virus and the Host Innate Immune Response date: 2020-05-11 words: 11098.0 sentences: 688.0 pages: flesch: 48.0 cache: ./cache/cord-327000-oyg3oyx1.txt txt: ./txt/cord-327000-oyg3oyx1.txt summary: This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. Porcine epidemic diarrhea virus (PEDV) is the etiological agent of porcine epidemic diarrhea (PED) that causes an acute and highly contagious enteric disease of swine characterized by vomiting, diarrhea, dehydration, and anorexia in pigs of all ages, especially resulting in severe diarrhea and high mortality rate in piglets. Nsp3 is the largest nsp protein, containing two papain-like protease (PLP1 and PLP2) domains, of which PEDV PLP2 acts as a viral deubiquitinase (DUB), to negatively regulate type I IFN signaling [80] . The evasive strategies utilized by PEDV are classified into four major types: (1) inhibition of RLRs-mediated IFN production pathways, (2) inhibition of the activation of transcription factors responsible for IFN induction, (3) disruption of the signal cascades induced by IFN, and (4) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. abstract: Porcine epidemic diarrhea virus (PEDV), a swine enteropathogenic coronavirus (CoV), is the causative agent of porcine epidemic diarrhea (PED). PED causes lethal watery diarrhea in piglets, which has led to substantial economic losses in many countries and is a great threat to the global swine industry. Interferons (IFNs) are major cytokines involved in host innate immune defense, which induce the expression of a broad range of antiviral effectors that help host to control and antagonize viral infections. PEDV infection does not elicit a robust IFN response, and some of the mechanisms used by the virus to counteract the host innate immune response have been unraveled. PEDV evades the host innate immune response by two main strategies including: 1) encoding IFN antagonists to disrupt innate immune pathway, and 2) hiding its viral RNA to avoid the exposure of viral RNA to immune sensors. This review highlights the immune evasion mechanisms employed by PEDV, which provides insights for the better understanding of PEDV-host interactions and developing effective vaccines and antivirals against CoVs. url: https://doi.org/10.3390/pathogens9050367 doi: 10.3390/pathogens9050367 id: cord-007208-wnkjdg6y author: Li, Sheng-Hsiang title: Demonstration of a Glycoprotein Derived From the Ceacam10 Gene in Mouse Seminal Vesicle Secretions(1) date: 2005-09-01 words: 5610.0 sentences: 289.0 pages: flesch: 56.0 cache: ./cache/cord-007208-wnkjdg6y.txt txt: ./txt/cord-007208-wnkjdg6y.txt summary: Here we report the purification and identification of an androgen-stimulated 36-kDa glycoprotein, a minor protein component of mouse SVS that is able to enhance sperm motility in vitro. The following materials were obtained from commercial sources: DEAE-Sephacel (Amersham Pharmacia Biotech, Uppsala, Sweden); Protein PAK SP 5PW column (Waters, Milford, MA); Vydac 218TP54 C 18 column (Separations Group, Hesperia, CA); AminoLink coupling gel, bicinchoninic protein assay kit (Pierce, Rockford, IL); testosterone propionate, nitroblue tetrazolium, 5-bromo-4-chloro-3-indolyl phosphate (BCIP), PMSF, periodic acid Schiff reagent, and silanated glass slides (Sigma Chemical Co., St Louis, MO); cDNA integrity kit, alkaline phosphataseconjugated streptavidin, and biotin-conjugated goat anti-rabbit immunoglobulin G (IgG; Kirkegaard & Perry Laboratories, Gaithersburg, MD); rhodamine-conjugated goat anti-rabbit IgG (Zymed Laboratories, San Francisco, CA); Nuclear Fast Red (Vector Laboratories, Burlingame, CA); enhanced chemiluminescent substrate and [␣32 A) Fractionation of soluble mouse SVS proteins by ion exchange chromatography on a DEAE-Sephacel column. A novel heat-labile phospholipid-binding protein, SVS VII, in mouse seminal vesicle as a sperm motility enhancer abstract: CEACAM10 was purified from mouse seminal vesicle secretions by a series of purification steps that included ion exchange chromatography on a DEAE-Sephacel column and ion exchange high-performance liquid chromatography on a sulfopropyl column. It was shown to be a 36-kDa glycoprotein with an N-linked carbohydrate moiety. The circular dichromoism spectrum of CEACAM10 in 50 mM phosphate buffer at pH 7.4 appeared as one negative band arising from the β form at 217 nm. CEACAM10 was expressed predominantly in seminal vesicles of adult mice. Both CEACAM10 and its mRNA were demonstrated on the luminal epithelium of the mucosal folds in the seminal vesicle. The amount of Ceacam10 mRNA in the seminal vesicle was correlated with the stage of animal maturation. Castration of adult mice resulted in cessation of Ceacam10 expression, while treatment of castrated mice with testosterone propionate in corn oil restored Ceacam10 expression in the seminal vesicle. During the entire course of pregnancy, Ceacam10 might be silent in the embryo. A cytochemical study illustrated the presence of the CEACAM10 binding region on the entire surface of mouse sperm. CEACAM10-sperm binding greatly enhanced sperm motility in vitro. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109865/ doi: 10.1095/biolreprod.105.039651 id: cord-006951-tj22dh5o author: Li, Siyu title: The effect of RNA stiffness on the self-assembly of virus particles date: 2018-01-31 words: 4913.0 sentences: 218.0 pages: flesch: 59.0 cache: ./cache/cord-006951-tj22dh5o.txt txt: ./txt/cord-006951-tj22dh5o.txt summary: While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging. In this paper, we vary the degree of branching as well as the effective Kuhn length and linear charge density of a model RNA, and study their impact on the optimal length of encapsulated genome by capsid proteins. abstract: Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between an ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104906/ doi: 10.1088/1361-648x/aaa159 id: cord-323585-iv2dcpqj author: Li, Su title: eEF1A Interacts with the NS5A Protein and Inhibits the Growth of Classical Swine Fever Virus date: 2015-08-10 words: 6142.0 sentences: 343.0 pages: flesch: 59.0 cache: ./cache/cord-323585-iv2dcpqj.txt txt: ./txt/cord-323585-iv2dcpqj.txt summary: The NS5A protein of classical swine fever virus (CSFV) is involved in the RNA synthesis and viral replication. The GST or GST-NS5A fusion proteins expressed in Escherichia coli BL21(DE3) were purified with glutathione Sepharose 4B resin and incubated with the lysate of HEK293T cells overexpressing the Myc-tagged eEF1A. The immunoprecipitate was analyzed by Western blotting using the anti-Flag MAb (1:1000) and a rabbit anti-Myc PAb (1:500); (D) Co-IP analysis of eEF1A and NS5A by the anti-Myc MAb. HEK293T cells were cotransfected with the indicated plasmids (+) or empty vectors (''), the cell lysate was collected at 48 h post-transfection (hpt), incubated with the anti-Myc MAb and Protein G-Agarose. The bound proteins were analyzed by immunoblotting using the anti-Myc monoclonal antibody (MAb) (1:1000); (B) eEF1A interacts with the CSFV IRES in a dose-dependent manner. The bound proteins were analyzed by immunoblotting using the anti-Myc monoclonal antibody (MAb) (1:1000); (B) eEF1A interacts with the CSFV IRES in a dose-dependent manner. abstract: The NS5A protein of classical swine fever virus (CSFV) is involved in the RNA synthesis and viral replication. However, the NS5A-interacting cellular proteins engaged in the CSFV replication are poorly defined. Using yeast two-hybrid screen, the eukaryotic elongation factor 1A (eEF1A) was identified to be an NS5A-binding partner. The NS5A–eEF1A interaction was confirmed by coimmunoprecipitation, glutathione S-transferase (GST) pulldown and laser confocal microscopy assays. The domain I of eEF1A was shown to be critical for the NS5A–eEF1A interaction. Overexpression of eEF1A suppressed the CSFV growth markedly, and conversely, knockdown of eEF1A enhanced the CSFV replication significantly. Furthermore, eEF1A, as well as NS5A, was found to reduce the translation efficiency of the internal ribosome entry site (IRES) of CSFV in a dose-dependent manner, as demonstrated by luciferase reporter assay. Streptavidin pulldown assay revealed that eEF1A could bind to the CSFV IRES. Collectively, our results suggest that eEF1A interacts with NS5A and negatively regulates the growth of CSFV. url: https://www.ncbi.nlm.nih.gov/pubmed/26266418/ doi: 10.3390/v7082833 id: cord-264051-ps0x2es1 author: Li, Wei title: Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network date: 2020-11-05 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The COVID-19 pandemic is a widespread and deadly public health crisis. The pathogen SARS-CoV-2 replicates in the lower respiratory tract and causes fatal pneumonia. Although tremendous efforts have been put into investigating the pathogeny of SARS-CoV-2, the underlying mechanism of how SARS-CoV-2 interacts with its host is largely unexplored. Here, by comparing the genomic sequences of SARS-CoV-2 and human, we identified five fully conserved elements in SARS-CoV-2 genome, which were termed as “human identical sequences (HIS)”. HIS are also recognized in both SARS-CoV and MERS-CoV genome. Meanwhile, HIS-SARS-CoV-2 are highly conserved in the primate. Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, and hyaluronan synthase 2 (HAS2), which further increases hyaluronan formation. Noteworthily, hyaluronan level in plasma of COVID-19 patients is tightly correlated with severity and high risk for acute respiratory distress syndrome (ARDS) and may act as a predictor for the progression of COVID-19. HIS antagomirs, which downregulate hyaluronan level effectively, and 4-Methylumbelliferone (MU), an inhibitor of hyaluronan synthesis, are potential drugs to relieve the ARDS related ground-glass pattern in lung for COVID-19 treatment. Our results revealed that unprecedented HIS elements of SARS-CoV-2 contribute to the cytokine storm and ARDS in COVID-19 patients. Thus, blocking HIS-involved activating processes or hyaluronan synthesis directly by 4-MU may be effective strategies to alleviate COVID-19 progression. url: https://doi.org/10.1101/2020.11.04.361576 doi: 10.1101/2020.11.04.361576 id: cord-288960-v6l6o5va author: Li, Yang title: Regulating STING in health and disease date: 2017-06-07 words: 12297.0 sentences: 689.0 pages: flesch: 41.0 cache: ./cache/cord-288960-v6l6o5va.txt txt: ./txt/cord-288960-v6l6o5va.txt summary: Possibly via RIG-I -dependent RNA detection which may in turn induce STING [6] Vesicular stomatitis virus Negative strand ssRNA virus Unknown [6] Human immunodeficiency virus Negative strand ssRNA virus dsDNA reverse transcribed from viral RNA induces cGAS-STING pathway [28] Influenza A virus Negative strand ssRNA virus Possibly via membrane fusion or unknown mechanism independent of DNA recognition [29] Mycobacteria tuberculosis Bacteria producing c-di-GMP c-di-GMP [30, 31] Streptococcus pneumoniae Bacteria dsDNA Bacterial dsDNA [32] Streptococcus pyrogenes Bacteria dsDNA Bacterial dsDNA [33] Staphylococcus aureus Bacteria producing c-di-AMP c-di-AMP [34] Listeria monocytogenes Bacteria producing c-di-AMP c-di-AMP [35] Vibrio cholera Bacteria producing 3′-3′ cGAMP 3′-3′ cGAMP [36, 37] Abbreviations: dsDNA double-stranded DNA, ssRNA single-stranded RNA The type I interferon signal adaptor protein STING is responsible for mediating double-stranded DNA sensing responses and the detection of bacterial cyclic dinucleotides c-di-AMP, c-di-GMP, and 3′-3′ cGAMP. abstract: The presence of cytosolic double-stranded DNA molecules can trigger multiple innate immune signalling pathways which converge on the activation of an ER-resident innate immune adaptor named “STimulator of INterferon Genes (STING)”. STING has been found to mediate type I interferon response downstream of cyclic dinucleotides and a number of DNA and RNA inducing signalling pathway. In addition to its physiological function, a rapidly increasing body of literature highlights the role for STING in human disease where variants of the STING proteins, as well as dysregulated STING signalling, have been implicated in a number of inflammatory diseases. This review will summarise the recent structural and functional findings of STING, and discuss how STING research has promoted the development of novel therapeutic approaches and experimental tools to improve treatment of tumour and autoimmune diseases. url: https://doi.org/10.1186/s12950-017-0159-2 doi: 10.1186/s12950-017-0159-2 id: cord-341513-e6p3lrlf author: Li, Yunchuan title: Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection date: 2017-09-29 words: 6136.0 sentences: 341.0 pages: flesch: 47.0 cache: ./cache/cord-341513-e6p3lrlf.txt txt: ./txt/cord-341513-e6p3lrlf.txt summary: title: Microarray Analysis Identifies the Potential Role of Long Non-Coding RNA in Regulating Neuroinflammation during Japanese Encephalitis Virus Infection To determine the role of lncRNAs in inflammatory cytokine production, the cells were transfected with siE52329, siN54010 or non-specific control siRNA, and then infected with JEV. To examine the role of lncRNA E52329 and N54010 in regulating the kinase activity of MKK4/JNK pathway, BV2 cells were transfected with siE52329, siN54010 or non-specific control siRNA, and then infected with JEV. The results of our study reveal the first experimental evidence demonstrating the complex regulation of lncRNAs by JEV infection in mice brain and microglial cells. Third, the integration of microarray platform, quantitative real-time PCR, GO analysis, pathways analysis, and lncRNA-mRNA coexpression network analysis has allowed us to conduct an active comparative genomics and bioinformatics study to reveal host lncRNAs expression patterns associated with JEV infection. abstract: Japanese encephalitis virus (JEV) is the leading cause of epidemic encephalitis worldwide. JEV-induced neuroinflammation is characterized by profound neuronal cells damage accompanied by activation of glial cells. Albeit long non-coding RNAs (lncRNAs) have been emerged as important regulatory RNAs with profound effects on various biological processes, it is unknown how lncRNAs regulate JEV-induced inflammation. Here, using microarray approach, we identified 618 lncRNAs and 1,007 mRNAs differentially expressed in JEV-infected mice brain. The functional annotation analysis revealed that differentially regulated transcripts were predominantly involved in various signaling pathways related to host immune and inflammatory responses. The lncRNAs with their potential to regulate JEV-induced inflammatory response were identified by constructing the lncRNA-mRNA coexpression network. Furthermore, silencing of the two selected lncRNAs (E52329 and N54010) resulted in reducing the phosphorylation of JNK and MKK4, which are known to be involved during inflammatory response. Collectively, we first demonstrated the transcriptomic landscape of lncRNAs in mice brain infected with JEV and analyzed the coexpression network of differentially regulated lncRNAs and mRNAs during JEV infection. Our results provide a better understanding of the host response to JEV infection and suggest that the identified lncRNAs may be used as potential therapeutic targets for the management of Japanese encephalitis. url: https://www.ncbi.nlm.nih.gov/pubmed/29033949/ doi: 10.3389/fimmu.2017.01237 id: cord-320351-47d0nby0 author: Li, Zhouxiao title: The emerging landscape of circular RNAs in immunity: breakthroughs and challenges date: 2020-07-10 words: 5971.0 sentences: 339.0 pages: flesch: 39.0 cache: ./cache/cord-320351-47d0nby0.txt txt: ./txt/cord-320351-47d0nby0.txt summary: Recently conducted researches indicated that circRNAs can be used as a miRNA sponge to inhibit targeted mRNA functions, showing interaction to RNA-binding proteins (RBPs) and translating proteins [9] . In contrast to the sensitive strains, the expression of 2909 circRNAs in A549 / Taxol was noticeably enriched and 8372 circRNAs were noticeably declined, demonstrating that abnormal cir-cRNA is likely to alter the occurrence of paclitaxel resistance [33] .Circ-PVT1 was found to facilitate paclitaxel resistance of gastric cancer cells by controlling ZEB1 expressing via the sponging process for miR-124-3p [34] . Lymphoblastic lymphoma [52] -T cell structure and degradation of circRNAs regulating PKR Activation in innate immunity circ-CDR1as B cell serving as the miR-7 "sponge" to increase expression of PTEN and restrain SLE [66] Other immune-related diseases circ_ 0057980 Circular RNA circ-PVT1 contributes to paclitaxel resistance of gastric cancer cells through the regulation of ZEB1 expression by sponging miR-124-3p abstract: Circular RNAs (circRNAs) are covalently linked RNAs that exhibit individual strand with a closed-loop framework compared with a conserving, steady and abundant linear counterpart. In recent years, as high-throughput sequencing advancement has been developing, functional circRNAs have been increasingly recognized, and more extensive analyses expounded their effect on different diseases. However, the study on the function of circRNAs in the immune system remains insufficient. This study discusses the basic principles of circRNAs regulation and the systems involved in physiology-related and pathology-related processes. The effect of circRNAs on immune regulation is elucidated. The ongoing development of circRNAs and basic immunology has multiplied their potential in treating diseases. Such perspective will summarize the status and effect of circRNAs on various immune cells in cancer, autoimmune diseases and infections. Moreover, this study will primarily expound the system of circRNAs in T lymphocytes, macrophages and other immune cells, which creates a novel perspective and lay a theoretical basis for treating diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32665846/ doi: 10.1186/s40364-020-00204-5 id: cord-033692-txfuuu7d author: Lim, Byeonghwi title: Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection date: 2020-10-13 words: 7927.0 sentences: 371.0 pages: flesch: 44.0 cache: ./cache/cord-033692-txfuuu7d.txt txt: ./txt/cord-033692-txfuuu7d.txt summary: In this study, we investigated the molecular mechanisms of PRRSV infection by integrating the differences in the expression of various genes in tissues responsible for respiration (lungs) and immunity (bronchial lymph nodes [BLNs] , and tonsils) using RNA-Seq data at serial time points. To validate the results of specific groups, GSEA based on the KEGG database were performed using log 2 -normalised TMM counts at each time point for each tissue to identify the maximum gene expression changes for each group, and the GSEA results were consistent with the KEGG enrichment analyses of DEGs. GSEA using the 3-dpi data for all tissues revealed many significant pathways related to viral infection, among which influenza A showed the highest NES ( Figure 5A ). Significant KEGG terms related to viral infections and immune signalling were identified through KEGG enrichment analyses performed for each up-and down-regulated genes (343 and 287 genes, respectively), based on the time point for each tissue with a maximum FC value in the GCN, which was constructed using serial DEGs ( Figure 4A ). abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) infection is the most important viral disease causing severe economic losses in the swine industry. However, mechanisms underlying gene expression control in immunity-responsible tissues at different time points during PRRSV infection are poorly understood. We constructed an integrated gene co-expression network and identified tissue- and time-dependent biological mechanisms of PRRSV infection through bioinformatics analysis using three tissues (lungs, bronchial lymph nodes [BLNs], and tonsils) via RNA-Seq. Three groups with specific expression patterns (i.e., the 3-dpi, lung, and BLN groups) were discovered. The 3 dpi-specific group showed antiviral and innate-immune signalling similar to the case for influenza A infection. Moreover, we observed adaptive immune responses in the lung-specific group based on various cytokines, while the BLN-specific group showed down-regulated AMPK signalling related to viral replication. Our study may provide comprehensive insights into PRRSV infection, as well as useful information for vaccine development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552595/ doi: 10.1186/s13567-020-00850-5 id: cord-269193-a647hwu9 author: Lin, Debby A. title: Evolutionary relatedness of the predicted gene product of RNA segment 2 of the Tick-Borne Dhori virus and the PB1 polymerase gene of influenza viruses date: 1991-05-31 words: 2946.0 sentences: 152.0 pages: flesch: 57.0 cache: ./cache/cord-269193-a647hwu9.txt txt: ./txt/cord-269193-a647hwu9.txt summary: Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. The viral RNAs have been shown to encode information in the negative-sense (Clerx et al., 1983; Fuller et al., 1987; Freedman-Faulstich and Fuller, 1990) and it was previously shown that the Dhori nucleoprotein (encoded by RNA segment 5) shares conserved amino acid sequences with the influenza A, B, and C virus nucleoproteins (Fuller et al., 1987) . The PBl polymerase proteins are the most highly conserved among the proteins of the influenza A, B, and C viruses (Yamashita et a/,, 1989 ) and they are most likely required for nucleotide addition during viral RNA synthesis (Braam et al., 1983) . abstract: Abstract The complete nucleotide sequence of the second largest RNA segment of Dhori/India/1313/61 virus was determined and the deduced amino acid sequence was compared with the polymerase (P) proteins of influenza A, B, and C viruses. RNA segment 2 (2224 nucleotides) of Dhori virus contains a single long open reading frame that can encode a 716-amino amid polypeptide (81.3 kDa). The predicted polypeptide shares between 27 and 31% sequence identities with the PB1 polypeptides of influenza A, B, and C viruses. Among the regions most highly conserved are the sequences around the Asp-Asp motif common to many RNA polymerases. In spite of the high level of sequence identity between the Dhori RNA segment 2 gene product and the influenza A, B, and C virus PB1 proteins the amino acid composition of the Dhori protein indicates an acidic charge feature at pH 7.0 in contrast to the basic nature of the PB1 proteins of the influenza viruses. We suggest that the Dhori PB1-like protein be designated the Pα protein of this virus. url: https://www.ncbi.nlm.nih.gov/pubmed/2024457/ doi: 10.1016/0042-6822(91)90641-n id: cord-312741-0au4nctt author: Lin, Panpan title: Coronavirus in human diseases: Mechanisms and advances in clinical treatment date: 2020-10-01 words: 14665.0 sentences: 840.0 pages: flesch: 42.0 cache: ./cache/cord-312741-0au4nctt.txt txt: ./txt/cord-312741-0au4nctt.txt summary: 160, 161 Once the PAMPs from invaded viruses are detected, RIG-I and MDA5 interact with the mitochondrial antiviral signaling protein (MAVs) that is a mitochondrial membrane-bound F I G U R E 2 Escape mechanisms of innate immune response of SARS-CoV and MERS-CoV adaptor molecule, followed by the activation of several kinase complexes and multiple subsequent transcription factors (IRF3, IRF7, and NF-κB). Antiviral peptides analogous derived from these regions exhibited inhibition to the spike protein-mediated cell-cell fusion and viral entry in viruses such as SARS-CoV, MERS-CoV, as well as HCoV-229E. Receptor-binding domain of severe acute respiratory syndrome coronavirus spike protein contains multiple conformation-dependent epitopes that induce highly potent neutralizing antibodies Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response Inhibition of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infectivity by peptides analogous to the viral spike protein abstract: Coronaviruses (CoVs), a subfamily of coronavirinae, are a panel of single‐stranded RNA virus. Human coronavirus (HCoV) strains (HCoV‐229E, HCoV‐OC43, HCoV‐HKU1, HCoV‐NL63) usually cause mild upper respiratory diseases and are believed to be harmless. However, other HCoVs, associated with severe acute respiratory syndrome, Middle East respiratory syndrome, and COVID‐19, have been identified as important pathogens due to their potent infectivity and lethality worldwide. Moreover, currently, no effective antiviral drugs treatments are available so far. In this review, we summarize the biological characters of HCoVs, their association with human diseases, and current therapeutic options for the three severe HCoVs. We also highlight the discussion about novel treatment strategies for HCoVs infections. url: https://www.ncbi.nlm.nih.gov/pubmed/33173860/ doi: 10.1002/mco2.26 id: cord-328300-zehltghv author: Lin, Shing-Yen title: Structural Basis for the Identification of the N-Terminal Domain of Coronavirus Nucleocapsid Protein as an Antiviral Target date: 2014-02-24 words: 6628.0 sentences: 345.0 pages: flesch: 53.0 cache: ./cache/cord-328300-zehltghv.txt txt: ./txt/cord-328300-zehltghv.txt summary: CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein''s N-terminal domain (N-NTD). We report the crystal structures of HCoV-OC43 N-NTD complexed with ribonucleoside 5′-monophosphates as a model for understanding the molecular interactions that govern CoV N-NTD binding to RNA. To begin to elucidate how RNA and the N protein interact, we determined the crystal structure of HCoV-OC43 N-NTD complexed with AMP. These amino acids are sequentially and structurally conserved in other HCoV N proteins ( Figure S2 , Supporting Information); therefore, they are likely essential for RNA recognition and interaction in all coronavirus N proteins. Previous studies indicated that the positively charged amino acid, Arg 106, located at the cleft in the HCoV-OC43 N-NTD structure, is conserved in all CoV N proteins and interacts nonspecifically with the RNA phosphate backbone. abstract: [Image: see text] Coronaviruses (CoVs) cause numerous diseases, including Middle East respiratory syndrome and severe acute respiratory syndrome, generating significant health-related and economic consequences. CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein’s N-terminal domain (N-NTD). Using human CoV-OC43 (HCoV-OC43) as a model for CoV, we present the 3D structure of HCoV-OC43 N-NTD complexed with ribonucleoside 5′-monophosphates to identify a distinct ribonucleotide-binding pocket. By targeting this pocket, we identified and developed a new coronavirus N protein inhibitor, N-(6-oxo-5,6-dihydrophenanthridin-2-yl)(N,N-dimethylamino)acetamide hydrochloride (PJ34), using virtual screening; this inhibitor reduced the N protein’s RNA-binding affinity and hindered viral replication. We also determined the crystal structure of the N-NTD–PJ34 complex. On the basis of these findings, we propose guidelines for developing new N protein-based antiviral agents that target CoVs. url: https://www.ncbi.nlm.nih.gov/pubmed/24564608/ doi: 10.1021/jm500089r id: cord-264159-e9071tyv author: Lin, Weikang Nicholas title: The Role of Single-Cell Technology in the Study and Control of Infectious Diseases date: 2020-06-10 words: 13339.0 sentences: 580.0 pages: flesch: 36.0 cache: ./cache/cord-264159-e9071tyv.txt txt: ./txt/cord-264159-e9071tyv.txt summary: In pathophysiological studies of infectious disease, single-cell omics offer excellent spatial-temporal resolution that help to not only reconstruct the uneven subcellular distribution of pathogen across the entire host cell population, but also reveal the sequence of immune events accompanied by the change of immune cell profiles. Moreover, viral mutation can be correlated with host gene expression status at the single-cell level to further investigate their potential mutual effect on one another throughout the course of infection and reveal the dynamic host responses and pathogen adaptations in the progression of infection [32] . Technologies that enable the simultaneous measurement of multiple parameters facilitate high-resolution characterization of transcripts and protein at the single-cell level and boost our understanding of how host immune responses are initiated and orchestrated against infection. As covered earlier in this review, the main applications of scRNA-seq in infectious disease study comprise of the following: (1) studying effect of host cell heterogeneity on infection, (2) identifying host immune responses, and (3) antibody discovery. abstract: The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. The extensive characterization of genomic and phenotypic biomarkers, in addition to host–pathogen interactions at the single-cell level, has resulted in the discovery of previously unknown infection mechanisms as well as potential treatment options. In this article, we review the various single-cell technologies and their applications in the ongoing fight against infectious diseases, as well as discuss the potential opportunities for future development. url: https://www.ncbi.nlm.nih.gov/pubmed/32531928/ doi: 10.3390/cells9061440 id: cord-314572-1pou702r author: Lin, Ya-Hui title: Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator date: 2016-10-14 words: 7182.0 sentences: 337.0 pages: flesch: 47.0 cache: ./cache/cord-314572-1pou702r.txt txt: ./txt/cord-314572-1pou702r.txt summary: Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. In a first step to constructing a ligand-responsive −1 PRF stimulator, we designed Switch-0 RNA with a theophylline aptamer replacing the stem 3 of SARS-PK ( Figure 1A and C). We rationalized that such an engineered switch hairpin of reasonable stability (predicted free energy of −12.7 kcal/mole (37)) would be the dominant conformation that could interfere with the formation of pseudoknot stem 2 in the absence of theophylline (Supplementary Figure S2A) . To improve the dynamic range of ligand response and to see if theophylline aptamers can be functional while existing in both positive and negative regulators of −1 PRF, we fused previously designed theophylline-dependent upstream attenuator, theoOFF2 (24) with Switch-1 ( Figure 5A ) and examined theophylline-dependent −1 PRF activity in vitro. abstract: Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate −1 programmed ribosomal frameshifting (PRF), suggesting −1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by difficulty in identifying a specific ligand-responsive pseudoknot that also functions as a ligand-dependent -1 PRF stimulator. We addressed this problem by using the −1 PRF stimulation pseudoknot of SARS-CoV (SARS-PK) to build a ligand-dependent −1 PRF stimulator. In particular, the extra stem of SARS-PK was replaced by an RNA aptamer of theophylline and designed to couple theophylline binding with the stimulation of −1 PRF. Conformational and functional analyses indicate that the engineered theophylline-responsive RNA functions as a mammalian riboswitch with robust theophylline-dependent −1 PRF stimulation activity in a stable human 293T cell-line. Thus, RNA–ligand interaction repertoire provided by in vitro selection becomes accessible to ligand-specific −1 PRF stimulator engineering using SARS-PK as the scaffold for synthetic biology application. url: https://www.ncbi.nlm.nih.gov/pubmed/27521370/ doi: 10.1093/nar/gkw718 id: cord-002764-px0cz6qn author: Lin, Yuan title: Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs date: 2017-11-17 words: 8369.0 sentences: 429.0 pages: flesch: 51.0 cache: ./cache/cord-002764-px0cz6qn.txt txt: ./txt/cord-002764-px0cz6qn.txt summary: These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline–rich-motif (polyPRM) ligand. These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline-rich-motif (polyPRM) ligand. Tyrosine mutations also block recruitment of IDRs into hydrogels and/or phase-separated liquids formed by the RNA-binding protein hnRNPA2 (47) and FUS (29) , as well as into RNA granules in cells (29) . We found that, when tethered to a polySH3 domain protein that phase-separates when mixed with a cognate poly-proline-rich motif (polyPRM) ligand, wildtype FUS decreases the threshold concentration for LLPS by 8-fold. abstract: Liquid–liquid phase separation (LLPS) is thought to contribute to the establishment of many biomolecular condensates, eukaryotic cell structures that concentrate diverse macromolecules but lack a bounding membrane. RNA granules control RNA metabolism and comprise a large class of condensates that are enriched in RNA-binding proteins and RNA molecules. Many RNA granule proteins are composed of both modular domains and intrinsically disordered regions (IDRs) having low amino acid sequence complexity. Phase separation of these molecules likely plays an important role in the generation and stability of RNA granules. To understand how folded domains and IDRs can cooperate to modulate LLPS, we generated a series of engineered proteins. These were based on fusions of an IDR derived from the RNA granule protein FUS (fused in sarcoma) to a multivalent poly-Src homology 3 (SH3) domain protein that phase-separates when mixed with a poly-proline–rich-motif (polyPRM) ligand. We found that the wild-type IDR promotes LLPS of the polySH3–polyPRM system, decreasing the phase separation threshold concentration by 8-fold. Systematic mutation of tyrosine residues in Gly/Ser-Tyr-Gly/Ser motifs of the IDR reduced this effect, depending on the number but not on the position of these substitutions. Mutating all tyrosines to non-aromatic residues or phosphorylating the IDR raised the phase separation threshold above that of the unmodified polySH3–polyPRM pair. These results show that low-complexity IDRs can modulate LLPS both positively and negatively, depending on the degree of aromaticity and phosphorylation status. Our findings provide plausible mechanisms by which these sequences could alter RNA granule properties on evolutionary and cellular timescales. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704491/ doi: 10.1074/jbc.m117.800466 id: cord-319681-kjet3e50 author: Lin, Zhaoru title: Spacer-length dependence of programmed −1 or −2 ribosomal frameshifting on a U(6)A heptamer supports a role for messenger RNA (mRNA) tension in frameshifting date: 2012-06-28 words: 8862.0 sentences: 391.0 pages: flesch: 57.0 cache: ./cache/cord-319681-kjet3e50.txt txt: ./txt/cord-319681-kjet3e50.txt summary: The mRNA signal for À1 FS is composed of two elements, a slippery sequence with consensus X_XXY_ YYZ (underlines denote zero frame; X can be any base, Y is A or U, Z is not G in eukaryotic systems) where the ribosome changes frame, and a downstream stimulatory RNA structure, a stem-loop or pseudoknot (reviewed in 3, 4) . A version of the À1 FS reporter plasmid with the IBV slippery sequence (p2lucIBV-AON) was also Spacer-length dependence of programmed À1 or À2 ribosomal frameshifting on a U 6 A heptamer supports a role for mRNA tension in frameshifting Based on the published literature, including our own studies of 80S ribosomes stalled at the IBV frameshift-stimulatory pseudoknot (22, 37) , we proposed a mechanical model of frameshifting in which a failure of intrinsic ribosomal helicase activity (15, 28) to unwind efficiently the stimulatory RNA during the translocation step leads to the build up of tension in the mRNA and subsequently, breakage of codon:anticodon contacts and realignment of the tRNAs in the À1 reading frame. abstract: Programmed −1 ribosomal frameshifting is employed in the expression of a number of viral and cellular genes. In this process, the ribosome slips backwards by a single nucleotide and continues translation of an overlapping reading frame, generating a fusion protein. Frameshifting signals comprise a heptanucleotide slippery sequence, where the ribosome changes frame, and a stimulatory RNA structure, a stem–loop or RNA pseudoknot. Antisense oligonucleotides annealed appropriately 3′ of a slippery sequence have also shown activity in frameshifting, at least in vitro. Here we examined frameshifting at the U(6)A slippery sequence of the HIV gag/pol signal and found high levels of both −1 and −2 frameshifting with stem–loop, pseudoknot or antisense oligonucleotide stimulators. By examining −1 and −2 frameshifting outcomes on mRNAs with varying slippery sequence-stimulatory RNA spacing distances, we found that −2 frameshifting was optimal at a spacer length 1–2 nucleotides shorter than that optimal for −1 frameshifting with all stimulatory RNAs tested. We propose that the shorter spacer increases the tension on the mRNA such that when the tRNA detaches, it more readily enters the −2 frame on the U(6)A heptamer. We propose that mRNA tension is central to frameshifting, whether promoted by stem–loop, pseudoknot or antisense oligonucleotide stimulator. url: https://www.ncbi.nlm.nih.gov/pubmed/22743270/ doi: 10.1093/nar/gks629 id: cord-003130-p2h8p5bm author: Lindqvist, Richard title: Tick-Borne Flaviviruses and the Type I Interferon Response date: 2018-06-21 words: 8350.0 sentences: 481.0 pages: flesch: 48.0 cache: ./cache/cord-003130-p2h8p5bm.txt txt: ./txt/cord-003130-p2h8p5bm.txt summary: There are more than 70 viruses in the genus flavivirus, and they are transmitted by arthropods such as mosquitoes (dengue virus (DENV), Japanese encephalitis virus (JEV) and West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV) and ticks (tick-borne encephalitis virus (TBEV), Langat virus (LGTV), Kyasanur forest disease virus (KFDV), Omsk hemorrhagic fever virus (OHFV), Powassan virus (POWV), and Louping-ill virus (LIV)) [1] [2] [3] [4] [5] . Two other ISGs which have been shown to be antivirally active against TBEV are virus inhibitory protein endoplasmic reticulum associated interferon inducible (viperin) and tripartite motif-79α (TRIM79α). The role of interferon in tick-borne encephalitis virus-infected l cells. A functional toll-like receptor 3 gene (tlr3) may be a risk factor for tick-borne encephalitis virus (tbev) infection Analysis of tick-borne encephalitis virus-induced host responses in human cells of neuronal origin and interferon-mediated protection abstract: Flaviviruses are globally distributed pathogens causing millions of human infections every year. Flaviviruses are arthropod-borne viruses and are mainly transmitted by either ticks or mosquitoes. Mosquito-borne flaviviruses and their interactions with the innate immune response have been well-studied and reviewed extensively, thus this review will discuss tick-borne flaviviruses and their interactions with the host innate immune response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071234/ doi: 10.3390/v10070340 id: cord-345371-pjbviagq author: Lisi, Lucia title: Approaching Coronavirus Disease 2019: mechanisms of action of repurposed drugs with potential activity against SARS-CoV-2 date: 2020-07-23 words: 10648.0 sentences: 512.0 pages: flesch: 37.0 cache: ./cache/cord-345371-pjbviagq.txt txt: ./txt/cord-345371-pjbviagq.txt summary: The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. Here, we review the recently published literature on the pharmacological treatments used so far and/or undergoing evaluation in clinical trials, with focus on the biochemical mechanisms of action of repurposed or investigational drugs, classified as agents directly targeting the virus ( Figure 1 and Table 1 ) and those used to treat the respiratory distress and inflammation associated with the cytokine release syndrome ( Figure 2 and Table 2 ). abstract: On March 11, 2020, the World Health Organization (WHO) declared the severe acute respiratory syndrome caused by coronavirus 2 (SARS-CoV-2) a global pandemic. As of July 2020, SARS-CoV-2 has infected more than 14 million people and provoked more than 590,000 deaths, worldwide. From the beginning, a variety of pharmacological treatments has been empirically used to cope with the life-threatening complications associated with Corona Virus Disease 2019 (COVID-19). Thus far, only a couple of them and not consistently across reports have been shown to further decrease mortality, respect to what can be achieved with supportive care. In most cases, and due to the urgency imposed by the number and severity of the patients’ clinical conditions, the choice of treatment has been limited to repurposed drugs, approved for other indications, or investigational agents used for other viral infections often rendered available on a compassionate-use basis. The rationale for drug selection was mainly, though not exclusively, based either i) on the activity against other coronaviruses or RNA viruses in order to potentially hamper viral entry and replication in the epithelial cells of the airways, and/or ii) on the ability to modulate the excessive inflammatory reaction deriving from dysregulated host immune responses against the SARS-CoV-2. In several months, an exceptionally large number of clinical trials have been designed to evaluate the safety and efficacy of anti-COVID-19 therapies in different clinical settings (treatment or pre- and post-exposure prophylaxis) and levels of disease severity, but only few of them have been completed so far. This review focuses on the molecular mechanisms of action that have provided the scientific rationale for the empirical use and evaluation in clinical trials of structurally different and often functionally unrelated drugs during the SARS-CoV-2 pandemic. url: https://www.ncbi.nlm.nih.gov/pubmed/32710969/ doi: 10.1016/j.bcp.2020.114169 id: cord-330954-ft14aa2n author: Liu, B. M. title: Epidemiological characteristics of COVID-19 patients in convalescence period date: 2020-06-03 words: 3783.0 sentences: 179.0 pages: flesch: 54.0 cache: ./cache/cord-330954-ft14aa2n.txt txt: ./txt/cord-330954-ft14aa2n.txt summary: The discharged patients must meet the following criteria: (1) the body temperature returns to normal for more than 3 days; (2) respiratory symptoms improve significantly; (3) pulmonary imaging shows that the acute exudative lesions were significantly absorbed and improved; (4) the SARS-CoV-2 ribonucleic acid (RNA) detection results of two consecutive respiratory specimens are negative (sampling interval should be at least 24 h). We recorded the clinical manifestations, RNA detection results of oropharyngeal swab specimens, SARS-CoV-2 IgM−IgG antibodies detection results (data were collected on the 28th day after discharge), chest computed tomography (CT) images and medication of these patients. A case report of four mild-to-moderate COVID-19 patients (all were medical staff) showed that all convalescent patients without clinical symptoms presented RP findings of RNA detection in throat swab specimens at 5−13 days after discharge [14] . Another study found that among 62 COVID-19 convalescent medical staff, two patients without clinical symptoms showed RP findings of RNA detection in throat swab specimens at 5−6 days after discharge [15] . abstract: This study aimed to investigate the clinical characteristics and to analyse the epidemiological features of coronavirus disease 2019 (COVID-19) patients during convalescence. In this study, we enrolled 71 confirmed cases of COVID-19 who were discharged from hospital and transferred to isolation wards from 6 February to 26 March 2020. They were all employees of Zhongnan Hospital of Wuhan University or their family members of which three cases were <18 years of age. Clinical data were collected and analysed statistically. Forty-one cases (41/71, 57.7%) comprised medical faculty, young and middle-aged patients (aged ⩽60 years) accounted for 81.7% (58/71). The average isolation time period for all adult patients was 13.8 ± 6.1 days. During convalescence, RNA detection results of 35.2% patients (25/71) turned from negative to positive. The longest RNA reversed phase time was 7 days. In all, 52.9% of adult patients (36/68) had no obvious clinical symptoms, and the remaining ones had mild and non-specific clinical symptoms (e.g. cough, sputum, sore throat, disorders of the gastrointestinal tract etc.). Chest CT signs in 89.7% of adult patients (61/68) gradually improved, and in the others, the lesions were eventually absorbed and improved after short-term repeated progression. The main chest CT manifestations of adult patients were normal, GGO or fibre streak shadow, and six patients (8.8%) had extrapulmonary manifestations, but there was no significant correlation with RNA detection results (r = −0.008, P > 0.05). The drug treatment was mainly symptomatic support therapy, and antibiotics and antiviral drugs were ineffective. It is necessary to re-evaluate the isolation time and standard to terminate isolation for discharged COVID-19 patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32487271/ doi: 10.1017/s0950268820001181 id: cord-001963-4wjvykx7 author: Liu, Chia-Lin title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development date: 2016-02-26 words: 5457.0 sentences: 304.0 pages: flesch: 56.0 cache: ./cache/cord-001963-4wjvykx7.txt txt: ./txt/cord-001963-4wjvykx7.txt summary: title: Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development By interrupting the stacking interaction between Y148 and an RNA base, we identified an influenza virus NP inhibitor, (E, E)-1,7-bis(4-hydroxy-3-methoxyphenyl) -1,6-heptadiene-3,5-dione; this inhibitor reduced the NP''s RNA-binding affinity and hindered viral replication. As shown in Fig. 7A , upon H7 treatment at 15μM, the M1 viral RNA synthesis in the influenza virus-infected cells was reduced by 75% at T2. NP is the most abundant RNA-binding viral protein in influenza virus-infected cells and is responsible for recognizing RNA and forming a filamentous nucleocapsid 24 . Using fluorescence titration and an SPR assay of the NPs, we identified one potential natural compound, curcumin (H7), that targets Y148 of influenza virus NP and potently interferes with its RNA-binding activity. abstract: Nucleoprotein (NP) is the most abundant type of RNA-binding viral protein in influenza A virus–infected cells and is necessary for viral RNA transcription and replication. Recent studies demonstrated that influenza NP is a valid target for antiviral drug development. The surface of the groove, covered with numerous conserved residues between the head and body domains of influenza A NP, plays a crucial role in RNA binding. To explore the mechanism by which NP binds RNA, we performed a series of site-directed mutagenesis in the RNA-binding groove, followed by surface plasmon resonance (SPR), to characterize the interactions between RNA and NP. Furthermore, a role of Y148 in NP stability and NP-RNA binding was evaluated. The aromatic residue of Y148 was found to stack with a nucleotide base. By interrupting the stacking interaction between Y148 and an RNA base, we identified an influenza virus NP inhibitor, (E, E)-1,7-bis(4-hydroxy-3-methoxyphenyl) -1,6-heptadiene-3,5-dione; this inhibitor reduced the NP’s RNA-binding affinity and hindered viral replication. Our findings will be useful for the development of new drugs that disrupt the interaction between RNA and viral NP in the influenza virus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4768256/ doi: 10.1038/srep21662 id: cord-016261-jms7hrmp author: Liu, Chunmei title: Profiling and Searching for RNA Pseudoknot Structures in Genomes date: 2005 words: 4330.0 sentences: 221.0 pages: flesch: 53.0 cache: ./cache/cord-016261-jms7hrmp.txt txt: ./txt/cord-016261-jms7hrmp.txt summary: Profiling models based solely on sequence content such as Hidden Markov Model (HMM) [12] may miss structural homologies when directly used to search genomes for noncoding RNAs containing complex secondary structures. ERPIN searches genomes by sequentially looking for single stem loop motifs contained in the noncoding RNA gene, and reports a hit when significant alignment scores are observed for all the motifs at their corresponding locations. In this paper, we propose a new method to search for RNA pseudoknot structures using a model of multiple CMs. Unlike the model of Brown and Wilson, we use independent CM components to profile the interleaving stems in a pseudoknot. Finally, in order to test the ability of our program to cope with noncoding RNA genes with complex pseudoknot structures, we carried out an experiment where the complete DNA genomes of two bacteria were searched to find the locations of the tmRNA genes. abstract: We developed a new method that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for structures that contain pseudoknot in genomes of a variety of organisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120494/ doi: 10.1007/11567752_2 id: cord-269866-3tpyj04y author: Liu, D. X. title: Identification of two new polypeptides encoded by mRNA5 of the coronavirus infectious bronchitis virus date: 1992-01-31 words: 3164.0 sentences: 137.0 pages: flesch: 50.0 cache: ./cache/cord-269866-3tpyj04y.txt txt: ./txt/cord-269866-3tpyj04y.txt summary: We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. abstract: Abstract The second smallest subgenomic messenger RNA, mRNA5, of the coronavirus infectious bronchitis virus includes in its “5′ unique region” two separate open reading frames (5a and 5b), whose coding function has not so far been established, and thus it may represent a dicistronic messenger RNA. We report here that two polypeptides with the sizes expected for the 5a and 5b products can be synthesised by in vitro translation of a single artificial mRNA containing both the 5a and 5b ORFs. To establish whether these polypeptides represent genuine virus gene products, both the 5a and 5b coding sequences were expressed as bacterial fusion proteins, and these were used to raise monospecific antisera. Antisera raised against both the 5a and 5b-specific sequences recognized specifically proteins of the expected size in infectious bronchitis virus-infected chicken kidney and Vero cells, indicating that 5a and 5b do represent genuine virus genes, and suggesting that mRNA5 is indeed functionally dicistronic. url: https://www.sciencedirect.com/science/article/pii/0042682292900946 doi: 10.1016/0042-6822(92)90094-6 id: cord-343350-04e6wvov author: Liu, Haipeng title: Antiviral immunity in crustaceans date: 2009-02-15 words: 8002.0 sentences: 441.0 pages: flesch: 43.0 cache: ./cache/cord-343350-04e6wvov.txt txt: ./txt/cord-343350-04e6wvov.txt summary: White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis Preliminary study on haemocyte response to white spot syndrome virus infection in black tiger shrimp Penaeus monodon Time-course and levels of apoptosis in various tissues of black tiger shrimp Penaeus monodon infected with white-spot syndrome virus Protein expression profiling of the shrimp cellular response to white spot syndrome virus infection Cloning and characterization of a caspase gene from black tiger shrimp (Penaeus monodon)-infected with white spot syndrome virus (WSSV) Immunological responses of Penaeus monodon to DNA vaccine and its efficacy to protect shrimp against white spot syndrome virus (WSSV) Multiple envelope proteins are involved in white spot syndrome virus (WSSV) infection in crayfish Identification of white spot syndrome virus (WSSV) envelope proteins involved in shrimp infection DNA fragmentation, an indicator of apoptosis, in cultured black tiger shrimp Penaeus monodon infected with white spot syndrome virus (WSSV) abstract: Viral diseases of shrimp have caused negative effects on the economy in several countries in Asia, South America and America, where they have numerous shrimp culture industries. The studies on the immunity of shrimp and other crustaceans have mainly focused on general aspects of immunity and as a consequence little is known about the antiviral responses in crustaceans. The aim of this review is to update recent knowledge of innate immunity against viral infections in crustaceans. Several antiviral molecules have been isolated and characterized recently from decapods. Characterization and identification of these molecules might provide a promising strategy for protection and treatment of these viral diseases. In addition dsRNA-induced antiviral immunity is also included. url: https://www.ncbi.nlm.nih.gov/pubmed/19223016/ doi: 10.1016/j.fsi.2009.02.009 id: cord-258678-0atfsivf author: Liu, Hong Yan title: A Universal Protein Tag for Delivery of SiRNA-Aptamer Chimeras date: 2013-11-07 words: 4788.0 sentences: 282.0 pages: flesch: 51.0 cache: ./cache/cord-258678-0atfsivf.txt txt: ./txt/cord-258678-0atfsivf.txt summary: Here, we report the development of a small and simple protein tag that complements the therapeutic and targeting functionalities of chimera with two functional domains: a dsRNA binding domain (dsRBD) for siRNA docking and a pH-dependent polyhistidine to disrupt endosomal membrane. Therefore, it is of critical importance to design a delivery system that is simple for potential regulatory approval and mass production, universal for all siRNAaptamer chimera, neutral and siRNA-binding specific to ensure aptamer targeting, and small to avoid major alteration of chimera''s biodistribution profile. To assess their dsRNA binding activity, siRNA-aptamer chimera labeled with fluorophore FAM were incubated with the protein tags and probed with gel electrophoresis (1% agarose). To evaluate the targeting specificity of the aptamer block, PSMA-positive LNCaP cells and PSMA-negative PC3 cells were treated with complex of chimera and dsRBD-His 18 (chimera/protein tag molar ratio at 152, 100 nM chimera) in serum free medium for 2 hours, followed by incubation in complete medium for another 12 h. abstract: siRNA-aptamer chimeras have emerged as one of the most promising approaches for targeted delivery of siRNA due to the modularity of their diblock RNA structure, relatively lower cost over other targeted delivery approaches, and, most importantly, the outstanding potential for clinical translation. However, additional challenges must be addressed for efficient RNA interference (RNAi), in particular, endosomal escape. Currently, vast majority of siRNA delivery vehicles are based on cationic materials, which form complexes with negatively charged siRNA. Unfortunately, these approaches complicate the formulations again by forming large complexes with heterogeneous sizes, unfavorable surface charges, colloidal instability, and poor targeting ligand orientation. Here, we report the development of a small and simple protein tag that complements the therapeutic and targeting functionalities of chimera with two functional domains: a dsRNA binding domain (dsRBD) for siRNA docking and a pH-dependent polyhistidine to disrupt endosomal membrane. The protein selectively tags along the siRNA block of individual chimera, rendering the overall size of the complex small, desirable for deep tissue penetration, and the aptamer block accessible for target recognition. More interestingly, we found that extending the c-terminal polyhistidine segment in the protein tag to 18 amino acids completely abolishes the RNA binding function of dsRBD. url: https://www.ncbi.nlm.nih.gov/pubmed/24196104/ doi: 10.1038/srep03129 id: cord-331916-n744pymd author: Liu, Jue title: Inhibition of porcine circovirus type 2 replication in mice by RNA interference date: 2006-04-10 words: 6657.0 sentences: 350.0 pages: flesch: 52.0 cache: ./cache/cord-331916-n744pymd.txt txt: ./txt/cord-331916-n744pymd.txt summary: Specific inhibition of endogenous or pathogen mRNA by RNAi can be triggered by the introduction of 21 -23 nucleotide (nt) duplexes of RNA (siRNA) or by transcription of DNA precursor into short hairpin RNAs (shRNA) homologous to target sequences (Brummelkamp et al., 2002; Elbashir et al., 2001a; Paddison et al., 2002) , opening up possibilities for controlling replicative processes of pathogens. To further examine the ability of ORF1 shRNA to suppress viral gene expression in PCV2-infected PK15 cells, single nucleotide mutations were introduced into pSIR3 sequence as shown in Fig. 4A . As shown in Fig. 4B , a mutant with one nucleotide mutation in the 5V-end of the sense strand (pSIR3-m1) still had an effective reduction in the synthesis of ORF1 and ORF2 proteins, whereas with a nucleotide substitution at the center (pSIR3-m2) or 3V-end (pSIR3-m3) of the sense sequence, the resultant shRNAs failed to significantly suppress expression of PCV2 ORF1 and ORF2 in the transfected cells, further verifying the specificity of RNAi as demonstrated (Amarzguioui et al., 2003; Harborth et al., 2003) . abstract: Porcine circovirus type 2 (PCV2) is the primary causative agent of an emerging swine disease, postweaning multisystemic wasting syndrome (PMWS) for which no antiviral treatment is available. To exploit the possibility of using RNA interference (RNAi) as a therapeutic approach against the disease, plasmid-borne short hairpin RNAs (shRNAs) were generated to target the PCV2 genome. Transfection of these shRNAs into cultured PK15 cells caused a significant reduction in viral RNA production that was accompanied by inhibiting viral DNA replication and protein synthesis in infected cells. The effect was further tested in vivo in a mouse model that has been developed for PCV2 infection. Mice injected with shRNA before PCV2 infection showed substantially decreased microscopic lesions in inguinal lymph nodes compared to controls. In situ hybridization and immunohistochemical analyses showed that shRNA caused a significant inhibition in the level of viral DNA and protein synthesis detected in the lymph nodes of the treated mice relative to the controls. Taken together, these results indicate that shRNAs are capable of inhibiting PCV2 infection in vitro as well as in vivo and thus may constitute an effective therapeutic strategy for PCV2 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/16427679/ doi: 10.1016/j.virol.2005.12.006 id: cord-347917-fmb5nyxu author: Liu, Junli title: Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection date: 2020-01-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine delta coronavirus (PDCoV) is a novel emerging enterocytetropic virus causing diarrhea, vomiting, dehydration, and mortality in suckling piglets. Long non-coding RNAs (lncRNAs) are known to be important regulators during virus infection. Here, we describe a comprehensive transcriptome profile of lncRNA in PDCoV-infected swine testicular (ST) cells. In total, 1,308 annotated and 1,190 novel lncRNA candidate sequences were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these lncRNAs might be involved in numerous biological processes. Clustering analysis of differentially expressed lncRNAs showed that 454 annotated and 376 novel lncRNAs were regulated after PDCoV infection. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to metabolism and TNF signaling. Our study provided comprehensive information about lncRNAs that would be a useful resource for studying the pathogenesis of and designing antiviral therapy for PDCoV infection. url: https://doi.org/10.3389/fmicb.2019.03036 doi: 10.3389/fmicb.2019.03036 id: cord-355676-2y8vowbi author: Liu, Pinghua title: A Previously Unrecognized Unr Stem-Loop Structure in the Coronavirus 5’ Untranslated Region Plays a Functional role in Replication date: 2006 words: 1329.0 sentences: 76.0 pages: flesch: 62.0 cache: ./cache/cord-355676-2y8vowbi.txt txt: ./txt/cord-355676-2y8vowbi.txt summary: The RNA secondary structure prediction algorithm Vienna RNA 1.5 4 was used to predict the secondary structures of group 1 and group 2 coronavirus 5'' UTRs. A reverse genetic system based on in vitro assembly of cloned cDNAs (A-G) was used to recover wild-type MHV-A59 1000 and mutant viruses. The assembled fragment containing either the wild-type sequence, or with mutations in SL2, was ligated into MHV-A59-1000 RNA was electroporated into BHK-R cells to recover infectious virus as described. Analysis of the entire 30 kb MHV and SARS-CoV genomes reveals that SL2-like stem loops are extremely rare (appearing just 3 and 5 other times, respectively); this suggests an important role in coronavirus replication. Consistent with the predicted structure of the UNR loop, the U49A mutant was viable and produced a virus with a near normal plaque size (Figs 4A-B) . abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037499/ doi: 10.1007/978-0-387-33012-9_3 id: cord-271188-ewlxy5po author: Liu, Wei title: Depriving Iron Supply to the Virus Represents a Promising Adjuvant Therapeutic Against Viral Survival date: 2020-04-20 words: 4237.0 sentences: 245.0 pages: flesch: 42.0 cache: ./cache/cord-271188-ewlxy5po.txt txt: ./txt/cord-271188-ewlxy5po.txt summary: Abbreviations 311, 2-hydroxy-1-naphthylaldehyde benzoyl hydrazine; 3CL pro , 3C-like protease; ABCE1, ATP binding cassette subfamily E member 1; ACE, angiotensin-converting enzyme 2; ADK, aryl diketoacids; AIDS, acquired immunodeficiency syndrome; APN, aminopeptidase N; AT2, small population of type II alveolar cells; BMP, bone morphogenetic proteins; Bp4aT, 2-benzoylpyridine 4-allyl-3thiosemicarbazone; Bp4eT, 2-benzoylpyridine 4-ethyl-3thiosemicarbazone; COVID-19, novel coronavirus pneumonia; CoVs, coronaviruses; DFO, deferoxamine; DFP, deferiprone; DPP4, dipeptidyl-peptidase 4.; E, envelope; EPDTC, Nethyl-Nphenyldithiocarbamic acid zinc; ER, endoplasmic reticulum; HCMV, human cytomegalovirus; HFE, homeostatic iron regulator protein; HIV, human immunodeficiency virus; HSA, human serum albumin; IP10, interferon-inducible protein 10; M, membrane; MBD, metal-binding domain; MCP1, monocyte chemotactic protein 1; MERS, Middle East respiratory syndrome; N, nucleocapsid; PBMC, peripheral blood mononuclear cells; PL pro , papain-like protease; PMA, phenylmercuric acetate; PPY, phenyl-1-pyridin-2yl-ethanone; RdRp, RNA-dependent RNA polymerase; ROS, reactive oxygen species; S, spike; SARS, severe acute respiratory syndrome; SARS-CoV-2, the 2019 novel coronavirus; SCD, sickle cell disease; TDT, toluene-3,4-dithiolato zinc; TfR1, transferrin receptor1 abstract: PURPOSE OF THE REVIEW: The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) in China is lifting widespread concerns. Thus, therapeutic options are urgently needed, and will be discussed in this review. RECENT FINDINGS: Iron-containing enzymes are required for viruses most likely including coronaviruses (CoVs) to complete their replication process. Moreover, poor prognosis occurred in the conditions of iron overload for patients upon infections of viruses. Thus, limiting iron represents a promising adjuvant strategy in treating viral infection through oral uptake or venous injection of iron chelators, or through the manipulation of the key iron regulators. For example, treatment with iron chelator deferiprone has been shown to prolong the survival of acquired immunodeficiency syndrome (AIDS) patients. Increasing intracellular iron efflux via increasing iron exporter ferroportin expression also exhibits antiviral effect on human immunodeficiency virus (HIV). The implications of other metals besides iron are also briefly discussed. SUMMARY: For even though we know little about iron regulation in COVID-19 patients thus far, it could be deduced from other viral infections that iron chelation might be an alternative beneficial adjuvant in treating COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32318324/ doi: 10.1007/s40588-020-00140-w id: cord-003305-ya0siivm author: Liu, Weichi title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase date: 2018-11-16 words: 8861.0 sentences: 427.0 pages: flesch: 54.0 cache: ./cache/cord-003305-ya0siivm.txt txt: ./txt/cord-003305-ya0siivm.txt summary: The intra-molecular NTD interactions with the RdRP palm that controls the active site closure, together with the observation of the NTD deletion mutant N-91 exhibited higher level of misincorporation in the de novo RNA synthesis, suggesting a unique mode of fidelity modulation. In order to quantitatively assess whether the fidelity levels are modulated by the intra-molecular NTD-RdRP interface interactions, we established the 32 P-radioactivity based NTP misincorporation assays using the T30/P2 construct utilized in the aforementioned de novo-mode synthesis assessment ( Figure 1B and C) . The effect of E472A mutation was highly consistent with AA mutation ( Figure 4B and Supplementary Figure S3A Since polymerase misincorporation level can be affected by the type of misincorporation and the sequence context of the misincorporation site, we established the second type of regular NTP misincorporation assays using the same T30/P2 construct for a more adequate assessment of the RdRP fidelity modulation brought by the NTD. abstract: Typically not assisted by proofreading, the RNA-dependent RNA polymerases (RdRPs) encoded by the RNA viruses may need to independently control its fidelity to fulfill virus viability and fitness. However, the precise mechanism by which the RdRP maintains its optimal fidelity level remains largely elusive. By solving 2.1–2.5 Å resolution crystal structures of the classical swine fever virus (CSFV) NS5B, an RdRP with a unique naturally fused N-terminal domain (NTD), we identified high-resolution intra-molecular interactions between the NTD and the RdRP palm domain. In order to dissect possible regulatory functions of NTD, we designed mutations at residues Y471 and E472 to perturb key interactions at the NTD–RdRP interface. When crystallized, some of these NS5B interface mutants maintained the interface, while the others adopted an ‘open’ conformation that no longer retained the intra-molecular interactions. Data from multiple in vitro RdRP assays indicated that the perturbation of the NTD–RdRP interactions clearly reduced the fidelity level of the RNA synthesis, while the processivity of the NS5B elongation complex was not affected. Collectively, our work demonstrates an explicit and unique mode of polymerase fidelity modulation and provides a vivid example of co-evolution in multi-domain enzymes. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237809/ doi: 10.1093/nar/gky848 id: cord-353484-q7d0ysbo author: Liu, Xue title: COVID-19: Progress in diagnostics, therapy and vaccination date: 2020-06-19 words: 8557.0 sentences: 465.0 pages: flesch: 41.0 cache: ./cache/cord-353484-q7d0ysbo.txt txt: ./txt/cord-353484-q7d0ysbo.txt summary: Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. Another type of rapid diagnostic test (RDT) that detects the presence of viral antigens expressed by SARS-CoV-2 virus in a respiratory tract sample is of low complexity and may provide results typically within 30 minutes [68, 69] . Studies in Vero E6 cells have suggested that favipiravir can cripple the SARS-CoV-2 virus (EC50 = 61.88 μM) [88] , and patients with COVID-19 are being recruited in randomized trials to evaluate the efficacy of favipiravir plus other antivirals (e.g., ClinicalTrials.gov: ChiCTR2000029600, ChiCTR2000029544). As no specific therapeutic agents or vaccines are available for COVID-19, this therapy is the only strategy that is immediately available for use to prevent and treat a novel, emerging infectious disease such as SARS-CoV-2 infection [121, 122] . abstract: Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently become a pandemic. As the sudden emergence and rapid spread of SARS-CoV-2 is endangering global health and the economy, the development of strategies to contain the virus's spread are urgently needed. At present, various diagnostic kits to test for SARS-CoV-2 are available for use to initiate appropriate treatment faster and to limit further spread of the virus. Several drugs have demonstrated in vitro activity against SARS-CoV-2 or potential clinical benefits. In addition, institutions and companies worldwide are working tirelessly to develop treatments and vaccines against COVID-19. However, no drug or vaccine has yet been specifically approved for COVID-19. Given the urgency of the outbreak, we focus here on recent advances in the diagnostics, treatment, and vaccine development for SARS-CoV-2 infection, helping to guide strategies to address the current COVID-19 pandemic. url: https://doi.org/10.7150/thno.47987 doi: 10.7150/thno.47987 id: cord-320169-dtv7to3l author: Liu, Yen-Chin title: COVID-19: the First Documented Coronavirus Pandemic in History date: 2020-05-05 words: 1935.0 sentences: 127.0 pages: flesch: 51.0 cache: ./cache/cord-320169-dtv7to3l.txt txt: ./txt/cord-320169-dtv7to3l.txt summary: The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. The spike glycoprotein of SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2) in human and Chinese horseshoe bats, civet for cell entry, that is also dependent on S protein priming by the serine protease TMPRSS2. Domestic animals can suffer from disease as intermediate hosts that cause virus transmission from natural hosts to humans; for example, SARS-CoV and MERS-CoV crossed the species barriers into masked palm civets and camels, respectively [30, 31] [ Table 1 ]. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. abstract: The novel human coronavirus disease COVID-19 has become the fifth documented pandemic since the 1918 flu pandemic. COVID-19 was first reported in Wuhan, China, and subsequently spread worldwide. The coronavirus was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses based on phylogenetic analysis. SARS-CoV-2 is believed to be a spillover of an animal coronavirus and later adapted the ability of human-to-human transmission. Because the virus is highly contagious, it rapidly spreads and continuously evolves in the human population. In this review article, we discuss the basic properties, potential origin, and evolution of the novel human coronavirus. These factors may be critical for studies of pathogenicity, antiviral designs, and vaccine development against the virus. url: https://doi.org/10.1016/j.bj.2020.04.007 doi: 10.1016/j.bj.2020.04.007 id: cord-284156-btb4oodz author: Liu, Yiliu title: Host and Viral Modulation of RIG-I-Mediated Antiviral Immunity date: 2017-01-03 words: 7021.0 sentences: 397.0 pages: flesch: 38.0 cache: ./cache/cord-284156-btb4oodz.txt txt: ./txt/cord-284156-btb4oodz.txt summary: Retinoic acid-inducible gene-I (RIG-I) is critical in triggering antiviral and inflammatory responses for the control of viral replication in response to cytoplasmic virus-specific RNA structures. They function as cytoplasmic sensors for the recognition of a variety of RNA viruses and subsequent activation of downstream signaling to drive type I IFN production and antiviral gene expressions. (c) Interactions between RIG-I-TRIM25 complex and 14-3-3ϵ promote RIG-I translocation to mitochondrial mitochondrial antiviral signaling protein (MAVS) for downstream signaling, leading to interferon production. Protein purification and mass spectrometry analysis identified that phosphorylation of Thr170 in the CARDs antagonizes RIG-I signaling by inhibiting TRIM25-mediated Lys172 ubiquitination and MAVS binding (68) . Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Inhibition of dengue and chikungunya virus infections by RIG-I-mediated type I interferon-independent stimulation of the innate antiviral response abstract: Innate immunity is the first line of defense against invading pathogens. Rapid and efficient detection of pathogen-associated molecular patterns via pattern-recognition receptors is essential for the host to mount defensive and protective responses. Retinoic acid-inducible gene-I (RIG-I) is critical in triggering antiviral and inflammatory responses for the control of viral replication in response to cytoplasmic virus-specific RNA structures. Upon viral RNA recognition, RIG-I recruits the mitochondrial adaptor protein mitochondrial antiviral signaling protein, which leads to a signaling cascade that coordinates the induction of type I interferons (IFNs), as well as a large variety of antiviral interferon-stimulated genes. The RIG-I activation is tightly regulated via various posttranslational modifications for the prevention of aberrant innate immune signaling. By contrast, viruses have evolved mechanisms of evasion, such as sequestrating viral structures from RIG-I detections and targeting receptor or signaling molecules for degradation. These virus–host interactions have broadened our understanding of viral pathogenesis and provided insights into the function of the RIG-I pathway. In this review, we summarize the recent advances regarding RIG-I pathogen recognition and signaling transduction, cell-intrinsic control of RIG-I activation, and the viral antagonism of RIG-I signaling. url: https://www.ncbi.nlm.nih.gov/pubmed/28096803/ doi: 10.3389/fimmu.2016.00662 id: cord-262076-b5u5hp2r author: Liu, Ying Poi title: Inhibition of HIV-1 by multiple siRNAs expressed from a single microRNA polycistron date: 2008-03-16 words: 6881.0 sentences: 414.0 pages: flesch: 56.0 cache: ./cache/cord-262076-b5u5hp2r.txt txt: ./txt/cord-262076-b5u5hp2r.txt summary: We show that the expression of individual miRNAs is greatly enhanced in multiplex hairpin transcripts that are properly processed into functional miRNAs. HIV-1 replication can be potently inhibited by simultaneous expression of four antiviral miRNAs. These combined results indicate that the multiplex miRNA strategy is a promising therapeutic approach against escape-prone viral pathogens. By repeating this procedure we obtained constructs expressing different combinations of 1, 2, 3, 4 and 6 pri-miRNAs. The RNA structures formed by the transcripts were predicted with the Mfold program (47) at http://frontend.bioinfo.rpi.edu/ applications/mfold/ and found to be similar to the predicted conformation of the wild-type pri-miRNAs. The firefly luciferase (FL) reporters containing HIV-1 target sequences pol47 (Luc-A pol47 ), pol1 (Luc-B pol1 ), gag5 (Luc-C gag5 ), r/t5 (Luc-D r/t5 ), ldr9 (Luc-E ldr9 ) and the anti-HIV shRNAs have been described previously (32) . abstract: RNA interference (RNAi) is a powerful approach to inhibit human immunodeficiency virus type 1 (HIV-1) replication. However, HIV-1 can escape from RNAi-mediated antiviral therapy by selection of mutations in the targeted sequence. To prevent viral escape, multiple small interfering RNAs (siRNAs) against conserved viral sequences should be combined. Ideally, these RNA inhibitors should be expressed simultaneously from a single transgene transcript. In this study, we tested a multiplex microRNA (miRNA) expression strategy by inserting multiple effective anti-HIV siRNA sequences in the miRNA polycistron mir-17-92. Individual anti-HIV miRNAs that resemble the natural miRNA structures were optimized by varying the siRNA position in the hairpin stem to obtain maximal effectiveness against luciferase reporters and HIV-1. We show that an antiviral miRNA construct can have a greater intrinsic inhibitory activity than a conventional short hairpin (shRNA) construct. When combined in a polycistron setting, the silencing activity of an individual miRNA is strongly boosted. We demonstrate that HIV-1 replication can be efficiently inhibited by simultaneous expression of four antiviral siRNAs from the polycistronic miRNA transcript. These combined results indicate that a multiplex miRNA strategy may be a promising therapeutic approach to attack escape-prone viral pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/18346971/ doi: 10.1093/nar/gkn109 id: cord-002006-pwlybr2h author: Liu, Yuan-yuan title: Specific interference shRNA-expressing plasmids inhibit Hantaan virus infection in vitro and in vivo date: 2016-03-14 words: 3906.0 sentences: 197.0 pages: flesch: 50.0 cache: ./cache/cord-002006-pwlybr2h.txt txt: ./txt/cord-002006-pwlybr2h.txt summary: AIM: To investigate the antiviral effects of vectors expressing specific short hairpin RNAs (shRNAs) against Hantaan virus (HTNV) infection in vitro and in vivo. In mice infected with lethal doses of HTNV, intraperitoneal injection of pSilencer-S or pSilencer-M (30 μg) considerably increased the survival rates and mean time to death, and significantly reduced the mean virus yields and viral RNA level, and alleviated virus-induced pathological lesions in lungs, brains and kidneys. Based on these results and the viral antigen expression results detected by IFA (data not shown), we concluded that the shRNAs that targeted the S and M segments of the HTNV gene were able to inhibit RNA transcript and virus production in the HTNV-infected cells and that shRNA-S1 and shRNA-M2 exhibited a stronger inhibitory effect against HTNV. The RNAi pSilencer-S and pSilencer-M plasmids were constructed, and their antiviral effects were further evaluated by detecting the viral protein synthesis and RNA transcript and progeny virus titers in the HTNV-infected cells. abstract: AIM: To investigate the antiviral effects of vectors expressing specific short hairpin RNAs (shRNAs) against Hantaan virus (HTNV) infection in vitro and in vivo. METHODS: Based on the effects of 4 shRNAs targeting different regions of HTNV genomic RNA on viral replication, the most effective RNA interference fragments of the S and M genes were constructed in pSilencer-3.0-H1 vectors, and designated pSilencer-S and pSilencer-M, respectively. The antiviral effect of pSilencer-S/M against HTNV was evaluated in both HTNV-infected Vero-E6 cells and mice. RESULTS: In HTNV-infected Vero-E6 cells, pSilencer-S and pSilencer-M targeted the viral nucleocapsid proteins and envelope glycoproteins, respectively, as revealed in the immunofluorescence assay. Transfection with pSilencer-S or pSilencer-M (1, 2, 4 μg) markedly inhibited the viral antigen expression in dose- and time-dependent manners. Transfection with either plasmid (2 μg) significantly decreased HTNV-RNA level at 3 day postinfectin (dpi) and the progeny virus titer at 5 dpi. In mice infected with lethal doses of HTNV, intraperitoneal injection of pSilencer-S or pSilencer-M (30 μg) considerably increased the survival rates and mean time to death, and significantly reduced the mean virus yields and viral RNA level, and alleviated virus-induced pathological lesions in lungs, brains and kidneys. CONCLUSION: Plasmid-based shRNAs potently inhibit HTNV replication in vitro and in vivo. Our results provide a basis for development of shRNA as therapeutics for HTNV infections in humans. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820803/ doi: 10.1038/aps.2015.165 id: cord-319194-ukuia48s author: Liò, Pietro title: Phylogenomics and bioinformatics of SARS-CoV date: 2004-02-04 words: 4488.0 sentences: 201.0 pages: flesch: 45.0 cache: ./cache/cord-319194-ukuia48s.txt txt: ./txt/cord-319194-ukuia48s.txt summary: Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. Figure 1 shows the maximum likelihood tree produced using a set of homologous replicases from five SARS-CoV strains, 12 other coronaviruses representing both groups 1 and 2 of the genus [2, 3] , one torovirus (Breda virus) and one okavirus [yellow head (YH) virus], which were determined to most closely represent the consensus coronavirus sequence by a PSI-Blast search [12] . abstract: Tracing the history of molecular changes in coronaviruses using phylogenetic methods can provide powerful insights into the patterns of modification to sequences that underlie alteration to selective pressure and molecular function in the SARS-CoV (severe acute respiratory syndrome coronavirus) genome. The topology and branch lengths of the phylogenetic relationships among the family Coronaviridae, including SARS-CoV, have been estimated using the replicase polyprotein. The spike protein fragments S1 (involved in receptor-binding) and S2 (involved in membrane fusion) have been found to have different mutation rates. Fragment S1 can be further divided into two regions (S1A, which comprises approximately the first 400 nucleotides, and S1B, comprising the next 280) that also show different rates of mutation. The phylogeny presented on the basis of S1B shows that SARS-CoV is closely related to MHV (murine hepatitis virus), which is known to bind the murine receptor CEACAM1. The predicted structure, accessibility and mutation rate of the S1B region is also presented. Because anti-SARS drugs based on S2 heptads have short half-lives and are difficult to manufacture, our findings suggest that the S1B region might be of interest for anti-SARS drug discovery. url: https://api.elsevier.com/content/article/pii/S0966842X04000216 doi: 10.1016/j.tim.2004.01.005 id: cord-268337-o6lo55o8 author: Lloyd, Richard E. title: Translational control by viral proteinases date: 2005-11-21 words: 9416.0 sentences: 495.0 pages: flesch: 49.0 cache: ./cache/cord-268337-o6lo55o8.txt txt: ./txt/cord-268337-o6lo55o8.txt summary: Human immunodeficiency virus-1 (HIV-1) infection of cells resulted in partial cleavages of eIF4GI that was mapped to three sites in two regions on either side of the eIF3-binding domain ( Fig. 1) (Ohlmann et al., 2002; Ventoso et al., 2001) . Translation assays based on luciferase reporter constructs in cells indicated that expression of HIV protease (HIV PR) primarily inhibited translation of capped mRNAs. Interestingly, comparison of translation function of eIF4GI C-terminal cleavage products produced by L pro and HIV PR revealed that the slightly shorter HIV PR-derived fragment was defective in supporting translation of the PV-IRES but not the EMCV IRES. Demonstration in vitro that eucaryotic initiation factor 3 is active but a cap-binding protein complex is inactive in poliovirus-infected HeLa cells Eukaryotic initiation factor 4GII (eIF4GII), but not eIF4GI, cleavage correlates with inhibition of host cell protein synthesis after human rhinovirus infection Cleavage of eukaryotic initiation factor eIF4G and inhibition of host-cell protein synthesis during feline calicivirus infection abstract: Most RNA viruses have evolved strategies to regulate cellular translation in order to promote preferential expression of the viral genome. Positive strand RNA viruses express large portions, or all of their proteome via translation of large polyproteins that are processed by embedded viral proteinases or host proteinases. Several of these viral proteinases are known to interact with host proteins, particularly with the host translation machinery, and thus, encompass the dual functions of processing of viral polyproteins and exerting translation control. Picornaviruses are perhaps the best characterized in regards to interaction of their proteinases with the host translation machinery and will be emphasized here. However, new findings have shown that similar paradigms exist in other viral systems which will be discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/16303201/ doi: 10.1016/j.virusres.2005.10.016 id: cord-342901-ca2xxkb2 author: Lloyd, Richard E. title: Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses date: 2015-05-31 words: 16221.0 sentences: 823.0 pages: flesch: 50.0 cache: ./cache/cord-342901-ca2xxkb2.txt txt: ./txt/cord-342901-ca2xxkb2.txt summary: Though PTB was the first, a wide spectrum of factors, largely nuclear RBPs, have also been proposed as poliovirus ITAFs, including Lupus autoantigen (La) (Meerovitch et al., 1993 (Meerovitch et al., , 1989 , poly(rC)binding proteins (PCBPs) (Blyn et al., 1996; Gamarnik and Andino, 1997) , upstream of N-ras (UNR) (Anderson et al., 2007; Boussadia et al., 2003; Hunt et al., 1999) , SRp20 (Bedard et al., 2007) and glycyl-tRNA synthetase (GARS) (Andreev et al., 2012) (Table 1 ). In addition, certain ITAFs play crucial roles in regulating the conversion of translation-competent genomic RNAs into replicationcompetent RNAs. PTB was known as a nuclear splicing factor when its role as an ITAF of poliovirus and EMCV was discovered; a classic hijacked nuclear protein pressed into a new role required for the virus. abstract: Abstract Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. url: https://www.ncbi.nlm.nih.gov/pubmed/25818028/ doi: 10.1016/j.virol.2015.03.001 id: cord-309048-emmtplv3 author: Lomonossoff, George P. title: TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications date: 2018-07-26 words: 9017.0 sentences: 407.0 pages: flesch: 46.0 cache: ./cache/cord-309048-emmtplv3.txt txt: ./txt/cord-309048-emmtplv3.txt summary: (1999) displayed peptides of either 10 or 15 amino acids from the spike protein of the coronavirus murine hepatitis virus on the surface of assembled particles. coli-produced protein with a minimum of 20% of plant-made TMV CP, an approach that enabled efficient RNA-guided assembly of TMV-CP His6 into particles of the expected length (Eiben et al., 2014) . Assembly of the particle of tobacco mosaic virus from RNA and disks of protein β-Structure of the coat protein subunits in spherical particles generated by tobacco mosaic virus thermal denaturation Expression of tobacco mosaic virus coat protein and assembly of pseudovirus particles in Escherichia coli In vitro assembly of tobacco mosaic virus coat protein variants derived from fission yeast expression clones or plants Modified tobacco mosaic virus particles as scaffolds for display of protein antigens for vaccine applications Display of peptides on the surface of tobacco mosaic virus particles Assembly of hybrid RNAs with tobacco mosaic virus coat protein. abstract: Ever since its initial characterization in the 19th century, tobacco mosaic virus (TMV) has played a prominent role in the development of modern virology and molecular biology. In particular, research on the three-dimensional structure of the virus particles and the mechanism by which these assemble from their constituent protein and RNA components has made TMV a paradigm for our current view of the morphogenesis of self-assembling structures, including viral particles. More recently, this knowledge has been applied to the development of novel reagents and structures for applications in biomedicine and bionanotechnology. In this article, we review how fundamental science has led to TMV being at the vanguard of these new technologies. url: https://doi.org/10.1016/bs.aivir.2018.06.003 doi: 10.1016/bs.aivir.2018.06.003 id: cord-302368-uhhtvdif author: Longhini, Andrew P. title: Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations date: 2016-04-07 words: 6542.0 sentences: 323.0 pages: flesch: 49.0 cache: ./cache/cord-302368-uhhtvdif.txt txt: ./txt/cord-302368-uhhtvdif.txt summary: Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Additionally, we show that the measurements of relaxation parameters using CPMG, R 1 , and CEST are possible for both small and large RNAs. Furthermore, we demonstrate substantial improvements in signalto-noise and line width for relaxation optimized spectroscopy (TROSY) experiments compared to the traditional heteronuclear single quantum coherence (HSQC) exNucleic Acids Research, 2016, Vol. 44, No. 6 e52 periments for isolated two-spin systems approximated by our purine and pyrimidine labeling schemes (30) (31) (66) (67) . Thus, RNAs synthesized with our selective site-specifically labeled NTPs should benefit from TROSY based NMR experiments that reduce the problems of crowding, fast signal decay, low resolution, and decreased S/N ratios (12, 34, 31, (66) (67) (80) (81) . abstract: Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis (48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB. url: https://doi.org/10.1093/nar/gkv1333 doi: 10.1093/nar/gkv1333 id: cord-314369-o4nis91y author: Lopez-Lopes, G. I. S. title: Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19. date: 2020-08-01 words: 3684.0 sentences: 211.0 pages: flesch: 55.0 cache: ./cache/cord-314369-o4nis91y.txt txt: ./txt/cord-314369-o4nis91y.txt summary: Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. During the initial months of the COVID-19 swabs and other collection methods were used by LHW in the institute to identify SARS-Cov-2 RNA in upper respiratory tract, but occasionally throat wash (TW) was alternatively used. We compared the CT obtained at this survey to results generated from contemporary swab collections, sent as routine testing at the institute, that provide SARS-CoV-2 rtPCR testing to clinical services. The study did not compare the rate of positivity in paired samples, and only one individual was documented that performed both a swab test (negative) and a positive throat wash collection at a same day. The study suggests that throat wash may be a valid alternative to the detection of SARS-CoV-2 RNA. abstract: Background: SARS-CoV-2 RNA detection with real time PCR is currently the central diagnostic tool to determine ongoing active infection. Nasopharyngeal and oral swabs are the main collection tool of biological material used as the source of viral RNA outside a hospital setting. However, limitation in swabs availability, trained health professional with proper PPE and potential risk of aerosols may hinder COVID diagnosis. Self-collection with swabs, saliva and throat wash to obtain oropharyngeal wash has been suggested as having comparable performance of regular swab. We performed throat wash (TW) based surveillance with laboratory heath workers and other employees (LHW) at a laboratory research institute. Methods: Consecutive volunteer testing of LWH and external household and close contacts were included. TW self-collection was performed in 5 mL of sterile saline that was returned to original vial after approximate 5 secs of gargle. RNA extraction and rtPCR were performed as part of routine COVID protocols using Allplex (Seegene, Korea). Results: Four hundred and twenty two volunteers, 387 (93%) LHW and 43 (7%) contacts participated in the survey. One or more positive COVID rtPCR was documented in 63 (14.9% CI95 12%-19%) individuals. No correlation was observed between with direct activities with COVID samples to positivity, with infection observed in comparable rates among different laboratory areas, administrative or supportive activities. Among 63 with detected SARS-CoV-2 RNA, 59 with clinical information, 58% reported symptoms at a median of 4 days prior to collection, most with mild disease. Over a third (38%) of asymptomatic cases developed symptoms 1-3 days after collection. Although overall CT values of TW were higher than that of contemporary swab tests from hospitalized cases, TW from symptomatic cases had comparable CTs. Conclusions: The study suggests that TW may be a valid alternative to the detection of SARS-CoV-2 RNA. The proportion of asymptomatic and pre-symptomatic cases is elevated and reinforces the need of universal precautions and frequent surveys to limit the spread of the disease. url: http://medrxiv.org/cgi/content/short/2020.07.29.20163998v1?rss=1 doi: 10.1101/2020.07.29.20163998 id: cord-287658-c2lljdi7 author: Lopez-Rincon, Alejandro title: Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning date: 2020-09-10 words: 4766.0 sentences: 253.0 pages: flesch: 55.0 cache: ./cache/cord-287658-c2lljdi7.txt txt: ./txt/cord-287658-c2lljdi7.txt summary: The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. For example, we can use this sequencing data with cDNA, resulting from the PCR of the original viral RNA; e,g, Real-Time PCR amplicons to identify the SARS-CoV-2 16 . The global impact of SARS-CoV-2 prompted researchers to apply effective alignment-free methods to the classification of the virus: For example, in 26 the authors propose the use of Machine Learning Digital Signal Processing for separating the virus from similar strains, with remarkable accuracy. We calculated the frequency of appearance of different primer sets'' sequences used in SARS-CoV-2 RT-PCR tests developed by WHO referral laboratories and compared it to our primer design in the dataset from the GISAID ( Table 2) repository. abstract: In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from available repositories, separating the genome of different virus strains from the Coronavirus family with considerable accuracy. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets on existing datasets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from NGDC, separating the genome of different virus strains from the Coronavirus family with accuracy 98.73%. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. The proposed methodology has a substantial added value over existing methods, as it is able to both identify promising primer sets for a virus from a limited amount of data, and deliver effective results in a minimal amount of time. Considering the possibility of future pandemics, these characteristics are invaluable to promptly create specific detection methods for diagnostics. url: https://doi.org/10.1101/2020.03.13.990242 doi: 10.1101/2020.03.13.990242 id: cord-322234-1zyy536y author: Lorusso, Alessio title: One-step real-time RT-PCR for pandemic influenza A virus (H1N1) 2009 matrix gene detection in swine samples date: 2009-12-17 words: 4162.0 sentences: 195.0 pages: flesch: 51.0 cache: ./cache/cord-322234-1zyy536y.txt txt: ./txt/cord-322234-1zyy536y.txt summary: To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. Swine and equine influenza virus isolates and the clinical samples from pigs infected experimentally with 2009 (H1N1)v were subjected to the USDA-validated qRT-PCR procedure for the general detection of type A influenza virus RNA (matrix screening assay), following procedures described previously (Spackman and Suarez, 2008) . All endemic North American swine influenza virus isolates were negative for (H1N1) 2009 specific matrix gene RNA using the present qRT-PCR assay, whereas the (H1N1) 2009 strains used as positive control were positive. abstract: In the spring of 2009, a novel (H1N1) influenza A virus began to spread among humans worldwide. Although the 2009 H1N1 is related genetically to swine influenza viruses, human infection has not been connected to pig exposure. Because the virus is now circulating widely in the human population, swine herds are at increased risk of becoming infected. In order to investigate potential outbreaks of the 2009 pandemic virus in pigs, a quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) for the detection of the (H1N1) 2009 RNA in clinical specimens was developed. To evaluate the applicability of the test as a diagnostic tool in the screening of field specimens from swine, 64 field isolates of North American swine, 5 equine and 48 avian influenza viruses collected during diagnostic investigations were analyzed retrospectively as well as samples collected during an experimental in vivo infection with two novel H1N1 isolates, A/California/04/2009 (H1N1)v virus and A/Mexico/4108/2009 (H1N1)v. The sensitivity of the qRT-PCR was shown to be higher with respect to standard techniques such as virus isolation and the reproducibility was satisfactory. The present unique and highly sensitive assay is able to detect as little as 1 × 10(1) copies of RNA per μl of template and it represents a rapid and useful approach for the screening and quantitation of (H1N1) 2009 RNA in porcine specimens. url: https://www.sciencedirect.com/science/article/pii/S0166093409005205 doi: 10.1016/j.jviromet.2009.12.002 id: cord-329866-io9fvy58 author: Lorusso, Eleonora title: Discrepancies between feline coronavirus antibody and nucleic acid detection in effusions of cats with suspected feline infectious peritonitis date: 2019-08-31 words: 2810.0 sentences: 126.0 pages: flesch: 48.0 cache: ./cache/cord-329866-io9fvy58.txt txt: ./txt/cord-329866-io9fvy58.txt summary: With the aim to contribute to fill this diagnostic gap, a total of 61 effusions from cats with suspected effusive FIP were collected intra-vitam for detection of feline coronavirus (FCoV) antibodies and RNA by means of indirect immunofluorescence (IIF) assay and real-time RT-PCR (qRT-PCR), respectively. Fifty-one (48 ascitic and 3 pleuric fluids) of the 61 tested samples had FCoV antibody (Table 2 and Fig. 1 ), although only 37 positive effusions contained antibody levels ≥ 1:1600, which are considered highly suggestive of FIP diagnosis (Hartmann et al., 2003) . A recent paper (Meli et al., 2013) has investigated the agreement between FCoV antibody titres and RNA detection in the effusions of 13 cats with confirmed FIP, showing a correlation between high amounts of virus and lower signals in IIF assay, likely due to the fact that antibodies bound to viral antigens of the effusions are not able to bind to the antigens of the FCoV-infected cells used in serological tests. abstract: Abstract Intra-vitam diagnosis of feline infectious peritonitis (FIP) is a challenge for veterinary diagnosticians, since there are no highly specific and sensitive assays currently available. With the aim to contribute to fill this diagnostic gap, a total of 61 effusions from cats with suspected effusive FIP were collected intra-vitam for detection of feline coronavirus (FCoV) antibodies and RNA by means of indirect immunofluorescence (IIF) assay and real-time RT-PCR (qRT-PCR), respectively. In 5 effusions there was no evidence for either FCoV RNA or antibodies, 51 and 52 specimens tested positive by IIF and qRT-PCR, respectively, although antibody titres≥1:1600, which are considered highly suggestive of FIP, were detected only in 37 effusions. Three samples with high antibody levels tested negative by qRT-PCR, whereas 18 qRT-PCR positive effusions contained no or low-titre antibodies. qRT-PCR positive samples with low antibody titres mostly contained low FCoV RNA loads, although the highest antibody titres were detected in effusions with C T values>30. In conclusion, combining the two methods, i.e., antibody and RNA detection would help improving the intra-vitam diagnosis of effusive FIP. url: https://api.elsevier.com/content/article/pii/S0034528817306495 doi: 10.1016/j.rvsc.2017.10.004 id: cord-341176-83khavoh author: Lotfi, Melika title: CRISPR/Cas13: A potential therapeutic option of COVID-19 date: 2020-09-17 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can be considered as the most important current global issue, as it has caused the novel coronavirus disease (COVID-19) pandemic, which has resulted in high mortality and morbidity rates all around the world. Although scientists are trying to discover novel therapies and develop and evaluate various previous treatments, at the time of writing this paper, there was no definite therapy and vaccine for COVID-19. So, as COVID-19 has called ideas for treatment, controlling, and diagnosis, we discussed the application of Clustered Regularly Interspaced Short Palindromic Repeats/Cas13 (CRISPR/Cas13) as a treatment of COVID-19, which received less attention compared with other potential therapeutic options. url: https://doi.org/10.1016/j.biopha.2020.110738 doi: 10.1016/j.biopha.2020.110738 id: cord-280003-ndpuezpo author: Lou, Bin title: Serology characteristics of SARS-CoV-2 infection since the exposure and post symptoms onset date: 2020-03-27 words: 3024.0 sentences: 190.0 pages: flesch: 57.0 cache: ./cache/cord-280003-ndpuezpo.txt txt: ./txt/cord-280003-ndpuezpo.txt summary: Serial sera of COVID-19 patients were collected and total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 were detected. The first detectible serology marker is total antibody and followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 day post exposure (d.p.e) or 9, 10 and 12 days post onset, separately. In order to answer some of the questions, we investigated the characteristics of antibody responses in 80 Covid-19 patients during their hospitalization periods, through detecting total antibody, IgM and IgG using immunoassays. A total of 80 Covid-19 patients and 100 to 300 healthy people were tested for antibodies against SARS-CoV-2 using different immunoassays. The present data showed that the sensitivity of total antibody detection was higher than that of IgM and IgG (p<0.001) while the specificities are overall comparable when the same testing technic (ELISA, CLMA or LFIA) is used. abstract: Background Timely diagnosis of SARS-CoV-2 infection is the prerequisite for treatment and preventive quarantine. The serology characteristics and complement diagnosis value of antibody test to RNA test needs to be demonstrated. Method A patient cohort study was conducted at the first affiliated hospital of Zhejiang University, China. Serial sera of COVID-19 patients were collected and total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 were detected. The antibody dynamics during the infection were described. Results The seroconversion rate for Ab, IgM and IgG in COVID-19 patients was 98.8% (79/80), 93.8% (75/80) and 93.8% (75/80), respectively. The first detectible serology marker is total antibody and followed by IgM and IgG, with a median seroconversion time of 15, 18 and 20 day post exposure (d.p.e) or 9, 10 and 12 days post onset, separately. The antibody levels increased rapidly since 6 d.p.o and accompanied with the decline of viral load. For patients in the early stage of illness (0-7d.p.o),Ab showed the highest sensitivity (64.1%) compared to the IgM and IgG (33.3% for both, p<0.001). The sensitivities of Ab, IgM and IgG detection increased to 100%, 96.7% and 93.3% two weeks later, respectively. Conclusions Typical acute antibody response is induced during the SARS-CoV-2 infection. The serology testing provides important complementation to RNA test for pathogenic specific diagnosis and helpful information to evaluate the adapted immunity status of patient. It should be strongly recommended to apply well-validated antibody tests in the clinical management and public health practice to improve the control of COVID-19 infection. url: https://doi.org/10.1101/2020.03.23.20041707 doi: 10.1101/2020.03.23.20041707 id: cord-307817-2vy28i4m author: Lou, Zhiyong title: Current progress in antiviral strategies date: 2014-01-14 words: 7555.0 sentences: 343.0 pages: flesch: 36.0 cache: ./cache/cord-307817-2vy28i4m.txt txt: ./txt/cord-307817-2vy28i4m.txt summary: The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Based on the complex structure of the PA C-terminal domain (PA C ) and the first 25 amino acids of PB1 [99] , a subset of modifications on N-terminal peptide of PB1 was shown to diminish the binding affinity of PA and PB1, inhibit polymerase activity, and attenuate the replication of influenza virus [100] [101] [102] . Because both the polymerase complex and NP show significant conservation between different influenza viruses, these results demonstrated that targeting the formation of viral RNP is a valid approach to the development of small molecule therapies against serious antiviral resistance to currently available drugs, such as adamantanes or neuraminidase inhibitors. abstract: The prevalence of chronic viral infectious diseases, such as human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus; the emergence and re-emergence of new viral infections, such as picornaviruses and coronaviruses; and, particularly, resistance to currently used antiviral drugs have led to increased demand for new antiviral strategies and reagents. Increased understanding of the molecular mechanisms of viral infection has provided great potential for the discovery of new antiviral agents that target viral proteins or host factors. Virus-targeting antivirals can function directly or indirectly to inhibit the biological functions of viral proteins, mostly enzymatic activities, or to block viral replication machinery. Host-targeting antivirals target the host proteins that are involved in the viral life cycle, regulating the function of the immune system or other cellular processes in host cells. Here we review key targets and considerations for the development of both antiviral strategies. url: https://www.sciencedirect.com/science/article/pii/S0165614713002265 doi: 10.1016/j.tips.2013.11.006 id: cord-009376-a35a92gh author: Lovatt, Archie title: Applications of quantitative PCR in the biosafety and genetic stability assessment of biotechnology products date: 2002-01-07 words: 9214.0 sentences: 523.0 pages: flesch: 48.0 cache: ./cache/cord-009376-a35a92gh.txt txt: ./txt/cord-009376-a35a92gh.txt summary: Applications of Q-PCR within biotechnology are discussed with particular emphasis on the following areas of biosafety and genetic stability testing: (a) determination of the biodistribution of gene therapy vectors in animals; (b) quantification of the residual DNA in final product therapeutics; (c) detection of viral and bacterial nucleic acid in contaminated cell banks and final products; (d) quantification of the level of virus removal in process validation viral clearance studies; (e) specific detection of retroviral RT activity in vaccines with high sensitivity; and (f) transgene copy number determination for monitoring genetic stability during production. We are developing Q-PCR assays for these repeat regions for rodent and primate residual DNA to obtain sensitivity in the fg range, however, one advantage of using a gene such as ␤-actin is gene stability, as this target should not undergo copy number changes within a stable cell line. abstract: High throughput screening, increased accuracy and the coupling of real-time quantitative PCR (Q-PCR) to robotic set-up systems are beginning to revolutionise biotechnology. Applications of Q-PCR within biotechnology are discussed with particular emphasis on the following areas of biosafety and genetic stability testing: (a) determination of the biodistribution of gene therapy vectors in animals; (b) quantification of the residual DNA in final product therapeutics; (c) detection of viral and bacterial nucleic acid in contaminated cell banks and final products; (d) quantification of the level of virus removal in process validation viral clearance studies; (e) specific detection of retroviral RT activity in vaccines with high sensitivity; and (f) transgene copy number determination for monitoring genetic stability during production. Methods employed for Q-PCR assay validation as required in ICH Topic Q2A Validation of Analytical Methods: Definitions and Terminology (1st June 1995) are also reviewed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148957/ doi: 10.1016/s1389-0352(01)00043-5 id: cord-329794-msxrdhb3 author: Lu, Aili title: Attenuation of SARS coronavirus by a short hairpin RNA expression plasmid targeting RNA-dependent RNA polymerase date: 2004-06-20 words: 2679.0 sentences: 172.0 pages: flesch: 61.0 cache: ./cache/cord-329794-msxrdhb3.txt txt: ./txt/cord-329794-msxrdhb3.txt summary: Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Here, we provide the evidence that RNAi targeting at coronavirus RDRP using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Design of specific shRNA expression plasmids targeting at coronavirus RDRP Coronavirus isolated from SARS patients has a large genomic RNA (approximately 30 kb). After transfecton, about 40-90% of RDRP gene expression was inhibited, depending on the sequence of the shRNA inserts, based on RT-PCR analysis in both HeLa and 293 cells transfected with RDRP (data not shown). shRNA reduced the expression of SARS RDRP mRNA in 293 and HeLa cells As shown in Fig. 1A , based on the RT-PCR analysis, the expression of extraneous RDRP gene was observed peaking at 48 h after the transfection. abstract: Abstract Severe acute respiratory syndrome (SARS) is a highly contagious and sometimes a lethal disease, which spread over five continents in 2002–2003. Laboratory analysis showed that the etiologic agent for SARS is a new type of coronavirus. Currently, there is no specific treatment for this disease. RNA interference (RNAi) is a recently discovered antiviral mechanism in plant and animal cells that induces a specific degradation of double-stranded RNA. Here, we provide evidences that RNAi targeting at coronavirus RNA-dependent RNA polymerase (RDRP) using short hairpin RNA (shRNA) expression plasmids can specifically inhibit expression of extraneous coronavirus RDRP in 293 and HeLa cells. Moreover, this construct significantly reduced the plaque formation of SARS coronaviruses in Vero-E6 cells. The data may suggest a new approach for treatment of SARS patients. url: https://www.sciencedirect.com/science/article/pii/S0042682204002181 doi: 10.1016/j.virol.2004.03.031 id: cord-317537-wgu5cd0y author: Lu, Hsiang-Chia title: Cymbidium mosaic potexvirus isolate-dependent host movement systems reveal two movement control determinants and the coat protein is the dominant date: 2009-05-25 words: 8155.0 sentences: 474.0 pages: flesch: 57.0 cache: ./cache/cord-317537-wgu5cd0y.txt txt: ./txt/cord-317537-wgu5cd0y.txt summary: All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 4I) , and statistics analysis (ANOVA) of real-time RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV clone-infected protoplasts at 24 h postinoculation revealed no significant difference in percentage between these clones (P = 0.91). All constructs were replication competent in protoplasts as assayed by northern blot hybridization (Fig. 6J) , and statistics analysis (ANOVA) of realtime RT-PCR quantification of average relative percentage (from 3 independent experiments) of CymMV RNA from CymMV cloneinfected protoplasts at 24 h post-inoculation revealed no significant difference in percentage between these clones (P = 0.83). Our results indicated that the important amino acids of the CP that allowed for the CymMV systemic infection are located within the previously predicted RNA binding domain ( Fig. 7A; 1) . abstract: Little is known about how plant viruses of a single species exhibit different movement behavior in different host species. Two Cymbidium mosaic potexvirus (CymMV) isolates, M1 and M2, were studied. Both can infect Phalaenopsis orchids, but only M1 can systemically infect Nicotiana benthamiana plants. Protoplast inoculation and whole-mount in situ hybridization revealed that both isolates can replicate in N. benthamiana; however, M2 was restricted to the initially infected cells. Genome shuffling between M1 and M2 revealed that two control modes are involved in CymMV host dependent movement. The M1 coat protein (CP) plays a dominant role in controlling CymMV movement between cells, because all chimeric CymMV viruses containing the M1 CP systemically infected N. benthamiana plants. Without the M1 CP, one chimeric virus containing the combination of the M1 triple gene block proteins (TGBps), the M2 5′ RNA (1–4333), and the M2 CP effectively moved in N. benthamiana plants. Further complementation analysis revealed that M1 TGBp1 and TGBp3 are co-required to complement the movement of the chimeric viruses in N. benthamiana. The amino acids within the CP, TGBp1 and TGBp3 which are required or important for CymMV M2 movement in N. benthamiana plants were mapped. The required amino acids within the CP map to the predicted RNA binding domain. RNA–protein binding assays revealed that M1 CP has higher RNA binding affinity than does M2 CP. Yeast two-hybrid assays to detect all possible interactions of M1 TGBps and CP, and only TGBp1 and CP self-interactions were observed. url: https://api.elsevier.com/content/article/pii/S004268220900172X doi: 10.1016/j.virol.2009.02.049 id: cord-293163-udcw1mx5 author: Lu, Patrick Y. title: Modulation of angiogenesis with siRNA inhibitors for novel therapeutics date: 2005-02-04 words: 6378.0 sentences: 329.0 pages: flesch: 34.0 cache: ./cache/cord-293163-udcw1mx5.txt txt: ./txt/cord-293163-udcw1mx5.txt summary: The functional validation of angiogenic factors for their specific role has been greatly facilitated by the use of RNAi inhibitors, revealing a network involving the early activation of the VEGF pathway and interactions among MMPs and adhesion molecules, leading to the regulation of signal transduction pathways. MMP9 and MMP2 are important for the mobilization of sequestered VEGF and initiation of tumor angiogenesis [17] , whereas specific integrins mediate interactions between endothelial cells and the BM by activating the integrin receptor signaling that controls many key functions, such as proliferation [18] . The involvement, revealed by siRNA, of diacylglycerol kinase a (Dgka) in hepatocyte growth factor (HGF)-stimulated cell migration, which impaired angiogenesis in vitro, indicated its essential role in both proliferative and migratory response to VEGF, and suggested that it is a novel therapeutic target for controlling angiogenesis [43] . abstract: Cancer and many other serious diseases are characterized by the uncontrolled growth of new blood vessels. Recently, RNA interference (RNAi) has reinvigorated the therapeutic prospects for inhibiting gene expression and promises many advantages over binding inhibitors, including high specificity, which is essential for targeted therapeutics. This article describes the latest developments using small-interfering RNA (siRNA) inhibitors to downregulate various angiogenic and tumor-associated factors, both in cell-culture assays and in animal disease models. The majority of research efforts are currently focused on understanding gene function, as well as proof-of-concept for siRNA-mediated anti-angiogenesis. The prospects for siRNA therapeutics, both advantages and looming hurdles, are evaluated. url: https://www.sciencedirect.com/science/article/pii/S1471491405000237 doi: 10.1016/j.molmed.2005.01.005 id: cord-001829-rwnbxmt4 author: Lu, Yi-Fan title: IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance date: 2015-11-04 words: 7156.0 sentences: 384.0 pages: flesch: 48.0 cache: ./cache/cord-001829-rwnbxmt4.txt txt: ./txt/cord-001829-rwnbxmt4.txt summary: Genome-wide association studies performed on diverse patient populations have identified polymorphisms near the interferon-λ 3 (IFNL3; formerly IL28B) gene that predict the efficacy of interferon-based therapy for chronic infection. The differential effects on mRNA versus protein levels strongly suggest that the IFNL3 3′ UTR regulates gene expression by repressing the efficiency of mRNA translation rather than mRNA abundance in HeLa cells. We used polysome profiling to examine whether the variant IFNL3 reporter mRNAs were differentially associated with translating ribosomes in stable HeLa cell lines. Although rs4803217 is not independently associated with patient phenotypes in the cohort we analyzed, this SNP occurs in the 3′ UTR of IFNL3 and showed clear functional effects on reporter gene expression, suggesting a role for this variant in control of HCV infection. abstract: Polymorphisms near the interferon lambda 3 (IFNL3) gene strongly predict clearance of hepatitis C virus (HCV) infection. We analyzed a variant (rs4803217 G/T) located within the IFNL3 mRNA 3′ untranslated region (UTR); the G allele (protective allele) is associated with elevated therapeutic HCV clearance. We show that the IFNL3 3′ UTR represses mRNA translation and the rs4803217 allele modulates the extent of translational regulation. We analyzed the structures of IFNL3 variant mRNAs at nucleotide resolution by SHAPE-MaP. The rs4803217 G allele mRNA forms well-defined 3′ UTR structure while the T allele mRNA is more dynamic. The observed differences between alleles are among the largest possible RNA structural alterations that can be induced by a single nucleotide change and transform the UTR from a single well-defined conformation to one with multiple dynamic interconverting structures. These data illustrate that non-coding genetic variants can have significant functional effects by impacting RNA structure. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631997/ doi: 10.1038/srep16037 id: cord-282618-tjvjlyn9 author: Luke, J M title: Improved antibiotic-free plasmid vector design by incorporation of transient expression enhancers date: 2010-11-25 words: 6241.0 sentences: 336.0 pages: flesch: 43.0 cache: ./cache/cord-282618-tjvjlyn9.txt txt: ./txt/cord-282618-tjvjlyn9.txt summary: To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. A neomycin resistance gene (NeoR) without an upstream Kozak sequence was cloned downstream of an enhanced green fluorescent protein (EGFP) transgene in different configurations similar to that used with PREs. Quantifiable neoR translation products were present in all tested configurations, as was biologically active neoR protein after plasmid transfection into both HEK293 and CHO cell lines (Supplementary Table S1 ). The assay was in the same format as in (a), except for the fact that Pol III inhibitor-treated cells were transfected with EGFP plasmids containing the CMV-HTLV-I R promoter with or without VA1; (c) Inhibition of PKR, not of adenosine deaminase acting on RNA (ADAR) or RNA interference (RNAI), was required for VA1 expression enhancement effect. abstract: Methods to improve plasmid-mediated transgene expression are needed for gene medicine and gene vaccination applications. To maintain a low risk of insertional mutagenesis-mediated gene activation, expression-augmenting sequences would ideally function to improve transgene expression from transiently transfected intact plasmid, but not from spurious genomically integrated vectors. We report herein the development of potent minimal, antibiotic-free, high-manufacturing-yield mammalian expression vectors incorporating rationally designed additive combinations of expression enhancers. The SV40 72 bp enhancer incorporated upstream of the cytomegalovirus (CMV) enhancer selectively improved extrachromosomal transgene expression. The human T-lymphotropic virus type I (HTLV-I) R region, incorporated downstream of the CMV promoter, dramatically increased mRNA translation efficiency, but not overall mRNA levels, after transient transfection. A similar mRNA translation efficiency increase was observed with plasmid vectors incorporating and expressing the protein kinase R-inhibiting adenoviral viral associated (VA)1 RNA. Strikingly, HTLV-I R and VA1 did not increase transgene expression or mRNA translation efficiency from plasmid DNA after genomic integration. The vector platform, when combined with electroporation delivery, further increased transgene expression and improved HIV-1 gp120 DNA vaccine-induced neutralizing antibody titers in rabbits. These antibiotic-free vectors incorporating transient expression enhancers are safer, more potent alternatives to improve transgene expression for DNA therapy or vaccination. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/gt.2010.149) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/21107439/ doi: 10.1038/gt.2010.149 id: cord-332270-fusfdkjw author: Lukiw, Walter J. title: Biomarkers for Alzheimer’s Disease (AD) and the Application of Precision Medicine date: 2020-09-21 words: 5193.0 sentences: 198.0 pages: flesch: 29.0 cache: ./cache/cord-332270-fusfdkjw.txt txt: ./txt/cord-332270-fusfdkjw.txt summary: The ongoing search for valid biomarkers for AD is being carried out globally in at least a dozen major geriatric, bioinformatic, neurobiological, neuro-genetic and neurological bioscience arenas: (i) those involving the age, gender, and geriatrics of the ''prospectiveAD patient''; (ii) in the genetics and epigenetics of the AD patient including messenger RNA (mRNA) and microRNA (miRNA) signaling patterns, complexity and genomic methylation research; (iii) in multiple biofluids from AD patients including the blood (plasma/serum) of the systemic circulation, the glymphatic system, the cerebrospinal fluid (CSF) and/or urine; (iv); through the detailed analysis of molecular cargos from both biofluids and tissue-compartmentalized exosomes and extracellular microvesicles (EXs and EMVs); (v) throughout the peripheral nervous system (PNS; typically using skin biopsies); (vi) via clinically-based geriatric, psychiatric, and neurological assessment and testing; (vii) via advances in neuro-radiological labeling techniques and neuroimaging technologies including CAT, PET, PET-SN, MRI, fMRI; UHF-MRI, DOT, MEG, SPECT, cranial ultrasound, functional ultrasound (fUS) imaging, and immunohistochemistry involving confocal laser scanning microscopy and other advanced microscopic and neuroimaging techniques; (viii) from the quantitation and characterization of the load of microbial and microbial-derived components in the AD-affected brain; (ix) via the identification, quantitation, and characterization of AD-specific lesions including amyloid peptide-enriched SPs and NFTs; (x) after post-mortem examination and biopsies of AD cases, again matched up against those same biomarkers in age-and gender-matched neurologically normal controls to corroborate the prospective diagnosis of AD; (xi) via the comprehensive analysis of the potential contribution of overlapping progressive, age-related neurological disorders to AD-type change; and lastly (xii), through the assessment of the socioeconomic, environmental, and lifestyle factors of the ''prospectiveAD patient'' ( Table 1 ). abstract: An accurate diagnosis of Alzheimer’s disease (AD) currently stands as one of the most difficult and challenging in all of clinical neurology. AD is typically diagnosed using an integrated knowledge and assessment of multiple biomarkers and interrelated factors. These include the patient’s age, gender and lifestyle, medical and genetic history (both clinical- and family-derived), cognitive, physical, behavioral and geriatric assessment, laboratory examination of multiple AD patient biofluids, especially within the systemic circulation (blood serum) and cerebrospinal fluid (CSF), multiple neuroimaging-modalities of the brain’s limbic system and/or retina, followed up in many cases by post-mortem neuropathological examination to finally corroborate the diagnosis. More often than not, prospective AD cases are accompanied by other progressive, age-related dementing neuropathologies including, predominantly, a neurovascular and/or cardiovascular component, multiple-infarct dementia (MID), frontotemporal dementia (FTD) and/or strokes or ‘mini-strokes’ often integrated with other age-related neurological and non-neurological disorders including cardiovascular disease and cancer. Especially over the last 40 years, enormous research efforts have been undertaken to discover, characterize, and quantify more effectual and reliable biological markers for AD, especially during the pre-clinical or prodromal stages of AD so that pre-emptive therapeutic treatment strategies may be initiated. While a wealth of genetic, neurobiological, neurochemical, neuropathological, neuroimaging and other diagnostic information obtainable for a single AD patient can be immense: (i) it is currently challenging to integrate and formulate a definitive diagnosis for AD from this multifaceted and multidimensional information; and (ii) these data are unfortunately not directly comparable with the etiopathological patterns of other AD patients even when carefully matched for age, gender, familial genetics, and drug history. Four decades of AD research have repeatedly indicated that diagnostic profiles for AD are reflective of an extremely heterogeneous neurological disorder. This commentary will illuminate the heterogeneity of biomarkers for AD, comment on emerging investigative approaches and discuss why ‘precision medicine’ is emerging as our best paradigm yet for the most accurate and definitive prediction, diagnosis, and prognosis of this insidious and lethal brain disorder. url: https://doi.org/10.3390/jpm10030138 doi: 10.3390/jpm10030138 id: cord-287153-jbuuph6w author: Lund, Morten title: Experimental Piscine orthoreovirus infection mediates protection against pancreas disease in Atlantic salmon (Salmo salar) date: 2016-10-21 words: 7435.0 sentences: 399.0 pages: flesch: 54.0 cache: ./cache/cord-287153-jbuuph6w.txt txt: ./txt/cord-287153-jbuuph6w.txt summary: The most prevalent viral diseases in Norwegian salmon aquaculture are heart and skeletal muscle inflammation (HSMI) caused by Piscine orthoreovirus (PRV), and pancreas disease (PD) caused by Salmonid alphavirus (SAV). The SAV RNA level in heart was significantly lower in the co-infected fish at 4 and 6 WPC-SAV compared to the SAV3 controls (p < 0.05). Using a non-parametric rank test of the ordinal histopathological score, changes in pancreas were found to be significantly lower at 4 and 6 WPC-SAV in both early and late co-infection compared to the SAV control groups (p < 0.05), except at 4 WPC-SAV in the PRV-SAV3-late group (Figures 6 and 7) . Microarray analysis was performed on hearts sampled at 4 and 6 WPC-SAV from the late co-infection and differences between the SAV3 control and PRV-SAV3-late group were analyzed (Table 2) . SAV RNA levels in heart were significantly lower 6 WPC-SAV in the early co-infected groups compared to the SAV controls. abstract: Viral diseases are among the main challenges in farming of Atlantic salmon (Salmo salar). The most prevalent viral diseases in Norwegian salmon aquaculture are heart and skeletal muscle inflammation (HSMI) caused by Piscine orthoreovirus (PRV), and pancreas disease (PD) caused by Salmonid alphavirus (SAV). Both PRV and SAV target heart and skeletal muscles, but SAV additionally targets exocrine pancreas. PRV and SAV are often present in the same locations and co-infections occur, but the effect of this crosstalk on disease development has not been investigated. In the present experiment, the effect of a primary PRV infection on subsequent SAV infection was studied. Atlantic salmon were infected with PRV by cohabitation, followed by addition of SAV shedder fish 4 or 10 weeks after the initial PRV infection. Histopathological evaluation, monitoring of viral RNA levels and host gene expression analysis were used to assess disease development. Significant reduction of SAV RNA levels and of PD specific histopathological changes were observed in the co-infected groups compared to fish infected by SAV only. A strong correlation was found between histopathological development and expression of disease related genes in heart. In conclusion, experimentally PRV infected salmon are less susceptible to secondary SAV infection and development of PD. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13567-016-0389-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/27769313/ doi: 10.1186/s13567-016-0389-y id: cord-313161-07iwwsfz author: Lundstrom, Kenneth title: Alphavirus-Based Vaccines date: 2014-06-16 words: 6844.0 sentences: 322.0 pages: flesch: 30.0 cache: ./cache/cord-313161-07iwwsfz.txt txt: ./txt/cord-313161-07iwwsfz.txt summary: Furthermore, sequential immunization with SIN and VEE replicon particles expressing the type 1 HIV gp140 envelope (Env) and trimeric Env protein in MF59 adjuvant provided partial protection in macaques against intravenous challenges with high doses of simian-human immunodeficiency virus (SHIV) [61] . In another study, chimeric VEE/SIN replicon particles were applied for the expression of measles virus hemagglutinin (H) and fusion (F) proteins, which elicited high-titer neutralizing antibody and IFNɤ-producing T-cells in macaques after intradermal vaccination [48] . Furthermore, vaccination with recombinant particles expressing the P1A gene [105] and the human papilloma virus (HPV) E7 gene [89] from SFV and VEE vectors, respectively, provided protection against further tumor development in mice. When TRAMP mice were prophylactically immunized with a prostate stem cell antigen (PSCA) DNA plasmid followed by VEE-PSCA particle administration, a specific immune response and anti-tumor protection were observed in 90% of vaccinated animals [102] . abstract: Alphavirus vectors have demonstrated high levels of transient heterologous gene expression both in vitro and in vivo and, therefore, possess attractive features for vaccine development. The most commonly used delivery vectors are based on three single-stranded encapsulated alphaviruses, namely Semliki Forest virus, Sindbis virus and Venezuelan equine encephalitis virus. Alphavirus vectors have been applied as replication-deficient recombinant viral particles and, more recently, as replication-proficient particles. Moreover, in vitro transcribed RNA, as well as layered DNA vectors have been applied for immunization. A large number of highly immunogenic viral structural proteins expressed from alphavirus vectors have elicited strong neutralizing antibody responses in multispecies animal models. Furthermore, immunization studies have demonstrated robust protection against challenges with lethal doses of virus in rodents and primates. Similarly, vaccination with alphavirus vectors expressing tumor antigens resulted in prophylactic protection against challenges with tumor-inducing cancerous cells. As certain alphaviruses, such as Chikungunya virus, have been associated with epidemics in animals and humans, attention has also been paid to the development of vaccines against alphaviruses themselves. Recent progress in alphavirus vector development and vaccine technology has allowed conducting clinical trials in humans. url: https://doi.org/10.3390/v6062392 doi: 10.3390/v6062392 id: cord-291026-99cit4ig author: Lung, O. title: Insulated Isothermal Reverse Transcriptase PCR (iiRT‐PCR) for Rapid and Sensitive Detection of Classical Swine Fever Virus date: 2015-01-27 words: 4566.0 sentences: 206.0 pages: flesch: 55.0 cache: ./cache/cord-291026-99cit4ig.txt txt: ./txt/cord-291026-99cit4ig.txt summary: In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. Archived viral nucleic acid from 18 laboratory-amplified non-CSF viruses including eight other pestiviruses (BVDV 1-Hastings, Singer and NY1 strains; BVDV 2-Ames 125c, 890, 24515 strains; BDV-Coos Bay; HoBi atypical pestivirus), African swine fever virus-Lisbon, swine vesicular disease virus-ITL 19/92, porcine respiratory and reproductive syndrome virus-YNL, swine influenza virus (H3N2), porcine circovirus 1 (PCV1, derived from infectious clone based on GenBank accession no. The iiRT-PCR assay accurately detected all CSFV RNA samples which represented all three genotypes, and eight of 11 subgenotypes that were available for testing and gave negative results for three BVDV type 1 strains, three BVDV type 2 strains, BDV, HoBi atypical pestivirus, ASFV and nine other viruses that affect livestock. abstract: Classical swine fever (CSF) is an OIE‐listed disease that can have a severe impact on the swine industry. User‐friendly, sensitive, rapid diagnostic tests that utilize low‐cost field‐deployable instruments for CSF diagnosis can be useful for disease surveillance and outbreak monitoring. In this study, we describe validation of a new probe‐based insulated isothermal reverse transcriptase PCR (iiRT‐PCR) assay for rapid detection of classical swine fever virus (CSFV) on a compact, user‐friendly device (POCKIT (™) Nucleic Acid Analyzer) that does not need data interpretation by the user. The assay accurately detected CSFV RNA from a diverse panel of 33 CSFV strains representing all three genotypes plus an additional in vitro‐transcribed RNA from cloned sequences representing a vaccine strain. No cross‐reactivity was observed with a panel of 18 viruses associated with livestock including eight other pestivirus strains (bovine viral diarrhoea virus type 1 and type 2, border disease virus, HoBi atypical pestivirus), African swine fever virus, swine vesicular disease virus, swine influenza virus, porcine respiratory and reproductive syndrome virus, porcine circovirus 1, porcine circovirus 2, porcine respiratory coronavirus, vesicular exanthema of swine virus, bovine herpes virus type 1 and vesicular stomatitis virus. The iiRT‐PCR assay accurately detected CSFV as early as 2 days post‐inoculation in RNA extracted from serum samples of experimentally infected pigs, before appearance of clinical signs. The limit of detection (LOD (95%)) calculated by probit regression analysis was 23 copies per reaction. The assay has a sample to answer turnaround time of less than an hour using extracted RNA or diluted or low volume of neat serum. The user‐friendly, compact device that automatically analyses and displays results could potentially be a useful tool for surveillance and monitoring of CSF in a disease outbreak. url: https://doi.org/10.1111/tbed.12318 doi: 10.1111/tbed.12318 id: cord-271504-t3y1w9ef author: Luo, Zichao title: Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community date: 2020-06-16 words: 14361.0 sentences: 795.0 pages: flesch: 42.0 cache: ./cache/cord-271504-t3y1w9ef.txt txt: ./txt/cord-271504-t3y1w9ef.txt summary: A confirmed case should have at least one of the following criteria: (i) a positive result for 2019-nCoV nucleic acid, using real-time PCR tests from respiratory or blood samples; (ii) a high homogeneity between viral gene sequencing from respiratory or blood samples and known 2019-nCoV; and (iii) serum samples positive for IgM or IgG to 2019-nCoV, or seroconversion in IgG, or a fourfold or more significant increase in IgG antibody titer to 2019-nCoV in the recovery phase than in the acute phase [25] . Using blood samples taken from alleged COVID-19 patients, the researchers detected antibodies targeting the spike protein that prevented the virus from killing cells in laboratory tests. showed a promising in vitro inhibitory effect of this serine protease inhibitor in SARS-CoV and 2019-nCoV on human lung cells, showing potential as a viable option for COVID-19 treatment [113] . Given that antiviral drugs have previously demonstrated reasonable inhibition of coronaviruses and therapeutic efficacy against coronavirus outbreaks, umifenovir, chloroquine, hydroxychloroquine, lopinavir-ritonavir, and ribavirin have been recommended in the latest guidelines for diagnosis and treatment of COVID-19, updated on 17 February 2020 [189] . abstract: The World Health Organization (WHO) has declared the outbreak of 2019 novel coronavirus, known as 2019-nCoV, a pandemic, as the coronavirus has now infected over 2.6 million people globally and caused more than 185,000 fatalities as of April 23, 2020. Coronavirus disease 2019 (COVID-19) causes a respiratory illness with symptoms such as dry cough, fever, sudden loss of smell, and, in more severe cases, difficulty breathing. To date, there is no specific vaccine or treatment proven effective against this viral disease. Early and accurate diagnosis of COVID-19 is thus critical to curbing its spread and improving health outcomes. Reverse transcription-polymerase chain reaction (RT-PCR) is commonly used to detect the presence of COVID-19. Other techniques, such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and microfluidics, have allowed better disease diagnosis. Here, as part of the effort to expand screening capacity, we review advances and challenges in the rapid detection of COVID-19 by targeting nucleic acids, antigens, or antibodies. We also summarize potential treatments and vaccines against COVID-19 and discuss ongoing clinical trials of interventions to reduce viral progression. url: https://www.ncbi.nlm.nih.gov/pubmed/32607499/ doi: 10.34133/2020/6925296 id: cord-332632-u2ud0vmq author: Lussi, Carmela title: What can pestiviral endonucleases teach us about innate immunotolerance? date: 2016-03-17 words: 8703.0 sentences: 394.0 pages: flesch: 44.0 cache: ./cache/cord-332632-u2ud0vmq.txt txt: ./txt/cord-332632-u2ud0vmq.txt summary: In particular, the unique extension of ''self'' to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host''s own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. Thus, the survival strategy of BVDV consists of being non-cytopathogenic and producing less dsRNA than its cp counterpart, and expressing the IFN antagonists N pro as the first protein in order to reduce or even avoid IFN production in infected cells and E rns to degrade immunostimulatory viral RNA before they might activate the host''s PRRs. Notably, both pestiviral IFN antagonists are not only required to constantly maintain innate immunotolerance during persistent infections, but they also play an important role in acute infections [25] . abstract: Pestiviruses including bovine viral diarrhea virus (BVDV), border disease virus (BDV) and classical swine fever virus (CSFV), occur worldwide and are important pathogens of livestock. A large part of their success can be attributed to the induction of central immunotolerance including B- and T-cells upon fetal infection leading to the generation of persistently infected (PI) animals. In the past few years, it became evident that evasion of innate immunity is a central element to induce and maintain persistent infection. Hence, the viral non-structural protease N(pro) heads the transcription factor IRF-3 for proteasomal degradation, whereas an extracellularly secreted, soluble form of the envelope glycoprotein E(rns) degrades immunostimulatory viral single- and double-stranded RNA, which makes this RNase unique among viral endoribonucleases. We propose that these pestiviral interferon (IFN) antagonists maintain a state of innate immunotolerance mainly pertaining its viral nucleic acids, in contrast to the well-established immunotolerance of the adaptive immune system, which is mainly targeted at proteins. In particular, the unique extension of ‘self’ to include the viral genome by degrading immunostimulatory viral RNA by E(rns) is reminiscent of various host nucleases that are important to prevent inappropriate IFN activation by the host’s own nucleic acids in autoimmune diseases such as Aicardi-Goutières syndrome or systemic lupus erythematosus. This mechanism of “innate tolerance” might thus provide a new facet to the role of extracellular RNases in the sustained prevention of the body’s own immunostimulatory RNA to act as a danger-associated molecular pattern that is relevant across various species. url: https://www.ncbi.nlm.nih.gov/pubmed/27021825/ doi: 10.1016/j.cytogfr.2016.03.003 id: cord-255090-2gpsu1y4 author: Lv, Ke title: Transient inhibition of foot-and-mouth disease virus replication by siRNAs silencing VP1 protein coding region date: 2009-06-30 words: 6335.0 sentences: 318.0 pages: flesch: 52.0 cache: ./cache/cord-255090-2gpsu1y4.txt txt: ./txt/cord-255090-2gpsu1y4.txt summary: In addition, variations within multiple regions of the quasispecies of FMDV were retrospectively revealed by sequencing of FMDV genes, and a single nucleotide substitution was identified as the main factor in resistance to RNAi. Our data demonstrated that the three siRNA molecules synthesized with T7 RNA polymerase could have transient inhibitory effects on the replication of FMDV. Recently, several laboratories used RNAi to inhibit foot-and-mouth virus infection in cell culture or in animals taking forms of chemically synthesized siRNA, plasmid encoding shRNA, and adenovirus encoding shRNA (Chen et al., 2004 (Chen et al., , 2006 de los Santos et al., 2005; Kahana et al., 2004; Mohapatra et al., 2005) , showing rapid decrease of FMDV replication. Furthermore, among the five siRNAs candidates, three siRNAs were confirmed efficacious to transiently inhibit the replication of FMDV in BHK-21 cells by determining the relative viral amount within infected cells and the virus titers in supernatants as well as the observation of the emergence of CPE. abstract: Abstract Foot-and-mouth disease virus (FMDV) is the causative agent of foot-and-mouth disease, a severe, clinically acute, vesicular disease of cloven-hoofed animals. RNA interference (RNAi) is a mechanism for silencing gene expression post-transcriptionally that is being exploited as a rapid antiviral strategy. To identify efficacious small interfering RNAs (siRNAs) to inhibit the replication of FMDV, candidate siRNAs corresponding to FMDV VP1 gene were designed and synthesized in vitro using T7 RNA polymerase. In reporter assays, five siRNAs showed significant sequence-specific silencing effects on the expression of VP1-EGFP fusion protein from plasmid pVP1-EGFP-N1, which was cotransfected with siRNA into 293T cells. Furthermore, using RT-qPCR, viral titration and viability assay, we identified VP1-siRNA517, VP1-siRNA113 and VP1-siRNA519 that transiently acted as potent inhibitors of FMDV replication when BHK-21 cells were infected with FMDV. In addition, variations within multiple regions of the quasispecies of FMDV were retrospectively revealed by sequencing of FMDV genes, and a single nucleotide substitution was identified as the main factor in resistance to RNAi. Our data demonstrated that the three siRNA molecules synthesized with T7 RNA polymerase could have transient inhibitory effects on the replication of FMDV. url: https://doi.org/10.1016/j.rvsc.2008.10.011 doi: 10.1016/j.rvsc.2008.10.011 id: cord-018804-wj35q88f author: Lázaro, Ester title: Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity date: 2007 words: 8510.0 sentences: 398.0 pages: flesch: 44.0 cache: ./cache/cord-018804-wj35q88f.txt txt: ./txt/cord-018804-wj35q88f.txt summary: High error prone replication, together with the short replication times and large population sizes typical of RNA viruses, instead of being a handicap for survival provides an extraordinary evolutionary advantage by permitting the generation of a wide reservoir of mutants with different phenotypic properties [7] . However, the fact that DNA organisms, which usually live in constant environments, have evolved corrector activities, whereas RNA viruses have not, suggests that replication with high error rates is a selected character that strongly favours viral adaptation to fast changing conditions. Quasi-species replicating during a long time in a near-constant environment in the absence of large population size fluctuations can present a low rate of fixation of mutations in the consensus sequence, despite the continuous occurrence of mutants that is characteristic of the underlying dynamics of the population. The infection of a new host constitutes a sudden change in the environment in which viral replication takes place, usually with the consequence of a drastic decrease in the average fitness of the virus population, which prevents further transmission. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123777/ doi: 10.1007/978-3-540-35306-5_15 id: cord-304014-k62mtr9j author: Ma, Xuelian title: Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection date: 2019-11-04 words: 4474.0 sentences: 325.0 pages: flesch: 54.0 cache: ./cache/cord-304014-k62mtr9j.txt txt: ./txt/cord-304014-k62mtr9j.txt summary: Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML). CONCLUSIONS: The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins. The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins. abstract: BACKGROUND: Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown. RESULTS: In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to inflammatory response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML). CONCLUSIONS: The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/31684870/ doi: 10.1186/s12864-019-6156-5 id: cord-293417-oqusfhei author: Ma, Yanlin title: Structures of the N- and C-terminal domains of MHV-A59 nucleocapsid protein corroborate a conserved RNA-protein binding mechanism in coronavirus date: 2010-07-01 words: 5142.0 sentences: 292.0 pages: flesch: 55.0 cache: ./cache/cord-293417-oqusfhei.txt txt: ./txt/cord-293417-oqusfhei.txt summary: The higher resolution provides more detailed structural information than previous reports, showing that the NTD structure from MHV shares a similar overall and topology structure with that of SARS-CoV and IBV, but varies in its potential surface, which indicates a possible difference in RNA-binding module. To gain insight into the precise mechanism of N protein, several crystallographic or NMR structural results were reported, including MHV N-terminal RNA binding domain (residues 60-195) (Grossoehme et al., 2009) , two proteaseresistant domains of the N protein from SARS-CoV (Huang et al., 2004; Luo et al., 2006; Yu et al., 2006; Chen et al., 2007; Saikatendu et al., 2007; Takeda et al., 2008) , and IBV (Beaudette strain and Gray strain) (Fan et al., 2005; Jayaram et al., 2006) . In overall ribbon posture, the high resolution structure of MHV-NTD determined using two forms of crystals with different packing modes is similar to previously reported SARS-CoV and IBV structures, with a remarkable difference in surface electrostatic distribution. abstract: Coronaviruses are the causative agent of respiratory and enteric diseases in animals and humans. One example is SARS, which caused a worldwide health threat in 2003. In coronaviruses, the structural protein N (nucleocapsid protein) associates with the viral RNA to form the filamentous nucleocapsid and plays a crucial role in genome replication and transcription. The structure of Nterminal domain of MHV N protein also implicated its specific affinity with transcriptional regulatory sequence (TRS) RNA. Here we report the crystal structures of the two proteolytically resistant N- (NTD) and C-terminal (CTD) domains of the N protein from murine hepatitis virus (MHV). The structure of NTD in two different crystal forms was solved to 1.5 Å. The higher resolution provides more detailed structural information than previous reports, showing that the NTD structure from MHV shares a similar overall and topology structure with that of SARS-CoV and IBV, but varies in its potential surface, which indicates a possible difference in RNA-binding module. The structure of CTD was solved to 2.0-Å resolution and revealed a tightly intertwined dimer. This is consistent with analytical ultracentrifugation experiments, suggesting a dimeric assembly of the N protein. The similarity between the structures of these two domains from SARS-CoV, IBV and MHV corroborates a conserved mechanism of nucleocapsid formation for coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/21203940/ doi: 10.1007/s13238-010-0079-x id: cord-354582-fniymnmf author: Ma, Zhiqian title: Reverse genetic systems: Rational design of coronavirus live attenuated vaccines with immune sequelae date: 2020-06-30 words: 8373.0 sentences: 423.0 pages: flesch: 44.0 cache: ./cache/cord-354582-fniymnmf.txt txt: ./txt/cord-354582-fniymnmf.txt summary: In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. Recently, reverse genetics techniques, including targeted RNA recombination, in vitro ligation and bacterial artificial chromosome systems, vaccinia virus vectors and transformation associated recombination (TAR) cloning, have been successfully used to manipulate the genome of coronaviruses (Fig. 2 ). Using a recombinant SARS-CoV strain with reduced nsp3 de-ADP-ribosylation activity showed that this mutant strain led to virus attenuation in mice but protected them from an otherwise lethal SARS-CoV infection and significantly enhanced the innate immune response, indicating that it is an important virulence factor for SARS-CoV . The N protein plays an important role in viral pathogenesis since BALB/c mice immunized with recombinant virus MVA-MERS-N exhibit stronger T cell responses and anti-N monoclonal antibodies protect mice from lethal infection by MHV (Nakanaga et al., 1986; Veit et al., 2018) . abstract: Since the end of 2019, the global COVID-19 outbreak has once again made coronaviruses a hot topic. Vaccines are hoped to be an effective way to stop the spread of the virus. However, there are no clinically approved vaccines available for coronavirus infections. Reverse genetics technology can realize the operation of RNA virus genomes at the DNA level and provide new ideas and strategies for the development of new vaccines. In this review, we systematically describe the role of reverse genetics technology in studying the effects of coronavirus proteins on viral virulence and innate immunity, cell and tissue tropism and antiviral drug screening. An efficient reverse genetics platform is useful for obtaining the ideal attenuated strain to prepare an attenuated live vaccine. url: https://doi.org/10.1016/bs.aivir.2020.06.003 doi: 10.1016/bs.aivir.2020.06.003 id: cord-016144-280kwlev author: Maan, Sushila title: Novel Molecular Diagnostics and Therapeutic Tools for Livestock Diseases date: 2018-04-26 words: 6526.0 sentences: 364.0 pages: flesch: 45.0 cache: ./cache/cord-016144-280kwlev.txt txt: ./txt/cord-016144-280kwlev.txt summary: Further, modifications in PCR-based molecular detection techniques have generated a vast array of fast, reliable and specific assays which have widespread applications in veterinary diagnostics. The sensitivity of any genome detection-based method can be enhanced to a very high degree by manipulating any of the three pillars of the assay, i.e. by amplification of target, signal and probe. Common real-time PCRs include (1) SYBR green method where the fluorescent dye SYBR green binds to random dsDNA and can also give nonspecific amplification and (2) dual dyelabelled probe method which involves the use of sequence-specific DNA probes that are labelled with a fluorescent reporter, permitting specific detection after hybridization of the probe with its complementary sequence. To overcome these limitations and to increase efficiency comparable to symmetric PCRs, linear after the exponential (LATE)-PCR was developed based on primer pairs purposely designed for use at unequal concentrations to yield specific single-stranded DNA products in a robust way (Pierce et al. abstract: Recent novelties in diverse diagnostics and therapeutic tools in animal health sector have paved a brighter and clearer way ahead. These are proved to be better in detection, management, control and eradication of animal sufferings caused by various infectious and non-infectious diseases. These innovations have potential impact that extends beyond the animal health and welfare. The advancements have significantly contributed towards improvement in the economy of the country as well as food security. In the present competitive era of evolution, the organisms have inculcated a number of new strategies for survival and spread. Therefore, science needs to continuously evolve more sensitive, specific and high-throughput tools to overcome pathogen cleverness to escape from host immune surveillance. For visible or remarkable changes, it is necessary to use full potential of these advanced molecular techniques into current animal health standards and practices. Under ‘One Health’ concept, the health of animals and humans has to be taken care simultaneously. At present, these advanced molecular diagnostic methods play a significant role in the detection of new and emerging pathogens of livestock. The acquired information also helps to study the interrelationships of pathogens, their hosts and their surroundings. Additionally new vaccines bridging human and animal health development may be discovered. Latest developments in the field of diagnostics and vaccine design through genomics approach have also laid the foundation to enhance the diagnosis and surveillance and in turn helped in the control of infectious diseases. Latest high-throughput DNA sequencing platforms are currently being used for identification and detailed analysis of both disease pathogen and host genomes. The high-throughput data generated using these platforms need to be analysed adopting the bioinformatics and computational genomics that have taken a very high pace nowadays. In the context of animal health, the data analysis may provide some key opportunities for the development of better diagnostic and therapeutic tools for emerging or re-emerging diseases. Such novel and potent technologies put forward a significantly new scenario of disease knowledge, which enables more accurate predictions leading to faster and greater management responses to combat potentially devastating disease crises. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120337/ doi: 10.1007/978-981-10-4702-2_14 id: cord-016499-5iqpl23p author: Mackay, Ian M. title: Rhinoviruses date: 2014-02-27 words: 23394.0 sentences: 1156.0 pages: flesch: 45.0 cache: ./cache/cord-016499-5iqpl23p.txt txt: ./txt/cord-016499-5iqpl23p.txt summary: A convenience population of 15 healthy children (1-9 years old) without asthma were followed during at least three seasons, and picornaviruses were detected in 5 % of 740 specimens (21 % of infections) not associated with symptoms, The impact of HRV typing and of sampling based only on symptoms. Clinical features and complete genome characterization of a distinct human rhinovirus genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines abstract: Picornaviruses, which include the human rhinoviruses (HRVs) and enteroviruses (EVs), are the most frequent cause of acute human illness worldwide. HRVs are the most prevalent cause of acute respiratory tract illnesses (ARIs) which usually commence in the upper respiratory tract (URT). ARIs are the leading cause of morbidity in children under 5 years and occur in all seasons. ARIs linked to HRV infections are associated with excessive and perhaps inappropriate antibiotic prescribing and with significant direct and indirect healthcare expenditure. ARI incidence is highest in the first 2 years of life, with up to thirteen episodes per year including up to six positive for an HRV, and it is not uncommon to average one infection per child-month. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120790/ doi: 10.1007/978-1-4899-7448-8_29 id: cord-259671-7de21oaq author: Madhugiri, Ramakanth title: RNA structure analysis of alphacoronavirus terminal genome regions date: 2014-12-19 words: 11161.0 sentences: 568.0 pages: flesch: 50.0 cache: ./cache/cord-259671-7de21oaq.txt txt: ./txt/cord-259671-7de21oaq.txt summary: Overall, the conservation pattern identified for 5′ and 3′-terminal RNA structural elements in the genomes of alphaand betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements. Other internal cis-acting elements include specific RNA signals required for genome packing, which have been characterized in a small number of coronaviruses Escors et al., 2003; Morales et al., 2013; Penzes et al., 1994) , and a complex RNA pseudoknot structure located in the ORF1a-ORF1b overlap region that mediates a (−1) ribosomal frameshift event and thus controls the expression of the second large ORF on the coronavirus genome RNA (ORF1b) (Brierley et al., 1987 (Brierley et al., , 1989 de Haan et al., 2002; Namy et al., 2006) . abstract: Coronavirus genome replication is mediated by a multi-subunit protein complex that is comprised of more than a dozen virally encoded and several cellular proteins. Interactions of the viral replicase complex with cis-acting RNA elements located in the 5′ and 3′-terminal genome regions ensure the specific replication of viral RNA. Over the past years, boundaries and structures of cis-acting RNA elements required for coronavirus genome replication have been extensively characterized in betacoronaviruses and, to a lesser extent, other coronavirus genera. Here, we review our current understanding of coronavirus cis-acting elements located in the terminal genome regions and use a combination of bioinformatic and RNA structure probing studies to identify and characterize putative cis-acting RNA elements in alphacoronaviruses. The study suggests significant RNA structure conservation among members of the genus Alphacoronavirus but also across genus boundaries. Overall, the conservation pattern identified for 5′ and 3′-terminal RNA structural elements in the genomes of alpha- and betacoronaviruses is in agreement with the widely used replicase polyprotein-based classification of the Coronavirinae, suggesting co-evolution of the coronavirus replication machinery with cognate cis-acting RNA elements. url: https://api.elsevier.com/content/article/pii/S0168170214004055 doi: 10.1016/j.virusres.2014.10.001 id: cord-322240-z8zkl2xh author: Maeda, Ken title: Isolation of Novel Adenovirus from Fruit Bat (Pteropus dasymallus yayeyamae) date: 2008-02-17 words: 1686.0 sentences: 95.0 pages: flesch: 51.0 cache: ./cache/cord-322240-z8zkl2xh.txt txt: ./txt/cord-322240-z8zkl2xh.txt summary: To date, only 1 case of disseminated infection has been reported in a solid-organ (kidney) transplant recipient; the diagnosis was made by molecular identifi cation in isolates from blood and marrow cultures. As a fi rst step in investigating unidentifi ed pathogens in bats and to help forecast the potential threat of emerging infectious diseases, we tried to isolate and characterize viruses that persistently infect bats. However, no viral nucleic acid sequence was detected from an RNA sample in the RV1-infected BKT1 cells. In addition, our success in DNA virus isolation might have resulted from usage of the adult animal latently and persistently infected with DNA viruses such as adenovirus and herpesvirus. Although its pathogenicity for humans is still unknown, knowledge of RV1 will be useful in epidemiologic studies of infectious diseases emerging from bats because persistently infecting viruses might be isolated together with primary pathogens. abstract: Isolation of Novel Adenovirus from Fruit Bat url: https://doi.org/10.3201/eid1402.070932 doi: 10.3201/eid1402.070932 id: cord-317244-4su5on6s author: Maganga, Gael D. title: Identification of an Unclassified Paramyxovirus in Coleura afra: A Potential Case of Host Specificity date: 2014-12-31 words: 3476.0 sentences: 191.0 pages: flesch: 50.0 cache: ./cache/cord-317244-4su5on6s.txt txt: ./txt/cord-317244-4su5on6s.txt summary: In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. To further investigate the presence of the virus in bat populations, a strain-specific real-time RT-PCR assay (primers: GB09-478-F, 59-GGCGGCTCTTAAAAGT-GAATG-39; GB09-478-R, 59-GCGGGGTCAAATTGGTCAT-39; probe: GB09-478-P, 59-TCCAGCACAAACATATCCGAGAAGGCTAG-39) was designed within the initial PCR fragment and was used to test total RNA extracted from mixed liver and spleen samples from each of all the other bat species. In order to determine the organ distribution of this virus in infected bats, total RNA was extracted from heart, liver, spleen, kidney, lung, intestine and brain samples from all 14 real-time RT-PCR-positive bats, as described previously, and screened, using the same strain-specific real-time RT-PCR assay shown above. abstract: Bats are known to harbor multiple paramyxoviruses. Despite the creation of two new genera, Aquaparamyxovirus and Ferlavirus, to accommodate this increasing diversity, several recently isolated or characterized viruses remain unclassified beyond the subfamily level. In the present study, among 985 bats belonging to 6 species sampled in the Belinga caves of Gabon, RNA of an unclassified paramyxovirus (Belinga bat virus, BelPV) was discovered in 14 African sheath-tailed bats (Coleura afra), one of which exhibited several hemorrhagic lesions at necropsy, and viral sequence was obtained in two animals. Phylogenetically, BelPV is related to J virus and Beilong virus (BeiPV), two other unclassified paramyxoviruses isolated from rodents. In the diseased BelPV-infected C. afra individual, high viral load was detected in the heart, and the lesions were consistent with those reported in wild rodents and mice experimentally infected by J virus. BelPV was not detected in other tested bat species sharing the same roosting sites and living in very close proximity with C. afra in the two caves sampled, suggesting that this virus may be host-specific for C. afra. The mode of transmission of this paramyxovirus in bat populations remains to be discovered. url: https://doi.org/10.1371/journal.pone.0115588 doi: 10.1371/journal.pone.0115588 id: cord-313138-y485ev30 author: Magor, Katharine E. title: Defense genes missing from the flight division date: 2013-04-24 words: 10638.0 sentences: 610.0 pages: flesch: 51.0 cache: ./cache/cord-313138-y485ev30.txt txt: ./txt/cord-313138-y485ev30.txt summary: Whether cause or effect, the lack of TLR8 in avian monocytes/ macrophages likely does contribute to the susceptibility of birds to RNA viruses (West Nile virus, Newcastle disease virus, influenza virus and others) and intracellular bacterial infections, including mycobacteria. The gene encoding RIG-I, DDX58, is not annotated in the chicken genome sequence, and is missing in some fish species, but MDA5 homologues are present in all vertebrate families (Zou et 2009). Riplet/RNF135 is a cytoplasmic E3-ligase identified by yeast two-hybrid as one of the proteins binding RIG-I, and is essential for RIG-I activation in human cell lines upon infection with an RNA virus (Oshiumi et al., 2009; Oshiumi et al., 2010) . The upregulation of IFIT5 following viral infection of chicken cells expressing duck RIG-I ( Barber et al., 2013) or infection of ducks (Vanderven et al., 2012) suggests IFIT5 is an important antiviral effector in avian species. abstract: Birds have a smaller repertoire of immune genes than mammals. In our efforts to study antiviral responses to influenza in avian hosts, we have noted key genes that appear to be missing. As a result, we speculate that birds have impaired detection of viruses and intracellular pathogens. Birds are missing TLR8, a detector for single-stranded RNA. Chickens also lack RIG-I, the intracellular detector for single-stranded viral RNA. Riplet, an activator for RIG-I, is also missing in chickens. IRF3, the nuclear activator of interferon-beta in the RIG-I pathway is missing in birds. Downstream of interferon (IFN) signaling, some of the antiviral effectors are missing, including ISG15, and ISG54 and ISG56 (IFITs). Birds have only three antibody isotypes and IgD is missing. Ducks, but not chickens, make an unusual truncated IgY antibody that is missing the Fc fragment. Chickens have an expanded family of LILR leukocyte receptor genes, called CHIR genes, with hundreds of members, including several that encode IgY Fc receptors. Intriguingly, LILR homologues appear to be missing in ducks, including these IgY Fc receptors. The truncated IgY in ducks, and the duplicated IgY receptor genes in chickens may both have resulted from selective pressure by a pathogen on IgY FcR interactions. Birds have a minimal MHC, and the TAP transport and presentation of peptides on MHC class I is constrained, limiting function. Perhaps removing some constraint, ducks appear to lack tapasin, a chaperone involved in loading peptides on MHC class I. Finally, the absence of lymphotoxin-alpha and beta may account for the observed lack of lymph nodes in birds. As illustrated by these examples, the picture that emerges is some impairment of immune response to viruses in birds, either a cause or consequence of the host-pathogen arms race and long evolutionary relationship of birds and RNA viruses. url: https://api.elsevier.com/content/article/pii/S0145305X13001146 doi: 10.1016/j.dci.2013.04.010 id: cord-102967-dx0tg077 author: Mahajan, Lakshmi S. title: Mapping RNA dependent RNA polymerase activity and immune gene expression using PRO-seq date: 2020-06-16 words: 2853.0 sentences: 163.0 pages: flesch: 57.0 cache: ./cache/cord-102967-dx0tg077.txt txt: ./txt/cord-102967-dx0tg077.txt summary: Coupled to PRO-seq in human blood samples, we propose to use PRO-seq as a single package method to detect (+)ssRNA virus RdRp activity and its interaction with host immune response through transcriptome-wide profiling of leukocyte gene expressions at once. This is different from Drosophila RNA Polymerase II, which appears to have comparable substrate specificity for all 4 biotin-NTPs. The ORF-proximal accumulation coincides with quadruplet rich regions of the template-strand of the DAV genome ( Figure 1D ). From this data, we did not detect significant PRO-seq sequences from (+)ssRNA viral genomes, indicating that none of the individuals had direct viral infections in the blood immune cells. Our PRO-seq data show expression levels of immune-response related genes from human peripheral blood leukocytes. PRO-seq density on DAV genome and base-quadruplet counts.The read count is indicated along the left side of each graph. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) abstract: Positive strand, single strand RNA viruses ((+)ssRNA viruses) are viruses with an RNA genome that have broad impacts on a wide range of hosts, including SARS-CoV-2 human respiratory infections. Their replication and gene expression are driven by RNA dependent RNA polymerases (RdRp). Detecting active RNA synthesis by RdRp is critical for assessing the infectivity and pathogenicity of (+)ssRNA viruses. Current approaches rely on viral RNA detection, which cannot distinguish viral titer from RdRp activity. Precision Run-On sequencing (PRO-seq) is a nuclear run-on based nascent RNA sequencing method, widely used to map eukaryotic RNA polymerases by using labeled nucleotide analogues. Here we provide evidence that PRO-seq also detects RdRp activity and can serve as a highly sensitive RdRp mapping method. Coupled to PRO-seq in human blood samples, we propose to use PRO-seq as a single package method to detect (+)ssRNA virus RdRp activity and its interaction with host immune response through transcriptome-wide profiling of leukocyte gene expressions at once. url: https://doi.org/10.1101/2020.06.15.151738 doi: 10.1101/2020.06.15.151738 id: cord-272573-wxqly479 author: Maia Chagas, Andre title: Leveraging open hardware to alleviate the burden of COVID-19 on global health systems date: 2020-04-24 words: 5074.0 sentences: 317.0 pages: flesch: 55.0 cache: ./cache/cord-272573-wxqly479.txt txt: ./txt/cord-272573-wxqly479.txt summary: Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics. Community and commercial open source efforts in diagnostic technology to date have focused on four areas: i) open platforms for scaling reactions as exemplified by Opentrons ( Fig 3A) [28] , an open source lab automation platform that has been working with BP Genomics and the Open Medicine Institute to automate up to 2,400 tests per day and achieve US FDA EUA approval and is now automating COVID-19 testing at the Biomedical Diagnostic Center (CBD) of Hospital Clinic of Barcelona; ii) trying to fill gaps where less attention is being paid by clinical diagnostics companies, such as Chia Bio''s Open qPCR (Fig 3B) environmental test kit for surveillance via surface swabs [111] ; iii) distributed reproduction of rapidly-published, lab-scale protocols, seen within the OpenCOVID initiative hosted by Just One Giant Lab [39] which involves many community labs worldwide; iv) initiatives such as the Open Enzyme Collection [93] , Free Genes [94] and Biomaker Challenge [112] which are investigating new approaches to foundational technologies such as reagents and instrumentation, with a view to building capacity and resources or global science and medicine to face a future pandemic. abstract: With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment. Shortcomings are evident across the board, from staffing, facilities for rapid and reliable testing to availability of hospital beds and key medical-grade equipment. The scale and breadth of the problem calls for an equally substantive response not only from frontline workers such as medical staff and scientists, but from skilled members of the public who have the time, facilities and knowledge to meaningfully contribute to a consolidated global response. Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics. url: https://www.ncbi.nlm.nih.gov/pubmed/32330124/ doi: 10.1371/journal.pbio.3000730 id: cord-025948-6dsx7pey author: Maitra, Arindam title: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility date: 2020-06-04 words: 7218.0 sentences: 382.0 pages: flesch: 56.0 cache: ./cache/cord-025948-6dsx7pey.txt txt: ./txt/cord-025948-6dsx7pey.txt summary: Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. We have initiated a study on sequencing of SARS-CoV-2 genome from swab samples obtained from infected individuals from different regions of West Bengal in Eastern India and report here the first nine sequences and the results of analysis of the sequence data with respect to other sequences reported from the country until date. The A2a clade is characterized by the signature nonsynonymous mutations leading to amino acid changes of P323L in the RdRp which is involved in replication of the viral genome and the change of D614G in the Spike glycoprotein which is essential for the entry of the virus in the host cell by binding to the ACE2 receptor. We have also detected emergence of mutations in the important regions of the viral genome including Spike, RdRP and nucleocapsid coding genes. abstract: Direct massively parallel sequencing of SARS-CoV-2 genome was undertaken from nasopharyngeal and oropharyngeal swab samples of infected individuals in Eastern India. Seven of the isolates belonged to the A2a clade, while one belonged to the B4 clade. Specific mutations, characteristic of the A2a clade, were also detected, which included the P323L in RNA-dependent RNA polymerase and D614G in the Spike glycoprotein. Further, our data revealed emergence of novel subclones harbouring nonsynonymous mutations, viz. G1124V in Spike (S) protein, R203K, and G204R in the nucleocapsid (N) protein. The N protein mutations reside in the SR-rich region involved in viral capsid formation and the S protein mutation is in the S(2) domain, which is involved in triggering viral fusion with the host cell membrane. Interesting correlation was observed between these mutations and travel or contact history of COVID-19 positive cases. Consequent alterations of miRNA binding and structure were also predicted for these mutations. More importantly, the possible implications of mutation D614G (in S(D) domain) and G1124V (in S(2) subunit) on the structural stability of S protein have also been discussed. Results report for the first time a bird’s eye view on the accumulation of mutations in SARS-CoV-2 genome in Eastern India. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12038-020-00046-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7269891/ doi: 10.1007/s12038-020-00046-1 id: cord-312001-8p7scli8 author: Majzoub, Karim title: The Innate Antiviral Response in Animals: An Evolutionary Perspective from Flagellates to Humans date: 2019-08-16 words: 10056.0 sentences: 548.0 pages: flesch: 46.0 cache: ./cache/cord-312001-8p7scli8.txt txt: ./txt/cord-312001-8p7scli8.txt summary: Consequently, animal cells have evolved devoted pathways which (1) sense and recognize pathogen-associated molecular patterns (PAMPs) and, more particularly, virus-associated molecular signatures; (2) initiate signaling cascades stemming from the site of detection, translocating the information to the nucleus; and (3) induce a transcriptional program that confers an antiviral state to the host ( Figure 1 ). While the cytosolic recognition of viral RNA is almost exclusively mediated by RLRs, several proteins have been proposed to play a role in DNA sensing and triggering innate immune responses, such as the DNA-dependent activator of IFN-regulatory factors (DAI), DDX41, RNA polymerase III, IFI16 and DNA-PK [62] [63] [64] [65] [66] [67] . Although the pathway leading to the transcriptional activation of Vago is still poorly understood in insects, these studies established that DExD/H-box helicase containing proteins, like Dicer and RLRs, may represent an evolutionarily conserved set of viral nucleic acid sensors that direct antiviral responses in animals [159] . abstract: Animal cells have evolved dedicated molecular systems for sensing and delivering a coordinated response to viral threats. Our understanding of these pathways is almost entirely defined by studies in humans or model organisms like mice, fruit flies and worms. However, new genomic and functional data from organisms such as sponges, anemones and mollusks are helping redefine our understanding of these immune systems and their evolution. In this review, we will discuss our current knowledge of the innate immune pathways involved in sensing, signaling and inducing genes to counter viral infections in vertebrate animals. We will then focus on some central conserved players of this response including Toll-like receptors (TLRs), RIG-I-like receptors (RLRs) and cGAS-STING, attempting to put their evolution into perspective. To conclude, we will reflect on the arms race that exists between viruses and their animal hosts, illustrated by the dynamic evolution and diversification of innate immune pathways. These concepts are not only important to understand virus-host interactions in general but may also be relevant for the development of novel curative approaches against human disease. url: https://doi.org/10.3390/v11080758 doi: 10.3390/v11080758 id: cord-298934-vtrfqozl author: Makino, Shinji title: Primary structure and translation of a defective interfering rna of murine coronavirus date: 1988-10-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract An intracellular defective-interfering (DI) RNA, DIssE, of mouse hepatitis virus (MHV) obtained after serial high multiplicity passage of the virus was cloned and sequenced. DIssE RNA is composed of three noncontiguous genomic regions, representing the first 864 nucleotides of the Fend, an internal 748 nucleotides of the polymerase gene, and 601 nucleotides from the 3′ end of the parental MHV genome. The DIssE sequence contains one large continuous open reading frame. Two protein products from this open reading frame were identified both by in vitro translation and in DI-infected cells. Sequence comparison of DIssE and the corresponding parts of the parental virus genome revealed that DIssE had three base substitutions within the leader sequence and also a deletion of nine nucleotides located at the junction of the leader and the remaining genomic sequence. The 5′ end of DIssE RNA was heterogeneous with respect to the number of UCUAA repeats within the leader sequence. The parental MHV genomic RNA appears to have extensive and stable secondary structures at the regions where DI RNA rearrangements occurred. These data suggest that MHV DI RNA may have been generated as a result of the discontinuous and nonprocessive manner of MHV RNA synthesis. url: https://api.elsevier.com/content/article/pii/0042682288905260 doi: 10.1016/0042-6822(88)90526-0 id: cord-335482-nx7odchj author: Makino, Shinji title: Defective interfering particles of mouse hepatitis virus date: 1984-02-29 words: 3840.0 sentences: 210.0 pages: flesch: 60.0 cache: ./cache/cord-335482-nx7odchj.txt txt: ./txt/cord-335482-nx7odchj.txt summary: We have observed marked reduction of infectivity in the course od serial undiluted passages of JHM virus in DBT cell culture. To avoid contamination of the standard virus stock with DI particles, plaque purified MHV (JHM strain) (Hirano et aL, 1981; Makino et al, 1983) was propagated on DBT cells at a multiplicity of infection (m.o.i.) of 0.0002 and at 15 hr postinfection (p.i.) culture fluid was harvested and clarified by low speed centrifugation. Preparation of the Standard JHM Virus for Interference Assay JHM virus was propagated on DBT cells after infection at an m.o.i. of 1.0 and was harvested at 14 hr p.i. The culture fluid was clarified by centrifugation at 8000 rpm for 30 min. To determine if the reduction in the yield of infectious virus was due to the presence of DI particles, a''n interference analysis was performed with several culture fluid samples at different passage levels. abstract: Abstract After six to eight serial undiluted passages of mouse hepatitis virus (JHM strain) in DBT cell culture, a decrease in the yield of infectious virus occurred, and with further passages fluctuating yields of infectious virus were observed. The serially passaged virus interfered with the multiplication of the standard JHM virus, but not with vesicular stomatitis virus. After sucrose equilibrium centrifugation of high passage virus, a single peak contained both infectious virus and interfering activity. This virus population resembled the original JHM virus in its structural proteins, but it contained an increased proportion of a protein with a molecular weight of 65 × 103. Genomic RNA from standard JHM virus contained a single species of RNA with a molecular weight of 5.4 × 106. After five undiluted passages, however, the virion population contained two RNA species with molecular weights of 5.4 × 106 and 5.2 × 106. RNase T1 resistant oligonucleotide finger-printing of these RNAs showed that the lower molecular weight RNA had lost several oligonucleotide spots that were present in the genomic RNA of the standard JHM virus. After several serial diluted passages of passage 10 virus, a single virus population was obtained which again had only standard virus RNA with a molecular weight of 5.4 × 106 and lacked interfering activity. These results indicated that defective interfering particles were generated by serial undiluted passages of JHM virus. url: https://www.ncbi.nlm.nih.gov/pubmed/6322437/ doi: 10.1016/0042-6822(84)90420-3 id: cord-293481-bmfj50fb author: Malin, Jakob J. title: Remdesivir against COVID-19 and Other Viral Diseases date: 2020-10-14 words: 9097.0 sentences: 428.0 pages: flesch: 42.0 cache: ./cache/cord-293481-bmfj50fb.txt txt: ./txt/cord-293481-bmfj50fb.txt summary: Remdesivir or GS-5734 is a prodrug of a nucleoside analog with direct antiviral activity against several single-stranded RNA viruses, including SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Recently, preliminary data from a randomized placebo-controlled clinical trial showed that remdesivir reduces the time to recovery in patients with COVID-19 (5) , leading to an emergency-use authorization (EUA) by the U.S. Food and Drug Administration (FDA) only 2 days after the first press release from the National Institute of Allergy and Infectious Diseases (NIAID) (6) . There were strong arguments for the antiviral effect of remdesivir against coronaviruses emerging from multiple cell-based in vitro models, including primary human airway epithelial (HAE) cell cultures (25) , and, for MERS-CoV, from a mouse model of pulmonary infection (28) . After the outbreak of SARS-CoV-2 in January 2020, remdesivir was rapidly tested in a Vero E6 cell-based model that made use of direct viral quantification by rtPCR along with the antimalaria and immune-modulating drug chloroquine and known antivirals such as ribavirin and penciclovir. abstract: Patients and physicians worldwide are facing tremendous health care hazards that are caused by the ongoing severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2) pandemic. Remdesivir (GS-5734) is the first approved treatment for severe coronavirus disease 2019 (COVID-19). It is a novel nucleoside analog with a broad antiviral activity spectrum among RNA viruses, including ebolavirus (EBOV) and the respiratory pathogens Middle East respiratory syndrome coronavirus (MERS-CoV), SARS-CoV, and SARS-CoV-2. First described in 2016, the drug was derived from an antiviral library of small molecules intended to target emerging pathogenic RNA viruses. In vivo, remdesivir showed therapeutic and prophylactic effects in animal models of EBOV, MERS-CoV, SARS-CoV, and SARS-CoV-2 infection. However, the substance failed in a clinical trial on ebolavirus disease (EVD), where it was inferior to investigational monoclonal antibodies in an interim analysis. As there was no placebo control in this study, no conclusions on its efficacy in EVD can be made. In contrast, data from a placebo-controlled trial show beneficial effects for patients with COVID-19. Remdesivir reduces the time to recovery of hospitalized patients who require supplemental oxygen and may have a positive impact on mortality outcomes while having a favorable safety profile. Although this is an important milestone in the fight against COVID-19, approval of this drug will not be sufficient to solve the public health issues caused by the ongoing pandemic. Further scientific efforts are needed to evaluate the full potential of nucleoside analogs as treatment or prophylaxis of viral respiratory infections and to develop effective antivirals that are orally bioavailable. url: https://doi.org/10.1128/cmr.00162-20 doi: 10.1128/cmr.00162-20 id: cord-003482-f1uvohf0 author: Malmlov, Ashley title: Experimental Zika virus infection of Jamaican fruit bats (Artibeus jamaicensis) and possible entry of virus into brain via activated microglial cells date: 2019-02-04 words: 7503.0 sentences: 400.0 pages: flesch: 53.0 cache: ./cache/cord-003482-f1uvohf0.txt txt: ./txt/cord-003482-f1uvohf0.txt summary: Quantitative probe-based reverse transcription PCR (qRT-PCR) was performed on seruminoculated Vero cell supernatants, serum, brain, lung, liver, spleen, kidney, urinary bladder, prostate and testes from bats from both studies. Brain and testicular tissues stained with both goat polyclonal goat anti-Iba1 (green) and monoclonal 4G-2 flavivirus E specific antibodies (red) showed co-localization (yellow) of ZIKV antigen in cytoplasm of activated microglial cells with their characteristic morphology in the cerebral cortex of infected bats 10 dpi in the time course study and 28 day dpi in the pilot study (Fig 9) . Two bat infection experiments were conducted in this investigation; 1) a pilot study to determine susceptibility of Jamaican fruit bats to ZIKV infection, and 2) a time course study to better understand pathophysiology and chronology of events pertaining to the dynamics of viremia, viral tropism, replication and shedding of the virus in a New World bat species. abstract: The emergence of Zika virus (ZIKV) in the New World has led to more than 200,000 human infections. Perinatal infection can cause severe neurological complications, including fetal and neonatal microcephaly, and in adults there is an association with Guillain-Barré syndrome (GBS). ZIKV is transmitted to humans by Aedes sp. mosquitoes, yet little is known about its enzootic cycle in which transmission is thought to occur between arboreal Aedes sp. mosquitos and non-human primates. In the 1950s and ‘60s, several bat species were shown to be naturally and experimentally susceptible to ZIKV with acute viremia and seroconversion, and some developed neurological disease with viral antigen detected in the brain. Because of ZIKV emergence in the Americas, we sought to determine susceptibility of Jamaican fruit bats (Artibeus jamaicensis), one of the most common bats in the New World. Bats were inoculated with ZIKV PRVABC59 but did not show signs of disease. Bats held to 28 days post-inoculation (PI) had detectable antibody by ELISA and viral RNA was detected by qRT-PCR in the brain, saliva and urine in some of the bats. Immunoreactivity using polyclonal anti-ZIKV antibody was detected in testes, brain, lung and salivary glands plus scrotal skin. Tropism for mononuclear cells, including macrophages/microglia and fibroblasts, was seen in the aforementioned organs in addition to testicular Leydig cells. The virus likely localized to the brain via infection of Iba1(+) macrophage/microglial cells. Jamaican fruit bats, therefore, may be a useful animal model for the study of ZIKV infection. This work also raises the possibility that bats may have a role in Zika virus ecology in endemic regions, and that ZIKV may pose a wildlife disease threat to bat populations. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382173/ doi: 10.1371/journal.pntd.0007071 id: cord-319664-gyktrd36 author: Mancini, Fabiola title: Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing date: 2020-06-18 words: 2082.0 sentences: 112.0 pages: flesch: 54.0 cache: ./cache/cord-319664-gyktrd36.txt txt: ./txt/cord-319664-gyktrd36.txt summary: Finally, to evaluate the performance of molecular assays a standard curve was generated by 10-fold dilutions of SARS-CoV-2 RNA, isolated and extracted at Istituto Superiore di Sanità in Rome, Italy, and quantified by a well-established copy number of RNA synthetic E gene (Wuhan coronavirus, EVAg, www. All specimens were also manually extracted and tested for the presence of SARS-CoV-2 by in-house rt-Realtime PCR and the 2019-nCoV TaqMan RT-PCR Kit. In particular, we investigated the RNA availability and virus detection using both the purified and thermal/non-extractive procedures also with this commercial kit because it is based on the same primers, probes and assays developed by the CDC and used in the inhouse molecular method. This study corroborates our results for in-house rt-Real Time PCR, showing a lower sensitivity of the heat treatment (range ΔCT value of 0.5-1.0) when compared with purified samples, but, dissimilar to our findings, a total inhibition was found by the commercial kit RealStar SARS-CoV-2 RT-PCR (Altona Diagnostics, Hamburg, Germany), where all positive samples failed in the detection of Sars-CoV-2 [14] . abstract: The RNA purification is the gold standard for the detection of SARS-CoV-2 in swab samples, but it is dependent on the availability of chemical reagents. In this study, we evaluated the heat treatment method without RNA extraction as a reliable option to nucleic acid purification. url: https://www.ncbi.nlm.nih.gov/pubmed/32552549/ doi: 10.1080/22221751.2020.1775500 id: cord-297790-tpjxt0w5 author: Mandl, Judith N. title: Going to Bat(s) for Studies of Disease Tolerance date: 2018-09-20 words: 9486.0 sentences: 393.0 pages: flesch: 40.0 cache: ./cache/cord-297790-tpjxt0w5.txt txt: ./txt/cord-297790-tpjxt0w5.txt summary: Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. It is likely that differences in evolutionary history of pathogen exposure between bats and humans have led to distinct adaptations in anti-viral immune responses and the ability to tolerate certain infections without disease while being susceptible to others. We summarize this work below, but comparisons of observations made across species suggest that although a number of species appear to be capable of avoiding the pathological effects of RNA virus infection, each bat species may have achieved this through distinct pathways, possibly involving changes to both increase pathogen replication control and to mitigate any immunopathology through decreased inflammatory responses and hence increased disease tolerance. abstract: A majority of viruses that have caused recent epidemics with high lethality rates in people, are zoonoses originating from wildlife. Among them are filoviruses (e.g., Marburg, Ebola), coronaviruses (e.g., SARS, MERS), henipaviruses (e.g., Hendra, Nipah) which share the common features that they are all RNA viruses, and that a dysregulated immune response is an important contributor to the tissue damage and hence pathogenicity that results from infection in humans. Intriguingly, these viruses also all originate from bat reservoirs. Bats have been shown to have a greater mean viral richness than predicted by their phylogenetic distance from humans, their geographic range, or their presence in urban areas, suggesting other traits must explain why bats harbor a greater number of zoonotic viruses than other mammals. Bats are highly unusual among mammals in other ways as well. Not only are they the only mammals capable of powered flight, they have extraordinarily long life spans, with little detectable increases in mortality or senescence until high ages. Their physiology likely impacted their history of pathogen exposure and necessitated adaptations that may have also affected immune signaling pathways. Do our life history traits make us susceptible to generating damaging immune responses to RNA viruses or does the physiology of bats make them particularly tolerant or resistant? Understanding what immune mechanisms enable bats to coexist with RNA viruses may provide critical fundamental insights into how to achieve greater resilience in humans. url: https://doi.org/10.3389/fimmu.2018.02112 doi: 10.3389/fimmu.2018.02112 id: cord-314560-rswa5zdn author: Manjunath, N. title: Interfering antiviral immunity: application, subversion, hope? date: 2006-06-06 words: 5875.0 sentences: 352.0 pages: flesch: 48.0 cache: ./cache/cord-314560-rswa5zdn.txt txt: ./txt/cord-314560-rswa5zdn.txt summary: RNA interference (RNAi), initially recognized as a natural antiviral mechanism in plants, has rapidly emerged as an invaluable tool to suppress gene expression in a sequence-specific manner in all organisms, including mammals. However, in recent years, a new type of genomic immunity mediated by RNA interference (RNAi) has emerged and has sparked intense interest as a potential treatment strategy for a variety of diseases, including viral infections, cancer and degenerative diseases [1] [2] [3] [4] . In RNAi, long double-stranded (ds) RNA generated during viral infection is cleaved by an enzyme termed Dicer into short, 21-23 nucleotide (nt) dsRNA molecules termed small interfering (si)RNAs that mediate sequence-specific gene silencing [5, 6] . A landmark development in the field occurred with the discovery that the introduction of 21-nt-long synthetic RNA resembling the Dicer-processed siRNA into mammalian cells induces sequence-specific gene silencing without evoking the interferon response [10] . abstract: RNA interference (RNAi), initially recognized as a natural antiviral mechanism in plants, has rapidly emerged as an invaluable tool to suppress gene expression in a sequence-specific manner in all organisms, including mammals. Its potential to inhibit the replication of a variety of viruses has been demonstrated in vitro and in vivo in mouse and monkey models. These results have generated profound interest in the use of this technology as a potential treatment strategy for viral infections for which vaccines and drugs are unavailable or inadequate. In this review, we discuss the progress made within the past 2–3 years towards harnessing the potential of RNAi for clinical application in viral infections and the hurdles that have yet to be overcome. url: https://www.ncbi.nlm.nih.gov/pubmed/16753342/ doi: 10.1016/j.it.2006.05.006 id: cord-314753-xflhxb13 author: Manso, Carmen F. title: Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples date: 2017-06-23 words: 6333.0 sentences: 296.0 pages: flesch: 48.0 cache: ./cache/cord-314753-xflhxb13.txt txt: ./txt/cord-314753-xflhxb13.txt summary: The percentage of reads mapping to RNA virus genomes in the rRNA-depleted BBV Panel samples was between 40 and 150-fold higher than in corresponding untreated controls. The depth plots in Fig. 3 again show unbiased and even coverages across both genomes, and the percentages of reads mapping to viral targets was again much higher in the rRNA-depleted sample than in the untreated comparator (61-fold and 85-fold for HCV and HPgV respectively). By depleting host-derived nucleic acids and making modifications to an existing library preparation protocol to account for ultra-low RNA input quantities, we have been able to reconstruct effectively full-length genomes of HCV, HEV and HIV from plasma samples with viral loads of 10 4 IU/ml (copies/ml for HIV) and substantial fractions of complete genomes at 10 3 IU/ml. Additionally, our system was able to recover viral sequences from a panel of diverse RNA viruses diluted in human plasma, with a broad correlation between the genomic coverage and depth metrics and approximate concentration. abstract: RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 10(4) and 10(3) IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/28646219/ doi: 10.1038/s41598-017-02239-5 id: cord-102931-vxkbctiz author: Mao, Kai title: Induction of RNA interference by C. elegans mitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme date: 2020-06-06 words: 8680.0 sentences: 503.0 pages: flesch: 49.0 cache: ./cache/cord-102931-vxkbctiz.txt txt: ./txt/cord-102931-vxkbctiz.txt summary: Here, we report that mitochondrial dysfunction in Caenorhabditis elegans activates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. elegans compared to most animals, and surprisingly, loss of function mutations in some of those genes cause an increase in the response to siRNAs: mutations in the RdRp RRF-3, the specialized Argonaute ERGO-1, the RNA helicase ERI-6/7, or the exoribonuclease ERI-1 enhance silencing by siRNAs (Fischer et al., 2008; Kennedy et al., 2004) . We find that reduction of function mutations in a wide range of mitochondrial components robustly enhanced RNA interference-mediated silencing of endogenous genes as well as a variety of reporters of RNAi. These antiviral responses to mitochondrial dysfunction are homologous to the RIG-I-based mitochondrial response in mammals because they depend on the RIG-I homologue, the DRH-1 RNA helicase. Our analysis of the eol-1 and drh-1 pathway from mitochondrial dysfunction to enhanced RNA interference and antiviral activity is a key output from mitochondria for anti-aging. abstract: RNA interference (RNAi) is an antiviral pathway common to many eukaryotes that detects and cleaves foreign nucleic acids. In mammals, mitochondrially localized proteins such as MAVS, RIG-I, and MDA5 mediate antiviral responses. Here, we report that mitochondrial dysfunction in Caenorhabditis elegans activates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. The induction of RNAi also requires the conserved RNA decapping enzyme EOL-1/DXO. The transcriptional induction of eol-1 requires DRH-1 as well as the mitochondrial unfolded protein response (UPRmt). Upon mitochondrial dysfunction, EOL-1 is concentrated into foci that depend on the transcription of mitochondrial RNAs that may form dsRNA, as has been observed in mammalian antiviral responses. The enhanced RNAi triggered by mitochondrial dysfunction contributes to the increase in longevity that is induced by mitochondrial dysfunction. url: https://doi.org/10.1101/2020.06.05.136978 doi: 10.1101/2020.06.05.136978 id: cord-354829-god79qzw author: Mao, Kaimin title: Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets date: 2020-09-23 words: 6328.0 sentences: 315.0 pages: flesch: 45.0 cache: ./cache/cord-354829-god79qzw.txt txt: ./txt/cord-354829-god79qzw.txt summary: title: Identification of robust genetic signatures associated with lipopolysaccharide-induced acute lung injury onset and astaxanthin therapeutic effects by integrative analysis of RNA sequencing data and GEO datasets Here we performed a statistical meta-analysis of five publicly available gene expression datasets from LPS-induced ALI mouse models, conducted RNA-sequencing (RNA-seq) to screen differentially expressed genes (DEGs) in response to LPS administration and AST treatment, and integrative analysis to determine robust genetic signatures associated with LPS-induced ALI onset and AST administration. We subsequently integrated the RNA-seq and microarray meta-analysis data, and 11 core DEGs (Timp1, Ly6i, Cxcl13, Irf7, Cxcl5, Ccl7, Isg15, Saa3, Saa1, Tgtp1, and Gbp11) that were upregulated in ALI models and downregulated significantly after AST treatment were identified ( Table 2) . To further identify the robust expression signature related to LPS-induced ALI and investigate the transcriptional changes in response to the treatment of ALI by AST, we performed RNA-seq on three groups of mice and integrated the data with the results of the above mentioned meta-analysis. abstract: Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) are life-threatening clinical conditions predominantly arising from uncontrolled inflammatory reactions. It has been found that the administration of astaxanthin (AST) can exert protective effects against lipopolysaccharide (LPS)-induced ALI; however, the robust genetic signatures underlying LPS induction and AST treatment remain obscure. Here we performed a statistical meta-analysis of five publicly available gene expression datasets from LPS-induced ALI mouse models, conducted RNA-sequencing (RNA-seq) to screen differentially expressed genes (DEGs) in response to LPS administration and AST treatment, and integrative analysis to determine robust genetic signatures associated with LPS-induced ALI onset and AST administration. Both the meta-analyses and our experimental data identified a total of 198 DEGs in response to LPS administration, and 11 core DEGs (Timp1, Ly6i, Cxcl13, Irf7, Cxcl5, Ccl7, Isg15, Saa3, Saa1, Tgtp1, and Gbp11) were identified to be associated with AST therapeutic effects. Further, the 11 core DEGs were verified by quantitative real-time PCR (qRT-PCR) and immunohistochemistry (IHC), and functional enrichment analysis revealed that these genes are primarily associated with neutrophils and chemokines. Collectively, these findings unearthed the robust genetic signatures underlying LPS administration and the molecular targets of AST for ameliorating ALI/ARDS which provide directions for further research. url: https://www.ncbi.nlm.nih.gov/pubmed/32969837/ doi: 10.18632/aging.104042 id: cord-024282-t5wl0bih author: Mao, Shunfu title: BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance date: 2020-02-01 words: 3451.0 sentences: 226.0 pages: flesch: 58.0 cache: ./cache/cord-024282-t5wl0bih.txt txt: ./txt/cord-024282-t5wl0bih.txt summary: title: BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance For example, RNA-Seq assembly tools typically require hyper-parameter tuning to achieve good performance for particular datasets. Results: Here we propose BOAssembler, a framework that enables end-to-end automatic tuning of RNA-Seq assemblers, based on Bayesian Optimization principles. The reference-based assembler together with its performance evaluation can be represented as an abstract function f (D, θ), where D includes both the read alignments used for assembly and the reference transcriptome (a set of ground truth RNA transcripts) used for evaluation, and θ refers to the parameters of f . After read alignments are assembled with given parameter θ, the assembly output (a set of RNA transcripts) will be compared with the reference transcriptome, and the quality of assembly is measured by scalar metrics such as precision p and sensitivity s. abstract: High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult task. For example, RNA-Seq assembly tools typically require hyper-parameter tuning to achieve good performance for particular datasets. This kind of tuning is usually unintuitive and time-consuming. Consequently, users often resort to default parameters, which do not guarantee consistent good performance for various datasets. Results: Here we propose BOAssembler, a framework that enables end-to-end automatic tuning of RNA-Seq assemblers, based on Bayesian Optimization principles. Experiments show this data-driven approach is effective to improve the overall assembly performance. The approach would be helpful for downstream (e.g. gene, protein, cell) analysis, and more broadly, for future bioinformatics benchmark studies. Availability: https://github.com/shunfumao/boassembler. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197064/ doi: 10.1007/978-3-030-42266-0_15 id: cord-288701-nx9fg4yn author: Mari, Viviana title: Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus date: 2015-12-17 words: 4827.0 sentences: 227.0 pages: flesch: 53.0 cache: ./cache/cord-288701-nx9fg4yn.txt txt: ./txt/cord-288701-nx9fg4yn.txt summary: The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. To overcome these limitations, we have developed a multiplex real-time RT-PCR assay for simultaneous detection of the different species of bovine pestiviruses, including the emerging HoBi-like group, allowing a rapid, sensitive and specific diagnosis of pestivirus infection and characterisation of the viral species. abstract: HoBi-like pestiviruses are emerging pestiviruses that infect cattle causing clinical forms overlapping to those induced by bovine viral diarrhea virus (BVDV) 1 and 2. As a consequence of their widespread distribution reported in recent years, molecular tools for rapid discrimination among pestiviruses infecting cattle are needed. The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. The assay was found to be sensitive, specific and repeatable, ensuring detection of as few as 10(0)–10(1) viral RNA copies. No cross-reactions between different pestiviral species were observed even in samples artificially contaminated with more than one pestivirus. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. url: https://api.elsevier.com/content/article/pii/S0166093415003870 doi: 10.1016/j.jviromet.2015.12.003 id: cord-353576-f29kmtot author: Maricic, T. title: A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 date: 2020-06-26 words: 3499.0 sentences: 200.0 pages: flesch: 60.0 cache: ./cache/cord-353576-f29kmtot.txt txt: ./txt/cord-353576-f29kmtot.txt summary: We then tested 1 l of mouthwash from each of the 20 individuals using two RT-qPCR kits advertised to allow direct detection of SARS-CoV-2 from nasopharyngeal swabs: Luna Universal Probe (NEB, Ipswich, USA) and PrimeDirect (Takara, Kyoto, Japan) as well as another kit, SuperScript III with Platinum Taq (Invitrogen, Waltham, USA). To systematically investigate how the NEB Luna assay performs compared to RNA extraction followed by the Roche assay for mouthwash samples, we investigated 62 gargle lavages from patients that were either negative or presented with various viral loads based on previous investigations. In the first scheme, the samples were tested individually using the direct RT-qPCR protocol and the results were evaluated and reported back to the facility by 7 p.m. To detect any inhibition that the mouthwash samples may introduce into the RT-qPCR reactions, we added a synthesized control RNA that was quantified in parallel with SARS-CoV-2 by a probe . abstract: SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast approach to detect SARS-CoV-2 in single or pooled gargle lavages ('mouthwashes'). With this approach, we test all staff at a nursing home daily over a period of three weeks in order to reduce the risk that the infection penetrates the facility. This or similar approaches could be implemented to protect hospitals, nursing homes and other institutions in this and future viral epidemics. url: https://doi.org/10.1101/2020.06.24.20139501 doi: 10.1101/2020.06.24.20139501 id: cord-325736-gs9d8y55 author: Marin, J title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma date: 2000-07-31 words: 1874.0 sentences: 135.0 pages: flesch: 61.0 cache: ./cache/cord-325736-gs9d8y55.txt txt: ./txt/cord-325736-gs9d8y55.txt summary: title: Persistence of Viruses in Upper Respiratory Tract of Children with Asthma Conclusions: The persistent presence of viruses in the upper respiratory tract of asthmatic children shows a possible connection between viral infections and asthma. 4 In this study nasopharyngeal swabs were taken from asthmatic children whose asthma was well controlled, and when they were at least 3 weeks free of any respiratory infections. The samples were examined for the presence of adenovirus DNA and rhinovirus and coronavirus RNA. Five microlitres of c-DNA product were subsequently amplified in 50µl PCR reaction mixture consisting of 10 reaction buffer, 25 mM MgCl 2 , 20 mM dNTP, 5 U/l of DNA Taq polymerase (all reagents provided by Perkin Elmer, New Jersey, USA) and 50 µM of each specific primer for rhinoviruses and coronaviruses (TIB MOLBIOL, Berlin, Germany) (Table I) . found that upper respiratory tract viruses were associated with over 80% of asthma exacerbations in children. abstract: Abstract Objectives: Nasopharyngeal swabs of 50 asthmatic children in the symptom-free period were examined for the presence of adenoviruses, rhinoviruses and coronaviruses. A control group of 20 healthy individuals was included in this study. Methods: A polymerase chain reaction was used to detect adenovirus DNA and rhinovirus and coronavirus complementary DNA. The fragments of amplified genetic material were visualized with the use of agarose gel electrophoresis. Results: Adenovirus DNA was found in 78.4% of asthmatic children, rhinovirus RNA in 32.4% and coronavirus RNA in 2.7%. Adenovirus DNA was detected in one of the 20 nasopharyngeal swabs of healthy controls; the rest of the control samples were negative. Conclusions: The persistent presence of viruses in the upper respiratory tract of asthmatic children shows a possible connection between viral infections and asthma. url: https://www.ncbi.nlm.nih.gov/pubmed/10942643/ doi: 10.1053/jinf.2000.0688 id: cord-270143-muxrxvyo author: Markotter, Wanda title: Paramyxo- and Coronaviruses in Rwandan Bats date: 2019-07-02 words: 4897.0 sentences: 254.0 pages: flesch: 49.0 cache: ./cache/cord-270143-muxrxvyo.txt txt: ./txt/cord-270143-muxrxvyo.txt summary: A high diversity of coronaand paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of coronaand paramyxoviral RNA using reverse transcription PCR assays. Although several surveillance studies have been implemented to detect potential zoonotic viruses in bats, including from countries in the Congo basin and East Africa, limited information is available for Rwanda. Confirmation of species identification of bats, in which viral RNA was detected, was performed by amplifying the cytochrome b (cyt b) or cytochrome oxidase one (COI) gene region and determining the DNA sequence. aegyptiacus-derived viral sequence (BatPV/Rou_aeg/UP438/RWA/2008) grouped within a Henipavirus-related clade and was near identical to a paramyxoviral sequence detected in the same host species previously reported from Kenya [36] . abstract: A high diversity of corona- and paramyxoviruses have been detected in different bat species at study sites worldwide, including Africa, however no biosurveillance studies from Rwanda have been reported. In this study, samples from bats collected from caves in Ruhengeri, Rwanda, were tested for the presence of corona- and paramyxoviral RNA using reverse transcription PCR assays. Positive results were further characterized by DNA sequencing and phylogenetic analysis. In addition to morphological identification of bat species, we also did molecular confirmation of species identities, contributing to the known genetic database available for African bat species. We detected a novel Betacoronavirus in two Geoffroy’s horseshoe bats (Rhinolophus clivosus) bats. We also detected several different paramyxoviral species from various insectivorous bats. One of these viral species was found to be homologous to the genomes of viruses belonging to the Jeilongvirus genus. Additionally, a Henipavirus-related sequence was detected in an Egyptian rousette fruit bat (Rousettus aegyptiacus). These results expand on the known diversity of corona- and paramyxoviruses and their geographical distribution in Africa. url: https://doi.org/10.3390/tropicalmed4030099 doi: 10.3390/tropicalmed4030099 id: cord-000729-iq30z094 author: Marsh, Glenn A. title: Cedar Virus: A Novel Henipavirus Isolated from Australian Bats date: 2012-08-02 words: 6101.0 sentences: 277.0 pages: flesch: 49.0 cache: ./cache/cord-000729-iq30z094.txt txt: ./txt/cord-000729-iq30z094.txt summary: The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrinB2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. As part of our on-going field studies on HeV genetic diversity and infection dynamics in the Queensland flying fox populations, urine samples were collected on a regular basis for PCR and virus isolation. CedPV is more closely related to HeV and NiV than henipavirus-like sequences detected in African bats [26, 32] as shown in a phylogenetic tree based on the only sequences available of a 550-nt L gene fragment (Fig. S5) . abstract: The genus Henipavirus in the family Paramyxoviridae contains two viruses, Hendra virus (HeV) and Nipah virus (NiV) for which pteropid bats act as the main natural reservoir. Each virus also causes serious and commonly lethal infection of people as well as various species of domestic animals, however little is known about the associated mechanisms of pathogenesis. Here, we report the isolation and characterization of a new paramyxovirus from pteropid bats, Cedar virus (CedPV), which shares significant features with the known henipaviruses. The genome size (18,162 nt) and organization of CedPV is very similar to that of HeV and NiV; its nucleocapsid protein displays antigenic cross-reactivity with henipaviruses; and it uses the same receptor molecule (ephrin- B2) for entry during infection. Preliminary challenge studies with CedPV in ferrets and guinea pigs, both susceptible to infection and disease with known henipaviruses, confirmed virus replication and production of neutralizing antibodies although clinical disease was not observed. In this context, it is interesting to note that the major genetic difference between CedPV and HeV or NiV lies within the coding strategy of the P gene, which is known to play an important role in evading the host innate immune system. Unlike HeV, NiV, and almost all known paramyxoviruses, the CedPV P gene lacks both RNA editing and also the coding capacity for the highly conserved V protein. Preliminary study indicated that CedPV infection of human cells induces a more robust IFN-β response than HeV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3410871/ doi: 10.1371/journal.ppat.1002836 id: cord-006068-w3if1hns author: Marshak-Rothstein, Ann title: Toll-like receptors in systemic autoimmune disease date: 2006 words: 10093.0 sentences: 442.0 pages: flesch: 41.0 cache: ./cache/cord-006068-w3if1hns.txt txt: ./txt/cord-006068-w3if1hns.txt summary: This Review summarizes recent in vitro and in vivo studies that point to an important connection between DNA-and RNA-containing immune complexes, the production of type I interferons (IFNs; that is, IFNα and IFNβ), the activation of TLRs and subsequent events in the development and/or the progression of systemic autoimmune diseases. . b | IFNα upregulates expression of Toll-like receptor 7 (TLR7) by B cells, promotes cell death and increased release of certain RNA autoantigens, and primes pDCs to respond more effectively to immune complexes. A limited number of studies have now provided data consistent with the idea that TLR7 and TLR9 have key roles in the production of pathogenic autoantibodies and/or in the development of clinical features of autoimmunity in experimental animals ( Mice that are homozygous for the lpr mutation do not express a functional form of the death receptor CD95 (also known as FAS), and they develop a lymphoproliferative disease that is similar to Canale-Smith syndrome in humans. abstract: Toll-like receptors (TLRs) have a crucial role in the early detection of pathogen-associated molecular patterns and the subsequent activation of the adaptive immune response. Whether TLRs also have an important role in the recognition of endogenous ligands has been more controversial. Numerous in vitro studies have documented activation of both autoreactive B cells and plasmacytoid dendritic cells by mammalian TLR ligands. The issue of whether these in vitro observations translate to an in vivo role for TLRs in either the initiation or the progression of systemic autoimmune disease is a subject of intense research; data are beginning to emerge showing that this is the case. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097510/ doi: 10.1038/nri1957 id: cord-016108-jlono0x7 author: Marthaler, Douglas title: Next-Generation Sequencing for Porcine Coronaviruses date: 2015-09-10 words: 1439.0 sentences: 97.0 pages: flesch: 57.0 cache: ./cache/cord-016108-jlono0x7.txt txt: ./txt/cord-016108-jlono0x7.txt summary: In this chapter, we describe a method to deep genome sequence porcine coronavirus on the Illumina MiSeq, avoiding the number of contaminating reads associated with the host and other microorganisms. (e) Remap the reads to the contig to verify accurate generation of the viral genome and suffi cient coverage. (a) Open the SeqManNGen program, select reference-based assembly, and load the Susscrofa genome and the correlating paired fastq fi les to the sample. However, the concentration by RT-PCR may not indicate successful generation of the complete viral genome since total RNA was used in the library preparation. If libraries have limited host contamination and have an acceptable concentration of viral RNA (Ct value <25), a 1 million read output per sample should be suffi cient for assembly. Since the MiSeq generates reads from total RNA, host reads need to be removed to facilitate de novo assembly, which can be done by fi rst mapping the reads to the swine genome and saving the unmapped reads. abstract: The outbreak of porcine epidemic diarrhea virus and the discovery of porcine deltacoronavirus in the USA have led to multiple questions about the evolution of coronaviruses in swine. Coronaviruses are enveloped virus, containing a positive-sense single-stranded RNA genome (26–30 kb) that can cause respiratory or enteric illness in swine. With current technologies, the complete viral genomes can be determined to understand viral diversity and evolution. In this chapter, we describe a method to deep genome sequence porcine coronavirus on the Illumina MiSeq, avoiding the number of contaminating reads associated with the host and other microorganisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120291/ doi: 10.1007/978-1-4939-3414-0_19 id: cord-312688-12san3m7 author: Martin, Baptiste title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry date: 2016-09-14 words: 10226.0 sentences: 530.0 pages: flesch: 50.0 cache: ./cache/cord-312688-12san3m7.txt txt: ./txt/cord-312688-12san3m7.txt summary: title: Filovirus proteins for antiviral drug discovery: A structure/function analysis of surface glycoproteins and virus entry After replication of the viral genome and RNA transcription, nascent viral particles are assembled in a process mediated by the matrix protein VP40, and virus budding occurs at the cell surface membrane in a process that involves hijacking the host ESCRT machinery (Hartlieb and Weissenhorn, 2006; Noda et al., 2006) . However, no direct interaction between both molecules has been demonstrated yet, and recent studies suggest that a 5 b 1 -integrin is not required for GP-mediated binding of internalization, but rather is a positive regulator of cathepsins, which play an important role in processing GP 1 into its fusion-competent form within the endosomes of infected cells (Schornberg et al., 2009) . After attachment mediated by interaction between the filovirus surface protein GP 1,2 (PDB: 3CSY) and various attachment factors, the complex is internalized and routed to the endosome, where GP 1,2 is processed to trigger fusion of viral and host membranes. abstract: This review focuses on the recent progress in our understanding of filovirus protein structure/function and its impact on antiviral research. Here we focus on the surface glycoprotein GP(1,2) and its different roles in filovirus entry. We first describe the latest advances on the characterization of GP gene-overlapping proteins sGP, ssGP and Δ-peptide. Then, we compare filovirus surface GP(1,2) proteins in terms of structure, synthesis and function. As they bear potential in drug-design, the discovery of small organic compounds inhibiting filovirus entry is a currently very active field. Although it is at an early stage, the development of antiviral drugs against Ebola and Marburg virus entry might prove essential to reduce outbreak-associated fatality rates through post-exposure treatment of both suspected and confirmed cases. url: https://api.elsevier.com/content/article/pii/S0166354216304077 doi: 10.1016/j.antiviral.2016.09.001 id: cord-286343-s8n1ldol author: Martin, Javier title: Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic date: 2020-10-09 words: 5925.0 sentences: 340.0 pages: flesch: 53.0 cache: ./cache/cord-286343-s8n1ldol.txt txt: ./txt/cord-286343-s8n1ldol.txt summary: We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory. However, it was clear that there was a large reduction of SARS-CoV-2 RNA concentration in sewage between 14th April and 12th May. Positive and negative results were independently confirmed using a second real-time PCR platform (Stratagene 3000P) in a different NIBSC laboratory (data not shown). abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease (COVID-19) pandemic, is frequently shed in faeces during infection, and viral RNA has recently been detected in sewage in some countries. We have investigated the presence of SARS-CoV-2 RNA in wastewater samples from South-East England between 14th January and 12th May 2020. A novel nested RT-PCR approach targeting five different regions of the viral genome improved the sensitivity of RT-qPCR assays and generated nucleotide sequences at sites with known sequence polymorphisms among SARS-CoV-2 isolates. We were able to detect co-circulating virus variants, some specifically prevalent in England, and to identify changes in viral RNA sequences with time consistent with the recently reported increasing global dominance of Spike protein G614 pandemic variant. Low levels of viral RNA were detected in a sample from 11th February, 3 days before the first case was reported in the sewage plant catchment area. SARS-CoV-2 RNA concentration increased in March and April, and a sharp reduction was observed in May, showing the effects of lockdown measures. We conclude that viral RNA sequences found in sewage closely resemble those from clinical samples and that environmental surveillance can be used to monitor SARS-CoV-2 transmission, tracing virus variants and detecting virus importations. url: https://www.ncbi.nlm.nih.gov/pubmed/33050264/ doi: 10.3390/v12101144 id: cord-300489-gzcb6uqw author: Martinez, Mitzi L. title: Detection of feline infectious peritonitis virus infection in cell cultures and peripheral blood mononuclear leukocytes of experimentally infected cats using a biotinylated cDNA probe date: 1993-03-31 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Abstract A dot blot hybridization assay, using a biotinylated cDNA probe, was able to detect feline infectious peritonitis virus (FIPV) RNA in Felis catus whole fetus (fcwf-4) cells infected with the FIPV isolates DF2, 79-1146, UCDI, and UCD2. The probe cross-hybridized in the dot blot assay with nucleic acid of a closely related feline coronavirus, feline enteric coronavirus (FECV)-79-1683. To construct the probe, a 2.5 kilobase cDNA, prepared from FIPV-DF2 genomic RNA, was molecularly cloned. The recombinant cDNA clone was digested with the restriction endonuclease Rsa I, and an 870 basepair Rsa I fragment was isolated from vector DNA by agarose electrophoresis and glassmilk purification. This fragment was complementary to the 3′ three fourths of the nucleocapsid gene. The hybridization probe was prepared by random primed labeling in the presence of biotin-11-dUTP. Using an avidin-alkaline phosphatase conjugate and chemiluminescent substrate detection system, virus could be detected in as few as 3000 infected cells. In an in vivo study, the probe was used to detect FIPV RNA in peripheral blood mononuclear leukocytes (PBML) isolated at various post-infection days (PID) from cats experimentally infected with the FIP-producing coronavirus isolate FIPV-79-1146 or FIPV-DF2. Viral RNA could be detected in as few as 12 000 PBML isolated from cats at PID 7 and in 50 000 PBML at PID 22. There was no consistent pattern, however, between hybridization results and prognosis or severity of disease at the time of sampling. Despite some cross-hybridization with FECV RNA, this probe should be useful for diagnosis of FIP, because cats infected with FECV most likely do not become viremic. url: https://www.sciencedirect.com/science/article/pii/037811359390016Z doi: 10.1016/0378-1135(93)90016-z id: cord-291225-75ys908n author: Martins, Nelson title: A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells date: 2018-12-12 words: 5964.0 sentences: 366.0 pages: flesch: 51.0 cache: ./cache/cord-291225-75ys908n.txt txt: ./txt/cord-291225-75ys908n.txt summary: title: A Transgenic Flock House Virus Replicon Reveals an RNAi Independent Antiviral Mechanism Acting in Drosophila Follicular Somatic Cells Here we describe transgenic Drosophila melanogaster lines encoding a Flock House Virus-derived replicon (FHV∆B2eGFP), expressing GFP as a reporter of viral replication. This replicon is efficiently controlled by the siRNA pathway in most somatic tissues, with GFP fluorescence providing a reliable marker for the activity of antiviral RNAi. Interestingly, in follicular somatic cells (FSC) of ovaries, this replicon is still partially repressed in an siRNA independent manner. We did not detect replicon derived Piwi-interacting RNAs in FSCs and identified 31 differentially expressed genes between restrictive and permissive FSCs. Altogether, our results uncovered a yet unidentified RNAi-independent mechanism controlling FHV replication in FSCs of ovaries and validate the FHV∆B2eGFP replicon as a tool to screen for novel tissue specific antiviral mechanisms. abstract: The small interfering RNA (siRNA) pathway is the main and best studied invertebrate antiviral response. Other poorly characterized protein based antiviral mechanisms also contribute to the control of viral replication in insects. In addition, it remains unclear whether tissue specific factors contribute to RNA and protein-based antiviral immunity mechanisms. In vivo screens to identify such factors are challenging and time consuming. In addition, the scored phenotype is usually limited to survival and/or viral load. Transgenic viral replicons are valuable tools to overcome these limitations and screen for novel antiviral factors. Here we describe transgenic Drosophila melanogaster lines encoding a Flock House Virus-derived replicon (FHV∆B2eGFP), expressing GFP as a reporter of viral replication. This replicon is efficiently controlled by the siRNA pathway in most somatic tissues, with GFP fluorescence providing a reliable marker for the activity of antiviral RNAi. Interestingly, in follicular somatic cells (FSC) of ovaries, this replicon is still partially repressed in an siRNA independent manner. We did not detect replicon derived Piwi-interacting RNAs in FSCs and identified 31 differentially expressed genes between restrictive and permissive FSCs. Altogether, our results uncovered a yet unidentified RNAi-independent mechanism controlling FHV replication in FSCs of ovaries and validate the FHV∆B2eGFP replicon as a tool to screen for novel tissue specific antiviral mechanisms. url: https://www.ncbi.nlm.nih.gov/pubmed/30530643/ doi: 10.1534/g3.118.200872 id: cord-263315-g7os15m1 author: Martins-da-Silva, Andrea title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response date: 2018-01-18 words: 6975.0 sentences: 460.0 pages: flesch: 48.0 cache: ./cache/cord-263315-g7os15m1.txt txt: ./txt/cord-263315-g7os15m1.txt summary: title: Identification of Secreted Proteins Involved in Nonspecific dsRNA-Mediated Lutzomyia longipalpis LL5 Cell Antiviral Response The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. In human and mouse plasmacytoid dendritic cells (pDCs), which are professional interferon-producing cells specialized in recognizing viral RNA and DNA through the endosomal Toll-like receptors (TLRs) TLR7 and TLR9, respectively, PLSCR1 was described as a TLR9-binding protein that plays a significant role in type-1 interferon responses in pDCs by regulating TLR9 expression and trafficking [57] . Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. Binding of FKBP51 to TRAF proteins facilitates the type-I interferon response induced by dsRNA transfection or Newcastle disease virus (NDV) infection in murine fibroblasts. abstract: Hematophagous insects transmit infectious diseases. Sand flies are vectors of leishmaniasis, but can also transmit viruses. We have been studying immune responses of Lutzomyia longipalpis, the main vector of visceral leishmaniasis in the Americas. We identified a non-specific antiviral response in L. longipalpis LL5 embryonic cells when treated with non-specific double-stranded RNAs (dsRNAs). This response is reminiscent of interferon response in mammals. We are investigating putative effectors for this antiviral response. Secreted molecules have been implicated in immune responses, including interferon-related responses. We conducted a mass spectrometry analysis of conditioned medium from LL5 cells 24 and 48 h after dsRNA or mock treatment. We identified 304 proteins. At 24 h, 19 proteins had an abundance equal or greater than 2-fold change, while the levels of 17 proteins were reduced when compared to control cells. At the 48 h time point, these numbers were 33 and 71, respectively. The two most abundant secreted peptides at 24 h in the dsRNA-transfected group were phospholipid scramblase, an interferon-inducible protein that mediates antiviral activity, and forskolin-binding protein (FKBP), a member of the immunophilin family, which mediates the effect of immunosuppressive drugs. The transcription profile of most candidates did not follow the pattern of secreted protein abundance. url: https://www.ncbi.nlm.nih.gov/pubmed/29346269/ doi: 10.3390/v10010043 id: cord-347992-coby2m6e author: Marton, Soledad title: In Vitro and Ex Vivo Selection Procedures for Identifying Potentially Therapeutic DNA and RNA Molecules date: 2010-06-28 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: It was only relatively recently discovered that nucleic acids participate in a variety of biological functions, besides the storage and transmission of genetic information. Quite apart from the nucleotide sequence, it is now clear that the structure of a nucleic acid plays an essential role in its functionality, enabling catalysis and specific binding reactions. In vitro selection and evolution strategies have been extremely useful in the analysis of functional RNA and DNA molecules, helping to expand our knowledge of their functional repertoire and to identify and optimize DNA and RNA molecules with potential therapeutic and diagnostic applications. The great progress made in this field has prompted the development of ex vivo methods for selecting functional nucleic acids in the cellular environment. This review summarizes the most important and most recent applications of in vitro and ex vivo selection strategies aimed at exploring the therapeutic potential of nucleic acids. url: https://www.ncbi.nlm.nih.gov/pubmed/20657381/ doi: 10.3390/molecules15074610 id: cord-263699-gosqpg3k author: Martínez, José L. title: Role of the Guanine Nucleotide Exchange Factor GBF1 in the Replication of RNA Viruses date: 2020-06-24 words: 12329.0 sentences: 463.0 pages: flesch: 42.0 cache: ./cache/cord-263699-gosqpg3k.txt txt: ./txt/cord-263699-gosqpg3k.txt summary: GBF1 has been shown not only to facilitate the intracellular traffic of different viral and cellular elements during infection, but also to modulate the replication of viral RNA, the formation and maturation of viral replication complexes, and the processing of viral proteins through mechanisms that do not depend on its canonical role in intracellular transport. In addition to the role of GBF1 in the transport of cellular and viral proteins relevant for RNA replication and viral assembly, it has also been observed that this factor can regulate the lipid composition of the membranous web induced by HCV. The role of GBF1 has been found, principally, to depend on its ability to activate distinct Arf proteins, to regulate different transport pathways that permit the communication between the viral replication organelles and cellular organelles (ER and LDs) involved in virus infection. abstract: The guanine nucleotide exchange factor GBF1 is a well-known factor that can activate different ADP-ribosylation factor (Arf) proteins during the regulation of different cellular vesicular transport processes. In the last decade, it has become increasingly evident that GBF1 can also regulate different steps of the replication cycle of RNA viruses belonging to different virus families. GBF1 has been shown not only to facilitate the intracellular traffic of different viral and cellular elements during infection, but also to modulate the replication of viral RNA, the formation and maturation of viral replication complexes, and the processing of viral proteins through mechanisms that do not depend on its canonical role in intracellular transport. Here, we review the various roles that GBF1 plays during the replication of different RNA viruses. url: https://doi.org/10.3390/v12060682 doi: 10.3390/v12060682 id: cord-263157-8jin6oru author: Martínez, Miguel Angel title: Progress in the Therapeutic Applications of siRNAs Against HIV-1 date: 2008-10-13 words: 9234.0 sentences: 466.0 pages: flesch: 45.0 cache: ./cache/cord-263157-8jin6oru.txt txt: ./txt/cord-263157-8jin6oru.txt summary: Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Importantly, this study made the extraordinary demonstration that cell transfection of synthetic 21 base pairs (bp) short interfering RNA (siRNA) duplexes can mediate RNAi in a sequence-specific manner; this finding enabled the specific regulation of gene expression in a variety of biological systems, including diseased cells. Soon after the demonstration that synthetic siRNAs were able to induce the RNAi mechanism in mammalian cells (15) , several studies reported that HIV-1 gene expression and replication ex vivo could be inhibited by virus-specific synthetic siR-NAs (16 22) or expressed siRNAs (16, 18) that were targeted to early or late phases of virus replication. To counteract this strategic weakness, co-expression of multiple siRNAs or shRNAs that target conserved RNA sequences could reduce the emergence of single siRNA-resistant virus with a comparable effect to that achieved by the multiple anti-HIV drug combination approach employed by HAART. abstract: Therapeutic options against the human immunodeficiency virus type 1 (HIV-1) continue to expand with the development of new drugs and new therapeutic strategies. Nevertheless, management of HIV-1 infected individuals has become increasingly complex. The emergence of drug-resistant variants, the growing recognition of the long-term toxicity of antiretroviral therapies and the persistence of viral reservoirs justify the continued efforts to develop new anti-HIV-1 strategies. Recent advances regarding the utility of RNA-mediated interference (RNAi) to specifically inhibit HIV-1 replication have opened new possibilities for the development of gene-based therapies against HIV-1 infection. Here, the recent advances in siRNA-based therapies are reviewed. url: https://www.ncbi.nlm.nih.gov/pubmed/19301656/ doi: 10.1007/978-1-60327-547-7_17 id: cord-341342-kyavg4vu author: Masters, P. S. title: Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus date: 1992 words: 5901.0 sentences: 279.0 pages: flesch: 57.0 cache: ./cache/cord-341342-kyavg4vu.txt txt: ./txt/cord-341342-kyavg4vu.txt summary: The RNase sensitivity of the ability of N protein to migrate into nondenaturing gels was not due to possible contaminating protease activity in the RNase preparations, since the same RNase-treated samples of translated N 148 P.S. Masters protein showed no degradation when analyzed by SDS-PAGE (Fig. 3, lanes an, lower) . Since the N mRNAs synthesized from the transcription vectors shown in Fig. 1 contained this portion of the leader sequence, it seemed possible that the N-RNA complex observed in nondenaturing PAGE was that of translated N protein binding to its own mRNA. That the observed complex was not due to translated N protein binding to the leader portion of its own mRNA was also supported by the observation that full-length N protein translated from a construct in which the MHV leader sequence was entirely deleted was also able to migrate into nondenaturing gels (data not shown). abstract: The interaction between the nucleocapsid (N) protein of mouse hepatitis virus (MHV) and RNA was studied in an effort to define portions of the N molecule that participate in binding to RNA. N mRNAs transcribed from SP6 and T7 vectors were translated in a rabbit reticulocyte lysate. Analysis of synthesized N protein in a nondenaturing gel system showed that it bound in vitro to an endogenous RNA in the reticulocyte lysate but not to its own mRNA. A set of deletion mutants was constructed in order to localize the RNA-binding activity of the N protein. It was found that removal of as much as 135 amino-terminal or 57 carboxy-terminal amino acids from the molecule had little or no effect on RNA binding. Moreover, deletion mutants lacking both termini still retained RNA-binding ability. By contrast, internal deletions or truncations extending beyond these two limits effectively abolished RNA binding by N protein. Thus, the RNA-binding region of N has been mapped to the second (central) of the three structural domains of the molecule. url: https://www.ncbi.nlm.nih.gov/pubmed/1322650/ doi: 10.1007/bf01309634 id: cord-002320-m99amd4y author: Mathur, Kalika title: Analysis of chikungunya virus proteins reveals that non-structural proteins nsP2 and nsP3 exhibit RNA interference (RNAi) suppressor activity date: 2016-11-30 words: 5671.0 sentences: 338.0 pages: flesch: 56.0 cache: ./cache/cord-002320-m99amd4y.txt txt: ./txt/cord-002320-m99amd4y.txt summary: Systematic analysis of all CHIKV proteins using a Sf21 RNAi sensor cell line based assay revealed that non-structural proteins nsP2 and nsP3 exhibited RNAi suppressor activity. Using cell lysate of the transfected cell expressing nsP2 and nsP3, we evaluated their ability to bind double stranded RNA by using [γ 32P] labeled shRNA of GFP and running the bound complex in a 6% polyacrylamide gel (Fig. 3e) . Having confirmed that both nsP2 and nsP3 exhibit RNAi suppressor activities, efforts were taken to characterise the proteins better and to identify those specific domains that were and NS4B (dengue virus) were taken as positive controls and empty vector was used as negative control. Taken together, the current study has identified CHIKV proteins nsP2 and nsP3 to exhibit RNAi suppressor activity in the in-vitro system that was further demonstrated in its natural hosts, namely, an Aedes and mammalian cell line. abstract: RNAi pathway is an antiviral defence mechanism employed by insects that result in degradation of viral RNA thereby curbing infection. Several viruses including flaviviruses encode viral suppressors of RNAi (VSRs) to counteract the antiviral RNAi pathway. Till date, no VSR has been reported in alphaviruses. The present study was undertaken to evaluate chikungunya virus (CHIKV) proteins for RNAi suppressor activity. We systematically analyzed all nine CHIKV proteins for RNAi suppressor activity using Sf21 RNAi sensor cell line based assay. Two non-structural proteins, namely, nsP2 and nsP3 were found to exhibit RNAi suppressor activity. We further validated the findings in natural hosts, namely in Aedes and in mammalian cell lines and further through EMSA and Agrobacterium infiltration in GFP silenced transgenic tobacco plants. Domains responsible for maximum RNAi suppressor activity were also identified within these proteins. RNA binding motifs in these domains were identified and their participation in RNAi suppression evaluated using site directed mutagenesis. Sequence alignment of these motifs across all species of known alphaviruses revealed conservation of these motifs emphasizing on a similar role of action in other species of alphaviruses as well. Further validation of RNAi suppressor activity of these proteins awaits establishment of specific virus infection models. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5128919/ doi: 10.1038/srep38065 id: cord-010161-bcuec2fz author: Matson, David O. title: IV, 6. Calicivirus RNA recombination date: 2004-09-14 words: 3335.0 sentences: 168.0 pages: flesch: 45.0 cache: ./cache/cord-010161-bcuec2fz.txt txt: ./txt/cord-010161-bcuec2fz.txt summary: With the description of statistically significant phylogenetic clades within CV genera, data were available to recognize strains that might be natural recombinants within CVs. Two examples are the well-characterized Argentine strain 320 (Arg320) and Snow Mountain virus (SMV), one of the prototype CVs, recognized to be recombinants when the RNA polymerase and capsid regions of these strains were characterized (Hardy et al., 1997; Jiang et al., 1999) (Fig. 2) . While SMV was likely also to be a recombinant virus, the capsid and RNA polymerase region amplicons of SMV were generated separately and that fact did not exclude the possibility of different sources of strains. Infection of single cells simultaneously by two CVs implies absence of immune or molecular and of 40 nt near the 5'' end of that strain''s capsid gene (ID="B" sequence for this Fig.) . The sequence data indicated that recombination in strain Arg320 occurred at the ORF1/capsid gene junction where high sequence identity exists between the putative parent clades. abstract: RNA recombination apparently contributed to the evolution of CVs. Nucleic acid sequence homology or identity and similar RNA secondary structure of CVs and non-CVs may provide a locus for recombination within CVs or with non-CVs should co-infections of the same cell occur. Natural recombinants have been demonstrated among other enteric viruses, including Picornaviridae (Kirkegaard and Baltimore, 1986; Furione et al., 1993), Astroviridae (Walter et al., 2001), and possibly rotaviruses (e.g., Desselberger, 1996; Suzuki et al., 1998), augmenting the natural diversity of these pathogens and complicating viral gastroenteritis prevention strategies based upon traditional vaccines. Such is the case for CVs and Astroviridae, whose recombinant strains may be a common portion of naturally circulating strains. The taxonomic — and perhaps biologic — limits of recombination are defined by the suggested recombination of Nanovirus and CV, viruses from hosts of different biologic orders; the relationship of picornaviruses and CVs, viruses in different families, as recombination partners; and the intra-generic recombination between different clades of NLVs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172178/ doi: 10.1016/s0168-7069(03)09032-3 id: cord-016652-x8t3lf1x author: Matthews, David title: Viruses and the Nucleolus date: 2011-05-23 words: 6630.0 sentences: 348.0 pages: flesch: 33.0 cache: ./cache/cord-016652-x8t3lf1x.txt txt: ./txt/cord-016652-x8t3lf1x.txt summary: This process is crucial for virus biology because if the viral proteins that are required for cytoplasmic functions such as RNA synthesis and encapsidation are sequestered in the nucleolus or nucleus, then progeny virus production will be affected as has been revealed by inhibitor and genetic studies (Lee et al. Viruses may interact with the nucleolus to usurp host cell functions and recruit nucleolar proteins to facilitate virus replication. Initial studies utilising the prototype g-2 herpesvirus, herpes virus saimiri (HVS), demonstrated that the HVS nucleolar trafficking ORF57 protein induces nucleolar redistribution of the host cell human TREX proteins, which are involved in mRNA nuclear export (Boyne and Whitehouse 2006) . The localisation of porcine reproductive and respiratory syndrome virus nucleocapsid protein to the nucleolus of infected cells and identification of a potential nucleolar localization signal sequence Sequence requirements for nucleolar localization of human T cell leukemia virus type I pX protein, which regulates viral RNA processing abstract: The nucleolus is a dynamic sub-nuclear structure integral to the function of a eukaryotic cell. Some of its major roles involve ribosome subunit biogenesis, RNA processing, cell cycle control and responding to cellular stress, such as infection. Our understanding of the relationship between viruses and the nucleolus has moved from a phenomenological approach describing protein localisation to functional studies involving genetic analysis and proteomic approaches. These advances have provided fundamental insights as to how and why the nucleolus is targeted by many different viruses both to usurp normal functioning and to recruit nucleolar proteins to facilitate virus replication. This knowledge has been exploited for therapeutic strategies involving targeted inhibition of virus replication and live-attenuated recombinant vaccines. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121007/ doi: 10.1007/978-1-4614-0514-6_14 id: cord-103914-ppgx7mci author: Maughan, Elizabeth F. title: Cell-intrinsic differences between human airway epithelial cells from children and adults date: 2020-04-20 words: 8186.0 sentences: 419.0 pages: flesch: 47.0 cache: ./cache/cord-103914-ppgx7mci.txt txt: ./txt/cord-103914-ppgx7mci.txt summary: Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We found no significant differences in the proportion of cells in these three cellular compartments in paediatric and adult biopsies either by immunohistochemistry ( Figure 1A /1B), or by assessing basal, mucosecretory or ciliated cellassociated gene expression (Table S2 ) in bulk RNA sequencing in which we had laser-capture microdissected the whole epithelium ( Figure 1C ; Figure S1 ). Analysing this laser-capture microdissected whole epithelium RNA sequencing dataset using DESeq2 (Love et al., 2014) with a false discovery rate (FDR) of 1% and log2 fold change threshold of 1.2, we identified 37 genes with significant differential expression between paediatric and adult donors of which 17 were upregulated in adults and 20 were expressed at higher levels in children ( Figure 2A ; Table S3 ). abstract: The airway epithelium is a key protective barrier whose integrity is preserved by the self-renewal and differentiation of basal progenitor cells. Epithelial cells are central to the pathogenesis of multiple lung diseases. In chronic diseases, increasing age is a principle risk factor. In acute diseases, such as COVID-19, children suffer less severe symptoms than adults and have a lower rate of mortality. Few studies have explored differences between airway epithelial cells in children and adults to explain this age dependent variation in diseases. Here, we perform bulk RNA sequencing studies in laser-capture microdissected whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We find that, while the cellular composition of the paediatric and adult tracheobronchial epithelium is broadly similar, in cell culture, paediatric airway epithelial cells displayed higher colony forming ability, better in vitro growth and outcompeted adult cells in competitive proliferation assays. In RNA sequencing experiments, we observed potentially important differences in airway epithelial gene expression between samples from children and adults. However, genes known to be associated with SARS-CoV-2 infection were not differentially expressed between children and adults. Our results chart cell-intrinsic differences in transcriptional profile and regenerative capacity between proximal airway epithelial cells of children and adults. url: https://doi.org/10.1101/2020.04.20.027144 doi: 10.1101/2020.04.20.027144 id: cord-017181-ywz6w2po author: Maus, Carsten title: Component-Based Modelling of RNA Structure Folding date: 2008 words: 5364.0 sentences: 284.0 pages: flesch: 51.0 cache: ./cache/cord-017181-ywz6w2po.txt txt: ./txt/cord-017181-ywz6w2po.txt summary: As this regulating process depends largely on structure formation, modelling of RNA folding would be a big step in the right direction for reflecting attenuation dynamics. Additionally, modelling interactions between mRNA and RNAP as well as mRNA and the ribosome are needed because both influence the kinetic folding process and RNA termination structures break up gene transcription. If observed structures are present during folding simulation, the macro level model can signalise this information and thus trigger dynamics to other components by adding new ports to itself (representing docking sites) or send messages over existing ports. Simulating the RNA folding with Kinfold [12] results in a five times higher amount of the 2-helix conformation than the single hairpin, but their total sum is about 60% of all molecules and thus less misfolded structures can be observed. The pattern observation function of the RNA folding model, which is realised at macro level, allows us to look for an intrinsic transcription termination structure [2] during simulation. abstract: RNA structure is fundamentally important for many biological processes. In the past decades, diverse structure prediction algorithms and tools were developed but due to missing descriptions in clearly defined modelling formalisms it’s difficult or even impossible to integrate them into larger system models. We present an RNA secondary structure folding model described in ml-Devs, a variant of the Devs formalism, which enables the hierarchical combination with other model components like RNA binding proteins. An example of transcriptional attenuation will be given where model components of RNA polymerase, the folding RNA molecule, and the translating ribosome play together in a composed dynamic model. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121681/ doi: 10.1007/978-3-540-88562-7_8 id: cord-265855-zf52vl11 author: Mayor-Ibarguren, Ander title: A Hypothesis for the Possible Role of Zinc in the Immunological Pathways Related to COVID-19 Infection date: 2020-07-10 words: 5324.0 sentences: 283.0 pages: flesch: 47.0 cache: ./cache/cord-265855-zf52vl11.txt txt: ./txt/cord-265855-zf52vl11.txt summary: Zinc deficiency may increase ACE-2 receptor activity on type 2 pneumocytes and other cells that are infected by SARS-COV-2, mainly in the lower respiratory tract. Although there are no specific data regarding zinc in this pathway for SARS-CoV-2, zinc may limit infection through upregulation of IFN-alpha production and an increase in its antiviral activity (77, 78) . Thus, patients with IL-6-174 GG polymorphism (C-carriers) may be susceptible to developing a severe infection due to SARS-CoV-2, leading to an increase in IL-6 levels that produce a cytokine storm related to impaired zinc homeostasis. We believe there is enough evidence to further investigate how zinc status or homeostasis is involved in the pathogenesis of severe illness produced by SARS-CoV-2 infection, and its potential role as an active treatment should be assessed in clinical trials. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32754165/ doi: 10.3389/fimmu.2020.01736 id: cord-321013-8pkrg0mx author: McBride, Ruth title: The Coronavirus Nucleocapsid Is a Multifunctional Protein date: 2014-08-07 words: 10761.0 sentences: 476.0 pages: flesch: 44.0 cache: ./cache/cord-321013-8pkrg0mx.txt txt: ./txt/cord-321013-8pkrg0mx.txt summary: The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The M protein is the main core shell component and a 16 amino acid domain (aa 237-252) on the CTD of M protein binds directly to N protein via an ionic interaction, leading to specific genome encapsidation in the budding viral particle [81] [82] [83] .The N protein therefore plays an essential structural role in the CoV virion through a network of interactions with (i) the genomic RNA; (ii) M protein and (iii) other N proteins. Amino acid residues critical for RNA-binding in the N-terminal domain of the nucleocapsid protein are essential determinants for the infectivity of coronavirus in cultured cells Structure of the SARS coronavirus nucleocapsid protein RNA-binding dimerization domain suggests a mechanism for helical packaging of viral RNA abstract: The coronavirus nucleocapsid (N) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. Recent studies have confirmed that N is a multifunctional protein. The aim of this review is to highlight the properties and functions of the N protein, with specific reference to (i) the topology; (ii) the intracellular localization and (iii) the functions of the protein. url: https://doi.org/10.3390/v6082991 doi: 10.3390/v6082991 id: cord-274353-tzlcpx7q author: McDermott, Amy title: Inner Workings: Molecular biologists offer “wartime service” in the effort to test for COVID-19 date: 2020-05-05 words: 1987.0 sentences: 99.0 pages: flesch: 46.0 cache: ./cache/cord-274353-tzlcpx7q.txt txt: ./txt/cord-274353-tzlcpx7q.txt summary: In order to legally perform diagnostic work on human samples in the United States, a lab needs certification from the Centers for Medicare & Medicaid Services, through its Clinical Laboratory Improvement Amendments (CLIA) program (2) . On March 12, for example, California Governor Gavin Newsom issued an executive order suspending certification and licensure requirements for any researcher with relevant skills who meets CLIA requirements to run the COVID-19 test; such a person may now temporarily run the assays under the supervision of a medical laboratory scientist in a CLIA-certified lab (4). To get around its limitations, UC Berkeley is temporarily extending the clinical lab''s CLIA certificate into the larger Innovative Genomics Institute on campus, and will staff it with volunteer researchers who have the relevant skills to run the assay, supervised by a licensed medical laboratory scientist. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/32295880/ doi: 10.1073/pnas.2006240117 id: cord-294138-h7sfd1wa author: McIver, David J. title: Coronavirus surveillance of wildlife in the Lao People’s Democratic Republic detects viral RNA in rodents date: 2020-06-01 words: 2780.0 sentences: 130.0 pages: flesch: 56.0 cache: ./cache/cord-294138-h7sfd1wa.txt txt: ./txt/cord-294138-h7sfd1wa.txt summary: Both countries were involved in the United States Agency for International Development''s (USAID) Emerging Pandemic Threats PREDICT program, and surveillance of bats in wildlife markets in rural areas in Laos using family-level PCR assays revealed the presence of CoV RNA in 41 animals [5] . Considering the significant interactions of wildlife and especially rodents with humans in Laos, we were interested in investigating the presence of CoVs in these animals, which can be primary or intermediate hosts for CoVs with zoonotic potential. Since there are abundant contact opportunities for wildlife pathogens and humans in Laos, and considering that coronavirus-zoonotic events can involve intermediate hosts, as in the cases of SARS and MERS, we focused our screening on non-bat species potentially capable of playing that role. It is worth noting that we targeted rodents most likely to be in contact with humans and transmit virus and found fewer CoV-RNA-positive animals than in other studies of rodents in the region or elsewhere. abstract: Coronaviruses can become zoonotic, as in the case of COVID-19, and hunting, sale, and consumption of wild animals in Southeast Asia increases the risk for such incidents. We sampled and tested rodents (851) and other mammals and found betacoronavirus RNA in 12 rodents. The sequences belong to two separate genetic clusters and are closely related to those of known rodent coronaviruses detected in the region and distantly related to those of human coronaviruses OC43 and HKU1. Considering the close human-wildlife contact with many species in and beyond the region, a better understanding of virus diversity is urgently needed for the mitigation of future risks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04683-7) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-020-04683-7 doi: 10.1007/s00705-020-04683-7 id: cord-017764-h1w9gbxk author: Meanwell, Nicholas A. title: The Discovery and Development of Daclatasvir: An Inhibitor of the Hepatitis C Virus NS5A Replication Complex date: 2018-06-08 words: 9250.0 sentences: 389.0 pages: flesch: 39.0 cache: ./cache/cord-017764-h1w9gbxk.txt txt: ./txt/cord-017764-h1w9gbxk.txt summary: A groundbreaking clinical trial that combined daclatasvir (1) with the protease inhibitor asunaprevir (52) established that a chronic HCV infection could be cured with small molecule therapy in the absence of immune stimulation, setting the stage for approval of this regimen for the treatment of GT-1b-infected subjects by the Japanese health authorities on July 4, 2014. The discovery of the hepatitis C virus (HCV) nonstructural 5A (NS5A) replication complex inhibitor daclatasvir (1) began with the development of a genotype 1b (GT-1b) replicon that was implemented as a phenotypic screen using a design that conferred a stringent triaging of hit molecules [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] . A screen of compounds selected from the library of HCV NS5A inhibitors assessed in the presence of 1 using the Tyr93Asn GT-1aresistant replicon, followed by SAR optimization, identified Syn-395 (52) as a molecule capable of restoring the sensitivity of resistant virus to the inhibitory effects of 1. Discovery of daclatasvir, a pan-genotypic hepatitis C virus NS5A replication complex inhibitor with potent clinical effect abstract: The discovery of the hepatitis C virus (HCV) NS5A replication inhibitor daclatasvir (1) had its origins in a phenotypic screening lead. However, during the optimization campaign, it was observed that some members of the chemotype underwent a radical dimerization under the assay conditions. This redirected the effort to focus on palindromic molecules, a species subsequently shown to complement the dimeric nature of the NS5A protein. The most challenging aspect of the discovery program was extending antiviral activity to encompass GT-1a virus which was accomplished only after the development of extensive structure-activity relationships. In clinical trials, oral administration of daclatasvir (1) produced a profound effect on viral load with onset that was more rapid than had been seen previously with either NS3 protease or NS5B polymerase inhibitors. A groundbreaking clinical trial that combined daclatasvir (1) with the protease inhibitor asunaprevir (52) established that a chronic HCV infection could be cured with small molecule therapy in the absence of immune stimulation, setting the stage for approval of this regimen for the treatment of GT-1b-infected subjects by the Japanese health authorities on July 4, 2014. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122418/ doi: 10.1007/7355_2018_47 id: cord-293646-d4qcckh1 author: Meanwell, Nicholas A. title: Chapter 22. Non-HIV antiviral agents date: 2003-12-31 words: 4178.0 sentences: 198.0 pages: flesch: 46.0 cache: ./cache/cord-293646-d4qcckh1.txt txt: ./txt/cord-293646-d4qcckh1.txt summary: The first small molecule inhibitor of Hepatitis C Virus (HCV), the NS3 protease inhibitor BILN-2061, entered phase 2 clinical trials, producing a striking reduction in viral load in treated individuals. Inhibitors of Hepatitis B Virus (HBV) -Adefovir dipivoxil iHepsera''") (1) was approved in the US for the treatment of HBV on September 20'', 2002 and in the European Union on March 1 lth, 2003, providing a second small molecule antiviral to add to lamivudine (3TC) and the injectable protein IFNa as the only approved agents for treating HBV infection. Pyridinedicarboxamide S represents the first report of a non-nucleoside inhibitor of HBV reverse transcriptase enantiomer of q is active in cell culture and appears to prevent proper formation of the viral nucleocapsrd. A significant advance towards establishing a correlation between replicon inhibition and clinical efficacy was recently accomplished with the disclosure of preliminary clinical data for BILN-2061, a selective inhibitor of the NS3 serine protease of HCV that is structurally related to 13. abstract: Publisher Summary This chapter focuses on non-HIV antiviral agents. The development of antiviral agents to treat non-HIV infections is largely focused on therapies for the treatment of chronic hepatitis infections B and C. Nucleoside analog continue to be the mainstay of Hepatitis B Virus (HBV) therapeutics. The first small molecule inhibitor of Hepatitis C Virus (HCV), the NS3 protease inhibitor BILN-2061, entered phase 2 clinical trials, producing a striking reduction in viral load in treated individuals. The development of the HCV replicon system and its application to screening for antiviral agents provided tangible benefit with the disclosure of mechanistically and structurally diverse HCV inhibitors. Adefovir dipivoxil has been approved in the United States and the European Union for the treatment of HBV, providing a second small molecule antiviral to add to lamivudine (3TC) and the injectable protein IFNα as the only approved agents for treating HBV infection. The chapter also provides details of the inhibitors of hepatitis B and C virus, the inhibitors of simplex virus and human cytomegalovirus, the inhibitors of respiratory viruses and the inhibitors of West Nile virus and Papilloma virus. url: https://www.sciencedirect.com/science/article/pii/S0065774303380236 doi: 10.1016/s0065-7743(03)38023-6 id: cord-253115-ekgdsv4f author: Mehta, Meenu title: Oligonucleotide therapy: An emerging focus area for drug delivery in chronic inflammatory respiratory diseases date: 2019-08-01 words: 7317.0 sentences: 457.0 pages: flesch: 39.0 cache: ./cache/cord-253115-ekgdsv4f.txt txt: ./txt/cord-253115-ekgdsv4f.txt summary: Commonly used drug delivery systems for respiratory diseases are polymer-based, lipid-based and peptide-based, and among these three, the lipid-based carriers are the most commonly used vectors for delivering RNAi. They include solid lipid nanoparticles, cationic liposomes, lipidoids, solid nanostructured lipid carriers and pH-responsive lipids [26] . The effective delivery of the drug and siRNA induced cell death of lung tumor cells by targeted gene silencing [56] . Glud et al., investigated pulmonary gene silencing effect of small interfering locked nucleic acid (siLNAs), targeting enhanced-greenfluorescent-protein (EGFP) in lung bronchoepithelium upon intravenous delivery of naked siLNAs and intranasal delivery of naked siLNA or chitosan based siLNA mucoadhesive nanoparticles. This study demonstrated that SAMiRNA nanoparticle is a stable siRNA silencing platform with less toxicity for effective in vivo targeting of genes involved in the pathogenesis of respiratory diseases [96] . Overcoming cisplatin resistance in non-small cell lung cancer with Mad2 silencing siRNA delivered systemically using EGFR-targeted chitosan nanoparticles abstract: Abstract Oligonucleotide-based therapies are advanced novel interventions used in the management of various respiratory diseases such as asthma and Chronic Obstructive Pulmonary Disease (COPD). These agents primarily act by gene silencing or RNA interference. Better methodologies and techniques are the need of the hour that can deliver these agents to tissues and cells in a target specific manner by which their maximum potential can be reached in the management of chronic inflammatory diseases. Nanoparticles play an important role in the target-specific delivery of drugs. In addition, oligonucleotides also are extensively used for gene transfer in the form of polymeric, liposomal and inorganic carrier materials. Therefore, the current review focuses on various novel dosage forms like nanoparticles, liposomes that can be used efficiently for the delivery of various oligonucleotides such as siRNA and miRNA. We also discuss the future perspectives and targets for oligonucleotides in the management of respiratory diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/31136735/ doi: 10.1016/j.cbi.2019.05.028 id: cord-342344-jjnf4yje author: Mello, C. J. title: Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR date: 2020-06-26 words: 3122.0 sentences: 190.0 pages: flesch: 55.0 cache: ./cache/cord-342344-jjnf4yje.txt txt: ./txt/cord-342344-jjnf4yje.txt summary: Diagnostic assays for the presence of SARS-CoV-2 currently use real-time reverse transcriptase PCR (RT-qPCR) to yield a binary (positive or negative) result based on an amplification cycle threshold (Ct) value 9-12 . Current PCR-based assays can detect the presence of very short SARS-CoV-2 RNA sequences but do not distinguish whether these sequences are derived from longer molecules present in the sample at the time of collection. To address these issues, we explored using droplet digital PCR (ddPCR) 19, 20 to more precisely quantify SARS-CoV-2 RNA in biological samples and evaluate the extent to which positive results reflect larger, intact viral nucleic acids. The results yielded definitive evidence of linkage: although only 822 of the 12,220 droplets (6.7%) were positive for either N1 or N2, 75% of the droplets that were positive for N2 (HEX) were also positive for N1 (FAM) (Fig. 2a, Table 1 ); we estimate (using a formula we previously described 21 , which accounts for chance co-encapsulation) that 71% of the detected RNA sequences were physically linked. abstract: Quantifying SARS-CoV-2 infectivity, formulating well-calibrated public-health policy, and managing the safety of workplaces would all be facilitated by precise measurement of the extent to which SARS-CoV-2 RNA is present in an intact form in biological specimens and human environments. We describe assays that use digital PCR in nanoliter droplets (droplet digital PCR) to measure these properties. Such assays could be broadly deployed to inform COVID-19 epidemiology, measure symptomatic and asymptomatic infectivity, and help manage the safety of environments in which people live, move, and work. url: http://medrxiv.org/cgi/content/short/2020.06.24.20139584v1?rss=1 doi: 10.1101/2020.06.24.20139584 id: cord-320325-sjab8zsk author: Mendez, Aaron S title: Site specific target binding controls RNA cleavage efficiency by the Kaposi''s sarcoma-associated herpesvirus endonuclease SOX date: 2018-12-14 words: 6508.0 sentences: 329.0 pages: flesch: 53.0 cache: ./cache/cord-320325-sjab8zsk.txt txt: ./txt/cord-320325-sjab8zsk.txt summary: Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. Using an RNA substrate that is efficiently cleaved by SOX in cells, we revealed that specific RNA sequences within and outside of the cleavage site significantly contribute to SOX binding efficiency and target processing. Given that both substrates contain the requisite unpaired bulge at the predicted cleavage site (see Figure 2A and Supplementary Figure S2 ), these observations suggest that additional sequence or structural features impact SOX targeting efficiency on individual RNAs. Two SOX point mutants, P176S and F179A, located in an unstructured region of the protein that bridges domains I and II have been shown to be selectively required for its endonucleolytic processing of RNA substrates (Supplementary Figure S3A and S3B) (8, 21) . abstract: A number of viruses remodel the cellular gene expression landscape by globally accelerating messenger RNA (mRNA) degradation. Unlike the mammalian basal mRNA decay enzymes, which largely target mRNA from the 5′ and 3′ end, viruses instead use endonucleases that cleave their targets internally. This is hypothesized to more rapidly inactivate mRNA while maintaining selective power, potentially though the use of a targeting motif(s). Yet, how mRNA endonuclease specificity is achieved in mammalian cells remains largely unresolved. Here, we reveal key features underlying the biochemical mechanism of target recognition and cleavage by the SOX endonuclease encoded by Kaposi's sarcoma-associated herpesvirus (KSHV). Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. The strength of SOX binding dictates cleavage efficiency, providing an explanation for the breadth of mRNA susceptibility observed in cells. Importantly, we establish that cleavage site specificity does not require additional cellular cofactors, as had been previously proposed. Thus, viral endonucleases may use a combination of RNA sequence and structure to capture a broad set of mRNA targets while still preserving selectivity. url: https://doi.org/10.1093/nar/gky932 doi: 10.1093/nar/gky932 id: cord-317773-jdq1d98i author: Meng, Qing-Wen title: Enhanced inhibition of Avian leukosis virus subgroup J replication by multi-target miRNAs date: 2011-12-22 words: 3614.0 sentences: 214.0 pages: flesch: 53.0 cache: ./cache/cord-317773-jdq1d98i.txt txt: ./txt/cord-317773-jdq1d98i.txt summary: RESULTS: In this study, the avian leukosis virus subgroup J (ALV-J) proviral genome, including the gag genes, were treated as targets for RNAi. Four pairs of miRNA sequences were designed and synthesized that targeted different regions of the gag gene. To avoid the generation of escape variants during virus infection, expression vectors of multi-target miRNAs were constructed using the multi-target serial strategy (against different regions of the gag, pol, and env genes). CONCLUSION: The strategy of multi-target miRNAs might be an effective method for inhibiting ALV replication and the acquisition of resistant mutations. In some studies, transfection of siRNA designed to target C virus (HCV) remarkably inhibited the expression of virus-specific proteins and protected cells against HCV RNA, in vitro [4, 5] . In another study, Hepatitis B virus (HBV) replication was successfully inhibited after plasmid expression of HBV siRNA transfected into mouse liver [6] . abstract: BACKGROUND: Avian leukosis virus (ALV) is a major infectious disease that impacts the poultry industry worldwide. Despite intensive efforts, no effective vaccine has been developed against ALV because of mutations that lead to resistant forms. Therefore, there is a dire need to develop antiviral agents for the treatment of ALV infections and RNA interference (RNAi) is considered an effective antiviral strategy. RESULTS: In this study, the avian leukosis virus subgroup J (ALV-J) proviral genome, including the gag genes, were treated as targets for RNAi. Four pairs of miRNA sequences were designed and synthesized that targeted different regions of the gag gene. The screened target (i.e., the gag genes) was shown to effectively suppress the replication of ALV-J by 19.0-77.3%. To avoid the generation of escape variants during virus infection, expression vectors of multi-target miRNAs were constructed using the multi-target serial strategy (against different regions of the gag, pol, and env genes). Multi-target miRNAs were shown to play a synergistic role in the inhibition of ALV-J replication, with an inhibition efficiency of viral replication ranging from 85.0-91.2%. CONCLUSION: The strategy of multi-target miRNAs might be an effective method for inhibiting ALV replication and the acquisition of resistant mutations. url: https://doi.org/10.1186/1743-422x-8-556 doi: 10.1186/1743-422x-8-556 id: cord-350640-sz6xj5o3 author: Menzel, Nicolas title: MAP-Kinase Regulated Cytosolic Phospholipase A2 Activity Is Essential for Production of Infectious Hepatitis C Virus Particles date: 2012-07-26 words: 10059.0 sentences: 549.0 pages: flesch: 49.0 cache: ./cache/cord-350640-sz6xj5o3.txt txt: ./txt/cord-350640-sz6xj5o3.txt summary: When transfecting our infectious firefly luciferase reporter virus genome Luc-Jc1 [14] into highly permissive Huh-7.5 human hepatoma cells [15] cultured in the presence or absence of serum, we measured comparable levels of luciferase activity 4 to 48 h after transfection ( Figure S1A ). Among the inhibitors tested, U0126 a selective inhibitor of the MAPK/ERK pathway, substantially decreased the production of infectious virus particles as is evident from the dose-dependent reduction of luciferase activity in the inoculated cells ( Figure 1B) . To investigate if PLA2G4A activity is relevant for the production of infectious HCV particles we treated Luc-Jc1 transfected cells with pyrrolidine-2 (Py-2), a specific inhibitor of this type of phospholipase [22, 23] . Irrespective of culturing these cells in the presence or absence of serum, we observed a strong and dose-dependent inhibition of production of infectious particles resulting in a more than 100-fold reduction of luciferase transduction at 5 and 20 mM of Py-2, respectively ( Figure 2B ). abstract: Hepatitis C virus (HCV) has infected around 160 million individuals. Current therapies have limited efficacy and are fraught with side effects. To identify cellular HCV dependency factors, possible therapeutic targets, we manipulated signaling cascades with pathway-specific inhibitors. Using this approach we identified the MAPK/ERK regulated, cytosolic, calcium-dependent, group IVA phospholipase A2 (PLA2G4A) as a novel HCV dependency factor. Inhibition of PLA2G4A activity reduced core protein abundance at lipid droplets, core envelopment and secretion of particles. Moreover, released particles displayed aberrant protein composition and were 100-fold less infectious. Exogenous addition of arachidonic acid, the cleavage product of PLA2G4A-catalyzed lipolysis, but not other related poly-unsaturated fatty acids restored infectivity. Strikingly, production of infectious Dengue virus, a relative of HCV, was also dependent on PLA2G4A. These results highlight previously unrecognized parallels in the assembly pathways of these human pathogens, and define PLA2G4A-dependent lipolysis as crucial prerequisite for production of highly infectious viral progeny. url: https://www.ncbi.nlm.nih.gov/pubmed/22911431/ doi: 10.1371/journal.ppat.1002829 id: cord-016209-6p9btua0 author: Merl, S. title: Targeting Viral Heart Disease by RNA Interference date: 2008 words: 7170.0 sentences: 429.0 pages: flesch: 41.0 cache: ./cache/cord-016209-6p9btua0.txt txt: ./txt/cord-016209-6p9btua0.txt summary: The use of highly specific siRNAs targeting distinct regions of the viral genome ( Fig. 1) as well as host genes that are relevant for virus entry and maturation represents a novel therapeutic strategy to cure or attenuate in particular coxsackievirus-mediated diseases. Several laboratories obtained significant inhibition of the HIV-1 replication applying both synthetic and vector-derived siRNAs/shRNAs directed against the viral genome and HIV-encoded RNAs, such as the TAR element, tat, rev, gag, env, vif, nef and reverse transcriptase (Boden et al. In our previous work, the application of the most effective siRNA directed against the RNA dependent RNA polymerase 3D resulted in an approximately fourfold prolonged survival of coxsackievirus-infected cells and an inhibition of viral replication by more than 10 5 -fold compared to control siRNAs (Merl and Wessely 2007) . Even though previous studies reported efficient suppression of hepatitis C virus replication by siRNAs targeting single-stranded regions inbetween two stem-loop motifs of the viral 5′ UTR (Yokota et al. abstract: Viral heart disease (VHD) is an important clinical disease entity both in pediatric as well as adult cardiology. Coxsackieviruses (CVBs) are considered an important cause for VHD in both populations. VHD may lead to dilated cardiomyopathy and heart failure which can ultimately require heart transplantation. However, no specific treatment modality is so far available. We and others have shown that coxsackieviral replication and cytotoxicity can be successfully targeted by RNA interference, thus leading to increased cell viability and even prolongation of survival in vivo. However, considerable limitations have to be solved before this novel therapeutic approach may enter the clinical trials arena. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120428/ doi: 10.1007/978-3-540-78709-9_6 id: cord-339456-82iks0xf author: Mikel, P. title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens date: 2015-02-25 words: 10033.0 sentences: 499.0 pages: flesch: 53.0 cache: ./cache/cord-339456-82iks0xf.txt txt: ./txt/cord-339456-82iks0xf.txt summary: title: Methods for Preparation of MS2 Phage-Like Particles and Their Utilization as Process Control Viruses in RT-PCR and qRT-PCR Detection of RNA Viruses From Food Matrices and Clinical Specimens The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Also MS2 phage-like particles have been used as the process control virus for the detection of pathogenic RNA viruses in clinical samples. prepared MS2 phage-like particles, also called armored RNA (aRNA), that carried the consensus RNA sequence from human immunodeficiency virus type 1 (HIV-1) packaged in the capsid which can serve as quantitative standard in detection of HIV-1 (Pasloske et al. MS2 phage-like particles carrying the plant-specific ribulose-1,5-bisphosphate carboxyl small subunit (rbcs) gene fragment were used as the process control virus in qRT-PCR detection of severe acute respiratory syndrome coronavirus (SARS-CoV) . abstract: RNA viruses are pathogenic agents of many serious infectious diseases affecting humans and animals. The detection of pathogenic RNA viruses is based on modern molecular methods, of which the most widely used methods are the reverse transcription polymerase chain reaction (RT-PCR) and the real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). All steps of RT-PCR and qRT-PCR should be strictly controlled to ensure the validity of obtained results. False-negative results may be caused not only by inhibition of RT or/and PCR steps but also by failure of the nucleic acid extraction step, particularly in the case of viral RNA extraction. The control of nucleic acid extraction generally involves the utilization of a non-pathogenic virus (process control virus) of similar structural properties to those of the target virus. Although in clinical samples the use of such process control virus is only recommended, in other kinds of settings such as food matrices its use is necessary. Currently, several different process control viruses are used for these purposes. Process control viruses can also be constructed artificially using technology for production of MS2 phage-like particles, which have many advantages in comparison with other used controls and are especially suited for controlling the detection and quantification of certain types of RNA viruses. The technology for production of MS2 phage-like particles is theoretically well established, uses the knowledge gained from the study of the familiar bacteriophage MS2 and utilizes many different approaches for the construction of the various process control viruses. Nevertheless, the practical use of MS2 phage-like particles in routine diagnostics is relatively uncommon. The current situation with regard to the use of MS2 phage-like particles as process control viruses in detection of RNA viruses and different methods of their construction, purification and use are summarized and discussed in this review. url: https://www.ncbi.nlm.nih.gov/pubmed/25711389/ doi: 10.1007/s12560-015-9188-2 id: cord-002376-970934vm author: Mikel, Pavel title: Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices date: 2016-12-01 words: 6581.0 sentences: 311.0 pages: flesch: 52.0 cache: ./cache/cord-002376-970934vm.txt txt: ./txt/cord-002376-970934vm.txt summary: The quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay is nowadays considered as the gold standard method for detection and quantification of enteric RNA viruses such as hepatitis A virus (HAV), hepatitis E virus (HEV) or human noroviruses (NoV) (Mattison et al., 2009; Blaise-Boisseau et al., 2010; Di Pasquale et al., 2010; Vasickova et al., 2012; Hennechart-Collette et al., 2014) . The present article is a followup study of a previously published theoretical concept (Mikel et al., 2015) and describes a method of preparation of MS2 PLP carrying a specific control sequence and their use as a PCV in RT-qPCR detection and quantification of enteric RNA viruses in swab, liver tissue, serum, feces, and vegetable samples. MS2 PLP were added in the amount of 5 × 10 6 particles to the different types of matrices (swabs, liver tissue, serum, feces, and leafy green vegetables) to reveal their ability to serve as PCV in the RT-qPCR detection of enteric RNA viruses. abstract: The detection and quantification of enteric RNA viruses is based on isolation of viral RNA from the sample followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). To control the whole process of analysis and in order to guarantee the validity and reliability of results, process control viruses (PCV) are used. The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. The MS2 PLP were derived from bacteriophage MS2 carrying a unique and specific de novo-constructed RNA target sequence originating from the DNA of two extinct species. The amount of prepared MS2 particles was quantified using four independent methods – UV spectrophotometry, fluorimetry, transmission electron microscopy and a specifically developed duplex RT-qPCR. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP. The extraction efficiencies were calculated for each individual matrix. The prepared particles fulfill all requirements for PCV – they are very stable, non-infectious, and are genetically distinct from the target RNA viruses. Due to these properties they represent a good morphological and physiochemical model. The use of MS2 PLP as a PCV in detection and quantification of enteric RNA viruses was evaluated in different types of matrices. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5234545/ doi: 10.3389/fmicb.2016.01911 id: cord-330213-reb9vo7x author: Miladi, Milad title: The landscape of SARS-CoV-2 RNA modifications date: 2020-07-18 words: 3213.0 sentences: 210.0 pages: flesch: 55.0 cache: ./cache/cord-330213-reb9vo7x.txt txt: ./txt/cord-330213-reb9vo7x.txt summary: From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. The long RNA sequencing reads generated for this study cover the entire SARS-CoV-2 genomic RNA as well as the different ORFs (Fig 1b,c, Fig. S1b ). Two sets of Galaxy workflows based on Tombo (16) and Nanocompore (17) tools were designed to compute the modification scores from the DRS data (Table S3) . Figure 5 : Direct RNA sequencing raw electrical signals of downsampled reads obtained from unmodified RNA (IVT, black), from samples generated for this study and from isolate from a published korean data set (Fr1-3 and Kr, red). abstract: In 2019 the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the first documented cases of severe lung disease COVID-19. Since then, SARS-CoV-2 has been spreading around the globe resulting in a severe pandemic with over 500.000 fatalities and large economical and social disruptions in human societies. Gaining knowledge on how SARS-Cov-2 interacts with its host cells and causes COVID-19 is crucial for the intervention of novel therapeutic strategies. SARS-CoV-2, like other coronaviruses, is a positive-strand RNA virus. The viral RNA is modified by RNA-modifying enzymes provided by the host cell. Direct RNA sequencing (DRS) using nanopores enables unbiased sensing of canonical and modified RNA bases of the viral transcripts. In this work, we used DRS to precisely annotate the open reading frames and the landscape of SARS-CoV-2 RNA modifications. We provide the first DRS data of SARS-CoV-2 in infected human lung epithelial cells. From sequencing three isolates, we derive a robust identification of SARS-CoV-2 modification sites within a physiologically relevant host cell type. A comparison of our data with the DRS data from a previous SARS-CoV-2 isolate, both raised in monkey renal cells, reveals consistent RNA modifications across the viral genome. Conservation of the RNA modification pattern during progression of the current pandemic suggests that this pattern is likely essential for the life cycle of SARS-CoV-2 and represents a possible target for drug interventions. url: https://doi.org/10.1101/2020.07.18.204362 doi: 10.1101/2020.07.18.204362 id: cord-276185-ysspkbj7 author: Milewska, Aleksandra title: APOBEC3-mediated restriction of RNA virus replication date: 2018-04-13 words: 5507.0 sentences: 317.0 pages: flesch: 54.0 cache: ./cache/cord-276185-ysspkbj7.txt txt: ./txt/cord-276185-ysspkbj7.txt summary: In experiments in vitro, three human APOBEC3 proteins (A3C, A3F and A3H) inhibited HCoV-NL63 infection and limited production of progeny virus, but did not cause hypermutation of the coronaviral genome. Although the precise molecular mechanism of deaminase-dependent inhibition of coronavirus replication remains elusive, our results further our understanding of APOBEC-mediated restriction of RNA virus infections. HCoV-NL63 infection resulted in upregulation of expression of A3A, A3C, A3D and A3F and A3C, A3F and A3H all inhibited HCoV-NL63 replication, we tested whether this inhibition was the result of the catalytic activity of the APOBECs. Plasmids encoding variants of A3C, A3F and A3H with Glu → Gln substitutions in the catalytic site were prepared 31 and mRNAs encoding active or inactive proteins were transfected into LLC-Mk2 cells, which were infected with HCoV-NL63 and cultured prior to visualisation of viral proteins with specific antibodies. abstract: APOBEC3 family members are cytidine deaminases with roles in intrinsic responses to infection by retroviruses and retrotransposons, and in the control of other DNA viruses, such as herpesviruses, parvoviruses and hepatitis B virus. Although effects of APOBEC3 members on viral DNA have been demonstrated, it is not known whether they edit RNA genomes through cytidine deamination. Here, we investigated APOBEC3-mediated restriction of Coronaviridae. In experiments in vitro, three human APOBEC3 proteins (A3C, A3F and A3H) inhibited HCoV-NL63 infection and limited production of progeny virus, but did not cause hypermutation of the coronaviral genome. APOBEC3-mediated restriction was partially dependent on enzyme activity, and was reduced by the use of enzymatically inactive APOBEC3. Moreover, APOBEC3 proteins bound to the coronaviral nucleoprotein, and this interaction also affected viral replication. Although the precise molecular mechanism of deaminase-dependent inhibition of coronavirus replication remains elusive, our results further our understanding of APOBEC-mediated restriction of RNA virus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/29654310/ doi: 10.1038/s41598-018-24448-2 id: cord-017732-1pwa6zsk author: Miller, W. Allen title: Ribosomal Frameshifting in Decoding Plant Viral RNAs date: 2009-07-21 words: 10588.0 sentences: 477.0 pages: flesch: 56.0 cache: ./cache/cord-017732-1pwa6zsk.txt txt: ./txt/cord-017732-1pwa6zsk.txt summary: As in animal viruses, the −1 ribosomal frameshift site in the viral mRNA consists of a canonical shifty heptanucleotide followed by a highly structured frameshift stimulatory element, and the gene translated as a result of frameshifting usually encodes the RNA-dependent RNA polymerase. We suggest that these experiments may not have revealed all of the sequence requirements for frameshifting on the full-length viral RNA because the frameshifting constructs tested contained a very short (10 codon) first (zero frame) ORF from the start codon through the shifty site which is followed immediately by a stop codon. The 25-kDa protein that could be generated by a frameshift followed by cleavage at the HC-Pro/P3 cleavage site is indicated (Chung et al., 2008) anticipate results of future research and structural analysis to determine how these diverse plant viral RNAs induce ribosomes to change reading frames by what may be novel mechanisms. abstract: Frameshifting provides an elegant mechanism by which viral RNA both encodes overlapping genes and controls expression levels of those genes. As in animal viruses, the −1 ribosomal frameshift site in the viral mRNA consists of a canonical shifty heptanucleotide followed by a highly structured frameshift stimulatory element, and the gene translated as a result of frameshifting usually encodes the RNA-dependent RNA polymerase. In plant viruses, the −1 frameshift stimulatory element consists of either (i) a small pseudoknot stabilized by many triple-stranded regions and a triple base pair containing a protonated cytidine at the helical junction, (ii) an unusual apical loop–internal loop interaction in which a stem-loop in the 3(′) untranslated region 4 kb downstream base pairs to a bulged stem-loop at the frameshift site, or (iii) a potential simple stem-loop. Other less well-characterized changes in reading frame occur on plant viral RNAs, including a possible +1 frameshift, and net −1 reading frame changes that do not utilize canonical frameshift signals. All these studies reveal the remarkable ways in which plant viral RNAs interact with ribosomes to precisely control protein expression at the ratios needed to sustain virus replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122378/ doi: 10.1007/978-0-387-89382-2_9 id: cord-332747-u46xryoo author: Mingorance, Lidia title: Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation date: 2018-09-18 words: 10355.0 sentences: 485.0 pages: flesch: 37.0 cache: ./cache/cord-332747-u46xryoo.txt txt: ./txt/cord-332747-u46xryoo.txt summary: To determine which aspects of the HCV replication cycle are limited by lipin1 silencing, single cycle infection experiments were conducted by inoculating control and lipin1-deficient cell cultures at MOI 10 with genotype 2a D183 virus. Once cultures reached >95% of HCV-positive cells, they were transduced with lentiviral vectors expressing control, HCV RNA-targeting or LPIN1-specific shRNAs. At day 7 post-transduction, cells were split and samples of the cells and supernatants were collected 24 hours later to determine infectious virus production rate by infectivity titration HCV (C) and RNA levels by RT-qPCR (D). This reduced abundance is illustrated by a significant reduction in the fraction of cells displaying vesicular structures in lipin1-deficient cell cultures (Fig 7H) despite comparable transfection efficiency and viral protein expression levels, indicating that lipin1 may be required in a critical step leading to formation of the HCV-induced vesicular compartment. abstract: Hepatitis C virus (HCV) infection constitutes a significant health burden worldwide, because it is a major etiologic agent of chronic liver disease, cirrhosis and hepatocellular carcinoma. HCV replication cycle is closely tied to lipid metabolism and infection by this virus causes profound changes in host lipid homeostasis. We focused our attention on a phosphatidate phosphate (PAP) enzyme family (the lipin family), which mediate the conversion of phosphatidate to diacylglycerol in the cytoplasm, playing a key role in triglyceride biosynthesis and in phospholipid homeostasis. Lipins may also translocate to the nucleus to act as transcriptional regulators of genes involved in lipid metabolism. The best-characterized member of this family is lipin1, which cooperates with lipin2 to maintain glycerophospholipid homeostasis in the liver. Lipin1-deficient cell lines were generated by RNAi to study the role of this protein in different steps of HCV replication cycle. Using surrogate models that recapitulate different aspects of HCV infection, we concluded that lipin1 is rate limiting for the generation of functional replicase complexes, in a step downstream primary translation that leads to early HCV RNA replication. Infection studies in lipin1-deficient cells overexpressing wild type or phosphatase-defective lipin1 proteins suggest that lipin1 phosphatase activity is required to support HCV infection. Finally, ultrastructural and biochemical analyses in replication-independent models suggest that lipin1 may facilitate the generation of the membranous compartment that contains functional HCV replicase complexes. url: https://www.ncbi.nlm.nih.gov/pubmed/30226904/ doi: 10.1371/journal.ppat.1007284 id: cord-291513-vpehn6nx author: Minich, Jeremiah title: Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment date: 2020-08-18 words: 6429.0 sentences: 326.0 pages: flesch: 55.0 cache: ./cache/cord-291513-vpehn6nx.txt txt: ./txt/cord-291513-vpehn6nx.txt summary: Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. Here we characterize the suitability of detecting SARS-CoV-2 RNA in experimental conditions as well as COVID-19 patient and built-environment samples using viral-inactivating storage solutions and alternative medical-grade and consumer-grade swabs. In a subset of seven COVID-19 patient nares samples stored in 95% EtOH, we also detected signi cantly higher SARS-CoV-2 viral load in RNA extracted from the swab head versus eluent ( Fig. 1b ; one-tailed paired Student''s t-test p = 0.03). Based on the results from these initial experiments, we conducted a proof-of-concept study in the clinical setting by performing RT-qPCR for the SARS-CoV-2 N1 amplicon and human RNase P gene on RNA extracted from the swab head of nasal samples collected using TMI and/or CGp swabs alongside the recommended SYN swabs. abstract: Background: Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 testing to include environmental surfaces would ideally be performed with inexpensive swabs that could be transported safely without concern of being a source of new infections. However, CDC-approved clinical-grade sampling supplies and techniques using a synthetic swab are expensive, potentially expose laboratory workers to viable virus and prohibit analysis of the microbiome due to the presence of antibiotics in viral transport media (VTM). To this end, we performed a series of experiments comparing the diagnostic yield using five consumer-grade swabs (including plastic and wood shafts and various head materials including cotton, synthetic, and foam) and one clinical grade swab for inhibition to RNA. For three of these swabs, we evaluated performance to detect SARS-CoV-2 in twenty intensive care unit (ICU) hospital rooms of patients with 16 COVID-19+. All swabs were placed in 95% ethanol and further evaluated in terms of RNase activity. SARS-CoV-2 was measured both directly from the swab and from the swab eluent. Results: Compared to samples collected in VTM, 95% ethanol demonstrated significant inhibition properties against RNases. When extracting directly from the swab head as opposed to the eluent, RNA recovery was approximately 2-4x higher from all six swab types tested as compared to the clinical standard of testing the eluent from a CDC-approved synthetic swab. The limit of detection (LoD) of SARs-CoV-2 from floor samples collected using the CGp or TMI swabs was similar or better than the CDC standard, further suggesting that swab type does not impact RNA recovery as measured by SARs-CoV-2. The LoD for TMI was between 0-362.5 viral particles while SYN and CGp were both between 725–1450 particles. Lastly microbiome analyses (16S rRNA) of paired samples (e.g., environment to host) collected using different swab types in triplicate indicated that microbial communities were not impacted by swab type but instead driven by the patient and sample type (floor or nasal). Conclusions: Compared to using a clinical-grade synthetic swab, detection of SARS-CoV-2 from environmental samples collected from ICU rooms of patients with COVID was similar using consumer grade swabs, stored in 95% ethanol. The yield was best from the swab head rather than the eluent and the low level of RNase activity in these samples makes it possible to perform concomitant microbiome analysis. url: https://doi.org/10.21203/rs.3.rs-56028/v1 doi: 10.21203/rs.3.rs-56028/v1 id: cord-349623-dw5o9i59 author: Miranda, José P. title: Analytical and Clinical Validation for RT-qPCR Detection of SARS-CoV-2 Without RNA Extraction date: 2020-10-15 words: 3813.0 sentences: 174.0 pages: flesch: 48.0 cache: ./cache/cord-349623-dw5o9i59.txt txt: ./txt/cord-349623-dw5o9i59.txt summary: Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise''s buffer pH 7.2. For the standard protocol, routinely used in the laboratory for the detection of SARS-CoV-2, an aliquot of 180 ul of the sample from the nasopharyngeal swab, including 10 ul of extraction control, was used to extract RNA with the MagNA Pure 96 DNA and Viral NA LV Kit (Roche Diagnostics, Cat. No. For the standardization of the direct SARS-CoV-2 detection protocol without RNA extraction steps, 50 ul aliquots from the primary sample (nasopharyngeal swabs) of 5 anonymized patients were subjected to heat shock (65, 70, or 95 • C) during different incubation times (5, 10, or 30 min), and then were quickly placed at 4 • C until the moment of amplification. abstract: Background: The recent COVID-19 pandemic has posed an unprecedented challenge to laboratory diagnosis, based on the amplification of SARS-CoV-2 RNA. With global contagion figures exceeding 4 million persons, the shortage of reagents for RNA extraction represents a bottleneck for testing globally. We present the validation results for an RT-qPCR protocol without prior RNA extraction. Due to its simplicity, this protocol is suitable for widespread application in resource-limited settings. Methods: Optimal direct protocol was selected by comparing RT-qPCR performance under a set of thermal (65, 70, and 95° for 5, 10, and 30 min) and amplification conditions (3 or 3.5 uL loading volume; 2 commercial RT-qPCR kits with a limit of detection below 10 copies/reaction) in nasopharyngeal swabs stored at 4°C in sterile Weise's buffer pH 7.2. The selected protocol was evaluated for classification concordance with a standard protocol (automated RNA extraction) in 130 routine samples and 50 historical samples with Cq values near to the clinical decision limit. Results: Optimal selected conditions for direct protocol were: thermal shock at 70°C for 10 min, loading 3.5 ul in the RT-qPCR. Prospective evaluation in 130 routine samples showed a 100% classification concordance with the standard protocol. The evaluation in historical samples, selected because their Cqs were at the clinical decision limit, showed 94% concordance with our confirmatory standard, which includes manual RNA extraction. Conclusions : Our results validate the use of this direct RT-qPCR protocol as a safe alternative for SARS-CoV-2 diagnosis in the case of a shortage of reagents for RNA extraction, with minimal clinical impact. url: https://www.ncbi.nlm.nih.gov/pubmed/33178714/ doi: 10.3389/fmed.2020.567572 id: cord-002482-2t09zqqi author: Miras, Manuel title: Non-canonical Translation in Plant RNA Viruses date: 2017-04-06 words: 13890.0 sentences: 732.0 pages: flesch: 51.0 cache: ./cache/cord-002482-2t09zqqi.txt txt: ./txt/cord-002482-2t09zqqi.txt summary: Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. In this review, we describe current knowledge on the mechanisms used by positive-sense single-stranded (+ss) RNA plant viruses to initiate translation, focusing on cis-acting sequences present in viral mRNAs. We also describe other protein translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. abstract: Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5′ cap structure and/or the 3′ poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. We also describe other translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. Finally, future research perspectives on the unusual translational strategies of +ssRNA viruses are discussed, including parallelisms between viral and host mRNAs mechanisms of translation, particularly for host mRNAs which are translated under stress conditions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5382211/ doi: 10.3389/fpls.2017.00494 id: cord-103899-6tqm99g1 author: Mirzaei, Rasoul title: The emerging role of microRNAs in the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection date: 2020-11-13 words: 9756.0 sentences: 554.0 pages: flesch: 47.0 cache: ./cache/cord-103899-6tqm99g1.txt txt: ./txt/cord-103899-6tqm99g1.txt summary: Hence, analyzing the role of these types of nucleotides in antiviral immune responses and the characterization of miRNA target genes might contribute to understanding the mechanisms of the interplay between the host and viruses, and in the future, potentially result in discovering therapeutic strategies for the prevention and treatment of acute COVID-19 infection. This review will summarize the recent discoveries associated with miRNAs in various respiratory infections caused by viruses, especially coronavirus, and address all feasible therapeutic options to mitigate the burden of VRIs. The humoral immunity is immunologically categorized as an acquired immune response in which T helper cells collaborate with B cells to differentiate these types of cells to plasma cells [17] [18] [19] . The immune responses against VRIs, such as IV, hRV, human coronavirus (HcoV), hMPV, and RSV, are correlated with the aberrant expression of several miRNAs in epithelial cells and participate in the pathogenesis of chronic and acute forms of respiratory disorders (Table 1 ) [16] . abstract: The novel coronavirus disease 2019 (COVID-19) pandemic has imposed significant public health problems for the human populations worldwide after the 1918 influenza A virus (IVA) (H1N1) pandemic. Although numerous efforts have been made to unravel the mechanisms underlying the coronavirus, a notable gap remains in our perception of the COVID-19 pathogenesis. The innate and adaptive immune systems have a pivotal role in the fate of viral infections, such as COVID-19 pandemic. MicroRNAs (miRNAs) are known as short noncoding RNA molecules and appear as indispensable governors of almost any cellular means. Several lines of evidence demonstrate that miRNAs participate in essential mechanisms of cell biology, regulation of the immune system, and the onset and progression of numerous types of disorders. The immune responses to viral respiratory infections (VRIs), including influenza virus (IV), respiratory syncytial virus (RSV), and rhinovirus (RV), are correlated with the ectopic expression of miRNAs. Alterations of the miRNA expression in epithelial cells may contribute to the pathogenesis of chronic and acute airway infections. Hence, analyzing the role of these types of nucleotides in antiviral immune responses and the characterization of miRNA target genes might contribute to understanding the mechanisms of the interplay between the host and viruses, and in the future, potentially result in discovering therapeutic strategies for the prevention and treatment of acute COVID-19 infection. In this article, we present a general review of current studies concerning the function of miRNAs in different VRIs, particularly in coronavirus infection, and address all available therapeutic prospects to mitigate the burden of viral infections. url: https://api.elsevier.com/content/article/pii/S1567576920336717 doi: 10.1016/j.intimp.2020.107204 id: cord-323691-5s5almd2 author: Mishin, Vasiliy P title: A ‘minimal’ approach in design of flavivirus infectious DNA date: 2001-12-04 words: 5060.0 sentences: 255.0 pages: flesch: 49.0 cache: ./cache/cord-323691-5s5almd2.txt txt: ./txt/cord-323691-5s5almd2.txt summary: Abstract The ''infectious DNA'' approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Substantial difficulties, however, were encountered in design of flavivirus ''infectious DNA'', requiring either modification of the viral genome cassette (Yamshchikov et al., 2001) to prevent unwanted expression of viral genome segments encoding toxic for Escherichia coli products, or deletion of the structural protein region (Varnavski et al., 2000) . For this reason we sought to investigate if the stability of constructs containing an unmodified virus genome cassette can be improved by preventing its deleterious expression at the transcriptional level, i.e. by minimizing spurious transcription from eukaryotic promoters in E. abstract: Abstract The ‘infectious DNA’ approach, which is based on in vivo transcription of (+)RNA virus genome cDNA cassettes from eukaryotic promoters in transfected cells, became a popular alternative to the classical scheme in the infectious clone methodology. Its use, however, is often limited by the instability of plasmids due to a transcriptional activity of eukaryotic promoters in Escherichia coli resulting in synthesis of products toxic for the bacterial host. Using a highly unstable representative infectious clone of Japanese encephalitis (JE) flavivirus, we tested a new approach in design of such problematic ‘infectious DNA’ constructs, which is based on minimizing unwanted transcription in the bacterial host. A plasmid containing full genome size JE cDNA under control of the minimal cytomegalovirus (CMV) promoter can be propagated in E. coli with growth and stability characteristics similar to that of constructs controlled by the T7 promoter. Transfection of this plasmid into susceptible cells leads to the establishment of a productive infectious cycle. Reinsertion of the CMV enhancer at the 3′-end of the JE cassette substantially increased the specific infectivity without affecting the stability and growth characteristics of the construct. This approach can be useful when stabilization of infectious clones by modification of a viral cDNA cassette is not the feasible or suitable alternative. url: https://www.ncbi.nlm.nih.gov/pubmed/11682130/ doi: 10.1016/s0168-1702(01)00371-9 id: cord-328659-miujzgtd author: Mishra, Akhilesh title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions date: 2020-07-27 words: 6064.0 sentences: 361.0 pages: flesch: 55.0 cache: ./cache/cord-328659-miujzgtd.txt txt: ./txt/cord-328659-miujzgtd.txt summary: title: Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. The rapid global spread of SARS-CoV-2 in a short period of time and the availability of a large number of fully sequenced genomes provide us with a unique opportunity of understanding the short-term temporal evolution of this virus in humans in a near real-time scale. By this approach we propose the classification of the SARS-CoV-2 virus genomes into 5 mutually exclusive lineages with unique set of co-occurring mutations and geographic distribution. Our analysis revealed a total of 40 nucleotide substitutions which occurred at > 1% in the SARS-CoV-2 genomes (Table 1 and Figure 1A ). We consider a specific mutation or a set of cooccurring mutations as "lineage-defining" for SARS-CoV-2, only when they are present in at least 2% (n=30) of the sequences analysed. abstract: The COVID-19 pandemic has spread across the globe at an alarming rate. However, unlike any of the previous global outbreaks the availability of a large number of SARS-CoV-2 sequences provides us with a unique opportunity to understand viral evolution in real time. We analysed 1448 full-length (>29000 nt) sequences available and identified 40 single-nucleotide substitutions occurring in >1% of the genomes. Majority of the substitutions were C to T or G to A. We identify C/Gs with an upstream TTT trinucleotide motif as hotspots for mutations in the SARS-CoV-2 genome. Interestingly, three of the 40 substitutions occur within highly conserved secondary structures in the 5’ and 3’ regions of the genomic RNA that are critical for the virus life cycle. Furthermore, clustering analysis revealed unique geographical distribution of SARS-CoV-2 variants defined by their mutation profile. Of note, we observed several co-occurring mutations that almost never occur individually. We define five mutually exclusive lineages (A1, B1, C1, D1 and E1) of SARS-CoV-2 which account for about three quarters of the genomes analysed. We identify lineage-defining leading mutations in the SARS-CoV-2 genome which precede the occurrence of sub-lineage defining trailing mutations. The identification of mutually exclusive lineage-defining mutations with geographically restricted patterns of distribution has potential implications for diagnosis, pathogenesis and vaccine design. Our work provides novel insights on the temporal evolution of SARS-CoV-2. Importance The SARS-CoV-2 / COVID-19 pandemic has spread far and wide with high infectivity. However, the severeness of the infection as well as the mortality rates differ greatly across different geographic areas. Here we report high frequency mutations in the SARS-CoV-2 genomes which show the presence of linage-defining, leading and trailing mutations. Moreover, we propose for the first time, five mutually exclusive clusters of SARS-CoV-2 which account for 75% of the genomes analysed. This will have implications in diagnosis, pathogenesis and vaccine design url: https://doi.org/10.1101/2020.05.07.082768 doi: 10.1101/2020.05.07.082768 id: cord-018437-yjvwa1ot author: Mitchell, Michael title: Taxonomy date: 2013-08-26 words: 9283.0 sentences: 561.0 pages: flesch: 48.0 cache: ./cache/cord-018437-yjvwa1ot.txt txt: ./txt/cord-018437-yjvwa1ot.txt summary: Classifi cation is based on the genomic nucleic acid used by the virus (DNA or RNA), strandedness (single or double stranded), and method of replication. The nucleocapsids of some viruses are surrounded by envelopes composed of lipid bilayers and host-or viral-encoded proteins. The sequence of negative-sense ssRNA is complementary to the coding sequence for translation, so mRNA must be synthesized by RNA polymerase, typically carried within the virion, before translation into viral proteins. Among the families of viruses able to infect humans and other vertebrate hosts, there are many species that target and cause disease in the lung. The nucleocapsid is surrounded by an envelope derived from host-cell membrane and viral envelope proteins, including hepatitis B surface antigen. The genome of human parainfl uenza viruses is ~15 kb in length with an organization and six reading frames (N, P, M, F, HN, L) typical of the Paramyxoviridae (Karron and Collins 2007 ) . abstract: This chapter addresses the classification and taxonomy of viruses with special attention to viruses that show pneumotropic properties. Information provided in this chapter supplements that provided in other chapters in Parts II–V of this volume that discuss individual viral pathogens. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123310/ doi: 10.1007/978-3-642-40605-8_3 id: cord-324944-ixh3ykrc author: Mitsakakis, Konstantinos title: Diagnostic tools for tackling febrile illness and enhancing patient management date: 2018-12-05 words: 20805.0 sentences: 961.0 pages: flesch: 45.0 cache: ./cache/cord-324944-ixh3ykrc.txt txt: ./txt/cord-324944-ixh3ykrc.txt summary: This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. In studies that have recorded the clinical presentation of patients (and not only their laboratory results), the causes of fever in outpatients could be classified into four main syndromes: 1) acute respiratory infections (ARI, of any type); 2) diarrhea (gastroenteritis); 3) fever with another clear focus (e.g. meningitis or skin infection); and 4) non-specific fevers [13] (each diagnostic platform described in Section 5 focuses on at least one of the aforementioned cases). abstract: Most patients with acute infectious diseases develop fever, which is frequently a reason to visit health facilities in resource-limited settings. The symptomatic overlap between febrile diseases impedes their diagnosis on clinical grounds. Therefore, the World Health Organization promotes an integrated management of febrile illness. Along this line, we present an overview of endemic and epidemic etiologies of fever and state-of-the-art diagnostic tools used in the field. It becomes evident that there is an urgent need for the development of novel technologies to fulfill end-users' requirements. This need can be met with point-of-care and near-patient diagnostic platforms, as well as e-Health clinical algorithms, which co-assess test results with key clinical elements and biosensors, assisting clinicians in patient triage and management, thus enhancing disease surveillance and outbreak alerts. This review gives an overview of diagnostic technologies featuring a platform based approach: (i) assay (nucleic acid amplification technologies are examined); (ii) cartridge (microfluidic technologies are presented); (iii) instrument (various detection technologies are discussed); and at the end proposes a way that such technologies can be interfaced with electronic clinical decision-making algorithms towards a broad and complete diagnostic ecosystem. url: https://www.sciencedirect.com/science/article/pii/S0167931718304556 doi: 10.1016/j.mee.2018.10.001 id: cord-273379-w8vy5rl8 author: Mizutani, Tetsuya title: Nascent Synthesis of Leader Sequence-Containing Subgenomic mRNAs in Coronavirus Genome-Length Replicative Intermediate RNA date: 2000-09-30 words: 4033.0 sentences: 184.0 pages: flesch: 48.0 cache: ./cache/cord-273379-w8vy5rl8.txt txt: ./txt/cord-273379-w8vy5rl8.txt summary: RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5′ 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. We purified genome-length RI without contamination of any detectable level of MHV subgenomic mRNAs. We used RNase protection assays to look for nascent subgenomic mRNAs containing the leader sequence in the genome-length RI. If leader-sequence-containing subgenomic mRNA 6 elongates on the genome-length RI, then the RNase protection assay using probe 1 and purified radiolabeled genome-length RI should produce a radiolabeled 300-nt-long RNA fragment (300-nt fragment) that corresponds to the 5Ј-end 300 nt of nascent mRNA 6 (see Fig. 3A ). RNase A treatment of the gel-purified genome-length RI produced RF 1 (Fig. 2B) , and the RNase protection assay demonstrated the presence of nascent leader-sequence-containing subgenomic mRNAs in the genome-length RI. abstract: Abstract Infection with coronavirus results in the accumulation of genomic-sized mRNA and six to eight subgenomic mRNAs that make up a 3′ coterminal nested-set structure. Genome-length negative-strand RNA and subgenomic-length negative-strand RNAs, each of which corresponds to each of the subgenomic mRNAs, also accumulate in infected cells. The present study examined whether the genome-length negative-strand RNA serves as a template for subgenomic mRNA synthesis. Genome-length replicative intermediate (RI) RNA was purified by two-dimensional gel electrophoresis of intracellular RNAs from cells infected with mouse hepatitis virus. RNase A treatment of the purified genome-length RI resulted in the production of the genome-length replicative form RNA, indicating that the genome-length RI included genome-length template RNA. RNase protection assays using the purified genome-length RI and two probes, which corresponded to the 5′ 300-nt region of mRNA 6 and to the same region of mRNA 7, showed the presence of nascent leader sequence-containing subgenomic mRNAs in the genome-length RI. These data demonstrated that the genome-length negative-strand RNA serves as a template for subgenomic mRNA synthesis. url: https://www.ncbi.nlm.nih.gov/pubmed/10998322/ doi: 10.1006/viro.2000.0489 id: cord-329429-ur8g68vp author: Miłek, Justyna title: Coronaviruses in Avian Species – Review with Focus on Epidemiology and Diagnosis in Wild Birds date: 2018-12-10 words: 3809.0 sentences: 187.0 pages: flesch: 50.0 cache: ./cache/cord-329429-ur8g68vp.txt txt: ./txt/cord-329429-ur8g68vp.txt summary: Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3''UTR or 5''UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. This taxonomic name includes IBV which causes a highly contagious disease of chickens, and genetically similar viruses isolated from other domestic galliformes: turkey coronavirus (TCoV), responsible for turkey enteritis, and the more recently detected guinea fowl coronavirus (GfCoV), the aetiological factor of fulminating disease in this species (2, 6, 27) . abstract: Coronaviruses (CoVs) are a large group of enveloped viruses with a single-strand RNA genome, which continuously circulate in mammals and birds and pose a threat to livestock, companion animals, and humans. CoVs harboured by avian species are classified to the genera gamma- and deltacoronaviruses. Within the gamma-CoVs the main representative is avian coronavirus, a taxonomic name which includes the highly contagious infectious bronchitis viruses (IBVs) in chickens and similar viruses infecting other domestic birds such as turkeys, guinea fowls, or quails. Additionally, IBVs have been detected in healthy wild birds, demonstrating that they may act as the vector between domestic and free-living birds. Moreover, CoVs other than IBVs, are identified in wild birds, which suggests that wild birds play a key role in the epidemiology of other gammaCoVs and deltaCoVs. Development of molecular techniques has significantly improved knowledge of the prevalence of CoVs in avian species. The methods adopted in monitoring studies of CoVs in different avian species are mainly based on detection of conservative regions within the viral replicase, nucleocapsid genes, and 3’UTR or 5’UTR. The purpose of this review is to summarise recent discoveries in the areas of epidemiology and diagnosis of CoVs in avian species and to understand the role of wild birds in the virus distribution. url: https://www.ncbi.nlm.nih.gov/pubmed/30584600/ doi: 10.2478/jvetres-2018-0035 id: cord-001397-nrq4ncdf author: Mlera, Luwanika title: The role of viral persistence in flavivirus biology date: 2014-05-12 words: 15593.0 sentences: 812.0 pages: flesch: 46.0 cache: ./cache/cord-001397-nrq4ncdf.txt txt: ./txt/cord-001397-nrq4ncdf.txt summary: Avenues for additional studies include determining if the multifunctional flavivirus protein NS5 has a role in viral persistence, the development of relevant animal models of viral persistence as well as investigating the host responses that allow vector borne flavivirus replication without detrimental effects on infected cells. The SL1 structure is essential for viral replication and acts as a promoter which is targeted initially by NS5 and then delivered to the 3 0 end via cyclization (Filomatori et al., 2006; Zhang et al., 2008; Lodeiro et al., 2009) Although there is low nucleotide conservation between flaviviruses and different CS homology (Hahn et al., 1987) , the 5 0 UTRs of TBFVs share the same genomic organization as the MBFVs (Kofler et al., 2006) Structural proteins Capsid (C) 11 kDa, 114 aa Cytosol/nucleus The capsid protein is a dimeric alpha-helical (Jones et al., 2003) protein and assembles into an icosahedral structure, measuring 30 nm in diameter, which initiates encapsidation of the associated genomic RNA in virus-induced membrane invaginations of the ER (Welsch et al., 2009 ). abstract: In nature, vector-borne flaviviruses are persistently cycled between either the tick or mosquito vector and small mammals such as rodents, skunks, and swine. These viruses account for considerable human morbidity and mortality worldwide. Increasing and substantial evidence of viral persistence in humans, which includes the isolation of RNA by RT-PCR and infectious virus by culture, continues to be reported. Viral persistence can also be established in vitro in various human, animal, arachnid and insect cell lines in culture. Although some research has focused on the potential roles of defective virus particles, evasion of the immune response through the manipulation of autophagy and/or apoptosis, the precise mechanism of flavivirus persistence is still not well understood. We propose additional research for further understanding of how viral persistence is established in different systems. Avenues for additional studies include determining if the multifunctional flavivirus protein NS5 has a role in viral persistence, the development of relevant animal models of viral persistence as well as investigating the host responses that allow vector borne flavivirus replication without detrimental effects on infected cells. Such studies might shed more light on the viral-host relationships, and could be used to unravel the mechanisms for establishment of persistence. url: https://academic.oup.com/femspd/article-pdf/71/2/137/17943040/71-2-137.pdf doi: 10.1111/2049-632x.12178 id: cord-291063-de7v4e5s author: Moens, Ugo title: Silencing Viral MicroRNA as a Novel Antiviral Therapy? date: 2009-05-28 words: 9122.0 sentences: 526.0 pages: flesch: 49.0 cache: ./cache/cord-291063-de7v4e5s.txt txt: ./txt/cord-291063-de7v4e5s.txt summary: The expressions of EBV-encoded miRNAs in clinical samples and computational analysis to predict putative targets were applied to unravel the biological functions of EBV miRNAs. These approaches showed that the miR-BARTs are abundantly expressed in latently infected epithelial cells, nasopharyngeal carcinomas, EBV-associated gastric carcinoma cell lines and tissues, Burkitt''s lymphomas latency type I, EBV positive primary effusion lymphomas, and diffuse large B-cell lymphomas, but at a significantly lower level in B cells. However, computational alignment of the potential HIV-1 miRNAs with specific human T-cell mRNAs identified potential cellular targets including genes encoding CD4, CD28 and interleukin-2, IL-3, and IL-12 [119] . The idea of targeting viral transcripts is not new, and RNA interference has been demonstrated to efficiently mediate inhibition of replication of human pathogenic viruses such as HIV-1, HCV, dengue virus, severe acute respiratory syndrome (SARS) coronavirus, poliovirus, human rhinovirus, influenza A virus, hepatitis D virus, HBV, HSV-1, HPV, JCV, EBV, and CMV in cell culture (reviewed in [12] ). abstract: Viruses are intracellular parasites that ensure their existence by converting host cells into viral particle producing entities or into hiding places rendering the virus invisible to the host immune system. Some viruses may also survive by transforming the infected cell into an immortal tumour cell. MicroRNAs are small non-coding transcripts that function as posttranscriptional regulators of gene expression. Viruses encode miRNAs that regulate expression of both cellular and viral genes, and contribute to the pathogenic properties of viruses. Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. This review describes the miRNAs encoded by human viruses, and discusses the possible therapeutic applications of anti-miRNAs against viral diseases. url: https://doi.org/10.1155/2009/419539 doi: 10.1155/2009/419539 id: cord-345957-wuk2arf9 author: Mohamed, Fakry F. title: Detection and genetic characterization of bovine kobuvirus from calves in Egypt date: 2018-02-08 words: 4245.0 sentences: 219.0 pages: flesch: 61.0 cache: ./cache/cord-345957-wuk2arf9.txt txt: ./txt/cord-345957-wuk2arf9.txt summary: When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Initially, kobuviruses included Aichivirus (AiV), bovine kobuvirus (BKoV), and porcine kobuvirus (PKoV) based on the hosts infected e.g. humans, cattle, 1 3 and swine, respectively. In this study, we report BKoV infections among cattle populations of Egypt, the full-length genome of one Egyptian strain (BKoV/ Egy-1/ KY407744) as well as the phylogenetic analysis of BKoV strains from Cairo and Sharkia provinces. The RNA samples (n = 36) were subjected to RT-PCR for the detection of BKoV using degenerate primers (Univ-Kobu-F and Univ-Kobu-R), which amplify a conserved region in the 3D (RdRp) gene of all kobuviruses [12] ( Table 1 ). abstract: Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-018-3758-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00705-018-3758-1 doi: 10.1007/s00705-018-3758-1 id: cord-285330-td4vr0zv author: Mohammadi, Ali title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus date: 2015-11-12 words: 3157.0 sentences: 180.0 pages: flesch: 56.0 cache: ./cache/cord-285330-td4vr0zv.txt txt: ./txt/cord-285330-td4vr0zv.txt summary: title: Viral quantity and pathological changes in broilers experimentally infected by IRFIBV32 isolate of infectious bronchitis virus An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. In this study, we identified IBV load in different tissues of experimentally infected broilers to clarify the replication strength of IRFIBV32 Isolate at intervals post challenge. Gross lesions were recorded and their trachea, lungs, kidneys, caecal tonsils, testes and ovaries were aseptically collected separately for the virus detection, titration and histopathological evaluations. We detected the viral RNA in the caecal tonsils of infected chicken from 1 to 20 dpi and the maximal loads of the virus were on 5 dpi. Pathogenesis and tissue distribution of avian infectious bronchitis virus isolate IRFIBV32 (793/b serotype) in experimentally infected broiler chickens Development and evaluation of a real-time Taqman RT-PCR assay for the detection of infectious bronchitis virus from infected chickens abstract: An Iranian isolate of avian infectious bronchitis virus IRFIBV32 was quantified in experimentally infected broilers using real-time reverse transcriptase polymerase chain reaction and histopathological changes was investigated. Thirty-six 3-week-old commercial broilers were inoculated by 10(5) ELD50/0.1 ml of the virus. On the various days post inoculation (dpi) different tissues were collected. The virus strongly started the replication in trachea at 1 dpi and reached to the maximum titer at 3 dpi. The highest IBV RNA level was shown in this organ. In lung, the virus was replicated with the titer lower than that of the trachea, but it rose up more at 5 dpi. The kidneys were the tissues with the least viral genome copy number, although the duration of the virus presence was considerable. The virus replicated in testes sooner than ovaries also disappeared sooner but the maximum viral yield in the ovaries was more. The virus titer in the studied tissues had an interesting fluctuation especially in caecal tonsils. Testes and ovaries were the organs that the virus could reactivate without using any chemical. The most severe lesions were observed in tracheae but they appeared in the lungs later. Lymphocyte infiltration in the kidneys was noted from 5 dpi even sooner than the lungs. There were no lesions in the caecal tonsils, testes and ovaries in spite of the virus replication in a high titer. url: https://www.ncbi.nlm.nih.gov/pubmed/26645044/ doi: 10.1007/s13337-015-0286-4 id: cord-295351-0zr2e8lh author: Mohd Ropidi, Muhammad Izzuddin title: Endoplasmic reticulum: a focal point of Zika virus infection date: 2020-01-20 words: 7845.0 sentences: 389.0 pages: flesch: 35.0 cache: ./cache/cord-295351-0zr2e8lh.txt txt: ./txt/cord-295351-0zr2e8lh.txt summary: Following ZIKV infection, the accumulation of misfolded virus polyproteins in the ER lumen overwhelms the ER protein-folding capacity leading to ER stress and triggers the activation of the UPR (Fig. 2) [47] . Following the dissociation of GRP78 that unmasks the GLS, ATF6 translocate to the Golgi apparatus and undergoes sequential proteolytic processing by Fig. 2 ZIKV-induced ER stress initiates host cell unfolded protein response (UPR). ZIKV infection induces ER stress due to the increased amount of unfolded/misfolded viral (red strand) and host cell (grey strand) protein aggregates in the ER lumen. To summarize, ZIKV virus bypasses the UPR by inhibiting stress granules assembly and reticulophagy to ensure continuous viral protein translation and virion production while simultaneously protecting the virus from host cell defense mechanisms. abstract: Zika virus (ZIKV) belongs to the Flavivirus genus of the Flaviviridae family. It is an arbovirus that can cause congenital abnormalities and is sexually transmissible. A series of outbreaks accompanied by unexpected severe clinical complications have captured medical attention to further characterize the clinical features of congenital ZIKV syndrome and its underlying pathophysiological mechanisms. Endoplasmic reticulum (ER) and ER-related proteins are essential in ZIKV genome replication. This review highlights the subcellular localization of ZIKV to the ER and ZIKV modulation on the architecture of the ER. This review also discusses ZIKV interaction with ER proteins such as signal peptidase complex subunit 1 (SPCS1), ER membrane complex (EMC) subunits, and ER translocon for viral replication. Furthermore, the review covers several important resulting effects of ZIKV infection to the ER and cellular processes including ER stress, reticulophagy, and paraptosis-like death. Pharmacological targeting of ZIKV-affected ER-resident proteins and ER-associated components demonstrate promising signs of combating ZIKV infection and rescuing host organisms from severe neurologic sequelae. url: https://www.ncbi.nlm.nih.gov/pubmed/31959174/ doi: 10.1186/s12929-020-0618-6 id: cord-271526-14nfqusv author: Molenkamp, Richard title: Identification of a Specific Interaction between the Coronavirus Mouse Hepatitis Virus A59 Nucleocapsid Protein and Packaging Signal date: 1997-12-08 words: 5535.0 sentences: 341.0 pages: flesch: 56.0 cache: ./cache/cord-271526-14nfqusv.txt txt: ./txt/cord-271526-14nfqusv.txt summary: To determine the specificity of the nucleocapsid pro-RNA-protein complexes (Fig. 3, lanes 8-10 and 12) , tein-Ps180 RNA interaction in UV cross-linking assays, clearly indicating that the observed supershift was not competition experiments were performed. This interaction was studied by gel retardation and UV Lysates were prepared from the virus peak fractions (pcross-linking assays using an RNA probe containing the lysate) and from the gradient bottom fractions (b-lysate; 69-nt Ps and the N protein from MHV-A59 infected cell negative control). A structural model for coronaviruses was flanked by non-MHV sequences could confer specific proposed, in which a spherical core, composed of a combination of N and M proteins, was present in addition to encapsidation to a heterologous RNA in MHV infected INTERACTION BETWEEN NUCLEOCAPSID PROTEIN AND PACKAGING SIGNAL of a murine coronavirus in the absence of helper virus. abstract: Abstract The coronavirus mouse hepatitis virus (MHV) is an enveloped positive stranded RNA virus. In infected cells MHV produces a 3′ coterminal nested set of subgenomic messenger RNAs. Only the genomic RNA, however, is encapsidated by the nucleocapsid protein and incorporated in infectious MHV virions. It is believed that an RNA packaging signal (Ps), present only in the genomic RNA, is responsible for this selectivity. Earlier studies mapped this signal to a 69-nt stem–loop structure positioned in the 3′ end of ORF1b. The selective encapsidation mechanism probably initiates by specific interaction of the packaging signal with the nucleocapsid protein. In this study we demonstrate thein vitrointeraction of the MHV-A59 nucleocapsid protein with the packaging signal of MHV using gel retardation and UV cross-linking assays. This interaction was observed not only with the nucleocapsid protein from infected cells but also with that from purified virions and from cells expressing a recombinant nucleocapsid protein. The specificity of the interaction was demonstrated by competition experiments with nonlabeled Ps containing RNAs, tRNA, and total cytoplasmic RNA. The results indicated that no virus specific modification of the N-protein or the presence of other viral proteins are required for thisin vitrointeraction. The assays described in this report provide us with a powerful tool for studying encapsidation (initiation) in more detail. url: https://api.elsevier.com/content/article/pii/S004268229798867X doi: 10.1006/viro.1997.8867 id: cord-275795-ee7qyw5h author: Monette, Anne title: T Lymphocytes as Measurable Targets of Protection and Vaccination Against Viral Disorders date: 2018-10-24 words: 28265.0 sentences: 1205.0 pages: flesch: 38.0 cache: ./cache/cord-275795-ee7qyw5h.txt txt: ./txt/cord-275795-ee7qyw5h.txt summary: We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. Since that time, the occurrence of epidemics and outbreaks are now at lower risk, following the introduction of massive vaccination programs able to induce immune system targeting of viruses causing severe disorders affecting distinct geographical locations, and with many epidemiological reports demonstrating long-term efficacy of viral control of non-naïve populations. This approach is being developed to use virus-infected cell-killing antibodies that produce an antiviral environment; these termed antibody-dependent cellular cytotoxicity (ADCC)-mediating antibodies, which are predicted to link innate and adaptive immune responses, and is becoming possible due to new technologies for rapid isolation and characterization of monoclonal antibodies targeting conserved regions of influenza virus, reviewed in Jegaskanda et al. abstract: Continuous epidemiological surveillance of existing and emerging viruses and their associated disorders is gaining importance in light of their abilities to cause unpredictable outbreaks as a result of increased travel and vaccination choices by steadily growing and aging populations. Close surveillance of outbreaks and herd immunity are also at the forefront, even in industrialized countries, where previously eradicated viruses are now at risk of re-emergence due to instances of strain recombination, contractions in viral vector geographies, and from their potential use as agents of bioterrorism. There is a great need for the rational design of current and future vaccines targeting viruses, with a strong focus on vaccine targeting of adaptive immune effector memory T cells as the gold standard of immunity conferring long-lived protection against a wide variety of pathogens and malignancies. Here, we review viruses that have historically caused large outbreaks and severe lethal disorders, including respiratory, gastric, skin, hepatic, neurologic, and hemorrhagic fevers. To observe trends in vaccinology against these viral disorders, we describe viral genetic, replication, transmission, and tropism, host-immune evasion strategies, and the epidemiology and health risks of their associated syndromes. We focus on immunity generated against both natural infection and vaccination, where a steady shift in conferred vaccination immunogenicity is observed from quantifying activated and proliferating, long-lived effector memory T cell subsets, as the prominent biomarkers of long-term immunity against viruses and their associated disorders causing high morbidity and mortality rates. url: https://www.sciencedirect.com/science/article/pii/S1937644818300844 doi: 10.1016/bs.ircmb.2018.07.006 id: cord-291749-revhbd0q author: Mongan, Arthur Elia title: Portable sequencer in the fight against infectious disease date: 2019-10-03 words: 3735.0 sentences: 222.0 pages: flesch: 40.0 cache: ./cache/cord-291749-revhbd0q.txt txt: ./txt/cord-291749-revhbd0q.txt summary: Diagnosis can be upheld by observing the cause of disease under the microscope or detecting the presence of nucleic acid and proteins of the pathogens. Sequencing of PCR amplicons or whole pathogen genomic DNA can be applied to comprehensively screen for infecting agents and their drug resistance phenotype, if exists, at the same time. Sequencing ensures detection of DNA composition unique to an organism, the presence of antimicrobials-destroying genes, or mutation that can change the function or conformation of proteins related to drug resistance. Targeted sequencing with MinION is powerful and fast to detect pathogens in clinical samples. A novel diagnostic method for malaria using loopmediated isothermal amplification (LAMP) and MinION TM nanopore sequencer Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis MinION nanopore sequencing of multiple displacement amplified Mycobacteria DNA direct from sputum. abstract: Infectious disease is still a major threat in the world today. Five decades ago, it was considered soon to be eradicated, but the adaptation of pathogens to environmental pressure, such as antimicrobials, encouraged the emergence and reemergence of infectious disease. The fight with infectious disease starts with prevention, diagnosis, and treatment. Diagnosis can be upheld by observing the cause of disease under the microscope or detecting the presence of nucleic acid and proteins of the pathogens. The molecular techniques span from classical polymerase chain reaction (PCR) to sequencing the nucleic acid composition. Here, we are reviewing the works have been undertaken to utilize a portable sequencer, MinION, in various aspects of infectious disease management. url: https://www.ncbi.nlm.nih.gov/pubmed/31582773/ doi: 10.1038/s10038-019-0675-4 id: cord-274567-xd37wxxf author: Monpoeho, S. title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid date: 2002-07-13 words: 3284.0 sentences: 161.0 pages: flesch: 47.0 cache: ./cache/cord-274567-xd37wxxf.txt txt: ./txt/cord-274567-xd37wxxf.txt summary: title: Application of a Real-Time Polymerase Chain Reaction with Internal Positive Control for Detection and Quantification of Enterovirus in Cerebrospinal Fluid A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. Detection of EVs by amplification of viral RNA from CSF using reverse transcriptase-polymerase chain reaction (RT-PCR) assay has already been reported [4, 5, 6 ]. The fluorogenic RT-PCR was applied to detection of EVs in the CSF of 104 patients presenting with signs of meningitis. Amplicor enterovirus polymerase chain reaction in patients with aseptic meningitis: a sensitive test limited by amplification inhibitors Comparison of use of cerebrospinal fluid, serum, and throat swab specimens in diagnosis of enteroviral acute neurological infection by a rapid RNA detection PCR assay abstract: A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) method based on TaqMan technology was developed to determine the presence and amount of enterovirus RNA. In order to prevent false-negative results, a one-step multiplex RT-PCR was optimized. It contains two dual-labelled fluorogenic probes to quantify the 5′ noncoding region of enterovirus and detect an internal positive control. In the present study, 104 cerebrospinal fluid samples collected during an outbreak of enteroviral meningitis were analyzed using this method. Amplification of the internal positive control was effective in all but two specimens, confirming the absence of PCR inhibitors and allowing the results of amplification to be validated. The sensitivity of the RT-PCR was 96.8%, while that of cell culture was 34.9%. Genomic viral loads found ranged between 3.3 and 5.9 log(10) copies per milliliter of cerebrospinal fluid (mean, 4.8 log(10) copies/ml). This fluorogenic enterovirus RT-PCR allows large numbers of samples to be screened rapidly. Moreover, its sensitivity and reproducibility make it highly reliable. With these characteristics, the enterovirus RT-PCR can be a useful tool that may offer considerable benefit in the clinical management of patients with enteroviral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/12172744/ doi: 10.1007/s10096-002-0766-5 id: cord-334315-ymkrgj0h author: Moon, Stephanie L. title: Cytoplasmic Viruses: Rage against the (Cellular RNA Decay) Machine date: 2013-12-05 words: 1995.0 sentences: 100.0 pages: flesch: 43.0 cache: ./cache/cord-334315-ymkrgj0h.txt txt: ./txt/cord-334315-ymkrgj0h.txt summary: This review describes the myriad ways that viruses deal with the general host RNA decay machinery that is active in the cell immediately upon viral infection-turning what, at first, appears to be very hostile territory for a foreign transcript into a sort of ''''promised land'''' for viral gene expression. Disparate RNA viruses have, therefore, evolved unique mechanisms by which they disarm host RNA decay pathways by inactivating or proteolytically degrading important nucleases to promote productive viral infections. In addition, to make a cell more amenable to virus production, these virally encoded nucleases may also create a new ''''sandbox'''' in the cytoplasm for viral RNAs by initiating the large-scale decay of cellular mRNAs and dramatically altering the landscape of host gene expression. Considering the importance of RNA stability in regulating transcript abundance, the inactivation or commandeering of cellular RNA decay factors by viruses is likely to significantly alter host gene expression. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/24339774/ doi: 10.1371/journal.ppat.1003762 id: cord-289407-8fje16z1 author: Moore, G. title: Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England date: 2020-09-25 words: 4720.0 sentences: 328.0 pages: flesch: 59.0 cache: ./cache/cord-289407-8fje16z1.txt txt: ./txt/cord-289407-8fje16z1.txt summary: Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. 6 Air samples taken during tracheostomy procedures, high flow nasal oxygen treatment, non-invasive ventilation and nebulisation have not contained SARS-CoV-2 RNA 7 and HCWs exposed to unrecognised COVID-19 patients undergoing similar high-risk AGPs have not become infected. . https://doi.org/10.1101/2020.09.24.20191411 doi: medRxiv preprint Several studies, utilising a range of air and surface sampling methods, have been carried out to determine the presence and prevalence of SARS-CoV-2 in the healthcare environment. [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] The detection of viral RNA in air samples differs with study with some reporting widespread airborne contamination 14, 18, 21 but many reporting low or non-detectable concentrations 13, 15, 16, 19 even in samples collected 10 cm from the face of positive patients. Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients abstract: Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. The presence of SARS-CoV-2 in the air and on environmental surfaces around hospitalised patients, with and without respiratory symptoms, was investigated. Environmental sampling was carried out within eight hospitals in England during the first wave of the COVID-19 outbreak. Samples were analysed using reverse transcription polymerase chain reaction (RT-PCR) and virus isolation assays. SARS-CoV-2 RNA was detected on 30 (8.9%) of 336 environmental surfaces. Ct values ranged from 28.8 to 39.1 equating to 2.2 x 105 to 59 genomic copies/swab. Concomitant bacterial counts were low, suggesting the cleaning performed by nursing and domestic staff across all eight hospitals was effective. SARS-CoV-2 RNA was detected in four of 55 air samples taken < 1 m from four different patients. In all cases, the concentration of viral RNA was low and ranged from < 10 to 460 genomic copies per m3 of air. Infectious virus was not recovered from any of the PCR positive samples analysed. Effective cleaning can reduce the risk of fomite (contact) transmission but some surface types may facilitate the survival, persistence and/or dispersal of SARS-CoV-2. The presence of low or undetectable concentrations of viral RNA in the air supports current guidance on the use of specific PPE ensembles for aerosol and non-aerosol generating procedures. url: http://medrxiv.org/cgi/content/short/2020.09.24.20191411v1?rss=1 doi: 10.1101/2020.09.24.20191411 id: cord-325925-010xj69x author: Mordecai, Gideon J title: Endangered wild salmon infected by newly discovered viruses date: 2019-09-03 words: 5549.0 sentences: 259.0 pages: flesch: 48.0 cache: ./cache/cord-325925-010xj69x.txt txt: ./txt/cord-325925-010xj69x.txt summary: Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. Together, sequencing of dead or moribund aquaculture salmon and live-sampled wild salmon, in-situ hybridization, and epidemiological surveys revealed that previously unknown viruses, some of which are associated with disease, infect wild salmon from different populations. High-throughput RT-PCR screening of >6000 wild juvenile Chinook and sockeye salmon showed dissimilar geographical distributions of infected fish, reflecting differences in epidemiological patterns of transmission and infection dynamics for each of the viruses ( Figure 2) . abstract: The collapse of iconic, keystone populations of sockeye (Oncorhynchus nerka) and Chinook (Oncorhynchus tshawytscha) salmon in the Northeast Pacific is of great concern. It is thought that infectious disease may contribute to declines, but little is known about viruses endemic to Pacific salmon. Metatranscriptomic sequencing and surveillance of dead and moribund cultured Chinook salmon revealed a novel arenavirus, reovirus and nidovirus. Sequencing revealed two different arenavirus variants which each infect wild Chinook and sockeye salmon. In situ hybridisation localised arenavirus mostly to blood cells. Population surveys of >6000 wild juvenile Chinook and sockeye salmon showed divergent distributions of viruses, implying different epidemiological processes. The discovery in dead and dying farmed salmon of previously unrecognised viruses that are also widely distributed in wild salmon, emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks, and the threat that these viruses may pose to aquaculture. url: https://doi.org/10.7554/elife.47615 doi: 10.7554/elife.47615 id: cord-146406-85usg3uh author: Morelli, Marco J. title: Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing date: 2011-01-27 words: 4376.0 sentences: 221.0 pages: flesch: 55.0 cache: ./cache/cord-146406-85usg3uh.txt txt: ./txt/cord-146406-85usg3uh.txt summary: Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the Inoculum used to initiate experimental infection. Some of the higher frequency polymorphisms identified encoded changes within codons associated with heparan sulphate binding and were present in both feet lesions revealing intermediate stages in the evolution of a tissue-culture adapted virus replicating within a mammalian host. The sequence diversity of viral populations within individual hosts is the starting 24 material for selection and subsequent evolution of RNA viruses such as foot--and--mouth 25 disease virus (FMDV). The sequence diversity of viral populations within individual hosts is the starting 24 material for selection and subsequent evolution of RNA viruses such as foot--and--mouth 25 disease virus (FMDV). Validation and analysis of sequence diversity in the samples 148 The frequency of site--specific polymorphisms was estimated from the frequency of 149 mismatches of the aligned reads to the reference genome. abstract: The sequence diversity of viral populations within individual hosts is the starting material for selection and subsequent evolution of RNA viruses such as foot-and-mouth disease virus (FMDV). Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the Inoculum used to initiate experimental infection. Genomic sequences were determined in duplicate sequencing runs, and the consensus sequence determined by NGS, for the Inoculum, was identical to that previously determined using the Sanger method. However, NGS reveals the fine polymorphic sub-structure of the viral population, from nucleotide variants present at just below 50% frequency to those present at fractions of 1%. Some of the higher frequency polymorphisms identified encoded changes within codons associated with heparan sulphate binding and were present in both feet lesions revealing intermediate stages in the evolution of a tissue-culture adapted virus replicating within a mammalian host. We identified 2,622, 1,434 and 1,703 polymorphisms in the Inoculum, and in the two foot lesions respectively: most of the substitutions occurred only in a small fraction of the population and represent the progeny from recent cellular replication prior to onset of any selective pressures. We estimated an upper limit for the genome-wide mutation rate of the virus within a cell to be 7.8 x 10-4 per nt. The greater depth of detection, achieved by NGS, demonstrates that this method is a powerful and valuable tool for the dissection of FMDV populations within-hosts. url: https://arxiv.org/pdf/1101.5371v1.pdf doi: nan id: cord-295130-e7j7kac0 author: Moreno-Contreras, Joaquín title: Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages date: 2020-09-22 words: 2906.0 sentences: 122.0 pages: flesch: 58.0 cache: ./cache/cord-295130-e7j7kac0.txt txt: ./txt/cord-295130-e7j7kac0.txt summary: In this study, we compared the RT-qPCR results from 253 paired samples obtained from saliva and swabs of ambulatory patients; the RNA in the swab samples was extracted using a commercial RNA purification kit, and the saliva samples were directly mixed with a lysis buffer, boiled, and used for the RT-qPCR protocol. To evaluate if saliva is a good source of viral RNA for the RT-qPCR, we determined the presence of the SARS-CoV-2 genome in paired saliva and swab samples from 253 ambulatory patients. Direct lysis of nasopharyngeal or oropharyngeal swab samples in viral transport medium using the QE buffer has been reported as a suitable method for direct RT-qPCR for SARS-CoV-2 detection, with rates similar to those of methods based on column purification (11, 15) . abstract: As part of any plan to lift or ease the confinement restrictions that are in place in many different countries, there is an urgent need to increase the capacity of laboratory testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Detection of the viral genome through reverse transcription-quantitative PCR (RT-qPCR) is the gold standard for this virus; however, the high demand of the materials and reagents needed to sample individuals, purify the viral RNA, and perform the RT-qPCR has resulted in a worldwide shortage of several of these supplies. Here, we show that directly lysed saliva samples can serve as a suitable source for viral RNA detection that is less expensive and can be as efficient as the classical protocol, which involves column purification of the viral RNA. In addition, it bypasses the need for swab sampling, decreases the risk of the health care personnel involved in the testing process, and accelerates the diagnostic procedure. url: https://doi.org/10.1128/jcm.01659-20 doi: 10.1128/jcm.01659-20 id: cord-263645-wupre5uj author: Morgan, Brittany S title: Insights into the development of chemical probes for RNA date: 2018-09-19 words: 7104.0 sentences: 341.0 pages: flesch: 43.0 cache: ./cache/cord-263645-wupre5uj.txt txt: ./txt/cord-263645-wupre5uj.txt summary: One important example is the development of chemical probes, which has greatly progressed the study of proteins and related diseases (11, 12) but has been challenging for non-ribosomal RNAs. This powerful chemical tool requires small molecules with well-defined biological activity, cell permeability, and selectivity to accurately and reliably probe specific mechanistic and phenotypic questions (11, 12) . While ligands that bind non-ribosomal RNA in vitro have been reported for decades, the development of chemical probes with evidence of specific small molecule:RNA engagement in cell or animal models has dramatically increased in the last four years. Recent studies report several drug-like small molecules that target a range of RNAs in animal models, including riboswitches (15) , miRNAs, (16, 17) splice sites (18) , and mature mRNAs (19) , at least one of which is currently in clinical trials (NCT02268552). abstract: Over the past decade, the RNA revolution has revealed thousands of non-coding RNAs that are essential for cellular regulation and are misregulated in disease. While the development of methods and tools to study these RNAs has been challenging, the power and promise of small molecule chemical probes is increasingly recognized. To harness existing knowledge, we compiled a list of 116 ligands with reported activity against RNA targets in biological systems (R-BIND). In this survey, we examine the RNA targets, design and discovery strategies, and chemical probe characterization techniques of these ligands. We discuss the applicability of current tools to identify and evaluate RNA-targeted chemical probes, suggest criteria to assess the quality of RNA chemical probes and targets, and propose areas where new tools are particularly needed. We anticipate that this knowledge will expedite the discovery of RNA-targeted ligands and the next phase of the RNA revolution. url: https://doi.org/10.1093/nar/gky718 doi: 10.1093/nar/gky718 id: cord-310967-15mv5yx7 author: Morris, Vincent L. title: Characterization of coronavirus JHM variants isolated from wistar furth rats with a viral-induced demyelinating disease date: 1989-03-31 words: 5838.0 sentences: 301.0 pages: flesch: 56.0 cache: ./cache/cord-310967-15mv5yx7.txt txt: ./txt/cord-310967-15mv5yx7.txt summary: One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In this report, we investigated viral variants that arose in the CNS of rats with a JHM-induced demyelinating disease and studied the effect of alterations in their mRNAs. When lo-day-old rats were inoculated with ATllf brain virus or ATlIe brain virus, the rats developed a rapid encephalitis instead of the more chronic demyelinating disease that has previously been seen with wild-type parental JHM virus (Sorensen et al., 1980; Jackson et al., 1984) and was observed with ATIIf cord virus-injected rats. In contrast, when 2-day-old rats were inoculated with ATllf cord virus, the more chronic CNS disease resulted instead of the rapid encephalitis that has been reported for wild-type JHM (Sorensen et a/., 1980; Parham et a/., 1986) and was observed with the ATIIf brain virus variant. abstract: Abstract Murine hepatitis virus (MHV) can cause neurological disease when inoculated intracerebrally (ic) into mice and rats. Specifically the JHM strain of MHV (MHV-JHM) generally causes an acute encephalitis when inoculated is into 2-day-old Wistar Furth rats. In contrast, JHM generally produces a chronic demyelinating disease with resulting posterior paralysis when inoculated is into 10-day-old Wistar Furth rats. In addition, while JHM readily produces a productive infection in a mouse fibroblast cell line (L-2), it does not form syncytia or replicate well in a tissue cell line of glial origin (G26-24). We have isolated and characterized three MHV-JHM viral variants from the central nervous system of two Wistar Furth rats with a MHV-JHM-induced demyelinating disease. The pattern of viral-specific mRNA for all three of these variants differed from what was observed for the wild-type parental MHV-JHM that had been passaged only in tissue culture. One of these variants, ATIIf cord virus, which induced a chronic demyelinating disease in 2- or 10-day-old intracerebrally inoculated Wistar Furth rats, had a deletion in the coding region of the peplomer glycoprotein mRNA. In addition, this variant formed massive syncytia and replicated well in G26-24 cells. We have not detected this deletion in the other two JHM variants, ATIIf brain virus and ATIIe brain virus. ATIIf brain virus and ATIIe brain virus primarily produced an acute encephalitis when reinoculated into 2-or 10-day-old Wistar Furth rats. In addition, these two variants did not form syncytia and had a reduced ability to replicate in G26-24 cells. url: https://www.ncbi.nlm.nih.gov/pubmed/2538027/ doi: 10.1016/0042-6822(89)90048-2 id: cord-325137-6c6er06a author: Moser, Lindsey A. title: A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses date: 2016-06-07 words: 9945.0 sentences: 514.0 pages: flesch: 53.0 cache: ./cache/cord-325137-6c6er06a.txt txt: ./txt/cord-325137-6c6er06a.txt summary: Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Thus, in some instances, large cDNAs, double-stranded DNAs (dsDNAs), or clones containing at least two-thirds of the genome may also be regulated as SAs. Positive-sense RNA viruses span multiple virus families, and the infectious nature of these genomic RNAs coupled with SA/biosafety/biosecurity concerns inhibit rapid removal from BSL-3/4 containment (7) or transport and handling of RNA samples that are known to contain viral genomes from outbreak settings. abstract: Several biosafety level 3 and/or 4 (BSL-3/4) pathogens are high-consequence, single-stranded RNA viruses, and their genomes, when introduced into permissive cells, are infectious. Moreover, many of these viruses are select agents (SAs), and their genomes are also considered SAs. For this reason, cDNAs and/or their derivatives must be tested to ensure the absence of infectious virus and/or viral RNA before transfer out of the BSL-3/4 and/or SA laboratory. This tremendously limits the capacity to conduct viral genomic research, particularly the application of next-generation sequencing (NGS). Here, we present a sequence-independent method to rapidly amplify viral genomic RNA while simultaneously abolishing both viral and genomic RNA infectivity across multiple single-stranded positive-sense RNA (ssRNA+) virus families. The process generates barcoded DNA amplicons that range in length from 300 to 1,000 bp, which cannot be used to rescue a virus and are stable to transport at room temperature. Our barcoding approach allows for up to 288 barcoded samples to be pooled into a single library and run across various NGS platforms without potential reconstitution of the viral genome. Our data demonstrate that this approach provides full-length genomic sequence information not only from high-titer virion preparations but it can also recover specific viral sequence from samples with limited starting material in the background of cellular RNA, and it can be used to identify pathogens from unknown samples. In summary, we describe a rapid, universal standard operating procedure that generates high-quality NGS libraries free of infectious virus and infectious viral RNA. IMPORTANCE This report establishes and validates a standard operating procedure (SOP) for select agents (SAs) and other biosafety level 3 and/or 4 (BSL-3/4) RNA viruses to rapidly generate noninfectious, barcoded cDNA amenable for next-generation sequencing (NGS). This eliminates the burden of testing all processed samples derived from high-consequence pathogens prior to transfer from high-containment laboratories to lower-containment facilities for sequencing. Our established protocol can be scaled up for high-throughput sequencing of hundreds of samples simultaneously, which can dramatically reduce the cost and effort required for NGS library construction. NGS data from this SOP can provide complete genome coverage from viral stocks and can also detect virus-specific reads from limited starting material. Our data suggest that the procedure can be implemented and easily validated by institutional biosafety committees across research laboratories. url: https://www.ncbi.nlm.nih.gov/pubmed/27822536/ doi: 10.1128/msystems.00039-15 id: cord-328633-c31xsyeo author: Moser, Michael J. title: Thermostable DNA Polymerase from a Viral Metagenome Is a Potent RT-PCR Enzyme date: 2012-06-04 words: 7868.0 sentences: 441.0 pages: flesch: 54.0 cache: ./cache/cord-328633-c31xsyeo.txt txt: ./txt/cord-328633-c31xsyeo.txt summary: Most RT-PCR protocols rely on two DNA polymerase (Pol) enzymes; a retroviral reverse transcriptase (RT) to copy RNA into cDNA and a thermostable DNA Pol to amplify the target sequence. Despite their wide use and general reliability, existing twoenzyme RT-PCR systems have several documented performance problems attributed to deficiencies inherent in retroviral RTs: 1) poor reagent stability, 2) low fidelity, 3) frequent rearrangements during cDNA synthesis, 4) secondary enzymatic activities (i.e. RNase H and strand switching), 5) bias for specific primers and templates, and 6) inhibition of PCR Pol enzymes [3, 4, 5, 6, 7] . We describe the discovery and biochemical attributes of one of these, 3173 Pol, its inherent RT activity and its incorporation into a single-enzyme PyroScriptH 2X RT-PCR Master Mix. The sensitivity, specificity and overall performance of this mix were compared to available one-and two-enzyme systems using a control MS2 RNA bacteriophage template, the clinically-relevant influenza A RNA and commonly used reference mRNA transcripts. abstract: Viral metagenomic libraries are a promising but previously untapped source of new reagent enzymes. Deep sequencing and functional screening of viral metagenomic DNA from a near-boiling thermal pool identified clones expressing thermostable DNA polymerase (Pol) activity. Among these, 3173 Pol demonstrated both high thermostability and innate reverse transcriptase (RT) activity. We describe the biochemistry of 3173 Pol and report its use in single-enzyme reverse transcription PCR (RT-PCR). Wild-type 3173 Pol contains a proofreading 3′-5′ exonuclease domain that confers high fidelity in PCR. An easier-to-use exonuclease-deficient derivative was incorporated into a PyroScript RT-PCR master mix and compared to one-enzyme (Tth) and two-enzyme (MMLV RT/Taq) RT-PCR systems for quantitative detection of MS2 RNA, influenza A RNA, and mRNA targets. Specificity and sensitivity of 3173 Pol-based RT-PCR were higher than Tth Pol and comparable to three common two-enzyme systems. The performance and simplified set-up make this enzyme a potential alternative for research and molecular diagnostics. url: https://doi.org/10.1371/journal.pone.0038371 doi: 10.1371/journal.pone.0038371 id: cord-341034-2oigu75k author: Moser, Theresa S. title: AMP-Activated Kinase Restricts Rift Valley Fever Virus Infection by Inhibiting Fatty Acid Synthesis date: 2012-04-19 words: 9932.0 sentences: 511.0 pages: flesch: 45.0 cache: ./cache/cord-341034-2oigu75k.txt txt: ./txt/cord-341034-2oigu75k.txt summary: We found that the energy regulator AMPK, which potently inhibits fatty acid synthesis, restricts infection of the Bunyavirus, Rift Valley Fever Virus (RVFV), an important re-emerging arthropod-borne human pathogen for which there are no effective vaccines or therapeutics. Furthermore, we found that AMPK is activated during RVFV infection, leading to the phosphorylation and inhibition of acetyl-CoA carboxylase, the first rate-limiting enzyme in fatty acid synthesis. Consistent with a role for AMPK both in early events during viral replication and in spread as measured by plaque assay Figure 1A ), we observed an increase in viral infection at early time points before virus spread, as well as increased spread in cells lacking AMPK by monitoring the production of RVFV N protein over time by microscopy ( Figure S1A-B) . We have found that energy-mediated activation of AMPK restricts infection of the Bunyavirus Rift Valley fever virus by decreasing levels of fatty acid synthesis. abstract: The cell intrinsic innate immune responses provide a first line of defense against viral infection, and often function by targeting cellular pathways usurped by the virus during infection. In particular, many viruses manipulate cellular lipids to form complex structures required for viral replication, many of which are dependent on de novo fatty acid synthesis. We found that the energy regulator AMPK, which potently inhibits fatty acid synthesis, restricts infection of the Bunyavirus, Rift Valley Fever Virus (RVFV), an important re-emerging arthropod-borne human pathogen for which there are no effective vaccines or therapeutics. We show restriction of RVFV both by AMPK and its upstream activator LKB1, indicating an antiviral role for this signaling pathway. Furthermore, we found that AMPK is activated during RVFV infection, leading to the phosphorylation and inhibition of acetyl-CoA carboxylase, the first rate-limiting enzyme in fatty acid synthesis. Activating AMPK pharmacologically both restricted infection and reduced lipid levels. This restriction could be bypassed by treatment with the fatty acid palmitate, demonstrating that AMPK restricts RVFV infection through its inhibition of fatty acid biosynthesis. Lastly, we found that this pathway plays a broad role in antiviral defense since additional viruses from disparate families were also restricted by AMPK and LKB1. Therefore, AMPK is an important component of the cell intrinsic immune response that restricts infection through a novel mechanism involving the inhibition of fatty acid metabolism. url: https://doi.org/10.1371/journal.ppat.1002661 doi: 10.1371/journal.ppat.1002661 id: cord-260705-huyyw5z6 author: Moshe, Adi title: Virus-Induced Aggregates in Infected Cells date: 2012-10-17 words: 5063.0 sentences: 265.0 pages: flesch: 39.0 cache: ./cache/cord-260705-huyyw5z6.txt txt: ./txt/cord-260705-huyyw5z6.txt summary: During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intraand intercellular transportation. In plant cells, both RNA and DNA viruses are associated with large inclusions detected in the cytoplasm and nucleus, however, their role in virus propagation or oppositely in virus restraint is less investigated than in infected mammalian cells. In general, mammalian and plant viruses make use of aggregates as scaffolds for anchoring the replication complex, increasing the local concentration of viral and host components required for replication and assembly, and shielding the process of replication from host defense. abstract: During infection, many viruses induce cellular remodeling, resulting in the formation of insoluble aggregates/inclusions, usually containing viral structural proteins. Identification of aggregates has become a useful diagnostic tool for certain viral infections. There is wide variety of viral aggregates, which differ by their location, size, content and putative function. The role of aggregation in the context of a specific virus is often poorly understood, especially in the case of plant viruses. The aggregates are utilized by viruses to house a large complex of proteins of both viral and host origin to promote virus replication, translation, intra- and intercellular transportation. Aggregated structures may protect viral functional complexes from the cellular degradation machinery. Alternatively, the activation of host defense mechanisms may involve sequestration of virus components in aggregates, followed by their neutralization as toxic for the host cell. The diversity of virus-induced aggregates in mammalian and plant cells is the subject of this review. url: https://www.ncbi.nlm.nih.gov/pubmed/23202461/ doi: 10.3390/v4102218 id: cord-015527-ph576eji author: Mostajo, Nelly F title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes date: 2019-09-30 words: 8386.0 sentences: 441.0 pages: flesch: 56.0 cache: ./cache/cord-015527-ph576eji.txt txt: ./txt/cord-015527-ph576eji.txt summary: Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species. abstract: Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108008/ doi: 10.1093/nargab/lqz006 id: cord-009662-ntjngiem author: Moulton, Jon D. title: Using Morpholinos to Control Gene Expression date: 2007-01-15 words: 11606.0 sentences: 583.0 pages: flesch: 48.0 cache: ./cache/cord-009662-ntjngiem.txt txt: ./txt/cord-009662-ntjngiem.txt summary: When delivering Morpholinos to cell cultures using Endo-Porter, starting with a 10 µM Morpholino concentration for both fluorescent delivery assays and functional experiments increases the chances that the fluorescence will be visible in the cytosol and that the first functional experiment will produce measurable results. However, assaying only for a phenotypic effect becomes problematic if the expected change in phenotype does not occur; if antisense activity is not separately assessed at the level of protein concentration or mRNA mass, the experimenter will not be able to discern whether (1) the oligo failed to reach and interact with its target mRNA to produce the knockdown or splice-block, or (2) the knockdown or spliceblock was successful but did not cause the expected phenotypic change. The negative control shows that the effects observed during the antisense experiment are due to the sequence of the targeting oligo and not to the backbone chemistry of the Morpholino or the cytosolic delivery method used. abstract: Morpholino oligonucleotides are stable, uncharged, water‐soluble molecules used to block complementary sequences of RNA, preventing processing, read‐through, or protein binding at those sites. Morpholinos are typically used to block translation of mRNA and to block splicing of pre‐mRNA, though they can block other interactions between biological macromolecules and RNA. Morpholinos are effective, specific, and lack non‐antisense effects. They work in any cell that transcribes and translates RNA, but must be delivered into the nuclear/cytosolic compartment to be effective. Morpholinos form stable base pairs with complementary nucleic acid sequences but apparently do not bind to proteins to a significant extent. They are not recognized by any proteins and do not undergo protein‐mediated catalysis; nor do they mediate RNA cleavage by RNase H or the RISC complex. This work focuses on techniques and background for using Morpholinos. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7162184/ doi: 10.1002/0471142700.nc0430s27 id: cord-275859-ix8du1er author: Mouzakis, Kathryn D. title: HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome date: 2012-12-15 words: 6721.0 sentences: 322.0 pages: flesch: 50.0 cache: ./cache/cord-275859-ix8du1er.txt txt: ./txt/cord-275859-ix8du1er.txt summary: In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Here, we investigate the role of the HIV-1 RNA structure in frameshifting, focusing on elucidating the relationships between frameshift efficiency and (i) the downstream RNA stem-loop thermodynamic stability, (ii) spacer length and (iii) surrounding genomic secondary structure. Our data further indicate that the base pairs important for frameshifting are located at a distance of 8 nt from the slippery site, which corresponds to the length of the spacer and is consistent with a structural model of the ribosome paused at the frameshift site. Instead, we observe a strong correlation (R 2 = 0.88) between frameshift efficiency and local stability of the first 3 bp at the base of the stem-loop using a one-phase exponential decay function ( Figure 3C and Supplementary Table S3 ). abstract: The human immunodeficiency virus (HIV) requires a programmed −1 ribosomal frameshift for Pol gene expression. The HIV frameshift site consists of a heptanucleotide slippery sequence (UUUUUUA) followed by a spacer region and a downstream RNA stem–loop structure. Here we investigate the role of the RNA structure in promoting the −1 frameshift. The stem–loop was systematically altered to decouple the contributions of local and overall thermodynamic stability towards frameshift efficiency. No correlation between overall stability and frameshift efficiency is observed. In contrast, there is a strong correlation between frameshift efficiency and the local thermodynamic stability of the first 3–4 bp in the stem–loop, which are predicted to reside at the opening of the mRNA entrance channel when the ribosome is paused at the slippery site. Insertion or deletions in the spacer region appear to correspondingly change the identity of the base pairs encountered 8 nt downstream of the slippery site. Finally, the role of the surrounding genomic secondary structure was investigated and found to have a modest impact on frameshift efficiency, consistent with the hypothesis that the genomic secondary structure attenuates frameshifting by affecting the overall rate of translation. url: https://www.ncbi.nlm.nih.gov/pubmed/23248007/ doi: 10.1093/nar/gks1254 id: cord-048478-ftlb5b95 author: Mroczek, Seweryn title: Apoptotic signals induce specific degradation of ribosomal RNA in yeast date: 2008-04-01 words: 9796.0 sentences: 418.0 pages: flesch: 45.0 cache: ./cache/cord-048478-ftlb5b95.txt txt: ./txt/cord-048478-ftlb5b95.txt summary: One striking characteristic, which accompanies apoptosis in both vertebrates and yeast, is a fragmentation of cellular DNA and mammalian apoptosis is often associated with degradation of different RNAs. We show that in yeast exposed to stimuli known to induce apoptosis, such as hydrogen peroxide, acetic acid, hyperosmotic stress and ageing, two large subunit ribosomal RNAs, 25S and 5.8S, became extensively degraded with accumulation of specific intermediates that differ slightly depending on cell death conditions. For example, in metazoans the programmed cell death (PCD) called apoptosis, in addition to irreversible DNA damage, which is considered an apoptotic hallmark (3) , also involves specific cleavage of several RNA species, including 28S rRNA, U1 snRNA or Ro RNP-associated Y RNAs (4) . Together, this strongly suggests that rRNA degradation observed in apoptotic and oxidative stress conditions is not simply a result of cell death but is produced in the process that requires enzymatic activity and functional cellular machinery. abstract: Organisms exposed to reactive oxygen species, generated endogenously during respiration or by environmental conditions, undergo oxidative stress. Stress response can either repair the damage or activate one of the programmed cell death (PCD) mechanisms, for example apoptosis, and finally end in cell death. One striking characteristic, which accompanies apoptosis in both vertebrates and yeast, is a fragmentation of cellular DNA and mammalian apoptosis is often associated with degradation of different RNAs. We show that in yeast exposed to stimuli known to induce apoptosis, such as hydrogen peroxide, acetic acid, hyperosmotic stress and ageing, two large subunit ribosomal RNAs, 25S and 5.8S, became extensively degraded with accumulation of specific intermediates that differ slightly depending on cell death conditions. This process is most likely endonucleolytic, is correlated with stress response, and depends on the mitochondrial respiratory status: rRNA is less susceptible to degradation in respiring cells with functional defence against oxidative stress. In addition, RNA fragmentation is independent of two yeast apoptotic factors, metacaspase Yca1 and apoptosis-inducing factor Aif1, but it relies on the apoptotic chromatin condensation induced by histone H2B modifications. These data describe a novel phenotype for certain stress- and ageing-related PCD pathways in yeast. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2396418/ doi: 10.1093/nar/gkm1100 id: cord-294592-zwvr57a0 author: Mukherjee, Moumita title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 date: 2020-08-11 words: 6099.0 sentences: 371.0 pages: flesch: 57.0 cache: ./cache/cord-294592-zwvr57a0.txt txt: ./txt/cord-294592-zwvr57a0.txt summary: title: Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV-2 Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. We have also looked at the possible regulation of viral genomic RNA through binding of host RNA binding proteins (RBPs) and miR-NAs in specific sequences of the viral UTRs. There are experimentally validated evidences of human RBPs binding to the regulated signals within the untranslated region of SARS-CoV RNA in order to control the viral RNA synthesis and turnover. abstract: BACKGROUND: The world is going through the critical phase of COVID-19 pandemic, caused by human coronavirus, SARS-CoV-2. Worldwide concerted effort to identify viral genomic changes across different sub-types has identified several strong changes in the coding region. However, there have not been many studies focusing on the variations in the 5’ and 3’ untranslated regions and their consequences. Considering the possible importance of these regions in host mediated regulation of viral RNA genome, we wanted to explore the phenomenon. METHODS: To have an idea of the global changes in 5’ and 3’-UTR sequences, we downloaded 8595 complete and high-coverage SARS-CoV-2 genome sequence information from human host in FASTA format from Global Initiative on Sharing All Influenza Data (GISAID) from 15 different geographical regions. Next, we aligned them using Clustal Omega software and investigated the UTR variants. We also looked at the putative host RNA binding protein (RBP) and microRNA binding sites in these regions by ‘RBPmap’ and ‘RNA22 v2’ respectively. Expression status of selected RBPs and microRNAs were checked in lungs tissue. RESULTS: We identified 28 unique variants in SARS-CoV-2 UTR region based on a minimum variant percentage cut-off of 0.5. Along with 241C>T change the important 5’-UTR change identified was 187A>G, while 29734G>C, 29742G>A/T and 29774C>T were the most familiar variants of 3’UTR among most of the continents. Furthermore, we found that despite the variations in the UTR regions, binding of host RBP to them remains mostly unaltered, which further influenced the functioning of specific miRNAs. CONCLUSION: Our results, shows for the first time in SARS-Cov-2 infection, a possible cross-talk between host RBPs-miRNAs and viral UTR variants, which ultimately could explain the mechanism of escaping host RNA decay machinery by the virus. The knowledge might be helpful in developing anti-viral compounds in future. url: https://www.ncbi.nlm.nih.gov/pubmed/32780783/ doi: 10.1371/journal.pone.0237559 id: cord-266127-phv08xe2 author: Mukhopadhyay, Urbi title: Biphasic regulation of RNA interference during rotavirus infection by modulation of Argonaute2 date: 2019-08-26 words: 7600.0 sentences: 432.0 pages: flesch: 46.0 cache: ./cache/cord-266127-phv08xe2.txt txt: ./txt/cord-266127-phv08xe2.txt summary: Consistent to our previous results, Rbx1 expression was successfully knocked down in response to Rbx1 siRNA in RV-SA11-infected cells lysed at 9 hpi as well as in mock-infected control but not in RV-SA11-infected cells harvested FIGURE 1 Host RNA interference is blocked during early hours of RV-SA11 infection. Together, the data suggest that actively replicating RV-SA11 triggers attenuation in protein levels of AGO2 leading to functional blocking of RNAi during early time points (2-6 hpi) of infection. Sensitivity of ectopic GFP (pEGFP-N1) expression to siGFP was also reduced in RV-NSP1overexpressing cells ( Figure S4A ), indicating that RV-NSP1 might FIGURE 3 Rotaviral nonstructural protein 1 triggers ubiquitination and proteasomal degradation of AGO2. Rotavirus nonstructural protein 1 suppresses virus-induced cellular apoptosis to facilitate viral growth by activating the cell survival pathways during early stages of infection abstract: RNA interference (RNAi) is an evolutionary ancient innate immune response in plants, nematodes, and arthropods providing natural protection against viral infection. Viruses have also gained counter‐defensive measures by producing virulence determinants called viral‐suppressors‐of‐RNAi (VSRs). Interestingly, in spite of dominance of interferon‐based immunity over RNAi in somatic cells of higher vertebrates, recent reports are accumulating in favour of retention of the antiviral nature of RNAi in mammalian cells. The present study focuses on the modulation of intracellular RNAi during infection with rotavirus (RV), an enteric virus with double‐stranded RNA genome. Intriguingly, a time point‐dependent bimodal regulation of RNAi was observed in RV‐infected cells, where short interfering RNA (siRNA)‐based RNAi was rendered non‐functional during early hours of infection only to be reinstated fully beyond that early infection stage. Subsequent investigations revealed RV nonstructural protein 1 to serve as a putative VSR by associating with and triggering degradation of Argonaute2 (AGO2), the prime effector of siRNA‐mediated RNAi, via ubiquitin–proteasome pathway. The proviral significance of AGO2 degradation was further confirmed when ectopic overexpression of AGO2 significantly reduced RV infection. Cumulatively, the current study presents a unique modulation of host RNAi during RV infection, highlighting the importance of antiviral RNAi in mammalian cells. url: https://doi.org/10.1111/cmi.13101 doi: 10.1111/cmi.13101 id: cord-324640-2zhaknbi author: Munday, Diane C. title: Quantitative Proteomic Analysis of A549 Cells Infected with Human Respiratory Syncytial Virus date: 2010-07-20 words: 12318.0 sentences: 588.0 pages: flesch: 39.0 cache: ./cache/cord-324640-2zhaknbi.txt txt: ./txt/cord-324640-2zhaknbi.txt summary: Although RNA synthesis and virus assembly occur in the cytoplasm, HRSV is known to induce nuclear responses in the host cell as replication alters global gene expression. More recently, 2DE was used to compare the potential effect of several different negative strand RNA viruses, including HRSV, parainfluenza virus, human metap-neumovirus, measles virus, and influenza virus, on the host cell proteome with common changes in proteins involved with apoptosis and endoplasmic reticulum stress being highlighted (27) . Together, the indirect immunofluorescence confocal microscopy images supported the observations from the quantitative proteomic analysis that the abundance of mitochondrial proteins (particularly pore proteins) was altered in HRSV-infected cells. Potential Disruption of Proteins Involved in Nucleocytoplasmic Trafficking-Network pathway analysis indicated that the abundance of nuclear pore complex components and proteins involved in the nucleocytoplasmic trafficking of proteins and RNA differed between HRSV-infected and mock-infected cells (Fig. 4) . abstract: Human respiratory syncytial virus (HRSV) is a major cause of pediatric lower respiratory tract disease to which there is no vaccine or efficacious chemotherapeutic strategy. Although RNA synthesis and virus assembly occur in the cytoplasm, HRSV is known to induce nuclear responses in the host cell as replication alters global gene expression. Quantitative proteomics was used to take an unbiased overview of the protein changes in transformed human alveolar basal epithelial cells infected with HRSV. Underpinning this was the use of stable isotope labeling with amino acids in cell culture coupled to LC-MS/MS, which allowed the direct and simultaneous identification and quantification of both cellular and viral proteins. To reduce sample complexity and increase data return on potential protein localization, cells were fractionated into nuclear and cytoplasmic extracts. This resulted in the identification of 1,140 cellular proteins and six viral proteins. The proteomics data were analyzed using Ingenuity Pathways Analysis to identify defined canonical pathways and functional groupings. Selected data were validated using Western blot, direct and indirect immunofluorescence confocal microscopy, and functional assays. The study served to validate and expand upon known HRSV-host cell interactions, including those associated with the antiviral response and alterations in subnuclear structures such as the nucleolus and ND10 (promyelocytic leukemia bodies). In addition, novel changes were observed in mitochondrial proteins and functions, cell cycle regulatory molecules, nuclear pore complex proteins and nucleocytoplasmic trafficking proteins. These data shed light into how the cell is potentially altered to create conditions more favorable for infection. Additionally, the study highlights the application and advantage of stable isotope labeling with amino acids in cell culture coupled to LC-MS/MS for the analysis of virus-host interactions. url: https://www.ncbi.nlm.nih.gov/pubmed/20647383/ doi: 10.1074/mcp.m110.001859 id: cord-003711-l3brhmzq author: Munnur, Deeksha title: Reversible ADP-ribosylation of RNA date: 2019-06-20 words: 6854.0 sentences: 410.0 pages: flesch: 58.0 cache: ./cache/cord-003711-l3brhmzq.txt txt: ./txt/cord-003711-l3brhmzq.txt summary: ADP-ribosylation is a reversible chemical modification catalysed by ADP-ribosyltransferases such as PARPs that utilize nicotinamide adenine dinucleotide (NAD(+)) as a cofactor to transfer monomer or polymers of ADP-ribose nucleotide onto macromolecular targets such as proteins and DNA. We further reveal that ADP-ribosylation of RNA mediated by PARP10 and TRPT1 can be efficiently reversed by several cellular ADP-ribosylhydrolases (PARG, TARG1, MACROD1, MACROD2 and ARH3), as well as by MACROD-like hydrolases from VEEV and SARS viruses. Importantly, PARP3 could only ADP-ribosylate DNA ends and did not have any activity on RNA oligos, while PARP10 specifically modified phosphorylated ssRNA oligo in the conditions tested ( Figure 1A and B). Since PARP10 can ADP-ribosylate both 5 and 3 phosphorylated ends of RNA, we tested both of these modified oligos as substrates for well characterized human ADP-ribosylhydrolases: PARG, TARG1, MACROD1, MACROD2 and ARH1-3. abstract: ADP-ribosylation is a reversible chemical modification catalysed by ADP-ribosyltransferases such as PARPs that utilize nicotinamide adenine dinucleotide (NAD(+)) as a cofactor to transfer monomer or polymers of ADP-ribose nucleotide onto macromolecular targets such as proteins and DNA. ADP-ribosylation plays an important role in several biological processes such as DNA repair, transcription, chromatin remodelling, host-virus interactions, cellular stress response and many more. Using biochemical methods we identify RNA as a novel target of reversible mono-ADP-ribosylation. We demonstrate that the human PARPs - PARP10, PARP11 and PARP15 as well as a highly diverged PARP homologue TRPT1, ADP-ribosylate phosphorylated ends of RNA. We further reveal that ADP-ribosylation of RNA mediated by PARP10 and TRPT1 can be efficiently reversed by several cellular ADP-ribosylhydrolases (PARG, TARG1, MACROD1, MACROD2 and ARH3), as well as by MACROD-like hydrolases from VEEV and SARS viruses. Finally, we show that TRPT1 and MACROD homologues in bacteria possess activities equivalent to the human proteins. Our data suggest that RNA ADP-ribosylation may represent a widespread and physiologically relevant form of reversible ADP-ribosylation signalling. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582358/ doi: 10.1093/nar/gkz305 id: cord-320709-2pnqpljt author: Munster, Vincent J. title: Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis) date: 2016-02-22 words: 3951.0 sentences: 219.0 pages: flesch: 53.0 cache: ./cache/cord-320709-2pnqpljt.txt txt: ./txt/cord-320709-2pnqpljt.txt summary: The Mx1, ISG56 and RANTES gene expression in the lungs of Jamaican fruit bats was analyzed as an indicator of the induction of an innate immune response to MERS-CoV infection. The tissue tropism of MERS-CoV in Jamaican fruit bats is comparable to the respiratory tract tropism observed in dromedary camels and humans 49, 50 . MERS-CoV and related batCoV-HKU4 can inhibit innate immune signaling in a variety of human cell lines in vitro via the ORF4b-encoded accessory proteins 52 Lungs of Jamaican fruit bat 5 were stained with α -cytokeratin as an epithelial marker (purple) and with a polyclonal α -coronavirus antibody (brown-red) to demonstrate that viral antigen was located along the basement membrane of alveolar pneumocytes of bat 1 at 2 dpi (indicated by black arrows). Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels abstract: The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) highlights the zoonotic potential of Betacoronaviruses. Investigations into the origin of MERS-CoV have focused on two potential reservoirs: bats and camels. Here, we investigated the role of bats as a potential reservoir for MERS-CoV. In vitro, the MERS-CoV spike glycoprotein interacted with Jamaican fruit bat (Artibeus jamaicensis) dipeptidyl peptidase 4 (DPP4) receptor and MERS-CoV replicated efficiently in Jamaican fruit bat cells, suggesting there is no restriction at the receptor or cellular level for MERS-CoV. To shed light on the intrinsic host-virus relationship, we inoculated 10 Jamaican fruit bats with MERS-CoV. Although all bats showed evidence of infection, none of the bats showed clinical signs of disease. Virus shedding was detected in the respiratory and intestinal tract for up to 9 days. MERS-CoV replicated transiently in the respiratory and, to a lesser extent, the intestinal tracts and internal organs; with limited histopathological changes observed only in the lungs. Analysis of the innate gene expression in the lungs showed a moderate, transient induction of expression. Our results indicate that MERS-CoV maintains the ability to replicate in bats without clinical signs of disease, supporting the general hypothesis of bats as ancestral reservoirs for MERS-CoV. url: https://doi.org/10.1038/srep21878 doi: 10.1038/srep21878 id: cord-308034-9b219k0v author: Murray, James L. title: A Role for H/ACA and C/D Small Nucleolar RNAs in Viral Replication date: 2014-01-30 words: 3654.0 sentences: 218.0 pages: flesch: 12.0 cache: ./cache/cord-308034-9b219k0v.txt txt: ./txt/cord-308034-9b219k0v.txt summary: We have employed gene-trap insertional mutagenesis to identify candidate genes whose disruption confer phenotypic resistance to lytic infection, in independent studies using 12 distinct viruses and several different cell lines. Expression of nine SNORA/Ds encoded within RCC1 (which also encodes the shorter non-coding SNHG3 gene), or SNHG1 were silenced with siRNAs for 2 days prior to infection with either cowpox virus (CPV), Dengue Fever virus (DFV), influenza A (FLU), human rhinovirus 16 (HRV16), herpes simplex virus 2 (HSV2), or respiratory syncytial virus (RSV). While a previous study showed that RCC1 supports HSV1 replication [21] , we did not observe that silencing RCC1 or the non-coding Small Nucleolar RNA Host Gene 3 (SNHG3) inhibits HSV2 (data not shown), whereas inhibiting expression of the RCC1encoded SNORA73A did. The discovery of these classes of non-coding genes prominently represented in the mutant clones selected in our virus surviving cell lines suggests an importance of SNORAs and SNORDs in facilitating viral replication. abstract: We have employed gene-trap insertional mutagenesis to identify candidate genes whose disruption confer phenotypic resistance to lytic infection, in independent studies using 12 distinct viruses and several different cell lines. Analysis of >2,000 virus-resistant clones revealed >1,000 candidate host genes, approximately 20 % of which were disrupted in clones surviving separate infections with 2–6 viruses. Interestingly, there were 83 instances in which the insertional mutagenesis vector disrupted transcripts encoding H/ACA-class and C/D-class small nucleolar RNAs (SNORAs and SNORDs, respectively). Of these, 79 SNORAs and SNORDs reside within introns of 29 genes (predominantly protein-coding), while 4 appear to be independent transcription units. siRNA studies targeting candidate SNORA/Ds provided independent confirmation of their roles in infection when tested against cowpox virus, Dengue Fever virus, influenza A virus, human rhinovirus 16, herpes simplex virus 2, or respiratory syncytial virus. Significantly, eight of the nine SNORA/Ds targeted with siRNAs enhanced cellular resistance to multiple viruses suggesting widespread involvement of SNORA/Ds in virus–host interactions and/or virus-induced cell death. url: https://www.ncbi.nlm.nih.gov/pubmed/24477674/ doi: 10.1007/s12033-013-9730-0 id: cord-264746-gfn312aa author: Muse, Spencer title: GENOMICS AND BIOINFORMATICS date: 2012-03-29 words: 10976.0 sentences: 583.0 pages: flesch: 58.0 cache: ./cache/cord-264746-gfn312aa.txt txt: ./txt/cord-264746-gfn312aa.txt summary: The success of this project (it came in almost 3 years ahead of time and 10% under budget, while at the same time providing more data than originally planned) depended on innovations in a variety of areas: breakthroughs in basic molecular biology to allow manipulation of DNA and other compounds; improved engineering and manufacturing technology to produce equipment for reading the sequences of DNA; advances in robotics and laboratory automation; development of statistical methods to interpret data from sequencing projects; and the creation of specialized computing hardware and software systems to circumvent massive computational barriers that faced genome scientists. Although the list of important biotechnologies changes on an almost daily basis, there are three prominent data types in today''s environment: (1) genome sequences provide the starting point that allows scientists to begin understanding the genetic underpinnings of an organism; (2) measurements of gene expression levels facilitate studies of gene regulation, which, among other things, help us to understand how an organism''s genome interacts with its environment; and (3) genetic polymorphisms are variations from individual to individual within species, and understanding how these variations correlate with phenotypes such as disease susceptibility is a crucial element of modern biomedical research. abstract: This chapter discusses the basic principles of molecular biology regarding genome science and describes the major types of data involved in genome projects, including technologies for collecting them. Genome science is heavily driven by new technological advances that allow for rapid and inexpensive collection of various types of data. The emergence of genomic science has not simply provided a rich set of tools and data for studying molecular biology. It has been the catalyst for an astounding burst of interdisciplinary research, and it has challenged long-established hierarchies found in most institutions of higher learning. The next generation of biologists needs to be as comfortable at a computer workstation as they are at the lab bench. Recognizing this fact, many universities have already reorganized their departments and their curricula to accommodate the demands of genomic science.The chapter discusses practical applications and uses of genomic data. For example, in the foreseeable future, are gene therapies that can repair genetic defects. url: https://api.elsevier.com/content/article/pii/B978012238662650015X doi: 10.1016/b978-0-12-238662-6.50015-x id: cord-004719-3stcx0dd author: Mushegian, A. R. title: Cell-to-cell movement of plant viruses: Insights from amino acid sequence comparisons of movement proteins and from analogies with cellular transport systems date: 1993 words: 6347.0 sentences: 280.0 pages: flesch: 44.0 cache: ./cache/cord-004719-3stcx0dd.txt txt: ./txt/cord-004719-3stcx0dd.txt summary: In several groups of positive-strand RNA viruses, the movement function is provided by the proteins encoded by the so-called triple gene block including two putative small membrane-associated proteins and a putative RNA helicase. It is concluded that classification of movement proteins based on comparison of their amino acid sequences does not correlate with the type of genome nucleic acid or with grouping of viruses based on phylogenetic analysis of replicative proteins or with the virus host range. Limited sequence similarities were observed between i) movement proteins of dianthoviruses and the MIP family of cellular integral membrane proteins, and ii) between movement proteins of bromoviruses and cucumoviruses and M1 protein of influenza viruses which is involved in nuclear export of viral ribonucleoproteins. With representative sequences of plant virus genomes from many groups available, efforts were made to identify regions of similarity between known movement proteins and to predict movement functions for uncharacterized ORFs. Early observations made by this approach have been reviewed previously (e.g. abstract: Cell-to-cell movement is a crucial step in plant virus infection. In many viruses, the movement function is secured by specific virus-encoded proteins. Amino acid sequence comparisons of these proteins revealed a vast superfamily containing a conserved sequence motif that may comprise a hydrophobic interaction domain. This superfamily combines proteins of viruses belonging to all principal groups of positive-strand RNA viruses, as well as single-stranded DNA containing geminiviruses, double-stranded DNA-containing pararetroviruses (caulimoviruses and badnaviruses), and tospoviruses that have negative-strand RNA genomes with two ambisense segments. In several groups of positive-strand RNA viruses, the movement function is provided by the proteins encoded by the so-called triple gene block including two putative small membrane-associated proteins and a putative RNA helicase. A distinct type of movement proteins with very high content of proline is found in tymoviruses. It is concluded that classification of movement proteins based on comparison of their amino acid sequences does not correlate with the type of genome nucleic acid or with grouping of viruses based on phylogenetic analysis of replicative proteins or with the virus host range. Recombination between unrelated or distantly related viruses could have played a major role in the evolution of the movement function. Limited sequence similarities were observed between i) movement proteins of dianthoviruses and the MIP family of cellular integral membrane proteins, and ii) between movement proteins of bromoviruses and cucumoviruses and M1 protein of influenza viruses which is involved in nuclear export of viral ribonucleoproteins. It is hypothesized that all movement proteins of plant viruses may mediate hydrophobic interactions between viral and cellular macromolecules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086723/ doi: 10.1007/bf01313766 id: cord-293988-f5gvwjyh author: Musso, Nicolò title: New SARS-CoV-2 Infection Detected in an Italian Pet Cat by RT-qPCR from Deep Pharyngeal Swab date: 2020-09-11 words: 3223.0 sentences: 186.0 pages: flesch: 54.0 cache: ./cache/cord-293988-f5gvwjyh.txt txt: ./txt/cord-293988-f5gvwjyh.txt summary: The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. The World Health Organization (WHO) declared COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a worldwide pandemic [1] . As the cat''s pathology evolved rapidly and harmfully (the animal died in as little as three days), with clinical signs and rate of disease progression similar to human COVID-19 patients, and because previously published papers reported different cases of feline infection [10, [13] [14] [15] [16] , a nasal swab was collected in order to verify a possible infection with SARS-CoV-2. abstract: The pandemic respiratory disease COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in Wuhan in December 2019 and then spread throughout the world; Italy was the most affected European country. Despite close pet–human contact, little is known about the predisposition of pets to SARS-CoV-2. Among these, felines are the most susceptible. In this study, a domestic cat with clear clinical signs of pneumonia, confirmed by Rx imaging, was found to be infected by SARS-CoV-2 using quantitative RT–qPCR from a nasal swab. This is the first Italian study responding to the request of the scientific community to focus attention on the possible role of pets as a viral reservoir. An important question remains unanswered: did the cat actually die due to SARS-CoV-2 infection? url: https://www.ncbi.nlm.nih.gov/pubmed/32932800/ doi: 10.3390/pathogens9090746 id: cord-001964-iy6qzq58 author: Muñoz-González, Sara title: Classical Swine Fever Virus vs. Classical Swine Fever Virus: The Superinfection Exclusion Phenomenon in Experimentally Infected Wild Boar date: 2016-02-26 words: 6933.0 sentences: 319.0 pages: flesch: 48.0 cache: ./cache/cord-001964-iy6qzq58.txt txt: ./txt/cord-001964-iy6qzq58.txt summary: The wild boars persistently infected with CSFV were protected from superinfection by the virulent CSFV Margarita strain, as evidenced by the absence of clinical signs and the absence of Margarita RNA detection in serum, swabs and tissue samples. Additionally, in PBMCs, a well-known target for CSFV viral replication, only the primary infecting virus RNA (Cat01 strain) could be detected, even after the isolation in ST cells, demonstrating SIE at the tissue level in vivo. Interestingly, the RNA of the vaccinal C-strain was undetectable by specific RT-PCR [8] in any of the samples analysed after vaccination, including blood, nasal and rectal swabs, or organs throughout the experiment, suggesting a phenomenon of homologous interference, also known as superinfection exclusion (SIE), between the high viral load generated by the primary persistent infection and the CSFV vaccine strain. abstract: Two groups with three wild boars each were used: Group A (animals 1 to 3) served as the control, and Group B (animals 4 to 6) was postnatally persistently infected with the Cat01 strain of CSFV (primary virus). The animals, six weeks old and clinically healthy, were inoculated with the virulent strain Margarita (secondary virus). For exclusive detection of the Margarita strain, a specific qRT-PCR assay was designed, which proved not to have cross-reactivity with the Cat01 strain. The wild boars persistently infected with CSFV were protected from superinfection by the virulent CSFV Margarita strain, as evidenced by the absence of clinical signs and the absence of Margarita RNA detection in serum, swabs and tissue samples. Additionally, in PBMCs, a well-known target for CSFV viral replication, only the primary infecting virus RNA (Cat01 strain) could be detected, even after the isolation in ST cells, demonstrating SIE at the tissue level in vivo. Furthermore, the data analysis of the Margarita qRT-PCR, by means of calculated ΔCt values, supported that PBMCs from persistently infected animals were substantially protected from superinfection after in vitro inoculation with the Margarita virus strain, while this virus was able to infect naive PBMCs efficiently. In parallel, IFN-α values were undetectable in the sera from animals in Group B after inoculation with the CSFV Margarita strain. Furthermore, these animals were unable to elicit adaptive humoral (no E2-specific or neutralising antibodies) or cellular immune responses (in terms of IFN-γ-producing cells) after inoculation with the second virus. Finally, a sequence analysis could not detect CSFV Margarita RNA in the samples tested from Group B. Our results suggested that the SIE phenomenon might be involved in the evolution and phylogeny of the virus, as well as in CSFV control by vaccination. To the best of our knowledge, this study was one of the first showing efficient suppression of superinfection in animals, especially in the absence of IFN-α, which might be associated with the lack of innate immune mechanisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4768946/ doi: 10.1371/journal.pone.0149469 id: cord-350600-73q8mve4 author: Myint, S. title: Detection of human coronavirus 229E in nasal washings using RNA:RNA hybridization date: 2005-12-09 words: 1996.0 sentences: 126.0 pages: flesch: 61.0 cache: ./cache/cord-350600-73q8mve4.txt txt: ./txt/cord-350600-73q8mve4.txt summary: A method is described for the detection of human coronavirus 229E (HCV 229E) in nasal washings using RNA:RNA filter hybridization. In this paper we describe a specific and sensitive test to detect one of these major groups, HCV 2293, in nasal washings. Briefly, using a method based on that of Gubler and Hoffmann [19831, cDNAs were generated from HCV 2293 RNA isolated from infected C16 cells [Phillpotts, 19831. The results of virus titration and probing of nasal washings from seven volunteers are presented in Table I . Three of the seven volunteers suffered a cold, and all three volunteers had detectable coronavirus RNA in their nasal washings. The results we have obtained show that the detection of HCV 2293 infection by nucleic acid hybridisation is a reliable and specific method. Hybridisation to known quantities of HCV 2293 RNA showed that less than 1 ng of virus-specific RNA from C16 cells infected with HCV 2293 could be detected. abstract: A method is described for the detection of human coronavirus 229E (HCV 229E) in nasal washings using RNA:RNA filter hybridization. Volunteers were inoculated with HCV 229E, and daily nasal washings were collected. These washings were then examined for the presence of viral RNA using a single‐stranded RNA probe. Nucleic acid hybridization is shown to be a sensitive technique for the diagnosis of HCV 229E infections. url: https://www.ncbi.nlm.nih.gov/pubmed/2584959/ doi: 10.1002/jmv.1890290113 id: cord-002398-0a3okta0 author: Myllykoski, Matti title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase date: 2017-01-31 words: 6151.0 sentences: 363.0 pages: flesch: 56.0 cache: ./cache/cord-002398-0a3okta0.txt txt: ./txt/cord-002398-0a3okta0.txt summary: Here, we studied the structure of the 2H family member LigT from Escherichia coli both in the apo form and complexed with different active-site ligands, including ATP, 2′-AMP, 3′-AMP, phosphate, and NADP(+). coli LigT bound to tRNA in solution, and provide a model for RNA binding by LigT, involving flexible loops lining the active site cavity. The crystal structure of LigT with 2 0 -AMP was superimposed on the corresponding complex of CNPase, in order to distinguish common and divergent ligand binding determinants in 2H enzymes. Structural data [29] from these enzymes incidate that the 2 0 ,5 0 -adenosine bisphophate substrate binds along the opposite side of the active site, compared to LigT and CNPase (Fig 7A) . As the different structures predicted an RNA-binding surface on LigT, we further modeled a 3-residue RNA molecule with a terminal 2 0 -phosphate into the active site. abstract: The 2H phosphoesterase family contains enzymes with two His-X-Ser/Thr motifs in the active site. 2H enzymes are found in all kingdoms of life, sharing little sequence identity despite the conserved overall fold and active site. For many 2H enzymes, the physiological function is unknown. Here, we studied the structure of the 2H family member LigT from Escherichia coli both in the apo form and complexed with different active-site ligands, including ATP, 2′-AMP, 3′-AMP, phosphate, and NADP(+). Comparisons to the well-characterized vertebrate myelin enzyme 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase) highlight specific features of the catalytic cycle and substrate recognition in both enzymes. The role played by the helix α7, unique to CNPases within the 2H family, is apparently taken over by Arg130 in the bacterial enzyme. Other residues and loops lining the active site groove are likely to be important for RNA substrate binding. We visualized conformational changes related to ligand binding, as well as the position of the nucleophilic water molecule. We also present a low-resolution model of E. coli LigT bound to tRNA in solution, and provide a model for RNA binding by LigT, involving flexible loops lining the active site cavity. Taken together, our results both aid in understanding the common features of 2H family enzymes and help highlight the distinct features in the 2H family members, which must result in different reaction mechanisms. Unique aspects in different 2H family members can be observed in ligand recognition and binding, and in the coordination of the nucleophilic water molecule and the reactive phosphate moiety. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5283653/ doi: 10.1371/journal.pone.0170355 id: cord-010977-fwz7chzf author: Myserlis, Pavlos title: Translational Genomics in Neurocritical Care: a Review date: 2020-02-20 words: 11990.0 sentences: 519.0 pages: flesch: 31.0 cache: ./cache/cord-010977-fwz7chzf.txt txt: ./txt/cord-010977-fwz7chzf.txt summary: In this review, we describe some of the approaches being taken to apply translational genomics to the study of diseases commonly encountered in the neurocritical care setting, including hemorrhagic and ischemic stroke, traumatic brain injury, subarachnoid hemorrhage, and status epilepticus, utilizing both forward and reverse genomic translational techniques. Termed "reverse translation," this approach starts with humans as the model system, utilizing genomic associations to derive new information about biological mechanisms that can be in turn studied further in vitro and in animal models for target refinement (Fig. 1) . These results highlight the value of reverse genomic translation in first identifying human-relevant genetic risk factors for disease, and using model systems to understand the pathways impacted by their introduction to select rationally-informed modalities for potential treatment. These observations provide vital information about cellular mechanisms impacted by human disease-associated genetic risk factors without requiring the expense and time investment of creating, validating, and studying animal models. abstract: Translational genomics represents a broad field of study that combines genome and transcriptome-wide studies in humans and model systems to refine our understanding of human biology and ultimately identify new ways to treat and prevent disease. The approaches to translational genomics can be broadly grouped into two methodologies, forward and reverse genomic translation. Traditional (forward) genomic translation begins with model systems and aims at using unbiased genetic associations in these models to derive insight into biological mechanisms that may also be relevant in human disease. Reverse genomic translation begins with observations made through human genomic studies and refines these observations through follow-up studies using model systems. The ultimate goal of these approaches is to clarify intervenable processes as targets for therapeutic development. In this review, we describe some of the approaches being taken to apply translational genomics to the study of diseases commonly encountered in the neurocritical care setting, including hemorrhagic and ischemic stroke, traumatic brain injury, subarachnoid hemorrhage, and status epilepticus, utilizing both forward and reverse genomic translational techniques. Further, we highlight approaches in the field that could be applied in neurocritical care to improve our ability to identify new treatment modalities as well as to provide important information to patients about risk and prognosis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13311-020-00838-1) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7223188/ doi: 10.1007/s13311-020-00838-1 id: cord-003284-hjx2d5rq author: Márquez-Jurado, Silvia title: An Alanine-to-Valine Substitution in the Residue 175 of Zika Virus NS2A Protein Affects Viral RNA Synthesis and Attenuates the Virus In Vivo date: 2018-10-07 words: 9917.0 sentences: 409.0 pages: flesch: 51.0 cache: ./cache/cord-003284-hjx2d5rq.txt txt: ./txt/cord-003284-hjx2d5rq.txt summary: Furthermore, using this infectious clone we have generated a mutant ZIKV containing a single amino acid substitution (A175V) in the NS2A protein that presented reduced viral RNA synthesis in cell cultures, was highly attenuated in vivo and induced fully protection against a lethal challenge with ZIKV wild-type. To analyze the genetic stability of the recombinant ZIKV harboring the point mutation A175V in the coding region of the NS2A protein (rZIKV-RGN-mNS2A), total RNA was purified from Vero cells infected with viruses from passage 1 (P1) to passage 5 (P5) using the RNeasy minikit (Qiagen), according to the manufacturer''s specifications. To investigate whether the reduced RNA synthesis of rZIKV-RGN-mNS2A in Vero cells could result in viral attenuation in vivo, the ability of the mutant virus to induce pathogenesis was analyzed in A129 mice and compared with that of the parental rZIKV-RGN ( Figure 6 ). abstract: The recent outbreaks of Zika virus (ZIKV), its association with Guillain–Barré syndrome and fetal abnormalities, and the lack of approved vaccines and antivirals, highlight the importance of developing countermeasures to combat ZIKV disease. In this respect, infectious clones constitute excellent tools to accomplish these goals. However, flavivirus infectious clones are often difficult to work with due to the toxicity of some flavivirus sequences in bacteria. To bypass this problem, several alternative approaches have been applied for the generation of ZIKV clones including, among others, in vitro ligation, insertions of introns and using infectious subgenomic amplicons. Here, we report a simple and novel DNA-launched approach based on the use of a bacterial artificial chromosome (BAC) to generate a cDNA clone of Rio Grande do Norte Natal ZIKV strain. The sequence was identified from the brain tissue of an aborted fetus with microcephaly. The BAC clone was fully stable in bacteria and the infectious virus was efficiently recovered in Vero cells through direct delivery of the cDNA clone. The rescued virus yielded high titers in Vero cells and was pathogenic in a validated mouse model (A129 mice) of ZIKV infection. Furthermore, using this infectious clone we have generated a mutant ZIKV containing a single amino acid substitution (A175V) in the NS2A protein that presented reduced viral RNA synthesis in cell cultures, was highly attenuated in vivo and induced fully protection against a lethal challenge with ZIKV wild-type. This BAC approach provides a stable and reliable reverse genetic system for ZIKV that will help to identify viral determinants of virulence and facilitate the development of vaccine and therapeutic strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6212934/ doi: 10.3390/v10100547 id: cord-304794-z2kx314h author: Métifiot, Mathieu title: G-quadruplexes in viruses: function and potential therapeutic applications date: 2014-11-10 words: 9102.0 sentences: 490.0 pages: flesch: 47.0 cache: ./cache/cord-304794-z2kx314h.txt txt: ./txt/cord-304794-z2kx314h.txt summary: Conversely, a G-quadruplex or G4 is formed by nucleic acid sequences (DNA or RNA) containing G-tracts or Gblocks (adjacent runs of guanines) and composed of various numbers of guanines. Short RNA templates from the central region of the HIV-1 genome contain G-rich sequences near the central polypurine tract (cPPT) at the 3 end of the pol gene (IN coding sequence); this is a region where one of the two primers used for synthesizing the (−) strand DNA is produced during reverse transcription. In addition, one could imagine alternative therapeutic strategies focused on targeting RNA structures within viral ORFs to interfere with the virus cycle as well as to promote antigen presentation and to stimulate the host immune response. Topology of a DNA G-quadruplex structure formed in the HIV-1 promoter: a potential target for anti-HIV drug development U3 Region in the HIV-1 genome adopts a G-quadruplex structure in its RNA and DNA sequence abstract: G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300 000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein–Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools. url: https://doi.org/10.1093/nar/gku999 doi: 10.1093/nar/gku999 id: cord-287758-da11ypiy author: Mônica Vitalino de Almeida, Sinara title: COVID-19 therapy: what weapons do we bring into battle? date: 2020-09-10 words: 17412.0 sentences: 1034.0 pages: flesch: 45.0 cache: ./cache/cord-287758-da11ypiy.txt txt: ./txt/cord-287758-da11ypiy.txt summary: The increase in studies related to SARS-CoV-2 during the first semester in 2020 has allowed the rather speedy identification of promising therapeutic targets for both developing immunotherapies and producing/identifying antiviral drugs. 5, 64 So far, structural proteins and enzymes that participate actively in the process of viral replication are the most investigated targets for the development of molecules for anti-CoVs therapies (FIG. Based on results from previous studies as well, nelfinavir was considered a likely therapy for COVID-19 after its indication for clinical trials as a promising anti-SARS drug. 218 In addition to this well-known antitumor effect, imatinib has also shown in-vitro antiviral properties against several virus, such as infectious bronchitis virus (a viral model for studying the role of tyrosine kinase activity during CoV infection), by interfering with virus-cell fusion, 219 and other RNA viruses including coxsackie virus, 220 hepatitis C virus, 221 Ebola, 222 among others, mainly by blocking viral entry or egress from the host cell. abstract: Urgent treatments, in any modality, to fight SARS-CoV-2 infections are desired by society in general, by health professionals, by Estate-leaders and, mainly, by the scientific community, because one thing is certain amidst the numerous uncertainties regarding COVID-19: knowledge is the means to discover or to produce an effective treatment against this global disease. Scientists from several areas in the world are still committed to this mission, as shown by the accelerated scientific production in the first half of 2020 with over 25,000 published articles related to the new coronavirus. Three great lines of publications related to COVID-19 were identified for building this article: The first refers to knowledge production concerning the virus and pathophysiology of COVID-19; the second regards efforts to produce vaccines against SARS-CoV-2 at a speed without precedent in the history of science; the third comprehends the attempts to find a marketed drug that can be used to treat COVID-19 by drug repurposing. In this review, the drugs that have been repurposed so far are grouped according to their chemical class. Their structures will be presented to provide better understanding of their structural similarities and possible correlations with mechanisms of actions. This can help identifying anti-SARS-CoV-2 promising therapeutic agents. url: https://doi.org/10.1016/j.bmc.2020.115757 doi: 10.1016/j.bmc.2020.115757 id: cord-348147-leni23pa author: Müller, B. title: Genetic diversity and recombination of murine noroviruses in immunocompromised mice date: 2007-05-29 words: 3482.0 sentences: 203.0 pages: flesch: 52.0 cache: ./cache/cord-348147-leni23pa.txt txt: ./txt/cord-348147-leni23pa.txt summary: Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. These specimens were obtained from 28 different mouse lines, including immunocompetent mice, lines with muta(4), b-TCR À=À (2), RAG2=gChain À=À (5), B6 Casp À=À (2), CD36=SRA À=À (2), CCL3 À=À (2), LFA À=À (2), LyZ À=À (2), PSEN tg (2), Bl6 wt (4) a GE genome equivalents; for more than one positive sample the mean was calculated b Includes partial sequences of the ORFs (underlined isolates; ORF1, RNA polymerase gene; ORF2, capsid gene) à Contains both regions tions in a number of immune effector molecules, and transgenic mouse lines (Table 1) . Like human noroviruses, the present sequence data indicate that murine norovirus strains are also genetically diverse and can, therefore, be subdivided in genetic clusters. abstract: Murine noroviruses (MNV) are newly identified pathogens which infect laboratory mice. In this study, we found a high prevalence (64.3%) of MNV in various breeding colonies of immunocompromised, transgenic and wild-type mouse lines. All mice survived infection with no signs of clinical disease. Faeces samples were collected from animals housed in two separate laboratory mouse colonies in Berlin, Germany, and screened using quantitative reverse transcription (RT)-PCR. We have determined the complete nucleotide sequences of 3 novel MNV strains. Furthermore, we sequenced two subgenomic regions within open reading frames (ORFs) 1 and 2 that are suitable for genotyping. Sequence analysis of the full-length and partial genomes obtained from naturally infected mice yielded valuable data on genetic diversity of murine noroviruses. The discordance of genotype affiliation of some MNVs shown in ORF1 and ORF2 suggests intertypic recombination events in vivo. url: https://www.ncbi.nlm.nih.gov/pubmed/17533553/ doi: 10.1007/s00705-007-0989-y id: cord-322410-k23engcx author: Naguib, Mahmoud M. title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses date: 2017-03-21 words: 5012.0 sentences: 259.0 pages: flesch: 52.0 cache: ./cache/cord-322410-k23engcx.txt txt: ./txt/cord-322410-k23engcx.txt summary: title: New real time and conventional RT-PCRs for updated molecular diagnosis of infectious bronchitis virus infection (IBV) in chickens in Egypt associated with frequent co-infections with avian influenza and Newcastle Disease viruses Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples. The specificity of RT-qPCR primer set was evaluated by examining different avian respiratory viruses circulating in poultry in Egypt including AIV H5N1, H9N2 and NDV as well as different coronaviruses including a panel of IBV reference strains as listed in the materials section. Within HVR 1, 2 sequences, however, the existence of two distinct Table 3 RT-qPCRs reveal frequent co-infections in Egyptian poultry samples with avian influenza (AIV), Newcastle Disease (NDV) and infectious bronchitis viruses (IBV). abstract: In Egypt, currently two geographically restricted genotypes of the infectious bronchitis coronavirus (IBV) are circulating with detrimental effects for poultry industry. A sensitive real-time RT-PCR assay targeting the IBV nucleocapsid gene (N) was developed to screen clinical samples for presence of IBV. Conventional RT-PCRs amplifying hypervariable regions (HVRs 1–2 and 3) of the IBV S1 gene were developed and amplificates used for nucleotide sequence-based typing of IBV field strains in Egyptian chickens directly from clinical samples. url: https://www.ncbi.nlm.nih.gov/pubmed/28336367/ doi: 10.1016/j.jviromet.2017.02.018 id: cord-349762-f5no10eq author: Nagura-Ikeda, Mayu title: Clinical Evaluation of Self-Collected Saliva by Quantitative Reverse Transcription-PCR (RT-qPCR), Direct RT-qPCR, Reverse Transcription–Loop-Mediated Isothermal Amplification, and a Rapid Antigen Test To Diagnose COVID-19 date: 2020-08-24 words: 4270.0 sentences: 233.0 pages: flesch: 54.0 cache: ./cache/cord-349762-f5no10eq.txt txt: ./txt/cord-349762-f5no10eq.txt summary: The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription–loop-mediated isothermal amplification (RT-LAMP). Here, we describe the clinical performance of various molecular diagnostic methods, including the RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, 3 direct RT-qPCR kits, and RT-LAMP, and a commercial SARS-CoV-2 RAT used on self-collected saliva specimens in diagnosing COVID-19. The RT-qPCR LDT, the cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed different sensitivities for detecting viral RNA in saliva specimens, but each can be selectively used according to the clinical setting and facilities if close attention is paid to any false-negative results. abstract: The clinical performances of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva. Saliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse transcription-PCR (RT-qPCR) laboratory-developed test (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse transcription–loop-mediated isothermal amplification (RT-LAMP). The viral antigen was detected by a rapid antigen immunochromatographic assay. Of the 103 samples, viral RNA was detected in 50.5 to 81.6% of the specimens by molecular diagnostic tests, and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at significantly higher percentages (65.6 to 93.4%) in specimens collected within 9 days of symptom onset than in specimens collected after at least 10 days of symptoms (22.2 to 66.7%) and in specimens collected from asymptomatic patients (40.0 to 66.7%). Self-collected saliva is an alternative specimen option for diagnosing COVID-19. The RT-qPCR LDT, a cobas SARS-CoV-2 high-throughput system, direct RT-qPCR kits (except for one commercial kit), and RT-LAMP showed sufficient sensitivities in clinical use to be selectively used in clinical settings and facilities. The rapid antigen test alone is not recommended for an initial COVID-19 diagnosis because of its low sensitivity. url: https://www.ncbi.nlm.nih.gov/pubmed/32636214/ doi: 10.1128/jcm.01438-20 id: cord-297760-uzzuoy9v author: Naito, Yuki title: siVirus: web-based antiviral siRNA design software for highly divergent viral sequences date: 2006-07-01 words: 1142.0 sentences: 80.0 pages: flesch: 59.0 cache: ./cache/cord-297760-uzzuoy9v.txt txt: ./txt/cord-297760-uzzuoy9v.txt summary: title: siVirus: web-based antiviral siRNA design software for highly divergent viral sequences siVirus () is a web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi). siVirus searches for functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. siVirus will be a useful tool for designing optimal siRNAs targeting highly divergent pathogens, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), influenza virus and SARS coronavirus, all of which pose enormous threats to global human health. Consequently, only a limited fraction of 21mers is suitable for use as antiviral siRNAs. In this study, we developed a novel web-based online software system, siVirus, which provides functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference abstract: siVirus () is a web-based online software system that provides efficient short interfering RNA (siRNA) design for antiviral RNA interference (RNAi). siVirus searches for functional, off-target minimized siRNAs targeting highly conserved regions of divergent viral sequences. These siRNAs are expected to resist viral mutational escape, since their highly conserved targets likely contain structurally/functionally constrained elements. siVirus will be a useful tool for designing optimal siRNAs targeting highly divergent pathogens, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), influenza virus and SARS coronavirus, all of which pose enormous threats to global human health. url: https://www.ncbi.nlm.nih.gov/pubmed/16845046/ doi: 10.1093/nar/gkl214 id: cord-298032-3zlu8g8y author: Nan, Yuchen title: Antisense Phosphorodiamidate Morpholino Oligomers as Novel Antiviral Compounds date: 2018-04-20 words: 10577.0 sentences: 524.0 pages: flesch: 46.0 cache: ./cache/cord-298032-3zlu8g8y.txt txt: ./txt/cord-298032-3zlu8g8y.txt summary: An earlier study showed that a 22mer PPMO targeting the translation start site region of EBOV VP35 positive-sense RNA exhibited sequence-specific, time-and dose-dependent inhibition of EBOV replication in cultured cells (Enterlein et al., 2006) . However, PPMO targeting conserved internal ribosome entry site (IRES) sequences have been shown to be highly effective in protecting cultured cells against infection by human rhinovirus type 14, coxsackievirus type B2, and poliovirus type 1 (PV1) (Stone et al., 2008) , with reduction of PV1 titers by up to 6 log10. In this study, virus replication in MDCK cells was significantly inhibited by three PPMO targeting either the translation start site region of PB1 or NP mRNA or the 3 -terminal region of NP viral RNA (vRNA). Inhibition of influenza virus infection in human airway cell cultures by an antisense peptide-conjugated morpholino oligomer targeting the hemagglutinin-activating protease TMPRSS2 abstract: Phosphorodiamidate morpholino oligomers (PMO) are short single-stranded DNA analogs that are built upon a backbone of morpholine rings connected by phosphorodiamidate linkages. As uncharged nucleic acid analogs, PMO bind to complementary sequences of target mRNA by Watson–Crick base pairing to block protein translation through steric blockade. PMO interference of viral protein translation operates independently of RNase H. Meanwhile, PMO are resistant to a variety of enzymes present in biologic fluids, a characteristic that makes them highly suitable for in vivo applications. Notably, PMO-based therapy for Duchenne muscular dystrophy (DMD) has been approved by the United States Food and Drug Administration which is now a hallmark for PMO-based antisense therapy. In this review, the development history of PMO, delivery methods for improving cellular uptake of neutrally charged PMO molecules, past studies of PMO antagonism against RNA and DNA viruses, PMO target selection, and remaining questions of PMO antiviral strategies are discussed in detail and new insights are provided. url: https://doi.org/10.3389/fmicb.2018.00750 doi: 10.3389/fmicb.2018.00750 id: cord-298233-qqhgmqrg author: Nan, Yuchen title: Molecular Biology and Infection of Hepatitis E Virus date: 2016-09-07 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Hepatitis E virus (HEV) is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotypes 3 and 4 are zoonotic, whereas those from genotypes 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy, and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus. url: https://doi.org/10.3389/fmicb.2016.01419 doi: 10.3389/fmicb.2016.01419 id: cord-270473-5tok4mqk author: Nanda, S. K. title: Mitochondrial HSP70, HSP40, and HSP60 bind to the 3′ untranslated region of the Murine hepatitis virus genome date: 2003-09-19 words: 7102.0 sentences: 384.0 pages: flesch: 53.0 cache: ./cache/cord-270473-5tok4mqk.txt txt: ./txt/cord-270473-5tok4mqk.txt summary: We have previously shown that mitochondrial-aconitase binds specifically to the 3′ terminal 42 nucleotides of the Murine hepatitis virus (MHV) RNA along with three additional proteins of 70, 58 and 40 kDa to form a stable RNA-protein complex. The assays were done essentially as previously described [22] except that the partially purified post-mitochondrial lysates (approximately 3 µg total protein) were incubated at 22 • C with purified m-apo-aconitase (8-10 µg, graciously supplied by M.C. Kennedy, Gannon University, Erie, PA) and MHV-JHM 3 UTR RNA in ATPase buffer (20 mM Hepes, pH 7.4, 100 mM KCl, 5 mM MgCl 2 , 0.1% NP-40, 1 mM DTT, 1 mM ATP containing 2 µCi [γ-32 P]ATP plus cocktails of protease and phosphatase inhibitors). Gel supershift assays with anti-phosphotyrosine antibodies (Fig. 2B ) demonstrate that at least one of the proteins in the complex formed with MHV 3 (+)42 containing RNAs and m-aconitase, mtHSP70, HSP60, and HSP40 is tyrosine phosphorylated. abstract: We have previously shown that mitochondrial-aconitase binds specifically to the 3′ terminal 42 nucleotides of the Murine hepatitis virus (MHV) RNA along with three additional proteins of 70, 58 and 40 kDa to form a stable RNA-protein complex. Supershift and western blot assays have identified these three proteins as mitochondrial HSP70 (mtHSP70), HSP60, and HSP40. A series of co-immunoprecipitation assays have established that these four MHV RNA binding proteins are associated, even in the absence of MHV RNA. However, the presence of a synthetic RNA containing the sequence bound by these four proteins does increase the amount of co-precipitated protein, in particular the amount of HSP60 which is brought down with antibodies directed against HSP40 and mtHSP70. We have provided evidence for the interaction of these four proteins with the 3′ end region of MHV RNA in infected cells by a series of immunoprecipitation RT-PCR assays. We believe it is likely that MHV RNA interacts with m-aconitase prior to its import into mitochondria in cooperation with extra-mitochondrial mtHSP70, HSP60, and HSP40. url: https://www.ncbi.nlm.nih.gov/pubmed/14689278/ doi: 10.1007/s00705-003-0196-4 id: cord-000143-2xvd5ogf author: Napthine, Sawsan title: Expression of the VP2 Protein of Murine Norovirus by a Translation Termination-Reinitiation Strategy date: 2009-12-22 words: 6886.0 sentences: 300.0 pages: flesch: 50.0 cache: ./cache/cord-000143-2xvd5ogf.txt txt: ./txt/cord-000143-2xvd5ogf.txt summary: In this process, following translation of an upstream open reading frame (ORF) and termination at the stop codon, a proportion of 40S subunits remain associated with the mRNA and reinitiate at the AUG of a downstream ORF, which is typically in close proximity. Recent studies of termination-reinitiation in the expression of the orthomyxovirus influenza BM2 protein have revealed a requirement for a shorter stretch of mRNA (45 nt) upstream of the stop-start window, but nevertheless, the RNA contains a similar TURBS Motif 1 [19] . Whilst in principle, reinitiation of translation of the MNV 49.7 VP2fluc ORF, following termination, could occur at the next available AUG, this is located 54 amino acids from the natural stop-start signal and initiation here would produce a substantially shorter product that would have been detectable by SDS-PAGE. abstract: BACKGROUND: Expression of the minor virion structural protein VP2 of the calicivirus murine norovirus (MNV) is believed to occur by the unusual mechanism of termination codon-dependent reinitiation of translation. In this process, following translation of an upstream open reading frame (ORF) and termination at the stop codon, a proportion of 40S subunits remain associated with the mRNA and reinitiate at the AUG of a downstream ORF, which is typically in close proximity. Consistent with this, the VP2 start codon (AUG) of MNV overlaps the stop codon of the upstream VP1 ORF (UAA) in the pentanucleotide UAA UG. PRINCIPAL FINDINGS: Here, we confirm that MNV VP2 expression is regulated by termination-reinitiation and define the mRNA sequence requirements. Efficient reintiation is dependent upon 43 nt of RNA immediately upstream of the UAA UG site. Chemical and enzymatic probing revealed that the RNA in this region is not highly structured and includes an essential stretch of bases complementary to 18S rRNA helix 26 (Motif 1). The relative position of Motif 1 with respect to the UAA UG site impacts upon the efficiency of the process. Termination-reinitiation in MNV was also found to be relatively insensitive to the initiation inhibitor edeine. CONCLUSIONS: The termination-reinitiation signal of MNV most closely resembles that of influenza BM2. Similar to other viruses that use this strategy, base-pairing between mRNA and rRNA is likely to play a role in tethering the 40S subunit to the mRNA following termination at the VP1 stop codon. Our data also indicate that accurate recognition of the VP2 ORF AUG is not a pre-requisite for efficient reinitiation of translation in this system. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793014/ doi: 10.1371/journal.pone.0008390 id: cord-298779-0mjizsoo author: Narendrula, Rashmi title: RNA disruption is associated with response to multiple classes of chemotherapy drugs in tumor cell lines date: 2016-02-24 words: 7172.0 sentences: 364.0 pages: flesch: 49.0 cache: ./cache/cord-298779-0mjizsoo.txt txt: ./txt/cord-298779-0mjizsoo.txt summary: The abnormal RNA disruption bands that occur upon chemotherapy drug exposure are smaller in molecular weight than the 28S and/or 18S rRNAs. To determine whether the abnormal bands originate from the 28S and/or 18S rRNAs, Northern blotting experiments were performed on total RNA prepared from A2780 cells after incubation in the absence or presence of docetaxel for up to 48 h (Fig. 4) . Previous studies have shown that a variety of apoptosisinducing agents with distinct mechanisms of action (glucocorticoids, okadaic acid, tumor necrosis factor (TNF), dexamethasone, a calcium ionophore and a tricothecene mycotoxin) were able to induce an ordered, apoptosis-associated rRNA degradation in several different cell types, including plant cells and the unicellular organism yeast [11-13, 15-17, 24] . However, this study is the first to report the ability of structurally distinct cytotoxic chemotherapy agents with different mechanisms of action to induce the formation of high molecular weight rRNA degradation fragments (Figs. abstract: BACKGROUND: Cellular stressors and apoptosis-inducing agents have been shown to induce ribosomal RNA (rRNA) degradation in eukaryotic cells. Recently, RNA degradation in vivo was observed in patients with locally advanced breast cancer, where mid-treatment tumor RNA degradation was associated with complete tumor destruction and enhanced patient survival. However, it is not clear how widespread chemotherapy induced “RNA disruption” is, the extent to which it is associated with drug response or what the underlying mechanisms are. METHODS: Ovarian (A2780, CaOV3) and breast (MDA-MB-231, MCF-7, BT474, SKBR3) cancer cell lines were treated with several cytotoxic chemotherapy drugs and total RNA was isolated. RNA was also prepared from docetaxel resistant A2780DXL and carboplatin resistant A2780CBN cells following drug exposure. Disruption of RNA was analyzed by capillary electrophoresis. Northern blotting was performed using probes complementary to the 28S and 18S rRNA to determine the origins of degradation bands. Apoptosis activation was assessed by flow cytometric monitoring of annexin-V and propidium iodide (PI) binding to cells and by measuring caspase-3 activation. The link between apoptosis and RNA degradation (disruption) was investigated using a caspase-3 inhibitor. RESULTS: All chemotherapy drugs tested were capable of inducing similar RNA disruption patterns. Docetaxel treatment of the resistant A2780DXL cells and carboplatin treatment of the A2780CBN cells did not result in RNA disruption. Northern blotting indicated that two RNA disruption bands were derived from the 3’-end of the 28S rRNA. Annexin-V and PI staining of docetaxel treated cells, along with assessment of caspase-3 activation, showed concurrent initiation of apoptosis and RNA disruption, while inhibition of caspase-3 activity significantly reduced RNA disruption. CONCLUSIONS: Supporting the in vivo evidence, our results demonstrate that RNA disruption is induced by multiple chemotherapy agents in cell lines from different tissues and is associated with drug response. Although present, the link between apoptosis and RNA disruption is not completely understood. Evaluation of RNA disruption is thus proposed as a novel and effective biomarker to assess response to chemotherapy drugs in vitro and in vivo. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-016-2197-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12885-016-2197-1 doi: 10.1186/s12885-016-2197-1 id: cord-252871-qfrpuy3t author: Nasir, Arshan title: Investigating the Concept and Origin of Viruses date: 2020-11-03 words: 5153.0 sentences: 298.0 pages: flesch: 46.0 cache: ./cache/cord-252871-qfrpuy3t.txt txt: ./txt/cord-252871-qfrpuy3t.txt summary: We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. In turn, the origin of archaeoviruses from Archaea, bacterioviruses from Bacteria, and eukaryoviruses from Eukarya also seems less likely as these viruses share several conserved protein folds involved in virion synthesis and other functions, indicating that they may have evolved prior to the diversification of LUCA into modern cells. abstract: The ongoing COVID-19 pandemic has piqued public interest in the properties, evolution, and emergence of viruses. Here, we discuss how these basic questions have surprisingly remained disputed despite being increasingly within the reach of scientific analysis. We review recent data-driven efforts that shed light into the origin and evolution of viruses and explain factors that resist the widespread acceptance of new views and insights. We propose a new definition of viruses that is not restricted to the presence or absence of any genetic or physical feature, detail a scenario for how viruses likely originated from ancient cells, and explain technical and conceptual biases that limit our understanding of virus evolution. We note that the philosophical aspects of virus evolution also impact the way we might prepare for future outbreaks. url: https://api.elsevier.com/content/article/pii/S0966842X20302304 doi: 10.1016/j.tim.2020.08.003 id: cord-341029-49360l2a author: Nasir, Arshan title: A phylogenomic data-driven exploration of viral origins and evolution date: 2015-09-25 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The origin of viruses remains mysterious because of their diverse and patchy molecular and functional makeup. Although numerous hypotheses have attempted to explain viral origins, none is backed by substantive data. We take full advantage of the wealth of available protein structural and functional data to explore the evolution of the proteomic makeup of thousands of cells and viruses. Despite the extremely reduced nature of viral proteomes, we established an ancient origin of the “viral supergroup” and the existence of widespread episodes of horizontal transfer of genetic information. Viruses harboring different replicon types and infecting distantly related hosts shared many metabolic and informational protein structural domains of ancient origin that were also widespread in cellular proteomes. Phylogenomic analysis uncovered a universal tree of life and revealed that modern viruses reduced from multiple ancient cells that harbored segmented RNA genomes and coexisted with the ancestors of modern cells. The model for the origin and evolution of viruses and cells is backed by strong genomic and structural evidence and can be reconciled with existing models of viral evolution if one considers viruses to have originated from ancient cells and not from modern counterparts. url: https://www.ncbi.nlm.nih.gov/pubmed/26601271/ doi: 10.1126/sciadv.1500527 id: cord-301233-nenw0f81 author: Naydenova, Katerina title: Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP date: 2020-10-21 words: 4059.0 sentences: 217.0 pages: flesch: 51.0 cache: ./cache/cord-301233-nenw0f81.txt txt: ./txt/cord-301233-nenw0f81.txt summary: Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Here we report the structure of the SARS-CoV-2 RdRp, comprising subunits nsp7, nsp8 and nsp12, in complex with template:primer double-stranded RNA and favipiravir ribonucleoside triphosphate (favipiravir-RTP), determined by cryoEM at 2.5Å resolution. In this study, we determined the cryoEM structure of favipiravir-RTP at the catalytic site of the SARS-CoV-2 RdRp, in complex with template:primer dsRNA, and investigated the influence of this nucleotide analogue inhibitor on RNA synthesis in vitro. abstract: The RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with SARS-CoV-2, despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses. url: https://doi.org/10.1101/2020.10.21.347690 doi: 10.1101/2020.10.21.347690 id: cord-277874-cr53ycrm author: Neault, N. title: SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence. date: 2020-09-03 words: 7079.0 sentences: 372.0 pages: flesch: 49.0 cache: ./cache/cord-277874-cr53ycrm.txt txt: ./txt/cord-277874-cr53ycrm.txt summary: We believe MPAD based SARS-CoV-2 protein quantitation represents a promising epidemiological tool with a sensitivity sufficiently superior to viral RNA measurement that, in addition to enabling early detection and population tracking of COVID-19 load, will also open the way to effective infection surveillance of specific facilities, schools and residences. Primary sludge and PEG precipitated influent fractions, collected from the contiguous cities of Ottawa and Gatineau in April through June 2020, were analysed for the presence of four SARS-CoV-2 structural proteins, N (nucleocapsid), M (membrane), S (spike), and E (envelope), by western blot. Next, in order to assure specificity for detection of SARS-CoV-2 proteins, we used MPAD with an expanded panel to simultaneously measure three viral proteins, N, S and M, along with six fecal content control proteins in PEG precipitated "influent solids" samples drawn from the Ottawa WRRF during the study period ( Fig 5) . abstract: The COVID-19 pandemic has given rise to diverse approaches to track infections. The causative agent, SARS-CoV-2 is a fecally-shed RNA virus, and many groups have assayed wastewater for viral RNA fragments by quantitative reverse transcription polymerase chain reaction (qRT-PCR) as a proxy of COVID-19 prevalence in the community. Most groups report low levels of viral RNA that often skirt the methods theoretical limits of detection and quantitation. Here, we demonstrate the presence of SARS-CoV-2 structural proteins in wastewater using traditional immunoblotting and quantitate them from wastewater solids using an immuno-linked PCR method called Multiplex Paired-antibody Amplified Detection (MPAD). In this longitudinal study, we corrected for stochastic variability inherent to wastewater-based epidemiology using multiple fecal content protein biomarkers. These normalized SARS-CoV-2 protein data correlated well with public health metrics. Our method of assaying SARS-CoV-2 protein from wastewater represents a promising and sensitive epidemiological tool to assess prevalence of fecally-shed pathogens in the community. url: http://medrxiv.org/cgi/content/short/2020.09.01.20185280v1?rss=1 doi: 10.1101/2020.09.01.20185280 id: cord-262753-jld1ygxt author: Neidermyer, William J. title: Global analysis of polysome-associated mRNA in vesicular stomatitis virus infected cells date: 2019-06-21 words: 9235.0 sentences: 461.0 pages: flesch: 46.0 cache: ./cache/cord-262753-jld1ygxt.txt txt: ./txt/cord-262753-jld1ygxt.txt summary: Analysis of sequence reads in the different fractions shows >60% of total cytoplasmic and polysome-associated reads map to the 5 viral genes by 6 hours post-infection, a time point at which robust host cell translational shut-off is observed. The cellular mRNAs that remain most polysome-associated following infection had longer half-lives, were typically larger, and were more AU rich, features that are shared with the viral mRNAs. Several of those mRNAs encode proteins known to positively affect viral replication, and using chemical inhibition and siRNA depletion we confirm that the host chaperone heat shock protein 90 (hsp90) and eukaryotic translation initiation factor 3A (eIF3A)—encoded by 2 such mRNAs—support viral replication. In the present study, we interrogate global mRNA translation in VSV infected cells using RNAseq analysis of the cytoplasmic mRNA transcriptome, and parallel sequencing of polysome-associated mRNAs. We obtain support for the model that an overabundance of viral mRNA contributes to host shut-off by leading to a re-distribution of cellular ribosomes onto viral mRNA. abstract: Infection of mammalian cells with vesicular stomatitis virus (VSV) results in the inhibition of cellular translation while viral translation proceeds efficiently. VSV RNA synthesis occurs entirely within the cytoplasm, where during transcription the viral polymerase produces 5 mRNAs that are structurally indistinct to cellular mRNAs with respect to their 5′ cap-structure and 3′-polyadenylate tail. Using the global approach of massively parallel sequencing of total cytoplasmic, monosome- and polysome-associated mRNA, we interrogate the impact of VSV infection of HeLa cells on translation. Analysis of sequence reads in the different fractions shows >60% of total cytoplasmic and polysome-associated reads map to the 5 viral genes by 6 hours post-infection, a time point at which robust host cell translational shut-off is observed. Consistent with an overwhelming abundance of viral mRNA in the polysome fraction, the reads mapping to cellular genes were reduced. The cellular mRNAs that remain most polysome-associated following infection had longer half-lives, were typically larger, and were more AU rich, features that are shared with the viral mRNAs. Several of those mRNAs encode proteins known to positively affect viral replication, and using chemical inhibition and siRNA depletion we confirm that the host chaperone heat shock protein 90 (hsp90) and eukaryotic translation initiation factor 3A (eIF3A)—encoded by 2 such mRNAs—support viral replication. Correspondingly, regulated in development and DNA damage 1 (Redd1) encoded by a host mRNA with reduced polysome association inhibits viral infection. These data underscore the importance of viral mRNA abundance in the shut-off of host translation in VSV infected cells and link the differential translatability of some cellular mRNAs with pro- or antiviral function. url: https://www.ncbi.nlm.nih.gov/pubmed/31226162/ doi: 10.1371/journal.ppat.1007875 id: cord-326225-crtpzad7 author: Neill, John D. title: Simultaneous rapid sequencing of multiple RNA virus genomes date: 2014-06-01 words: 3804.0 sentences: 204.0 pages: flesch: 55.0 cache: ./cache/cord-326225-crtpzad7.txt txt: ./txt/cord-326225-crtpzad7.txt summary: This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3′-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. There is a wealth of information in these isolates, but up till now, it has been time consuming and expensive to sequence these viral genomes, often requiring sets of strain-specific primers for PCR amplification and sequencing. These primers were developed so that the 20 base known sequence was used for PCR amplification of the library as well as served as a barcode for identifying each viral library following pooling and sequencing. This virus, a BVDV 1b strain isolated from alpaca (GenBank accession JX297520.1; Table 2 , library 3, barcode 10), was assembled from Ion Torrent data and was found to have only 1 base difference from the sequence determined earlier (data not shown). One virus, library 1, barcode 9, had only 658 viral sequence reads but 94.4% of the genome was assembled. abstract: Comparing sequences of archived viruses collected over many years to the present allows the study of viral evolution and contributes to the design of new vaccines. However, the difficulty, time and expense of generating full-length sequences individually from each archived sample have hampered these studies. Next generation sequencing technologies have been utilized for analysis of clinical and environmental samples to identify viral pathogens that may be present. This has led to the discovery of many new, uncharacterized viruses from a number of viral families. Use of these sequencing technologies would be advantageous in examining viral evolution. In this study, a sequencing procedure was used to sequence simultaneously and rapidly multiple archived samples using a single standard protocol. This procedure utilized primers composed of 20 bases of known sequence with 8 random bases at the 3′-end that also served as an identifying barcode that allowed the differentiation each viral library following pooling and sequencing. This conferred sequence independence by random priming both first and second strand cDNA synthesis. Viral stocks were treated with a nuclease cocktail to reduce the presence of host nucleic acids. Viral RNA was extracted, followed by single tube random-primed double-stranded cDNA synthesis. The resultant cDNAs were amplified by primer-specific PCR, pooled, size fractionated and sequenced on the Ion Torrent PGM platform. The individual virus genomes were readily assembled by both de novo and template-assisted assembly methods. This procedure consistently resulted in near full length, if not full-length, genomic sequences and was used to sequence multiple bovine pestivirus and coronavirus isolates simultaneously. url: https://doi.org/10.1016/j.jviromet.2014.02.016 doi: 10.1016/j.jviromet.2014.02.016 id: cord-253466-7gpije5d author: Netherton, Christopher title: A Guide to Viral Inclusions, Membrane Rearrangements, Factories, and Viroplasm Produced During Virus Replication date: 2007-08-31 words: 26372.0 sentences: 1363.0 pages: flesch: 45.0 cache: ./cache/cord-253466-7gpije5d.txt txt: ./txt/cord-253466-7gpije5d.txt summary: Significantly, Poliovirus infection causes enrichment of GEFs in membranes containing replicase proteins, and this would provide a mechanism for increasing levels of Arf1-GTP at sites of virus replication. There is evidence that Tobacco mosaic virus also uses the ER as a site of replication because the replicase enzyme and viral RNA are located on the ER of infected cells, and infection causes major changes in ER morphology (Reichel and Beachy, 1998) , including ER aggregation and formation of lamella structures. Even though these viruses infect a diverse range of hosts from different phyla, including vertebrates [poxviruses, African swine fever virus (ASFV)], arthropods (entomopox, ASFV, chloriridoviruses), amphibians and fish (Ranavirus, Megalocytivirus, and Lymphocystivirus genera of the Iridoviridae family), marine algae (phycodnaviruses), and protozoa (mimivirus), they all generate cytoplasmic factories as major sites of virus assembly and replication (illustrated in Fig. 4 ). Formation of DNA replication structures in herpes virus-infected cells requires a viral DNA binding protein abstract: Virus replication can cause extensive rearrangement of host cell cytoskeletal and membrane compartments leading to the “cytopathic effect” that has been the hallmark of virus infection in tissue culture for many years. Recent studies are beginning to redefine these signs of viral infection in terms of specific effects of viruses on cellular processes. In this chapter, these concepts have been illustrated by describing the replication sites produced by many different viruses. In many cases, the cellular rearrangements caused during virus infection lead to the construction of sophisticated platforms in the cell that concentrate replicase proteins, virus genomes, and host proteins required for replication, and thereby increase the efficiency of replication. Interestingly, these same structures, called virus factories, virus inclusions, or virosomes, can recruit host components that are associated with cellular defences against infection and cell stress. It is possible that cellular defence pathways can be subverted by viruses to generate sites of replication. The recruitment of cellular membranes and cytoskeleton to generate virus replication sites can also benefit viruses in other ways. Disruption of cellular membranes can, for example, slow the transport of immunomodulatory proteins to the surface of infected cells and protect against innate and acquired immune responses, and rearrangements to cytoskeleton can facilitate virus release. url: https://www.sciencedirect.com/science/article/pii/S0065352707700040 doi: 10.1016/s0065-3527(07)70004-0 id: cord-287093-9mertwj7 author: Netherton, Christopher L title: Virus factories, double membrane vesicles and viroplasm generated in animal cells date: 2011-10-12 words: 4308.0 sentences: 227.0 pages: flesch: 39.0 cache: ./cache/cord-287093-9mertwj7.txt txt: ./txt/cord-287093-9mertwj7.txt summary: In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses. In this review, we discuss how three supergroups of (+)strand RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses (NCLDV). The RNA-dependent RNA polymerases (RdRp) of the (+)strand RNA viruses are targeted to the cytoplasmic face of membrane-bound organelles and subsequent assembly of the replicase complex induces membrane curvature and the formation of densely packed membrane vesicles (reviewed in [1, 2] ) ( Figure 1 ). This suggests that replication may take place on CM and that genomes are transferred to vesicular packets for envelopment and budding, while excess viral RNA may be stored in DMVs. Picornaviruses generate densely packed DMVs between 200 and 400 nm in diameter, a series of single membraned vesicles resulting from fragmentation of the Golgi, and autophagosomes possibly generated as a bystander response to infection [11 ,12-16] . abstract: Many viruses reorganise cellular membrane compartments and the cytoskeleton to generate subcellular microenvironments called virus factories or ‘viroplasm’. These create a platform to concentrate replicase proteins, virus genomes and host proteins required for replication and also protect against antiviral defences. There is growing interest in understanding how viruses induce such large changes in cellular organisation, and recent studies are beginning to reveal the relationship between virus factories and viroplasm and the cellular structures that house them. In this review, we discuss how three supergroups of (+)RNA viruses generate replication sites from membrane-bound organelles and highlight research on perinuclear factories induced by the nucleocytoplasmic large DNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/22440839/ doi: 10.1016/j.coviro.2011.09.008 id: cord-297579-ohpm5ys0 author: Netzler, Natalie E. title: Norovirus antivirals: Where are we now? date: 2018-12-25 words: 6471.0 sentences: 375.0 pages: flesch: 37.0 cache: ./cache/cord-297579-ohpm5ys0.txt txt: ./txt/cord-297579-ohpm5ys0.txt summary: Despite the clinical significance of norovirus infection, antiviral studies have been hindered, because until recently, human norovirus could not be successfully propagated in cell culture. The cross-genotypic activity displayed by Nbs illustrates that these molecules have the potential to overcome the narrow antigenic spectrum typically displayed by conventional mAbs. However, despite these findings, mAb and Nb studies have been based mostly on VLP-binding and structural analysis of that binding (Table 1 ) and thus the effects of such compounds against norovirus in cell culture or in vivo need to be explored further before continued development toward clinical application. Most recently NTZ was shown to potently inhibit FCV replication in cell culture with an EC 50 of 0.6 µM, 189 and the GI norovirus replicon at a clinically relevant concentration (5 μg/mL), 190 which was later shown to result in a broad antiviral response. The viral polymerase inhibitor 2′-C-methylcytidine inhibits Norwalk virus replication and protects against norovirus-induced diarrhea and mortality in a mouse model abstract: Human noroviruses inflict a significant health burden on society and are responsible for approximately 699 million infections and over 200 000 estimated deaths worldwide each year. Yet despite significant research efforts, approved vaccines or antivirals to combat this pathogen are still lacking. Safe and effective antivirals are not available, particularly for chronically infected immunocompromised individuals, and for prophylactic applications to protect high‐risk and vulnerable populations in outbreak settings. Since the discovery of human norovirus in 1972, the lack of a cell culture system has hindered biological research and antiviral studies for many years. Recent breakthroughs in culturing human norovirus have been encouraging, however, further development and optimization of these novel methodologies are required to facilitate more robust replication levels, that will enable reliable serological and replication studies, as well as advances in antiviral development. In the last few years, considerable progress has been made toward the development of norovirus antivirals, inviting an updated review. This review focuses on potential therapeutics that have been reported since 2010, which were examined across at least two model systems used for studying human norovirus or its enzymes. In addition, we have placed emphasis on antiviral compounds with a defined chemical structure. We include a comprehensive outline of direct‐acting antivirals and offer a discussion of host‐modulating compounds, a rapidly expanding and promising area of antiviral research. url: https://www.ncbi.nlm.nih.gov/pubmed/30584800/ doi: 10.1002/med.21545 id: cord-276988-bvsz5q6d author: Neu, Carolin T. title: Post-Transcriptional Expression Control in Platelet Biogenesis and Function date: 2020-10-15 words: 11394.0 sentences: 581.0 pages: flesch: 38.0 cache: ./cache/cord-276988-bvsz5q6d.txt txt: ./txt/cord-276988-bvsz5q6d.txt summary: Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs. Blood platelets-the major players in hemostasis-are small anucleate cell fragments with a characteristic discoid shape and a diameter of 1 to 3 µm that originate from megakaryocytes (MKs). The m 7 G cap and poly(A) tail promote mRNA translation and stability, while the UTRs expose sequences for RNA-binding proteins (RBPs) and regulatory sites for microRNA (miRNA)-mediated translational and degradation control [45, [52] [53] [54] . Moreover, RNA-Seq analysis of platelet miRNAs in patients with myocardial infarction revealed nine differentially expressed platelet miRNAs compared to healthy controls, which were released upon platelet aggregation and taken up by endothelial cells via a vesicle-dependent mechanism [80] . Megakaryopoiesis, megakaryocyte maturation, as well as platelet formation, were shown to be highly complex processes that are regulated on multiple levels including epigenetic, transcriptional as well as post-transcriptional gene expression control mechanisms. abstract: Platelets are highly abundant cell fragments of the peripheral blood that originate from megakaryocytes. Beside their well-known role in wound healing and hemostasis, they are emerging mediators of the immune response and implicated in a variety of pathophysiological conditions including cancer. Despite their anucleate nature, they harbor a diverse set of RNAs, which are subject to an active sorting mechanism from megakaryocytes into proplatelets and affect platelet biogenesis and function. However, sorting mechanisms are poorly understood, but RNA-binding proteins (RBPs) have been suggested to play a crucial role. Moreover, RBPs may regulate RNA translation and decay following platelet activation. In concert with other regulators, including microRNAs, long non-coding and circular RNAs, RBPs control multiple steps of the platelet life cycle. In this review, we will highlight the different RNA species within platelets and their impact on megakaryopoiesis, platelet biogenesis and platelet function. Additionally, we will focus on the currently known concepts of post-transcriptional control mechanisms important for RNA fate within platelets with a special emphasis on RBPs. url: https://doi.org/10.3390/ijms21207614 doi: 10.3390/ijms21207614 id: cord-336628-0evl3wnd author: Neufeldt, Christopher J. title: SARS-CoV-2 infection induces a pro-inflammatory cytokine response through cGAS-STING and NF-κB date: 2020-07-21 words: 5880.0 sentences: 362.0 pages: flesch: 49.0 cache: ./cache/cord-336628-0evl3wnd.txt txt: ./txt/cord-336628-0evl3wnd.txt summary: Consistently, secreted cytokine profiles from both severe COVID-19 patients and SARS-CoV-2 infected lung epithelial cells, were enriched for pro-inflammatory cytokines and lacked type I/III IFNs. We also demonstrate that SARS-CoV-2 infection leads specifically to NF-κB but not IRF3 nuclear localization and that poly(I:C)-induced pathway activation is attenuated in infected cells. To confirm that the lack of IFN response in Calu-3 or A549-ACE2 cells infected with SARS-CoV-2 was not due to defects in the activation of innate immune pathways, we To test if IFNs could limit virus replication even after establishment of infection, A549-ACE2 cells were treated with high levels of various IFNs at the time point of infection or 6 h thereafter. these results indicate that SARS-CoV2-infection triggers the cGAS-STING pathway, leading to NF-κB-mediated induction of pro-inflammatory cytokines, and that this response can be controlled with STING inhibitors. abstract: SARS-CoV-2 is a novel virus that has rapidly spread, causing a global pandemic. In the majority of infected patients, SARS-CoV-2 leads to mild disease; however, in a significant proportion of infections, individuals develop severe symptoms that can lead to permanent lung damage or death. These severe cases are often associated with high levels of pro-inflammatory cytokines and low antiviral responses which can lead to systemic complications. We have evaluated transcriptional and cytokine secretion profiles from infected cell cultures and detected a distinct upregulation of inflammatory cytokines that parallels samples taken from infected patients. Building on these observations, we found a specific activation of NF-κB and a block of IRF3 nuclear translocation in SARS-CoV-2 infected cells. This NF-κB response is mediated by cGAS-STING activation and could be attenuated through STING targeting drugs. Our results show that SARS-CoV-2 curates a cGAS-STING mediated NF-κB driven inflammatory immune response in epithelial cells that likely contributes to inflammatory responses seen in patients and might be a target to suppress severe disease symptoms. url: https://doi.org/10.1101/2020.07.21.212639 doi: 10.1101/2020.07.21.212639 id: cord-303533-6s01qplg author: Neuman, Benjamin W. title: Does form meet function in the coronavirus replicative organelle? date: 2014-07-15 words: 3642.0 sentences: 177.0 pages: flesch: 39.0 cache: ./cache/cord-303533-6s01qplg.txt txt: ./txt/cord-303533-6s01qplg.txt summary: This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. Whatever their purpose, it is clear that the coronavirus organelle is dynamic [9] , closely tied to vesicular transport in the host cell [5, 10] , and consists mainly of paired membranes that form a variety of complex shapes including convoluted membranes and double-membrane vesicles (DMVs) [2, 11] . Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulum-targeted viral protein abstract: If we use the analogy of a virus as a living entity, then the replicative organelle is the part of the body where its metabolic and reproductive activities are concentrated. Recent studies have illuminated the intricately complex replicative organelles of coronaviruses, a group that includes the largest known RNA virus genomes. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle. url: https://www.sciencedirect.com/science/article/pii/S0966842X14001322 doi: 10.1016/j.tim.2014.06.003 id: cord-279418-3r1ijafm author: Nevers, Quentin title: Negri bodies and other virus membrane-less replication compartments() date: 2020-08-21 words: 6437.0 sentences: 406.0 pages: flesch: 44.0 cache: ./cache/cord-279418-3r1ijafm.txt txt: ./txt/cord-279418-3r1ijafm.txt summary: We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. With the rapid identification of cellular membraneless compartments and proteins that undergo LLPS in vitro, a major challenge in the field is to demonstrate unambiguously that a specific structure is indeed a phase-separated liquid body in the cellular context. Until now, only a few specific cellular factors, which directly interact with viral proteins such as the nucleoproteins and phosphoproteins of MNV, have been shown to concentrate in these structures. Upon Infection, Cellular WD Repeat-Containing Protein 5 (WDR5) Localizes to Cytoplasmic Inclusion Bodies and Enhances Measles Virus Replication The Ebola Virus Nucleoprotein Recruits the Nuclear RNA Export Factor NXF1 into Inclusion Bodies to Facilitate Viral Protein Expression The Cellular Protein CAD is Recruited into Ebola Virus Inclusion Bodies by the Nucleoprotein NP to Facilitate Genome Replication and Transcription abstract: Viruses reshape the organization of the cell interior to achieve different steps of their cellular cycle. Particularly, viral replication and assembly often take place in viral factories where specific viral and cellular proteins as well as nucleic acids concentrate. Viral factories can be either membrane-delimited or devoid of any cellular membranes. In the latter case, they are referred as membrane-less replication compartments. The most emblematic ones are the Negri bodies, which are inclusion bodies that constitute the hallmark of rabies virus infection. Interestingly, Negri bodies and several other viral replication compartments have been shown to arise from a liquid-liquid phase separation process and, thus, constitute a new class of liquid organelles. This is a paradigm shift in the field of virus replication. Here, we review the different aspects of membrane-less virus replication compartments with a focus on the Mononegavirales order and discuss their interactions with the host cell machineries and the cytoskeleton. We particularly examine the interplay between viral factories and the cellular innate immune response, of which several components also form membrane-less condensates in infected cells. url: https://doi.org/10.1016/j.bbamcr.2020.118831 doi: 10.1016/j.bbamcr.2020.118831 id: cord-016293-pyb00pt5 author: Newell-McGloughlin, Martina title: The flowering of the age of Biotechnology 1990–2000 date: 2006 words: 22402.0 sentences: 943.0 pages: flesch: 47.0 cache: ./cache/cord-016293-pyb00pt5.txt txt: ./txt/cord-016293-pyb00pt5.txt summary: In the course of the project, especially in the early years, the plan stated that "much new technology will be developed that will facilitate biomedical and a broad range of biological research, bring down the cost of many experiments (mapping and sequencing), and finding applications in numerous other fields." The plan built upon the 1988 reports of the Office of Technology Assessment and the National Research Council on mapping and sequencing the human genome. These DNA chips have broad commercial applications and are now used in many areas of basic and clinical research including the detection of drug resistance mutations in infectious organisms, direct DNA sequence comparison of large segments of the human genome, the monitoring of multiple human genes for disease associated mutations, the quantitative and parallel measurement of mRNA expression for thousands of human genes, and the physical and genetic mapping of genomes. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120537/ doi: 10.1007/1-4020-5149-2_4 id: cord-290813-6ylwj5je author: Ng, Enders K. O. title: Molecular Diagnosis of Severe Acute Respiratory Syndrome date: 2006 words: 3125.0 sentences: 179.0 pages: flesch: 53.0 cache: ./cache/cord-290813-6ylwj5je.txt txt: ./txt/cord-290813-6ylwj5je.txt summary: To date, based on the publicly released full genomic sequences of SARS-CoV, various molecular detection methods based on reverse-transcription polymerase chain reaction (RT-PCR) have been developed. Subsequently, together with the improvement of viral RNA extraction in which plasma or serum requires no ultracentrifugation, two real-time quantitative RT-PCR assays, one aimed toward the polymerase region and the other toward the nucleocapsid region of the virus genome ( Fig. 1) , were developed for measuring the concentration of SARS-CoV RNA in serum/plasma samples from SARS patients (13, 14) . With the use of the real-time quantitative RT-PCR assay, SARS-CoV RNA has recently been shown to be detectable in the plasma samples of pediatric patients during different stages of SARS (Fig. 4) (14) . Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome abstract: The etiologic agent of severe acute respiratory syndrome (SARS) has been identified as a new type of coronavirus, known as SARS-coronavirus (SARS-CoV). Although the SARS epidemic has subsided, many authorities, including the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC), have warned of the possible re-emergence of this highly infectious disease. Although antibody-based diagnosis of SARS has been demonstrated to be a reliable proof of SARS infection, it is not sensitive enough for detection during the early phase of the disease. To date, based on the publicly released full genomic sequences of SARS-CoV, various molecular detection methods based on reverse-transcription polymerase chain reaction (RT-PCR) have been developed. Although most of the assays have initially been focused on RNA extracted from nasopharyngeal aspirates, urine, and stools, several of the more recently developed assays have been based on the analysis of RNA extracted from plasma and serum. Such assays allow the more standardized quantitative expression of viral loads and are potentially useful for early SARS diagnosis. In this chapter, two real-time quantitative RT-PCR systems for the quantification of SARS-CoV RNA in serum are discussed. The two RT-PCR systems, one aimed toward the nucleocapsid region and the other toward the polymerase region of the virus genome, have a detection rate of up to 80% during the first week of illness. These quantitative systems are potentially useful for the early diagnosis of SARS and can also provide viral load information that might assist clinicians in making a prognostic evaluation of an infected individual. url: https://www.ncbi.nlm.nih.gov/pubmed/16916262/ doi: 10.1385/1-59745-074-x:163 id: cord-312544-vip4jtlv author: Ng, Lisa FP title: Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay date: 2006-03-02 words: 2142.0 sentences: 108.0 pages: flesch: 57.0 cache: ./cache/cord-312544-vip4jtlv.txt txt: ./txt/cord-312544-vip4jtlv.txt summary: METHODS: A one-step reverse-transcription PCR assay was developed to detect the H5N1 avian influenza A virus. RESULTS: Validation on 145 field specimens from Vietnam and Malaysia showed that the assay was specific without cross reactivity to a number of other infuenza strains as well as human respiratory related pathogens. In this study, we describe the development of a nucleic acid detection test that is rapid, specific and sensitive, thus allowing greatly improved detection of the H5N1 avian influenza A virus. To establish the specificity of the assays for H5N1 subtype detection, we then tested the primers on several known strains of influenza A viruses derived from avian sources (H3N8, H5N3, H7N3 and H9N2). A total of 145 field samples comprising of known and suspect cases from chickens, ducks and muscovies isolated from Vietnam and Malaysia during the 2004 to 2005 outbreak were tested for H5N1 RNA (Table Detection of H5N1 avian influenza A virus by one-step RT-PCR 2). abstract: BACKGROUND: Continuous outbreaks of the highly pathogenic H5N1 avian influenza A in Asia has resulted in an urgent effort to improve current diagnostics to aid containment of the virus and lower the threat of a influenza pandemic. We report here the development of a PCR-based assay that is highly specific for the H5N1 avian influenza A virus. METHODS: A one-step reverse-transcription PCR assay was developed to detect the H5N1 avian influenza A virus. The specificity of the assay was shown by testing sub-types of influenza A virus and other viral and bacterial pathogens; and on field samples. RESULTS: Validation on 145 field specimens from Vietnam and Malaysia showed that the assay was specific without cross reactivity to a number of other infuenza strains as well as human respiratory related pathogens. Detection was 100% from allantoic fluid in H5N1 positive samples, suggesting it to be a reliable sampling source for accurate detection. CONCLUSION: The assay developed from this study indicates that the primers are specific for the H5N1 influenza virus. As shown by the field tested results, this assay would be highly useful as a diagnostic tool to help identify and control influenza epidemics. url: https://www.ncbi.nlm.nih.gov/pubmed/16512903/ doi: 10.1186/1471-2334-6-40 id: cord-103638-n5kpvsvg author: Nguyen, Long T. title: Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection date: 2020-04-14 words: 5357.0 sentences: 388.0 pages: flesch: 60.0 cache: ./cache/cord-103638-n5kpvsvg.txt txt: ./txt/cord-103638-n5kpvsvg.txt summary: By extending the 3''or 5''-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes. However, the ENHANCE showed 5.4-fold and 3.4-fold and higher trans-cleavage activity compared to the wild-type crRNA for targeting the methylated dsDNA and ssDNA, respectively (Fig. 3e, Supplementary Fig. 20a) . While no clinical samples were tested, the results indicated the 3''DNA7-modified crRNA consistently demonstrated higher sensitivity for detecting CoV-2 dsDNA within 30 minutes as compared to the wild-type crCoV-2 ( Supplementary Figs. abstract: The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. However, the current CRISPR/Cas12a systems are limited to detecting DNA in a picomolar detection limit without an amplification step. Here, we developed a platform with engineered crRNAs and optimized conditions that enabled us to detect DNA, DNA/RNA heteroduplex and methylated DNA with higher sensitivity, achieving a limit of detection of in femtomolar range without any target pre-amplification step. By extending the 3’- or 5’-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. We applied this sensitive system to detect as low as 25 fM dsDNA from the PCA3 gene, an overexpressed biomarker in prostate cancer patients, in simulated urine over 6 hours. The same platform was used to detect as low as ~700 fM cDNA from HIV, 290 fM RNA from HCV, and 370 fM cDNA from SARS-CoV-2, all within 30 minutes without a need for target amplification. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes. url: https://doi.org/10.1101/2020.04.13.036079 doi: 10.1101/2020.04.13.036079 id: cord-003050-n25wnmq5 author: Nibert, Max L. title: A barnavirus sequence mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis date: 2018-03-07 words: 3324.0 sentences: 159.0 pages: flesch: 53.0 cache: ./cache/cord-003050-n25wnmq5.txt txt: ./txt/cord-003050-n25wnmq5.txt summary: The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on − 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. Based on similar genome sizes, coding organizations, and P2-and P3-region sequence similarities, both MBV and RsBV1 appear to be most closely related to plant viruses in the unassigned genus Sobemovirus [12, 16] . As a result, the consensus sequence for the apparent new barnavirus reported here (GenBank MG686618) is 4206 nt long, appears to be coding complete for ORFs 1-4 ( Fig. 1) , and was newly assembled from a total of 821 individual reads (reads per position: mean, 19; range, 2-35). abstract: Because so few viruses in the family Barnaviridae have been reported, we searched for more of them in public sequence databases. Here, we report the complete coding sequence of Colobanthus quitensis associated barnavirus 1, mined from a transcriptome of the Antarctic pearlwort Colobanthus quitensis. The 4.2-kb plus-strand sequence of this virus encompasses four main open reading frames (ORFs), as expected for barnaviruses, including ORFs for a protease-containing polyprotein, an RNA-dependent RNA polymerase whose translation appears to rely on − 1 ribosomal frameshifting, and a capsid protein that is likely to be translated from a subgenomic RNA. The possible derivation of this virus from a fungus associated with C. quitensis is discussed. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-018-3794-x) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5999160/ doi: 10.1007/s00705-018-3794-x id: cord-013176-6ckuya1w author: Ninfali, Paolino title: Antiviral Properties of Flavonoids and Delivery Strategies date: 2020-08-21 words: 8102.0 sentences: 372.0 pages: flesch: 35.0 cache: ./cache/cord-013176-6ckuya1w.txt txt: ./txt/cord-013176-6ckuya1w.txt summary: Quercetin, extracted from Embelia ribes (Mirsinaceae), exhibited antiviral effects against HCV, exerted through activity inhibition of the viral protease Non-Structural protein 3 (NS3), leading to a decrease in HCV replication [36] . The natural extract of Tetrastigma hemsleyanum (Vitaceae) contains many flavonoids, including vitexin, vitexin-2-O-rhamnoside, isorhamnetin, rutin, kaempferol, astragalin, quercitrin, quercetin and iso-quercetin, which were shown to be able to exert anti-influenza virus activity, with different efficiency, through the reduction of the number of plaques induced by the influenza virus in infected Madin-Darby Canine Kidney (MDCK) cells [21] . In future perspective, this approach could be considered in order to possibly improve the antiviral activity of some flavonoids, like baicalin, that was able, like fludarabine [65] , to act against HIV-1 chronic infection of human monocytes and macrophages, inhibiting the fusion of HIV virus envelope proteins with these cells [73] . abstract: This review summarizes the latest advancements in phytochemicals as functional antiviral agents. We focused on flavonoids, like apigenin, vitexin, quercetin, rutin and naringenin, which have shown a wide range of biological effects including antiviral activities. The molecular mechanisms of their antiviral effects mainly consist in the inhibition of viral neuraminidase, proteases and DNA/RNA polymerases, as well as in the modification of various viral proteins. Mixtures of different flavonoids or combination of flavonoids with antiviral synthetic drugs provide an enhancement of their antiviral effects. Recent strategies in drug delivery significantly contribute to overcoming the low bioavailability of flavonoids. Frequent viral infections worldwide have led to the need for new effective antiviral agents, which can be identified among the various phytochemicals. In this light, screening the antiviral activities of a cocktail of flavonoids would be advantageous in order to prevent viral infections and improve current antiviral therapies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551920/ doi: 10.3390/nu12092534 id: cord-344321-fjer281d author: Ning, Yi title: Aptamers used for biosensors and targeted therapy date: 2020-10-20 words: 16947.0 sentences: 1045.0 pages: flesch: 49.0 cache: ./cache/cord-344321-fjer281d.txt txt: ./txt/cord-344321-fjer281d.txt summary: Aptamers, first raised by two research groups independently in 1990 [1, 2] , are single-stranded DNA (ssDNA) or RNA sequences obtained through systematic evolution of ligands by exponential enrichment (SELEX) that can fold into secondary and three-dimensional shapes, enabling them to recognize various target molecules with high specificity and affinity, including proteins [3, 4] , small molecules [5, 6] , metal ions [7, 8] , bacterial cells [9, 10] , viruses [11, 12] , cancer cells [13, 14] , and even tissues [15] . developed a novel QD-Apt conjugate to be loaded with Dox for the targeted delivery of drugs to PC cells based on the mechanism of binary (Bi)-FRET (Fig. 15A) [215] . The Apt-Dox-Lip complex showed selective internalization and enhanced cytotoxicity to MCF-7 breast cancer cells and xenograft MCF-7 breast tumors in nude mice, suggesting that AS1411 aptamer-functionalized liposomes can specifically bind nucleolin overexpressed on the MCF-7 cell surface, and implement drug delivery with high selectivity. abstract: Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research. url: https://www.ncbi.nlm.nih.gov/pubmed/33096353/ doi: 10.1016/j.biopha.2020.110902 id: cord-000322-8ctsa9sd author: Ninove, Laetitia title: RNA and DNA Bacteriophages as Molecular Diagnosis Controls in Clinical Virology: A Comprehensive Study of More than 45,000 Routine PCR Tests date: 2011-02-09 words: 2892.0 sentences: 130.0 pages: flesch: 46.0 cache: ./cache/cord-000322-8ctsa9sd.txt txt: ./txt/cord-000322-8ctsa9sd.txt summary: Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids. Monitoring rt-PCR and rt-RT-PCR assays and validation of the results rely on the use of relevant external or internal controls (ECs or ICs) [1, 2] and commercial kits including such control systems are being increasingly improved for the molecular diagnosis of a number of pathogens such as HIV, hepatitis viruses, influenza viruses etc.. abstract: Real-time PCR techniques are now commonly used for the detection of viral genomes in various human specimens and require for validation both external and internal controls (ECs and ICs). In particular, ICs added to clinical samples are necessary to monitor the extraction, reverse transcription, and amplification steps in order to detect false-negative results resulting from PCR-inhibition or errors in the technical procedure. Here, we performed a large scale evaluation of the use of bacteriophages as ICs in routine molecular diagnosis. This allowed to propose simple standardized procedures (i) to design specific ECs for both DNA and RNA viruses and (ii) to use T4 (DNA) or MS2 (RNA) phages as ICs in routine diagnosis. Various technical formats for using phages as ICs were optimised and validated. Subsequently, T4 and MS2 ICs were evaluated in routine real-time PCR or RT-PCR virological diagnostic tests, using a series of 8,950 clinical samples (representing 36 distinct specimen types) sent to our laboratory for the detection of a variety of DNA and RNA viruses. The frequency of inefficient detection of ICs was analyzed according to the nature of the sample. Inhibitors of enzymatic reactions were detected at high frequency in specific sample types such as heparinized blood and bone marrow (>70%), broncho-alveolar liquid (41%) and stools (36%). The use of T4 and MS2 phages as ICs proved to be cost-effective, flexible and adaptable to various technical procedures of real-time PCR detection in virology. It represents a valuable strategy for enhancing the quality of routine molecular diagnosis in laboratories that use in-house designed diagnostic systems, which can conveniently be associated to the use of specific synthetic ECs. The high rate of inhibitors observed in a variety of specimen types should stimulate the elaboration of improved technical protocols for the extraction and amplification of nucleic acids. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3036576/ doi: 10.1371/journal.pone.0016142 id: cord-023766-qx0qdjmt author: Nirwan, Sonam title: Rhinovirus RNA Polymerase: Structure, Function, and Inhibitors date: 2018-11-02 words: 10466.0 sentences: 477.0 pages: flesch: 51.0 cache: ./cache/cord-023766-qx0qdjmt.txt txt: ./txt/cord-023766-qx0qdjmt.txt summary: Differences observed in the secondary structure of these polymerases reflect not only the substrate diversity but also divergent mechanisms for initiation of RNA synthesis (primer dependent for HRV and RHDV but primer independent for HCV and bacteriophage ϕ6). Conserved aspartic acid residues in the polymerase palm domains coordinate the two magnesium ions needed for the catalytic polymerization reaction of the enzyme, with one metal activating the primer 3 0 OH for the attack of the nucleotide α-phosphate, and the other metal serving to stabilize the triphosphate moiety ( Fig. 11 .1). The EC of PV polymerase provided a required view about how the template and the RNA strand interact as they thread through the active site and showed that viral RdRPs use a unique palm-based structural change to close their active site for catalysis (Gong and Peersen, 2010) . abstract: Human rhinovirus is responsible for causing 50% of common cold infections in infants and adults. It belongs to the picornavirus family of nonenveloped positive-strand RNA viruses. The RNA synthesis of rhinovirus is carried out by RNA-dependent RNA polymerase, also known as 3D(Pol). It catalyzes the synthesis of negative-strand RNA using a positive-strand template. The structure of the enzyme consists of three domains: palm, fingers, and thumb domains and Mg(2+) in the active site. These conserved structural features of the enzyme help in catalyzing phosphodiester bond formation between the two consecutive nucleotide units complimentary to the template RNA using a VPg primer. Owing to the presence of over 100 serotypes of the enzyme, designing specific inhibitors targeting the polymerase is a challenging task and until now no clinically approved antirhino viral drug is reported. In this review, we have given detailed information about the structure and function of the enzyme and also discussed some of the inhibitors and their in vivo activity against 3D(Pol). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173612/ doi: 10.1016/b978-0-12-815422-9.00011-5 id: cord-002763-n952re94 author: Niu, Xiaosai title: Transcriptome analysis of avian reovirus-mediated changes in gene expression of normal chicken fibroblast DF-1 cells date: 2017-11-25 words: 4307.0 sentences: 245.0 pages: flesch: 50.0 cache: ./cache/cord-002763-n952re94.txt txt: ./txt/cord-002763-n952re94.txt summary: title: Transcriptome analysis of avian reovirus-mediated changes in gene expression of normal chicken fibroblast DF-1 cells In this study, RNA-Seq technology was applied to investigate the transcriptome-wide changes of DF-1 cells upon ARV infection at the middle stage. CONCLUSIONS: Overall, the differential expression profile presented in this study can be used to expand our understanding of the comprehensive interactions between ARV and the host cells, and may be helpful for us to reveal the pathogenic mechanism on the molecular level. In this study, we tried to build a complete expression profile of ARV-mediated changes at the transcriptional level using RNA-Seq to unveil the complex interactions between ARV and host cells. The results show a similar pattern of ARV-mediated changes as was seen in the DEG analysis of RNA-Seq data (Fig. 4 ). abstract: BACKGROUND: Avian reovirus (ARV) is an important poultry pathogen that can cause immunosuppression. In this study, RNA-Seq technology was applied to investigate the transcriptome-wide changes of DF-1 cells upon ARV infection at the middle stage. RESULTS: Total RNA of ARV-infected or mock-infected samples at 10 and 18 h post infection (hpi) was extracted to build RNA-Seq datasets. Analysis of the sequencing data revealed that the expressions of numerous genes were altered, and a panel of differentially expressed genes were confirmed with RT-qPCR. At 10 hpi, 104 genes were down-regulated and 64 were up-regulated, while the expressions of 47 genes were increased and only one was down-regulated, which may play a role in retinoic acid biosynthesis, at 18 hpi in the ARV-infected cells. The similar profiles of up-regulated genes between the two groups of infected cells suggest that ARV infection activated a prolonged antiviral response of host cells. Alternative splicing analysis found no significantly changed events altered by ARV infection. CONCLUSIONS: Overall, the differential expression profile presented in this study can be used to expand our understanding of the comprehensive interactions between ARV and the host cells, and may be helpful for us to reveal the pathogenic mechanism on the molecular level. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4310-5) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702118/ doi: 10.1186/s12864-017-4310-5 id: cord-001748-7e8px4vx author: Nobach, Daniel title: Shedding of Infectious Borna Disease Virus-1 in Living Bicolored White-Toothed Shrews date: 2015-08-27 words: 4873.0 sentences: 249.0 pages: flesch: 47.0 cache: ./cache/cord-001748-7e8px4vx.txt txt: ./txt/cord-001748-7e8px4vx.txt summary: The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). In animals caught in 2013 (group 1: female #2, male #5, female #6), after an adaption phase of one month, samples of saliva, lacrimal fluid, skin surface, urine and excrements from the BoDV-1-infected shrews were taken weekly over a period of 4 weeks as necessary veterinary care. The five other shrews did not exhibit any evidence for BoDV-1-infection, neither infectious virus nor viral RNA was detected at any time point investigated. Current data from living shrews provide reliable evidence that natural BoDV-1-infection in these animals is indeed clinically inconspicuous over a long time period as already previously assumed [15, 18] despite persistent infection with shedding of infectious virus via various sites. Distribution of Borna Disease Virus Antigen and RNA in Tissues of naturally infected Bicolored White-Toothed Shrews, Crocidura leucodon, supporting their role as Reservoir Host Species abstract: BACKGROUND: Many RNA viruses arise from animal reservoirs, namely bats, rodents and insectivores but mechanisms of virus maintenance and transmission still need to be addressed. The bicolored white-toothed shrew (Crocidura leucodon) has recently been identified as reservoir of the neurotropic Borna disease virus 1 (BoDV-1). PRINCIPAL FINDINGS: Six out of eleven wild living bicoloured white-toothed shrews were trapped and revealed to be naturally infected with BoDV-1. All shrews were monitored in captivity in a long-term study over a time period up to 600 days that differed between the individual shrews. Interestingly, all six animals showed an asymptomatic course of infection despite virus shedding via various routes indicating a highly adapted host-pathogen interaction. Infectious virus and viral RNA were demonstrated in saliva, urine, skin swabs, lacrimal fluid and faeces, both during the first 8 weeks of the investigation period and for long time shedding after more than 250 days in captivity. CONCLUSIONS: The various ways of shedding ensure successful virus maintenance in the reservoir population but also transmission to accidental hosts such as horses and sheep. Naturally BoDV-1-infected living shrews serve as excellent tool to unravel host and pathogen factors responsible for persistent viral co-existence in reservoir species while maintaining their physiological integrity despite high viral load in many organ systems. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552160/ doi: 10.1371/journal.pone.0137018 id: cord-352361-jh31omg2 author: Nobach, Daniel title: No evidence for European bats serving as reservoir for Borna disease virus 1 or other known mammalian orthobornaviruses date: 2020-01-30 words: 3751.0 sentences: 209.0 pages: flesch: 41.0 cache: ./cache/cord-352361-jh31omg2.txt txt: ./txt/cord-352361-jh31omg2.txt summary: Although several rodents and other small mammals are known as important reservoirs for many viruses, bats (order: Chiroptera) represent the vast majority of identified natural reservoirs of several virus families/species to date [1, 14] . In conclusion, due to the continuous detection of new viruses in bats, the unclear situation regarding additional potential BoDV-1-reservoirs and molecular evidence for co-evolution of bats and bornaviruses, this study was conducted to investigate the potential presence of the most common orthobornaviruses in bats from endemic and non-endemic areas in Germany. Although the bicolored white-toothed shrew has been identified as indigenous reservoir of BoDV-1, other potential reservoirs or animal carriers are still unknown so that further investigations of small mammals including bat species are urgently needed. Distribution of Borna disease virus antigen and RNA in tissues of naturally infected bicolored white-toothed shrews, Crocidura leucodon, supporting their role as reservoir host species abstract: BACKGROUND: The majority of emerging infectious diseases are zoonotic in nature and originate from wildlife reservoirs. Borna disease, caused by Borna disease virus 1 (BoDV-1), is an infectious disease affecting mammals, but recently it has also been shown to cause fatal encephalitis in humans. The endemic character of Borna disease points towards a nature-bound reservoir, with only one shrew species identified as reservoir host to date. Bats have been identified as reservoirs of a variety of zoonotic infectious agents. Endogenous borna-like elements in the genome of certain bat species additionally point towards co-evolution of bats with bornaviruses and therefore raise the question whether bats could serve as a potential reservoir of orthobornaviruses. METHODS: Frozen brain samples (n = 257) of bats of seven different genera from Germany were investigated by orthobornaviral RT-PCR. Additionally, tissue slides of formalin-fixed paraffin-embedded material of a subset of these bats (n = 140) were investigated for orthobornaviral phosphoprotein by immunohistochemistry. RESULTS: The brain samples were tested by RT-PCR without any evidence of orthobornavirus specific amplicons. Immunohistochemistry revealed a faint immunoreaction in 3/140 bats but with an untypical staining pattern for viral antigen. CONCLUSIONS: RT-PCR-screening showed no evidence for orthobornaviral RNA in the investigated bats. However, immunohistochemistry results should be investigated further to elucidate whether the reaction might be associated with expressed endogenous bornaviral elements or other so far unknown bornaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32000801/ doi: 10.1186/s12985-020-1289-3 id: cord-281385-oxohdfpu author: Noble, Christian G. title: Crystal structure of dengue virus methyltransferase without S-adenosyl-L-methionine date: 2014-09-19 words: 2621.0 sentences: 152.0 pages: flesch: 58.0 cache: ./cache/cord-281385-oxohdfpu.txt txt: ./txt/cord-281385-oxohdfpu.txt summary: Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. The SAM-depleted and SAM-containing MTases exhibited comparable enzymatic activities (N-7 MTase, 2 0 -O MTase, and covalent GMP-MTase complex formation the natural product Sinefungin, showing that this is a viable approach to identify novel small molecules that bind to the same pocket. This conclusion was supported by two complementary structural and functional approaches: (i) the crystal structure unequivocally shows that absence of SAM does not affect the overall conformation of DENV MTase, including the SAM-binding pocket; (ii) depletion of SAM from the recombinant MTase did not change the activities of cap methylations and GMP-MTase complex formation. Structural and functional analysis of methylation and 5 0 -RNA sequence requirements of short capped RNAs by the methyltransferase domain of dengue virus NS5 abstract: Flavivirus methyltransferase is a genetically-validated antiviral target. Crystal structures of almost all available flavivirus methyltransferases contain S-adenosyl-L-methionine (SAM), the methyl donor molecule that co-purifies with the enzymes. This raises a possibility that SAM is an integral structural component required for the folding of dengue virus (DENV) methyltransferase. Here we exclude this possibility by solving the crystal structure of DENV methyltransferase without SAM. The SAM ligand was removed from the enzyme through a urea-mediated denaturation-and-renaturation protocol. The crystal structure of the SAM-depleted enzyme exhibits a vacant SAM-binding pocket, with a conformation identical to that of the SAM-enzyme co-crystal structure. Functionally, equivalent enzymatic activities (N-7 methylation, 2′-O methylation, and GMP-enzyme complex formation) were detected for the SAM-depleted and SAM-containing recombinant proteins. These results clearly indicate that the SAM molecule is not an essential component for the correct folding of DENV methyltransferase. Furthermore, the results imply a potential antiviral approach to search for inhibitors that can bind to the SAM-binding pocket and compete against SAM binding. To demonstrate this potential, we have soaked crystals of DENV methyltransferase without a bound SAM with the natural product Sinefungin and show that preformed crystals are capable of binding ligands in this pocket. url: https://www.ncbi.nlm.nih.gov/pubmed/25241250/ doi: 10.1016/j.antiviral.2014.09.003 id: cord-350083-kldu8q8x author: Oany, Arafat Rahman title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach date: 2015-08-08 words: 5019.0 sentences: 315.0 pages: flesch: 51.0 cache: ./cache/cord-350083-kldu8q8x.txt txt: ./txt/cord-350083-kldu8q8x.txt summary: title: Highly conserved regions in Ebola virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. To date, information regarding the processing, structure and functions of Ebola virus (EBOV) protein L (EBOL) demonstrates that it is an RNA-dependent RNA polymerase, with the assistance of VP35. In the present study, we have followed immunoinformatics approaches for designing potential conserved epitope candidate for the utility of vaccine development against the deadly Ebola virus, with an expectation of further wet lab validation. Protein variability server predicted the variability of the conserved region of the RNA-dependent RNA polymerase-L ( Fig. 10) to ensure that the proposed epitope is within the invariable region. Design of an epitope-based peptide vaccine against spike protein of human corona virus: an in silico approach abstract: PURPOSE: Ebola virus (EBOV) is such kind of virus which is responsible for 23,825 cases and 9675 deaths worldwide only in 2014 and with an average diseases fatality rate between 25 % and 90 %. Although, medical technology has tried to handle the problems, there is no Food and Drug Administration (FDA)-approved therapeutics or vaccines available for the prevention, post exposure, or treatment of Ebola virus disease (EVD). METHODS: In the present study, we used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of EBOV. BioEdit v7.2.3 sequence alignment editor, Jalview v2 and CLC Sequence Viewer v7.0.2 were used for the initial sequence analysis for securing the conservancy from the sequences. Later the Immune Epitope Database and Analysis Resource (IEDB-AR) was used for the identification of T-cell and B-cellepitopes associated with type I and II major histocompatibility complex molecules analysis. Finally, the population coverage analysis was employed. RESULTS: The core epitope “FRYEFTAPF” was found to be the most potential one, with 100 % conservancy among all the strains of EBOV. It also interacted with both type I and II major histocompatibility complex molecules and is considered as nonallergenic in nature. Finally, with impressive cumulative population coverage of 99.87 % for the both MHC-I and MHC-II class throughout the world population was found for the proposed epitope. CONCLUSION: To end, the projected peptide gave us a solid stand to propose for vaccine consideration and that might be experimented for its potency in eliciting immunity through humoral and cell mediated immune responses in vitro and in vivo. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40203-015-0011-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s40203-015-0011-4 doi: 10.1186/s40203-015-0011-4 id: cord-001228-4eh22ek7 author: Ofori, Leslie O. title: High-Affinity Recognition of HIV-1 Frameshift-Stimulating RNA Alters Frameshifting in Vitro and Interferes with HIV-1 Infectivity date: 2014-01-05 words: 6288.0 sentences: 339.0 pages: flesch: 53.0 cache: ./cache/cord-001228-4eh22ek7.txt txt: ./txt/cord-001228-4eh22ek7.txt summary: 32 Thus, as far as we are aware, there are no reported examples of synthetic molecules able to alter HIV-1 frameshifting and interfere with viral infectivity via selective, high-affinity binding to the FSS RNA. Building on our laboratory''s longstanding interest in understanding the factors that drive affinity and sequence selectivity in small molecule recognition of RNA, 33 we previously reported the use of an 11,325-member resin-bound dynamic combinatorial library 34 (designed based on the structure of DNA-binding, bisintercalating peptide antibiotics) to identify a compound (1) able to bind the HIV-1 FSS upper stem-loop with moderate affinity (K D = 4.1 ± 2.4 μM immobilized on an surface plasmon resonance (SPR) chip via one of its amine groups; K D = 350 ± 110 nM in solution as measured by fluorescence 35 ) and good selectivity. abstract: [Image: see text] The life cycle of the human immunodeficiency virus type 1 (HIV-1) has an absolute requirement for ribosomal frameshifting during protein translation in order to produce the polyprotein precursor of the viral enzymes. While an RNA stem-loop structure (the “HIV-1 Frameshift Stimulating Signal”, or HIV-1 FSS) controls the frameshift efficiency and has been hypothesized as an attractive therapeutic target, developing compounds that selectively bind this RNA and interfere with HIV-1 replication has proven challenging. Building on our prior discovery of a “hit” molecule able to bind this stem-loop, we now report the development of compounds displaying high affinity for the HIV-1 FSS. These compounds are able to enhance frameshifting more than 50% in a dual-luciferase assay in human embryonic kidney cells, and they strongly inhibit the infectivity of pseudotyped HIV-1 virions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954503/ doi: 10.1021/jm401438g id: cord-254916-y1rw9q11 author: Ogando, Natacha S. title: SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology date: 2020-06-22 words: 8571.0 sentences: 423.0 pages: flesch: 50.0 cache: ./cache/cord-254916-y1rw9q11.txt txt: ./txt/cord-254916-y1rw9q11.txt summary: The overall level of amino acid sequence identity of viral proteins ranges from about 65 % in the least conserved parts of the S protein to about 95 % in the most conserved replicative enzyme domains, prompting the coronavirus study group of the International Committee on the Taxonomy of Viruses to classify the new agent within the species Severe acute respiratory syndrome-related coronavirus, which also includes the 2003 SARS-CoV [1] . In this report, we describe a comparative study of the basic replication features of SARS-CoV and SARS-CoV-2 in Vero E6 cells, including growth kinetics, virus titres, plaque phenotype and an analysis of intracellular viral RNA and protein synthesis. One of them is the rapid evolution -during virus passaging in Vero cells -of a specific region of the SARS-CoV-2 S protein that contains the so-called furin-like cleavage site. abstract: The sudden emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 from the Chinese province of Hubei and its subsequent pandemic spread highlight the importance of understanding the full molecular details of coronavirus infection and pathogenesis. Here, we compared a variety of replication features of SARS-CoV-2 and SARS-CoV and analysed the cytopathology caused by the two closely related viruses in the commonly used Vero E6 cell line. Compared to SARS-CoV, SARS-CoV-2 generated higher levels of intracellular viral RNA, but strikingly about 50-fold less infectious viral progeny was recovered from the culture medium. Immunofluorescence microscopy of SARS-CoV-2-infected cells established extensive cross-reactivity of antisera previously raised against a variety of non-structural proteins, membrane and nucleocapsid protein of SARS-CoV. Electron microscopy revealed that the ultrastructural changes induced by the two SARS viruses are very similar and occur within comparable time frames after infection. Furthermore, we determined that the sensitivity of the two viruses to three established inhibitors of coronavirus replication (remdesivir, alisporivir and chloroquine) is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha. An important difference between the two viruses is the fact that – upon passaging in Vero E6 cells – SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative furin-like cleavage site in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays. url: https://www.ncbi.nlm.nih.gov/pubmed/32568027/ doi: 10.1099/jgv.0.001453 id: cord-291590-24psoaer author: Ogando, Natacha S. title: The enzymatic activity of the nsp14 exoribonuclease is critical for replication of Middle East respiratory syndrome-coronavirus date: 2020-06-20 words: 4299.0 sentences: 228.0 pages: flesch: 52.0 cache: ./cache/cord-291590-24psoaer.txt txt: ./txt/cord-291590-24psoaer.txt summary: In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. abstract: Coronaviruses (CoVs) stand out for their large RNA genome and complex RNA-synthesizing machinery comprising 16 nonstructural proteins (nsps). The bifunctional nsp14 contains an N-terminal 3’-to-5’ exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase) domain. While the latter presumably operates during viral mRNA capping, ExoN is thought to mediate proofreading during genome replication. In line with such a role, ExoN-knockout mutants of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) were previously found to have a crippled but viable hypermutation phenotype. Remarkably, using an identical reverse genetics approach, an extensive mutagenesis study revealed the corresponding ExoN-knockout mutants of another betacoronavirus, Middle East respiratory syndrome coronavirus (MERS-CoV), to be non-viable. This is in agreement with observations previously made for alpha- and gammacoronaviruses. Only a single MERS-CoV ExoN active site mutant could be recovered, likely because the introduced D191E substitution is highly conservative in nature. For 11 other MERS-CoV ExoN active site mutants, not a trace of RNA synthesis could be detected, unless – in some cases – reversion had first occurred. Subsequently, we expressed and purified recombinant MERS-CoV nsp14 and established in vitro assays for both its ExoN and N7-MTase activities. All ExoN knockout mutations that were lethal when tested via reverse genetics were found to severely decrease ExoN activity, while not affecting N7-MTase activity. Our study thus reveals an additional function for MERS-CoV nsp14 ExoN, which apparently is critical for primary viral RNA synthesis, thus differentiating it from the proofreading activity thought to boost long-term replication fidelity in MHV and SARS-CoV. Importance The bifunctional nsp14 subunit of the coronavirus replicase contains 3’-to-5’ exoribonuclease (ExoN) and N7-methyltransferase (N7-MTase) domains. For the betacoronaviruses MHV and SARS-CoV, the ExoN domain was reported to promote the fidelity of genome replication, presumably by mediating some form of proofreading. For these viruses, ExoN knockout mutants are alive while displaying an increased mutation frequency. Strikingly, we now established that the equivalent knockout mutants of MERS-CoV ExoN are non-viable and completely deficient in RNA synthesis, thus revealing an additional and more critical function of ExoN in coronavirus replication. Both enzymatic activities of (recombinant) MERS-CoV nsp14 were evaluated using newly developed in vitro assays that can be used to characterize these key replicative enzymes in more detail and explore their potential as target for antiviral drug development. url: https://doi.org/10.1101/2020.06.19.162529 doi: 10.1101/2020.06.19.162529 id: cord-000238-om92cx5q author: Ogbunugafor, C. Brandon title: On the possible role of robustness in the evolution of infectious diseases date: 2010-06-30 words: 6717.0 sentences: 347.0 pages: flesch: 39.0 cache: ./cache/cord-000238-om92cx5q.txt txt: ./txt/cord-000238-om92cx5q.txt summary: We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections. [14] [15] [16] In reviewing these results, we hope to highlight the importance of empirical work in RNA viruses for testing theory pertaining to robustness, as well as for better understanding the evolutionary biology and evolvability of infectious organisms in general. 1 However, theory and artificial-life data 9 support the idea that genetic robustness should be strongly favored when populations experience elevated mutation rates, suggesting that RNA viruses would be fruitful systems to explore how genetic robustness evolves. [33] [34] [35] Regardless, preliminary experiments showed that UVC exposure for periods up to 30 min greatly increased mortality in wild type phage 6 ͑Fig. 2͒, indicating that this environmental effect should produce strong selection for UVC resistance in populations of the virus. abstract: Robustness describes the capacity for a biological system to remain canalized despite perturbation. Genetic robustness affords maintenance of phenotype despite mutational input, necessarily involving the role of epistasis. Environmental robustness is phenotypic constancy in the face of environmental variation, where epistasis may be uninvolved. Here we discuss genetic and environmental robustness, from the standpoint of infectious disease evolution, and suggest that robustness may be a unifying principle for understanding how different disease agents evolve. We focus especially on viruses with RNA genomes due to their importance in the evolution of emerging diseases and as model systems to test robustness theory. We present new data on adaptive constraints for a model RNA virus challenged to evolve in response to UV radiation. We also draw attention to other infectious disease systems where robustness theory may prove useful for bridging evolutionary biology and biomedicine, especially the evolution of antibiotic resistance in bacteria, immune evasion by influenza, and malaria parasite infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909313/ doi: 10.1063/1.3455189 id: cord-272050-0u62j7nj author: Okamoto, Kimiyuki title: cis-Preferential requirement of a − 1 frameshift product p88 for the replication of Red clover necrotic mosaic virus RNA1 date: 2008-05-25 words: 5335.0 sentences: 262.0 pages: flesch: 50.0 cache: ./cache/cord-272050-0u62j7nj.txt txt: ./txt/cord-272050-0u62j7nj.txt summary: In contrast, cis-preferential function of the viral encoded proteins or a coupling between translation and replication has been reported for several viruses, including Alfalfa mosaic virus (AMV) (Neeleman and Bol, 1999; van Rossum et al., 1996) , Clover yellow mosaic virus (CYMV) (White et al., 1992) , Bovine coronavirus (Chang et al., 1994) , Cowpea mosaic virus (van Bokhoven et al., 1993) , Poliovirus (Hagino-Yamagishi and Nomoto, 1989; Johnson and Sarnow, 1991; Novak and Kirkegaard, 1994) , Turnip crinkle virus (TCV) (White et al., 1995) , Tobacco etch virus (Mahajan et al., 1996; Schaad et al., 1996) , Tobacco mosaic virus (TMV) (Lewandowski and Dawson, 2000) , Tomato bushy stunt virus (TBSV) (Oster et al., 1998) , Turnip yellow mosaic virus (TYMV) (Weiland and Dreher, 1993) , and Rubella virus (Liang and Gillam, 2001) . cis-Acting core RNA elements required for negative-strand RNA synthesis and cap-independent translation are separated in the 3¢-untranslated region of Red clover necrotic mosaic virus RNA1 abstract: The genome of Red clover necrotic mosaic virus (RCNMV) consists of RNA1 and RNA2. RNA1 encodes N-terminally overlapping replication proteins, p27 and p88, which are translated in a cap-independent manner. The 3′ untranslated region of RNA1 contains RNA elements essential for cap-independent translation and negative-strand RNA synthesis. In this study, we investigated how p27 and p88 were engaged in the replication of RCNMV genomic RNAs by using DNA vectors or in vitro transcribed RNAs in protoplasts and in a cell-free extract of evacuolated BY-2 protoplasts. Our results show a cis-preferential requirement of p88, but not of p27, for the replication of RNA1. This mechanism might help to facilitate a switch in the role of RNA1 from mRNA to a replication template. url: https://doi.org/10.1016/j.virol.2008.02.004 doi: 10.1016/j.virol.2008.02.004 id: cord-002222-rgqwm3vb author: Olarte-Castillo, Ximena A. title: Divergent Sapovirus Strains and Infection Prevalence in Wild Carnivores in the Serengeti Ecosystem: A Long-Term Study date: 2016-09-23 words: 7544.0 sentences: 339.0 pages: flesch: 46.0 cache: ./cache/cord-002222-rgqwm3vb.txt txt: ./txt/cord-002222-rgqwm3vb.txt summary: By screening a large number of predominantly fecal samples (n = 631) obtained from five carnivore species in the Serengeti ecosystem, East Africa, sapovirus RNA was detected in the spotted hyena (Crocuta crocuta, family Hyaenidae), African lion (Panthera leo, family Felidae), and bat-eared fox (Otocyon megalotis, family Canidae), but not in golden or silver-backed jackals (Canis aureus and C. Long-term monitoring of sapovirus in a population of individually known spotted hyenas from 2001 to 2012 revealed: i) a relatively high overall infection prevalence (34.8%); ii) the circulation of several genetically diverse variants; iii) large fluctuations in infection prevalence across years, indicative of outbreaks; iv) no significant difference in the likelihood of infection between animals in different age categories. A total of 20 partial RdRp gene sequences (16 from spotted hyenas, 3 from African lions and 1 from bat-eared foxes) were obtained and used for the phylogenetic analysis, together with publically available sequence data from 25 representatives of all sapovirus genogroups, divergent unclassified sapoviruses, and other genera in the Caliciviridae family, including Norovirus and Vesivirus. abstract: The genus Sapovirus, in the family Caliciviridae, includes enteric viruses of humans and domestic animals. Information on sapovirus infection of wildlife is limited and is currently lacking for any free-ranging wildlife species in Africa. By screening a large number of predominantly fecal samples (n = 631) obtained from five carnivore species in the Serengeti ecosystem, East Africa, sapovirus RNA was detected in the spotted hyena (Crocuta crocuta, family Hyaenidae), African lion (Panthera leo, family Felidae), and bat-eared fox (Otocyon megalotis, family Canidae), but not in golden or silver-backed jackals (Canis aureus and C. mesomelas, respectively, family Canidae). A phylogenetic analysis based on partial RNA-dependent RNA polymerase (RdRp) gene sequences placed the sapovirus strains from African carnivores in a monophyletic group. Within this monophyletic group, sapovirus strains from spotted hyenas formed one independent sub-group, and those from bat-eared fox and African lion a second sub-group. The percentage nucleotide similarity between sapoviruses from African carnivores and those from other species was low (< 70.4%). Long-term monitoring of sapovirus in a population of individually known spotted hyenas from 2001 to 2012 revealed: i) a relatively high overall infection prevalence (34.8%); ii) the circulation of several genetically diverse variants; iii) large fluctuations in infection prevalence across years, indicative of outbreaks; iv) no significant difference in the likelihood of infection between animals in different age categories. The likelihood of sapovirus infection decreased with increasing hyena group size, suggesting an encounter reduction effect, but was independent of socially mediated ano-genital contact, or the extent of the area over which an individual roamed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5035092/ doi: 10.1371/journal.pone.0163548 id: cord-283132-rfw8njpo author: Olsen, Christopher W. title: A review of feline infectious peritonitis virus: molecular biology, immunopathogenesis, clinical aspects, and vaccination date: 1993-07-31 words: 13945.0 sentences: 687.0 pages: flesch: 42.0 cache: ./cache/cord-283132-rfw8njpo.txt txt: ./txt/cord-283132-rfw8njpo.txt summary: List of abbreviations: ADE=antibody-dependent enhancement; BCV=bovine coronavirus; C'' =complement; C''-ADE=complement-mediated antibody-dependent enhancement; CCV=canine coronavirus; CNS=central nervous system; CR=complement receptor; CVLP=coronavirus-like particle; ds=double-stranded; DTH=delayed-type hypersensitivity; EAV=equine arteritis virus; FcR = Fc receptor; FECV = feline enteric coronavirus; FeLV = feline leukemia virus; FIP = feline infectious peritonitis; FIPV = feline infectious peritonitis virus; HCV-229E = human coronavirus 229E; HCV-OC43=human coronavirus OC43; HE=hemagglutinating esterase; HEV=hemagglutinating encephalomyelitis virus; HIV=human immunodeficiency virus; HRSV=human respiratory syncytial virus; IBV = infectious bronchitis virus; kB = kilobases; kDa = kilodaltons; LDHV = lactate dehydrogenase virus; M = membrane (protein); mAb = monoclonal antibody; MHC = major histocompatability; MHV=mouse hepatitis virus; mRNA=messenger RNA; N=nucleocapsid (protein); Nlinked = asparagine-linked (glycosylation); NS = nonstructural (protein); O-linked = serine-or th reonine-linked (glycosylation); ORF--open reading frame; Pol = polymerase (protein); PRCV = porcine respiratory coronavirus; RCV = rat coronavirus; RECV = rabbit enteric coronaivirus; RI = replicative intermediate; rHuIFN~ =recombinant human interferon alpha; S= spike (protein); SDAV = sialodacryoadenitis virus; SIV = simian immunodeficiency virus; SPF = specific-pathogen-free; TCIDs0=tissue culture infectious dose 50%; TCV=turkey coronavirus; TGEV=transmissible gastroenteritis virus; ts=temperature-sensitive; VN=virus neutralization (-izing). abstract: Abstract Feline infectious peritontis (FIP) has been an elusive and frustrating problem for veterinary practitioners and cat breeders for many years. Over the last several years, reports have begun to elucidate aspects of the molecular biology of the causal virus (FIPV). These papers complement a rapidly growing base of knowledge concerning the molecular organization and replication of coronaviruses in general. The fascinating immunopathogenesis of FIPV infection and the virus' interaction with macrophages has also been the subject of several recent papers. It is now clear that FIPV may be of interest to scientists other than veterinary virologists since its pathogenesis may provide a useful model system for other viruses whose infectivity is enhanced in the presence of virus-specific antibody. With these advances and the recent release of the first commercially-available FIPV vaccine, it is appropriate to review what is known about the organization and replication of coronaviruses and the pathogenesis of FIPV infection. url: https://www.sciencedirect.com/science/article/pii/037811359390126R doi: 10.1016/0378-1135(93)90126-r id: cord-004656-n4h295e5 author: Olson, Ann Louise title: Developmental Regulation of Angiotensinogen Gene Expression in Sheep date: 1990 words: 2412.0 sentences: 151.0 pages: flesch: 57.0 cache: ./cache/cord-004656-n4h295e5.txt txt: ./txt/cord-004656-n4h295e5.txt summary: In an effort to determine if this phenomenon is specific to the rat or applicable to other species, we compared the ontogenic changes in hepatic and renal angiotensinogen mRNA expression in fetal (60, 90, 118, and 138 d of gestation, term being 145 d), newborn (7 d postnatal), and adult sheep. Angiotensinogen mRNA sequences were detected in all fetal liver samples and appeared to increase 3-fold from 60 to 138 d gestation and then to decrease after birth. In an effort to determine if this phenomenon is specific to the rat or applicable to other species, we compared the ontogenic Received January 18, 1990 ; accepted April 16, 1990 changes in hepatic and renal angiotensinogen gene expression during the last trimester of gestation in fetal sheep. Northern blot analysis of liver and kidney RNA from fetal sheep (1 18 and 138 d gestational age) 1 and newborn lamb are shown in Figure 3 . abstract: ABSTRACT: It has been suggested that the liver is not the main source of angiotensinogen during fetal life in rats, but that the kidney is an important site of fetal angiotensinogen synthesis. In an effort to determine if this phenomenon is specific to the rat or applicable to other species, we compared the ontogenic changes in hepatic and renal angiotensinogen mRNA expression in fetal (60, 90, 118, and 138 d of gestation, term being 145 d), newborn (7 d postnatal), and adult sheep. Total RNA was extracted, subjected to Northern blotting and hybridized using a full-length rat radiolabeled antisense RNA. Angiotensinogen mRNA sequences were detected in all fetal liver samples and appeared to increase 3-fold from 60 to 138 d gestation and then to decrease after birth. In contrast, angiotensiogen mRNA could not be detected in renal cortical tissue of 118 or 138 d fetuses, or newborn or adult sheep. We conclude that, unlike in the rat, liver angiotensinogen gene expression is detectable during the 2nd trimester of gestation in sheep and is developmentally regulated. Furthermore, in contrast to the fetal rat, angiotensinogen mRNA sequences were undetectable in fetal sheep kidney. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7086511/ doi: 10.1203/00006450-199009000-00001 id: cord-351920-igmb2yfe author: Oma, Veslemøy Sunniva title: Bovine coronavirus in naturally and experimentally exposed calves; viral shedding and the potential for transmission date: 2016-06-13 words: 5526.0 sentences: 317.0 pages: flesch: 57.0 cache: ./cache/cord-351920-igmb2yfe.txt txt: ./txt/cord-351920-igmb2yfe.txt summary: The aims of the study were to investigate the duration and quantity of BCoV shedding in feces and nasal secretions related to clinical signs, the presence of virus in blood and tissues and to test the hypothesis that seropositive calves are not infectious to naïve in-contact calves three weeks after BCoV infection. In two experimental studies, infected calves were not protected against reinfection with a different BCoV strain three weeks after the first challenge, but did not develop clinical signs [19, 20] . The majority of experimental studies have used BCoV inoculation as challenge procedure, which may influence clinical signs and viral shedding, and thereby the transmission potential compared to natural infection. The present study showed that calves infected with BCoV shed viral RNA for five weeks, and harbored viral RNA in intestinal tissues and lymph nodes even longer. abstract: BACKGROUND: Bovine coronavirus (BCoV) is a widely distributed pathogen, causing disease and economic losses in the cattle industry worldwide. Prevention of virus spread is impeded by a lack of basic knowledge concerning viral shedding and transmission potential in individual animals. The aims of the study were to investigate the duration and quantity of BCoV shedding in feces and nasal secretions related to clinical signs, the presence of virus in blood and tissues and to test the hypothesis that seropositive calves are not infectious to naïve in-contact calves three weeks after BCoV infection. METHODS: A live animal experiment was conducted, with direct contact between animal groups for 24 h as challenge procedure. Four naïve calves were commingled with a group of six naturally infected calves and sequentially euthanized. Two naïve sentinel calves were commingled with the experimentally exposed group three weeks after exposure. Nasal swabs, feces, blood and tissue samples were analyzed for viral RNA by RT-qPCR, and virus isolation was performed on nasal swabs. Serum was analyzed for BCoV antibodies. RESULTS: The calves showed mild general signs, and the most prominent signs were from the respiratory system. The overall clinical score corresponded well with the shedding of viral RNA the first three weeks after challenge. General depression and cough were the signs that correlated best with shedding of BCoV RNA, while peak respiratory rate and peak rectal temperature appeared more than a week later than the peak shedding. Nasal shedding preceded fecal shedding, and the calves had detectable amounts of viral RNA intermittently in feces through day 35 and in nasal secretions through day 28, however virus isolation was unsuccessful from day six and day 18 from the two calves investigated. Viral RNA was not detected in blood, but was found in lymphatic tissue through day 42 after challenge. Although the calves were shedding BCoV RNA 21 days after infection the sentinel animals were not infected. CONCLUSIONS: Prolonged shedding of BCoV RNA can occur, but detection of viral RNA does not necessarily indicate a transmission potential. The study provides valuable information with regard to producing scientifically based biosecurity advices. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-016-0555-x) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12985-016-0555-x doi: 10.1186/s12985-016-0555-x id: cord-273723-srfypn7j author: Omar, Sarah title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis date: 2020-07-30 words: 2932.0 sentences: 135.0 pages: flesch: 46.0 cache: ./cache/cord-273723-srfypn7j.txt txt: ./txt/cord-273723-srfypn7j.txt summary: title: Duration of SARS-CoV-2 RNA detection in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 – an interval-censored survival analysis As far as we are aware, there are currently no published data on the duration of RNA positivity in the upper respiratory of patients with mild COVID-19 that could inform a public health assessment of RT-qPCR as a tool for monitoring home isolation. At 14 days after onset, the earliest moment to discontinue home isolation currently recommended in Germany [18] , 53.5% of COVID-19 patients still had detectable SARS-CoV-2 RNA (Figure 2) . Duration of SARS-CoV-2-RNA positivity in COVID-19 patients in home isolation, Rhineland-Palatinate, Germany, 2020 (n = 537) For cases where laboratory monitoring is indispensable, knowledge of the RT-qPCR threshold cycle may improve our judgement on whether a positive result indicates infectiousness or not [20] . abstract: We analysed consecutive RT-qPCR results of 537 symptomatic coronavirus disease (COVID-19) patients in home quarantine. Respectively 2, 3, and 4 weeks after symptom onset, 50%, 25% and 10% of patients had detectable RNA from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In patients with mild COVID-19, RNA detection is likely to outlast currently known periods of infectiousness by far and fixed time periods seem more appropriate in determining the length of home isolation than laboratory-based approaches. url: https://doi.org/10.2807/1560-7917.es.2020.25.30.2001292 doi: 10.2807/1560-7917.es.2020.25.30.2001292 id: cord-312886-o3ipzn05 author: Onomoto, Koji title: Antiviral innate immunity and stress granule responses date: 2014-08-19 words: 5136.0 sentences: 281.0 pages: flesch: 39.0 cache: ./cache/cord-312886-o3ipzn05.txt txt: ./txt/cord-312886-o3ipzn05.txt summary: Viral infection and stress granules Viral invasion and replication are detected by innate immune sensors in cells, triggering downstream signaling pathways that can ultimately result in the activation of systemic immune responses. In some cases these bodies have been given different names in an attempt to distinguish them from SGs; in this review, however, we refer to virusinduced SG-like granules collectively as SGs. Many viruses induce SGs through the activation of the eukaryotic translation initiation factor (eIF)2a kinases PKR and, in some cases, general control non-depressible 2 (GCN2), which are both triggered by detection of RNA in the cytoplasm [28] ( Figure 2 ). In the stress-recovered condition, GADD34 protein is rapidly downregulated by an unknown mechanism and the phosphorylated form of eIF2a reaccumulates in the cells, resulting in an oscillating pattern of SGs. In cases where viral infection appears to not induce SGs, accumulating evidence suggest that these viruses inhibit SG formation. abstract: Viral infection triggers the activation of antiviral innate immune responses in mammalian cells. Viral RNA in the cytoplasm activates signaling pathways that result in the production of interferons (IFNs) and IFN-stimulated genes. Some viral infections have been shown to induce cytoplasmic granular aggregates similar to the dynamic ribonucleoprotein aggregates termed stress granules (SGs), suggesting that these viruses may utilize this stress response for their own benefit. By contrast, some viruses actively inhibit SG formation, suggesting an antiviral function for these structures. We review here the relationship between different viral infections and SG formation. We examine the evidence for antiviral functions for SGs and highlight important areas of inquiry towards understanding cellular stress responses to viral infection. url: https://www.sciencedirect.com/science/article/pii/S1471490614001276 doi: 10.1016/j.it.2014.07.006 id: cord-274110-nyyunoha author: Orlinger, Klaus K. title: An inactivated West Nile Virus vaccine derived from a chemically synthesized cDNA system date: 2010-04-26 words: 5113.0 sentences: 271.0 pages: flesch: 50.0 cache: ./cache/cord-274110-nyyunoha.txt txt: ./txt/cord-274110-nyyunoha.txt summary: A cDNA comprising the complete genome of West Nile Virus (WNV) was generated by chemical synthesis using published sequence data, independent of any preformed viral components. The synthetic WNV, produced by transfection of in vitro transcribed RNA into cell culture, exhibited undistinguishable biological properties compared to the corresponding animal-derived wild-type virus. Taking advantage of the rapid progression of gene synthesis technology (for review [24] ), we intended to adopt such a synthetic approach to produce a flavivirus cDNA system for the generation of a synthetic WNV seed virus for use in vaccine development. The production and characterization of the resulting West Nile Virus, which fully matched the sequence of the in silico designed viral genome, confirms the feasibility and accuracy of the synthetic flavivirus reverse genetic system. Cover slips with fixed cells were dried, rehydrated with phosphate-buffered saline and treated with a polyclonal mouse anti-WNV serum (1:50 dilution) obtained after immunization of mice with a formalin-inactivated whole virus vaccine preparation. abstract: A cDNA comprising the complete genome of West Nile Virus (WNV) was generated by chemical synthesis using published sequence data, independent of any preformed viral components. The synthetic WNV, produced by transfection of in vitro transcribed RNA into cell culture, exhibited undistinguishable biological properties compared to the corresponding animal-derived wild-type virus. No differences were found concerning viral growth in mammalian and insect cell lines and concerning expression of viral proteins in cells. There were also no significant differences in virulence in mice following intranasal challenge. After immunizations of mice with experimental vaccines derived from the synthetic and wild-type viruses, protection from lethal challenge was achieved with similar amounts of antigen. Both vaccine preparations also induced comparable levels of neutralizing antibodies in mice. In addition, the synthetic approach turned out to be very accurate, since the rescued WNV genome contained no undesired mutations. Thus, the first flavivirus based on chemical gene synthesis was indistinguishable from the parent virus. This demonstrates that virus isolates from animal sources are dispensable to derive seed viruses for vaccine production or research. url: https://api.elsevier.com/content/article/pii/S0264410X10002860 doi: 10.1016/j.vaccine.2010.02.092 id: cord-317715-xtsi663k author: Ortiz-Riaño, Emilio title: D471G Mutation in LCMV-NP Affects its Ability to Self-associate and Results in a Dominant Negative Effect in Viral RNA Synthesis date: 2012-10-16 words: 9164.0 sentences: 483.0 pages: flesch: 52.0 cache: ./cache/cord-317715-xtsi663k.txt txt: ./txt/cord-317715-xtsi663k.txt summary: Reporter gene activation (FFL) is shown as percentage (%) of LCMV NP-NP wt interaction (pC-NP-VP16 and pC-NP-GAL4) after normalization of transfection efficiencies with the Renilla luciferase expression plasmid pRL SV40 (ii). Unexpectedly, the D471A substitution impeded both NP-NP and NP-Z interactions, as well as NP functions in replication and transcription of the LCMV MG and the ability of NP to counteract SeV-mediated induction of the host IFN-I response, suggesting that change D to A at position 471 might have affected the overall structure of NP without affecting its stability as reflected by its unchanged expression levels determined by WB using anti-VP16 ( Figures 6A and 6B ) or anti-HA ( Figures 6C and 6D) antibodies. (C) Replication and transcription activity: BHK-21 cells were co-transfected with the LCMV MG as described in Figure 3 together with expression plasmids for the viral polymerase (L) and wt or indicated mutant NPs, and pSV40-Cluc expression vector to normalize transfection efficiencies. abstract: Arenaviruses merit significant interest because several family members are etiological agents of severe hemorrhagic fevers, representing a major burden to public health. Currently, there are no FDA-licensed vaccines against arenaviruses and the only available antiviral therapy is limited to the use of ribavirin that is partially effective. Arenavirus nucleoprotein (NP) is found associated with the genomic RNA forming the viral ribonucleoproteins (vRNPs) that together with the polymerase (L) direct viral replication and transcription. Virion formation requires the recruitment of vRNPs into budding sites, a process in which the arenavirus matrix-like protein (Z) plays a major role. Therefore, proper NP-NP and NP-Z interactions are required for the generation of infectious progeny. In this work we demonstrate the role of the amino acid residue D471 in the self-association of lymphocytic choriomeningitis virus nucleoprotein (LCMV-NP). Amino acid substitutions at this position abrogate NP oligomerization, affecting its ability to mediate replication and transcription of a minigenome reporter plasmid. However, its ability to interact with the Z protein, counteract the cellular interferon response and bind to dsRNA analogs was retained. Additionally, we also document the dominant negative effect of D471G mutation on viral infection, suggesting that NP self-association is an excellent target for the development of new antivirals against arenaviruses. url: https://doi.org/10.3390/v4102137 doi: 10.3390/v4102137 id: cord-277306-r8jki3x4 author: Osborne, Christina title: Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans date: 2011-05-12 words: 5186.0 sentences: 223.0 pages: flesch: 56.0 cache: ./cache/cord-277306-r8jki3x4.txt txt: ./txt/cord-277306-r8jki3x4.txt summary: At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. To increase the sensitivity of RNA detection, based on our previously published bat CoV sequences [17] and new data from this study, we designed specific primers within the amplicons of alphacoronaviruses from bats of several species in the genus Myotis and big brown bats (Table S1 ). Although the number of big brown bats sampled at site #5 was small (4 in 2008 and 14 in 2009), the prevalence of CoV RNA in these bats during these two summers was high (29% to 100%) ( Table 2) . abstract: Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted. url: https://doi.org/10.1371/journal.pone.0019156 doi: 10.1371/journal.pone.0019156 id: cord-337339-0vkigjv2 author: Osterrieder, Nikolaus title: Age-Dependent Progression of SARS-CoV-2 Infection in Syrian Hamsters date: 2020-07-20 words: 4327.0 sentences: 220.0 pages: flesch: 47.0 cache: ./cache/cord-337339-0vkigjv2.txt txt: ./txt/cord-337339-0vkigjv2.txt summary: We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. Moreover, transgenic mice expressing human ACE2 represent a lethal SARS-CoV-2 infection model resulting in significant weight loss and permitting robust virus replication in the respiratory tract including the lungs [20] . In contrast to SARS-CoV-2 titers, histopathological changes differed markedly between young and aged Syrian hamsters over time: younger animals launched more severe reactions at early time points after infection, while lesions and inflammation in the lungs became more pronounced and widespread at later time points in the elderly. Based on the data presented here, we propose that comparative preclinical assessments of SARS-CoV-2 vaccines and other treatment options in young versus aged hamsters may yield valuable and relevant results, as this small animal model appears to mimic age-dependent differences in humans. abstract: In late 2019, an outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, resulted in high morbidity and mortality in infected humans. Complete understanding of COVID-19, the multi-faceted disease caused by SARS-CoV-2, requires suitable small animal models, as does the development and evaluation of vaccines and antivirals. Since age-dependent differences of COVID-19 were identified in humans, we compared the course of SARS-CoV-2 infection in young and aged Syrian hamsters. We show that virus replication in the upper and lower respiratory tract was independent of the age of the animals. However, older hamsters exhibited more pronounced and consistent weight loss. In situ hybridization in the lungs identified viral RNA in bronchial epithelium, alveolar epithelial cells type I and II, and macrophages. Histopathology revealed clear age-dependent differences, with young hamsters launching earlier and stronger immune cell influx than aged hamsters. The latter developed conspicuous alveolar and perivascular edema, indicating vascular leakage. In contrast, we observed rapid lung recovery at day 14 after infection only in young hamsters. We propose that comparative assessment in young versus aged hamsters of SARS-CoV-2 vaccines and treatments may yield valuable information, as this small-animal model appears to mirror age-dependent differences in human patients. url: https://www.ncbi.nlm.nih.gov/pubmed/32698441/ doi: 10.3390/v12070779 id: cord-286103-cgky6ar6 author: Otaki, Momoko title: Inhibition of measles virus and subacute sclerosing panencephalitis virus by RNA interference date: 2006-02-13 words: 3538.0 sentences: 228.0 pages: flesch: 56.0 cache: ./cache/cord-286103-cgky6ar6.txt txt: ./txt/cord-286103-cgky6ar6.txt summary: In this study, we adopted RNA interference (RNAi) strategy and examined whether small interfering RNAs (siRNAs) can be used to inhibit replication of MeV and SSPE virus. We report here that siRNAs targeted against L mRNA of MeV, either synthetic siRNAs or those generated by pcPUR + U6i-based expression plasmids, effectively and specifically inhibited replication of both MeV and SSPE virus without exhibiting any cytotoxic effect. We report here that siRNAs targeted against L mRNA of MeV, either synthetic ones or those generated by pcPUR + U6i-based expression plasmids, effectively inhibit replication of both MeV and SSPE virus. Indeed, we demonstrated in the present study that siRNAs targeted against selected portions of L mRNA of MeV, especially MV-L2 -L4 and -L5, either synthetic siRNAs or those expressed by pcPUR + U6i-based plasmids, effectively inhibited replication of both MeV and SSPE virus (Figs. abstract: Subacute sclerosing panencephalitis (SSPE) is a rare, but fatal outcome of measles virus (MeV) infection. SSPE develops after prolonged persistence of mutated MeV called SSPE virus. Although a combination therapy using interferon and inosiplex or ribavirin appears to prolong survival time to some extent, there is currently no effective treatment to completely cure SSPE and a new treatment strategy is greatly needed. In this study, we adopted RNA interference (RNAi) strategy and examined whether small interfering RNAs (siRNAs) can be used to inhibit replication of MeV and SSPE virus. We report here that siRNAs targeted against L mRNA of MeV, either synthetic siRNAs or those generated by pcPUR + U6i-based expression plasmids, effectively and specifically inhibited replication of both MeV and SSPE virus without exhibiting any cytotoxic effect. The L protein of MeV is a major component of RNA-dependent RNA polymerase that is essential for viral RNA replication, and yet it is least abundant among all the MeV proteins expressed. Therefore, mRNA encoding the L protein would be a good target for RNAi strategy. The present results imply the possibility that our siRNAs against MeV L mRNA are among the potential candidates to be used to treat patients with SSPE. url: https://www.sciencedirect.com/science/article/pii/S0166354206000295 doi: 10.1016/j.antiviral.2006.01.009 id: cord-008426-ktn8c0zx author: Othman, Yasmin title: Nucleotide sequence of the bean strain of southern bean mosaic virus() date: 1995-01-10 words: 5393.0 sentences: 276.0 pages: flesch: 57.0 cache: ./cache/cord-008426-ktn8c0zx.txt txt: ./txt/cord-008426-ktn8c0zx.txt summary: From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses. Southern bean mosaic virus (SBMV) is the type member of the sobemovirus group of small icosahedral positive-strand RNA viruses (for reviews see Sehgal, 1981 ; Tremaine and Hamilton, 1983; Hull, 1988) . The recently published nucleotide sequence (4450 nt) of rice yellow mottle virus (RYMV), another sobemovirus (Ngon A Yassi et aL, 1994) , shows that it has a similar genome organization to SBMV-C (Fig. 1) . Amino acid sequence of southern bean mosaic virus coat protein and its relation to the three dimensional structure of the virus abstract: The genome of the bean strain of southern bean mosaic virus (SBMV-B) comprises 4109 nucleotides and thus is slightlyshorter than those of the two other sequenced sobemoviruses (southern bean mosaic virus, cowpea strain (SBMV-C) and rice yellow mottle virus (RYMV)). SBMV-B has an overall sequence similarity with SBMV-C of 55% and with RYMV of 45%. Three potential open reading frames (ORFs) were recognized in SBMV-B which were in similar positions in the genomes of SBMV-C and RYMV. However, there was no analog of SBMV-C and RYMV ORF 3. From a comparison of the predicted sequences of the ORFs of these three sobemoviruses and of the noncoding regions, it is suggested that the two SBMV strains differ from one another as much as they do from RYMV and that they should be considered as different viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7130989/ doi: 10.1016/s0042-6822(95)80044-1 id: cord-268970-uz7q6z2f author: Ott, Isabel M. title: Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices date: 2020-08-04 words: 2790.0 sentences: 181.0 pages: flesch: 58.0 cache: ./cache/cord-268970-uz7q6z2f.txt txt: ./txt/cord-268970-uz7q6z2f.txt summary: Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. To explore the viability of broadly deploying affordable saliva-based surveillance approaches 8 , we characterized SARS-CoV-2 RNA stability and virus infectivity from saliva samples stored in widely available, sterile, nuclease-free laboratory plastic (polypropylene) tubes. Following RNA extraction 9 and RT-qPCR 10 testing for SARS-CoV-2 on the day of saliva collection 2 , the remaining sample volumes (n=20) were aliquoted and stored at -80°C, room temperature (recorded as ~19°C) and 30°C. Moreover, SARS-CoV-2 RNA remained relatively stable in saliva samples left for up to 25 days at room temperature (~19°C; Ct increase of 0.027, 95% CI: -0.019, 0.071) ( Figure 1B) . abstract: Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. Yet many of these are expensive, in limited supply, and not necessarily validated specifically for viral RNA. While saliva is a promising sample type as it can be reliably self-collected for the sensitive detection of SARS-CoV-2, the expense and availability of these collection tubes are prohibitive to mass testing efforts. Therefore, we investigated the stability of SARS-CoV-2 RNA and infectious virus detection from saliva without supplementation. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures which might be experienced when cold chain transport may be unavailable. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4°C, room temperature (~19°C), and 30°C for prolonged periods and found limited evidence for viral replication in stored saliva samples. This work demonstrates that expensive saliva collection options involving RNA stabilization and virus inactivation buffers are not always needed, permitting the use of cheaper collection options. Affordable testing methods are urgently needed to meet current testing demands and for continued surveillance in reopening strategies. url: https://doi.org/10.1101/2020.08.03.20165233 doi: 10.1101/2020.08.03.20165233 id: cord-306921-3afgpunj author: Owino, Collins Oduor title: Recent advances on the role of host factors during non-poliovirus enteroviral infections date: 2019-06-19 words: 11725.0 sentences: 568.0 pages: flesch: 39.0 cache: ./cache/cord-306921-3afgpunj.txt txt: ./txt/cord-306921-3afgpunj.txt summary: A small siRNA screen targeting human membrane trafficking genes identified vasolin-containing protein (VCP-p97) as an important protein essential after PV viral replication and it interacts and colocalizes with 2 BC/2C as well as 3AB/3B in poliovirus infected cells [83] . Human host factors-viral protein studies identified nuclear factor; adenosine-uridine (AU)-rich element RNA binding factor 1 (AUF1) is targeted for cleavage by CV-B3 viral 3C protease upon translocation to the cytoplasm for enhanced stability of the IRES dependent viral RNA production [112] , similar antiviral observations were made for poliovirus, coxsackievirus and human rhinovirus [113] . A subsequent study by Mohamud and colleagues demonstrated that SQSTM1 and another host factor calcium binding and coiled-coil domain-containing protein 2/nuclear dot 10 protein 52 (CALCOCO2) regulate CV-B3 virus infection by targeting autophagy receptors; via their interaction with viral protein 1 [177] . abstract: Non-polio enteroviruses are emerging viruses known to cause outbreaks of polio-like infections in different parts of the world with several cases already reported in Asia Pacific, Europe and in United States of America. These outbreaks normally result in overstretching of health facilities as well as death in children under the age of five. Most of these infections are usually self-limiting except for the neurological complications associated with human enterovirus A 71 (EV-A71). The infection dynamics of these viruses have not been fully understood, with most inferences made from previous studies conducted with poliovirus. Non-poliovirus enteroviral infections are responsible for major outbreaks of hand, foot and mouth disease (HFMD) often associated with neurological complications and severe respiratory diseases. The myriad of disease presentations observed so far in children calls for an urgent need to fully elucidate the replication processes of these viruses. There are concerted efforts from different research groups to fully map out the role of human host factors in the replication cycle of these viral infections. Understanding the interaction between viral proteins and human host factors will unravel important insights on the lifecycle of this groups of viruses. This review provides the latest update on the interplay between human host factors/processes and non-polio enteroviruses (NPEV). We focus on the interactions involved in viral attachment, entry, internalization, uncoating, replication, virion assembly and eventual egress of the NPEV from the infected cells. We emphasize on the virus- human host interplay and highlight existing knowledge gaps that needs further studies. Understanding the NPEV-human host factors interactions will be key in the design and development of vaccines as well as antivirals against enteroviral infections. Dissecting the role of human host factors during NPEV infection cycle will provide a clear picture of how NPEVs usurp the human cellular processes to establish an efficient infection. This will be a boost to the drug and vaccine development against enteroviruses which will be key in control and eventual elimination of the viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/31215493/ doi: 10.1186/s12929-019-0540-y id: cord-334082-fyxn0g3v author: O’Carroll, I.P. title: Viral Nucleic Acids date: 2015-08-20 words: 5495.0 sentences: 271.0 pages: flesch: 54.0 cache: ./cache/cord-334082-fyxn0g3v.txt txt: ./txt/cord-334082-fyxn0g3v.txt summary: This scheme in turn places two requirements on the nucleic acid: it must be replicated in the virus-producing cell, to provide the genetic material encased in the progeny virus particles; and it must encode the proteins needed for the production of the progeny particles, including at a minimum the structural proteins from which the particles will be assembled. The DNAs of ssDNA viruses are replicated by a mechanism similar to ''rolling circle'' replication, involving synthesis of dsDNA intermediates containing multiple tandem copies of the viral genome. These viruses are unique in that their genomic RNA is translated immediately upon infection; that is, the virus particle is simply a package that introduces an mRNA molecule into the cell. When the particle infects a new host cell, the RNA-dependent DNA polymerase or ''reverse transcriptase'' in the virus copies this RNA into dsDNA. abstract: Viral genomes exhibit extraordinary diversity with respect to nucleic acid type, size, complexity, and the information transfer pathways they follow. Thus, viral nucleic acids can be DNA or RNA, double-stranded or single-stranded, monopartite or multipartite, linear or circular, as short as 2 kb or up to 2500 kb long. The goal of a virus is to replicate itself. To do so, viruses have evolved various strategies to replicate their genomes and produce the structural and catalytic proteins needed for the formation of new viruses. This article is a brief introduction to viral genomes and viral replication. url: https://www.sciencedirect.com/science/article/pii/B9780123944474100616 doi: 10.1016/b978-0-12-394447-4.10061-6 id: cord-268071-ow2aijmj author: Pachetti, Maria title: Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant date: 2020-04-22 words: 4449.0 sentences: 236.0 pages: flesch: 53.0 cache: ./cache/cord-268071-ow2aijmj.txt txt: ./txt/cord-268071-ow2aijmj.txt summary: Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. Naturally occurring mutations in critical residues for drug efficacy can lead to drug resistance phenomena, with a significant loss in the binding affinity of these molecules to the RdRp. We focused our study on SARS-CoV-2 mutations in order to assess if new viral variants were spreading across the Countries. Among all mutation sites analyzed, RdRp mutant is particularly interesting given that the enzyme is directly involved in viral replication and its fidelity determines the mutagenic capabilities of SARS-CoV-2. In the present work we have compared the SARS-CoV-2 reference genome to those exported from the GISAID database with the aim of gaining important insights into virus mutations, their occurrence over time and within different geographic areas. abstract: BACKGROUND: SARS-CoV-2 is a RNA coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). RNA viruses are characterized by a high mutation rate, up to a million times higher than that of their hosts. Virus mutagenic capability depends upon several factors, including the fidelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Mutation rate drives viral evolution and genome variability, thereby enabling viruses to escape host immunity and to develop drug resistance. METHODS: We analyzed 220 genomic sequences from the GISAID database derived from patients infected by SARS-CoV-2 worldwide from December 2019 to mid-March 2020. SARS-CoV-2 reference genome was obtained from the GenBank database. Genomes alignment was performed using Clustal Omega. Mann–Whitney and Fisher-Exact tests were used to assess statistical significance. RESULTS: We characterized 8 novel recurrent mutations of SARS-CoV-2, located at positions 1397, 2891, 14408, 17746, 17857, 18060, 23403 and 28881. Mutations in 2891, 3036, 14408, 23403 and 28881 positions are predominantly observed in Europe, whereas those located at positions 17746, 17857 and 18060 are exclusively present in North America. We noticed for the first time a silent mutation in RdRp gene in England (UK) on February 9th, 2020 while a different mutation in RdRp changing its amino acid composition emerged on February 20th, 2020 in Italy (Lombardy). Viruses with RdRp mutation have a median of 3 point mutations [range: 2–5], otherwise they have a median of 1 mutation [range: 0–3] (p value < 0.001). CONCLUSIONS: These findings suggest that the virus is evolving and European, North American and Asian strains might coexist, each of them characterized by a different mutation pattern. The contribution of the mutated RdRp to this phenomenon needs to be investigated. To date, several drugs targeting RdRp enzymes are being employed for SARS-CoV-2 infection treatment. Some of them have a predicted binding moiety in a SARS-CoV-2 RdRp hydrophobic cleft, which is adjacent to the 14408 mutation we identified. Consequently, it is important to study and characterize SARS-CoV-2 RdRp mutation in order to assess possible drug-resistance viral phenotypes. It is also important to recognize whether the presence of some mutations might correlate with different SARS-CoV-2 mortality rates. url: https://www.ncbi.nlm.nih.gov/pubmed/32321524/ doi: 10.1186/s12967-020-02344-6 id: cord-269720-o81j3d1j author: Page, Kevin W. title: Sequence analysis of the leader RNA of two porcine coronaviruses: Transmissible gastroenteritis virus and porcine respiratory coronavirus date: 1990 words: 3553.0 sentences: 172.0 pages: flesch: 59.0 cache: ./cache/cord-269720-o81j3d1j.txt txt: ./txt/cord-269720-o81j3d1j.txt summary: Primer extension, of a synthetic oligonucleotide complementary to the 5′ end of the nucleoprotein gene of TGEV was used to produce a single-stranded DNA copy of the leader RNA from the nucleoprotein mRNA species from TGEV and PRCV, the sequences of which were determined by Maxam and Gilbert cleavage. Comparison of the leader RNAs of TGEV and PRCV with published leader RNAs of other coronaviruses was used to identify areas of conserved sequence and potential secondary structure that may be involved in the transcription of coronavirus subgenomic mRNA species. The site, ACTAAAC, is seven nucleotides upstream of the nucleoprotein initiation codon and has also been found to precede all the TGEV structural protein genes and two of the three potential genes shown to be at the 5'' end of mRNA species (15) (16) (17) . The two porcine coronavirus leader sequences were identical, indicating that the two viruses probably use the same RNA polymerase-leader complex binding site, ACTAAAC, for the synthesis of subgenomic mRNA species. abstract: The leader RNA sequence was determined for two pig coronaviruses, tranmissible gastroenteritis virus (TGEV), and porcine respiratory coronavirus (PRCV). Primer extension, of a synthetic oligonucleotide complementary to the 5′ end of the nucleoprotein gene of TGEV was used to produce a single-stranded DNA copy of the leader RNA from the nucleoprotein mRNA species from TGEV and PRCV, the sequences of which were determined by Maxam and Gilbert cleavage. Northern blot analysis, using a synthetic oligonucleotide complementary to the leader RNA, showed that the leader RNA sequence was present on all of the subgenomic mRNA species. The porcine coronavirus leader RNA sequences were compared to each other and to published coronavirus leader RNA sequences. Sequence homologies and secondary structure similarities were identified that may play a role in the biological function of these RNA sequences. url: https://www.ncbi.nlm.nih.gov/pubmed/1962975/ doi: 10.1007/bf00570024 id: cord-310947-aqau2n7q author: Pan, Ji''An title: Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication date: 2008-10-01 words: 6821.0 sentences: 302.0 pages: flesch: 43.0 cache: ./cache/cord-310947-aqau2n7q.txt txt: ./txt/cord-310947-aqau2n7q.txt summary: In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. However, the viral protein interaction maps have been generated until now only for a limited number of viruses, including T7 bacteriophage [1] , vaccinia virus [2] , potato virus A [3] , pea seed-borne mosaic virus [3] , wheat steak mosaic virus [4] , hepatitis C virus [5, 6] , porcine teschovirus [7] , Kaposi sarcoma-associated herpesvirus [8] , and very recently severe acute respiratory syndrome coronavirus (SARS-CoV) [9, 10] . abstract: Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV) and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp) 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12) provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins. url: https://www.ncbi.nlm.nih.gov/pubmed/18827877/ doi: 10.1371/journal.pone.0003299 id: cord-337026-osgi06o4 author: Panoutsopoulos, Alexios A. title: Conjunctivitis as a Sentinel of SARS-CoV-2 Infection: a Need of Revision for Mild Symptoms date: 2020-06-19 words: 3174.0 sentences: 171.0 pages: flesch: 48.0 cache: ./cache/cord-337026-osgi06o4.txt txt: ./txt/cord-337026-osgi06o4.txt summary: Given the uprising number of publications and case reports of COVID-19 patients showing conjunctivitis [61, 62] and the history of other coronaviruses that are found in tears, we have to consider the possibility of a separate, alternative viral mechanism through which the virus can enter the patient''s organism through epithelial cells of the eye [63] . The growing evidence on COVID-19 and its ocular implications and manifestations, in both animals and humans, is covered by many interesting reviews, all published 5 to 6 months after the novel coronavirus'' outbreak [64] [65] [66] [67] [68] , something that reveals the need to understand the virus from different perspectiveswhich at first may have seemed secondary in priority-in order to be able to reach a treatment. abstract: COVID-19 has been declared a pandemic by the World Health Organization on March 11, and since then, more than 3 million cases and a quarter million deaths have occurred due to it. Lately, there is a growing evidence for an ophthalmologic symptom (conjunctivitis) to be connected with the disease. This seems to happen in early stages of the infection by SARS-CoV-2, and thus, it is of major importance to understand the mechanism through which the virus can facilitate such a symptom. Here, we are proposing a molecular mechanism through which the novel coronavirus could act in order to affect the eye and use it as another, secondary but alternative, point of entry to the host organism. url: https://www.ncbi.nlm.nih.gov/pubmed/32838145/ doi: 10.1007/s42399-020-00360-7 id: cord-318164-6rqi17oz author: Paoli, D. title: Sperm cryopreservation during the SARS-CoV-2 pandemic date: 2020-10-10 words: 3258.0 sentences: 177.0 pages: flesch: 48.0 cache: ./cache/cord-318164-6rqi17oz.txt txt: ./txt/cord-318164-6rqi17oz.txt summary: This study therefore aimed to analyze the safety of sperm cryopreservation for cancer patients after the onset of the pandemic in Italy, through assessment of the risk of SARS-CoV-2 exposure and viral RNA testing of semen samples. CONCLUSION: This preliminary assessment suggests that a thorough evaluation (especially in the setting of a multidisciplinary team) and molecular confirmation of the absence of SARS-CoV-2 in seminal fluid from asymptomatic cancer patients may assist in ensuring the safety of sperm cryopreservation. This study thus aimed to evaluate the safety of sperm cryopreservation of cancer patients referred to our sperm bank after the onset of the pandemic in Italy through the assessment of the risk of SARS-CoV-2 exposure and, in selected volunteers, viral RNA testing of semen samples. This was further confirmed by testing seminal fluid samples from 10 asymptomatic cancer patients for SARS-CoV-2 RNA. abstract: PURPOSE: Sperm cryopreservation is fundamental in the management of patients undergoing gonadotoxic treatments. Concerns have risen in relation to SARS-CoV-2 and its potential for testicular involvement, since SARS-CoV-2-positive cryopreserved samples may have unknown effects on fertilization and embryo safety. This study therefore aimed to analyze the safety of sperm cryopreservation for cancer patients after the onset of the pandemic in Italy, through assessment of the risk of SARS-CoV-2 exposure and viral RNA testing of semen samples. METHODS: We recruited 10 cancer patients (mean age 30.5 ± 9.6 years) referred to our Sperm Bank during the Italian lockdown (from March 11th to May 4th 2020) who had not undergone a nasopharyngeal swab for SARS-CoV-2 testing. Patients were administered a questionnaire on their exposure to COVID-19, and semen samples were taken. Before cryopreservation, SARS-CoV-2 RNA was extracted from a 150 µl aliquot of seminal fluid in toto using QIAamp viral RNA kit (Qiagen) and amplified by a real time RT PCR system (RealStar SARS-CoV2 RT PCR, Altona Diagnostics) targeting the E and S genes. RESULTS: The questionnaire and medical interview revealed that all patients were asymptomatic and had had no previous contact with COVID-19 infected patients. All semen samples were negative for SARS-CoV-2 RNA. CONCLUSION: This preliminary assessment suggests that a thorough evaluation (especially in the setting of a multidisciplinary team) and molecular confirmation of the absence of SARS-CoV-2 in seminal fluid from asymptomatic cancer patients may assist in ensuring the safety of sperm cryopreservation. url: https://doi.org/10.1007/s40618-020-01438-8 doi: 10.1007/s40618-020-01438-8 id: cord-259927-xh9cw9ao author: Papadopoulos, Nikolaos G. title: Promising approaches for the treatment and prevention of viral respiratory illnesses date: 2017-07-21 words: 7342.0 sentences: 400.0 pages: flesch: 34.0 cache: ./cache/cord-259927-xh9cw9ao.txt txt: ./txt/cord-259927-xh9cw9ao.txt summary: When considering prevention or treatment of viral respiratory tract infections, potential targets include the causative pathogens themselves but also the immune response, disease transmission, or even just the symptoms. Here we provide an overview of the options and highlight some of the most promising approaches in vRTI treatment, including symptomatic medication, immunomodulatory drugs, antiviral agents, and natural products, as well as in vRTI prevention, ranging from vaccines to immunostimulators and public health policies. Early in vivo evidence suggested that azithromycin has anti-inflammatory and antiviral effects through induction of interferon-stimulated gene mRNA expression and reduced viral replication and release in patients with asthma and chronic obstructive lung disease. mAb therapies to viral infections, such as EBV (rituximab) or RSV (palivizumab), provide passive immunization and are licensed, whereas similar agents targeting influenza and other viruses are in preclinical development. abstract: Viral respiratory tract infections are the most common human ailments, leading to enormous health and economic burden. Hundreds of viral species and subtypes have been associated with these conditions, with influenza viruses, respiratory syncytial virus, and rhinoviruses being the most frequent and with the highest burden. When considering prevention or treatment of viral respiratory tract infections, potential targets include the causative pathogens themselves but also the immune response, disease transmission, or even just the symptoms. Strategies targeting all these aspects are developing concurrently, and several novel and promising approaches are emerging. In this perspective we overview the entire range of options and highlight some of the most promising approaches, including new antiviral agents, symptomatic or immunomodulatory drugs, the re-emergence of natural remedies, and vaccines and public health policies toward prevention. Wide-scale prevention through immunization appears to be within reach for respiratory syncytial virus and promising for influenza virus, whereas additional effort is needed in regard to rhinovirus, as well as other respiratory tract viruses. url: https://api.elsevier.com/content/article/pii/S0091674917311132 doi: 10.1016/j.jaci.2017.07.001 id: cord-355075-ieb35upi author: Papenfuss, Anthony T title: The immune gene repertoire of an important viral reservoir, the Australian black flying fox date: 2012-06-20 words: 8952.0 sentences: 480.0 pages: flesch: 54.0 cache: ./cache/cord-355075-ieb35upi.txt txt: ./txt/cord-355075-ieb35upi.txt summary: alecto transcriptome provides information on a variety of immune genes not previously identified in any bat species and represents an important starting point for examining the antiviral activity of these molecules. To enrich for sequences corresponding to cytokines and innate immune genes, the second dataset was derived from pooled total RNA obtained from mitogen-stimulated spleen, white blood cells and lymph node and unstimulated thymus and bone marrow obtained from one pregnant female and one adult male flying fox. A full length transcript, encoding a 667 amino acid protein was identified in our bat transcriptome datasets and found to be orthologous to Mx1 based on comparison with known mammalian Mx1 and Mx2 family members (Figure 4a and data not shown). Genes involved in the adaptive immune system, including MHC class I and II genes and T and B cell receptors and co-receptors were highly represented in both the thymus and pooled datasets providing evidence that bats have all of the components necessary to mount an adaptive immune response. abstract: BACKGROUND: Bats are the natural reservoir host for a range of emerging and re-emerging viruses, including SARS-like coronaviruses, Ebola viruses, henipaviruses and Rabies viruses. However, the mechanisms responsible for the control of viral replication in bats are not understood and there is little information available on any aspect of antiviral immunity in bats. Massively parallel sequencing of the bat transcriptome provides the opportunity for rapid gene discovery. Although the genomes of one megabat and one microbat have now been sequenced to low coverage, no transcriptomic datasets have been reported from any bat species. In this study, we describe the immune transcriptome of the Australian flying fox, Pteropus alecto, providing an important resource for identification of genes involved in a range of activities including antiviral immunity. RESULTS: Towards understanding the adaptations that have allowed bats to coexist with viruses, we have de novo assembled transcriptome sequence from immune tissues and stimulated cells from P. alecto. We identified about 18,600 genes involved in a broad range of activities with the most highly expressed genes involved in cell growth and maintenance, enzyme activity, cellular components and metabolism and energy pathways. 3.5% of the bat transcribed genes corresponded to immune genes and a total of about 500 immune genes were identified, providing an overview of both innate and adaptive immunity. A small proportion of transcripts found no match with annotated sequences in any of the public databases and may represent bat-specific transcripts. CONCLUSIONS: This study represents the first reported bat transcriptome dataset and provides a survey of expressed bat genes that complement existing bat genomic data. In addition, these data provide insight into genes relevant to the antiviral responses of bats, and form a basis for examining the roles of these molecules in immune response to viral infection. url: https://doi.org/10.1186/1471-2164-13-261 doi: 10.1186/1471-2164-13-261 id: cord-352891-ljmkqdzx author: Parang, Keykavous title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) date: 2020-05-17 words: 3165.0 sentences: 182.0 pages: flesch: 52.0 cache: ./cache/cord-352891-ljmkqdzx.txt txt: ./txt/cord-352891-ljmkqdzx.txt summary: title: Comparative Antiviral Activity of Remdesivir and Anti-HIV Nucleoside Analogs against Human Coronavirus 229E (HCoV-229E) Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. Therefore, HCoV-229E may be a good initial model for the evaluation of antiviral compounds that could have potential applications against other coronaviruses, such as SARS-COV-2, the coronavirus that causes COVID-19. We have previously shown that the conjugation of certain fatty acids to the anti-HIV NRTIs, such as FLT, 3TC and FTC, enhanced activity against X4, R5, cell-associated, and/or multi-drug resistant virus when compared with their parent nucleosides [24] [25] [26] [27] . A series of anti-HIV nucleosides and their fatty acyl derivatives were compared with remdesivir for antiviral activity against HCoV-229E in MRC-5 cells. abstract: Remdesivir is a nucleotide prodrug that is currently undergoing extensive clinical trials for the treatment of COVID-19. The prodrug is metabolized to its active triphosphate form and interferes with the action of RNA-dependent RNA polymerase of SARS-COV-2. Herein, we report the antiviral activity of remdesivir against human coronavirus 229E (HCoV-229E) compared to known anti-HIV agents. These agents included tenofovir (TFV), 4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA), alovudine (FLT), lamivudine (3TC), and emtricitabine (FTC), known as nucleoside reverse-transcriptase inhibitors (NRTIs), and a number of 5′-O-fatty acylated anti-HIV nucleoside conjugates. The anti-HIV nucleosides interfere with HIV RNA-dependent DNA polymerase and/or act as chain terminators. Normal human fibroblast lung cells (MRC-5) were used to determine the cytotoxicity of the compounds. The study revealed that remdesivir exhibited an EC(50) value of 0.07 µM against HCoV-229E with TC(50) of > 2.00 µM against MRC-5 cells. Parent NRTIs were found to be inactive against (HCoV-229E) at tested concentrations. Among all the NRTIs and 5′-O-fatty acyl conjugates of NRTIs, 5′-O-tetradecanoyl ester conjugate of FTC showed modest activity with EC(50) and TC(50) values of 72.8 µM and 87.5 µM, respectively. These data can be used for the design of potential compounds against other coronaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/32429580/ doi: 10.3390/molecules25102343 id: cord-264488-989t9ld1 author: Park, Il-Hyun title: Inhibition of hepatitis B virus replication by ligand-mediated activation of RNase L date: 2014-02-06 words: 5320.0 sentences: 269.0 pages: flesch: 54.0 cache: ./cache/cord-264488-989t9ld1.txt txt: ./txt/cord-264488-989t9ld1.txt summary: In the present study, the potential antiviral activity of RNase L against hepatitis B virus (HBV) was explored utilizing the recently reported infection protocol based on human hepatoma HepG2 cells stably complemented with the virus entry factor NTCP. These results suggest that HBV replication can be regulated through interferon-mediated RNA decay pathways and that activation of these host antiviral factors may represent a novel therapeutic strategy for HBV infection. Our data indicate that ligand-mediated activation of these enzymes results in a marked inhibition of HBV replication in both infected and transfected cells. With the newly established HepG2-NTCP cell culture system, which permits HBV infection, we showed that viral gene expression and replication can be profoundly reduced by 2-5Aor poly(I:C)-mediated activation of RNase L. In HBV1.2-transfected Huh-7 cells, it was further confirmed that this type of inhibition occurred mostly through viral RNA degradation via the ribonuclease function of RNase L. abstract: RNase L is a cellular endoribonuclease that is activated by 2′,5′-linked oligoadenylates (2–5A), which are unique and specific ligands synthesized by a family of interferon-inducible, dsRNA-activated enzymes named oligoadenylate synthetases. In the typical antiviral pathway, activated RNase L degrades viral and cellular RNAs, thus limiting viral replication and spread. Although the antiviral activity of RNase L has been demonstrated for several RNA viruses, there is little evidence regarding its role against DNA viruses. In the present study, the potential antiviral activity of RNase L against hepatitis B virus (HBV) was explored utilizing the recently reported infection protocol based on human hepatoma HepG2 cells stably complemented with the virus entry factor NTCP. Viral replication and expression in this cell type was markedly inhibited by poly(I:C)- or 2–5A-mediated activation of RNase L; however, the inhibition was significantly reversed by RNase L knockdown. Further analysis in HBV1.2-transfected Huh-7 hepatoma cells indicated that the antiviral activity of RNase L depends on its ribonuclease function. We also provide evidence for the specific roles of OAS family members in this process. These results suggest that HBV replication can be regulated through interferon-mediated RNA decay pathways and that activation of these host antiviral factors may represent a novel therapeutic strategy for HBV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/24509240/ doi: 10.1016/j.antiviral.2014.01.021 id: cord-007066-zn10rnrm author: Park, Noh Jin title: Characterization of RNA in Saliva date: 2006-06-01 words: 4637.0 sentences: 285.0 pages: flesch: 62.0 cache: ./cache/cord-007066-zn10rnrm.txt txt: ./txt/cord-007066-zn10rnrm.txt summary: RNA can enter the oral cavity through various routes, including saliva secretions from the 3 major salivary glands (the parotid, submandibular, and sublingual glands) and minor glands, gingival crevice fluid (GCF), and desquamated oral epithelial cells. It is therefore possible that the RPS9 PCR products in panels B and C of Fig. 1 are produced from both RPS9 and RPS9P2 mRNAs. Previous expression-based microarray analysis showed that 185 different transcripts were consistently detected in the supernatants of 10 healthy human saliva samples (6 ) . Although individual variations exist, we detected ␤-actin mRNA in all 3 major salivary glands, GCF, and desquamated oral epithelial cells ( Fig. 2A) , suggesting that RNA enters the oral cavity from different sites. In addition to the saliva samples, we also measured RNA-macromolecule associations in serum and found that ϳ8% and Ͻ1% of ␤-actin mRNA could be detected in serum filtered through 0.45 and 0.22 m pores, respectively (see Fig. 1c in the online Data Supplement). abstract: Background: We have previously shown that human mRNAs are present in saliva and can be used as biomarkers of oral cancer. In this study, we analyzed the integrity, sources, and stability of salivary RNA. Methods: We measured the integrity of salivary RNA with reverse transcription followed by PCR (RT-PCR) or RT-quantitative PCR (RT-qPCR). To study RNA entry sites into the oral cavity, we used RT-PCR analysis of salivary RNA from the 3 major salivary glands, gingival crevice fluid, and desquamated oral epithelial cells. We measured stability of the salivary β-actin mRNA by RT-qPCR of salivary RNA incubated at room temperature for different periods of time. We measured RNA association with other macromolecules by filtering saliva through pores of different sizes before performing RT-qPCR. To assess RNA–macromolecule interaction, we incubated saliva with Triton X-100 for different periods of time before performing RT-qPCR. Results: In most cases, we detected partial- to full-length salivary mRNAs and smaller amounts of middle and 3′ gene amplicons compared with the 5′. RNA was present in all oral fluids examined. Endogenous salivary β-actin mRNA degraded more slowly than exogenous β-actin mRNA, with half-lives of 12.2 and 0.4 min, respectively (P <0.001). Salivary RNA could not pass through 0.22 or 0.45 μm pores. Incubation of saliva with Triton X-100 accelerated degradation of salivary RNA. Conclusions: Saliva harbors both full-length and partially degraded forms of mRNA. RNA enters the oral cavity from different sources, and association with macromolecules may protect salivary RNA from degradation. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108156/ doi: 10.1373/clinchem.2005.063206 id: cord-288167-976qxja2 author: Park, Wan Beom title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection date: 2018-05-09 words: 1373.0 sentences: 87.0 pages: flesch: 52.0 cache: ./cache/cord-288167-976qxja2.txt txt: ./txt/cord-288167-976qxja2.txt summary: title: Replicative virus shedding in the respiratory tract of patients with Middle East respiratory syndrome coronavirus infection BACKGROUND: Information on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. In the present study, replicative MERS-CoV was detected in sputum or transtracheal aspirate for up to 4 weeks after symptom development in MERS-CoV-infected patients with severe pneumonia. In conclusion, replicative MERS-CoV was detected in lower respiratory tract specimens for up to 4 weeks after symptom development, which was well correlated with the detection of genomic RNA. In upper respiratory tract specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. Middle East respiratory syndrome coronavirus (MERS-CoV) genomic RNA (upE) titers in sputum and transtracheal aspirates with vs. abstract: BACKGROUND: Information on the duration of replicative Middle East respiratory syndrome coronavirus (MERS-CoV) shedding is important for infection control. The detection of MERS-CoV sub-genomic mRNAs indicates that the virus is replicative. This study examined the duration for detecting MERS-CoV sub-genomic mRNA compared with genomic RNA in diverse respiratory specimens. METHODS: Upper and lower respiratory samples were obtained from 17 MERS-CoV-infected patients. MERS-CoV sub-genomic mRNA was detected by reverse transcription PCR (RT-PCR) and MERS-CoV genomic RNA by real-time RT-PCR. RESULTS: In sputum and transtracheal aspirate, sub-genomic mRNA was detected for up to 4 weeks after symptoms developed, which correlated with the detection of genomic RNA. In oropharyngeal and nasopharyngeal swab specimens, the detection of sub-genomic mRNA and genomic RNA did not correlate. CONCLUSIONS: These findings suggest that MERS-CoV does not replicate well in the upper respiratory tract. url: https://api.elsevier.com/content/article/pii/S1201971218344114 doi: 10.1016/j.ijid.2018.05.003 id: cord-184744-oyc2djxk author: Parvez, Md Sorwer Alam title: Virtual Screening of Plant Metabolites against Main protease, RNA-dependent RNA polymerase and Spike protein of SARS-CoV-2: Therapeutics option of COVID-19 date: 2020-05-22 words: 3653.0 sentences: 224.0 pages: flesch: 49.0 cache: ./cache/cord-184744-oyc2djxk.txt txt: ./txt/cord-184744-oyc2djxk.txt summary: The present study evaluated the possibility of plant originated approved 117 therapeutics against the main protease protein (MPP), RNA-dependent RNA polymerase (RdRp) and spike protein (S) of SARS-CoV-2 including drug surface analysis by using molecular docking through drug repurposing approaches. The molecular interaction study revealed that Rifampin (-16.3 kcal/mol) were topmost inhibitor of MPP where Azobechalcone were found most potent plant therapeutics for blocking the RdRp (-15.9 kcal /mol) and S (-14.4 kcal/mol) protein of SARS-CoV-2. The main protease proteins, RNA-dependent RNA polymerase and spike protein of SARS-CoV-2 were employed to molecular docking study with the repurposed drug candidates from plant origin for find out the better drug option towards the COVID-19 pandemic. In the present study, five plantr based therapeutics such as Azobechalcone, Rifampin, Isolophirachalcone, Tetrandrine and Fangchinoline were suggested for potential inhibitors for the Main Protease protein, RNA dependent RNA polymerase and Spike protein of SARS-CoV-2 by using molecular docking based virtual screening study. abstract: Covid-19, a serious respiratory complications caused by SARS-CoV-2 has become one of the global threat to human healthcare system. The present study evaluated the possibility of plant originated approved 117 therapeutics against the main protease protein (MPP), RNA-dependent RNA polymerase (RdRp) and spike protein (S) of SARS-CoV-2 including drug surface analysis by using molecular docking through drug repurposing approaches. The molecular interaction study revealed that Rifampin (-16.3 kcal/mol) were topmost inhibitor of MPP where Azobechalcone were found most potent plant therapeutics for blocking the RdRp (-15.9 kcal /mol) and S (-14.4 kcal/mol) protein of SARS-CoV-2. After the comparative analysis of all docking results, Azobechalcone, Rifampin, Isolophirachalcone, Tetrandrine and Fangchinoline were exhibited as the most potential inhibitory plant compounds for targeting the key proteins of SARS-CoV-2. However, amino acid positions; H41, C145, and M165 of MPP played crucial roles for the drug surface interaction where F368, L371, L372, A375, W509, L514, Y515 were pivotal for RdRP. In addition, the drug interaction surface of S proteins also showed similar patterns with all of its maximum inhibitors. ADME analysis also strengthened the possibility of screened plant therapeutics as the potent drug candidates against SARS-C with the highest drug friendliness. url: https://arxiv.org/pdf/2005.11254v1.pdf doi: nan id: cord-254963-cnvxlv6h author: Paskey, Adrian C. title: Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples date: 2019-02-26 words: 6201.0 sentences: 267.0 pages: flesch: 45.0 cache: ./cache/cord-254963-cnvxlv6h.txt txt: ./txt/cord-254963-cnvxlv6h.txt summary: In order to test this newly expanded probe panel and to specifically assess the effect of hybridization-based viral enrichment on the sensitivity of HTS for detection of a single virus within a complex environmental sample, commercial bat guano was spiked with increasing concentrations of Influenza virus (IFV). As expected, a dose-dependent effect in the proportion of sequencing reads derived from IFV was observed as the number of spiked genome copies increased ( Fig. 1a and Additional file 1: Table S1 ), in both the unbiased shotgun sequence data as well as the virus enriched sequence data. Such limitations have been of particular concern for U.S. Department of Defense (DoD) laboratories tasked with biosurveillance and biodefense activities in regions with limited material resources and human We demonstrate here that hybridization-based viral target enrichment yields robust coverage of small genomes from clinical samples, even yielding full-length, deeply covered genomes at concentrations whereby Fig. 3 Detection of close relative viruses irrespective of extensive multiplexing. abstract: BACKGROUND: Sequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing. RESULTS: This study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage. CONCLUSIONS: Hybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5543-2) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12864-019-5543-2 doi: 10.1186/s12864-019-5543-2 id: cord-048198-zjufx4fo author: Pasternak, Alexander O. title: Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis date: 2001-12-17 words: 7614.0 sentences: 366.0 pages: flesch: 58.0 cache: ./cache/cord-048198-zjufx4fo.txt txt: ./txt/cord-048198-zjufx4fo.txt summary: Here we present results of a comprehensive co-variation mutagenesis study of equine arteritis virus TRSs, demonstrating that discontinuous RNA synthesis depends not only on base pairing between sense leader TRS and antisense body TRS, but also on the primary sequence of the body TRS. Synthesis of sg mRNAs initially was proposed to be primed by free leader transcripts, which would base-pair to the complementary TRS regions in the full-length minus strand, and would be extended subsequently to make sg plus strands ( Figure 1B ; Baric et al., 1983 Baric et al., , 1985 . 7220±7228, 2001 Using site-directed mutagenesis of TRSs of the arterivirus equine arteritis virus (EAV), we have shown previously that base pairing between the sense leader TRS and antisense body TRSs is crucial for sg mRNA synthesis (van Marle et al., 1999a) . abstract: Nidovirus subgenomic mRNAs contain a leader sequence derived from the 5′ end of the genome fused to different sequences (‘bodies’) derived from the 3′ end. Their generation involves a unique mechanism of discontinuous subgenomic RNA synthesis that resembles copy-choice RNA recombination. During this process, the nascent RNA strand is transferred from one site in the template to another, during either plus or minus strand synthesis, to yield subgenomic RNA molecules. Central to this process are transcription-regulating sequences (TRSs), which are present at both template sites and ensure the fidelity of strand transfer. Here we present results of a comprehensive co-variation mutagenesis study of equine arteritis virus TRSs, demonstrating that discontinuous RNA synthesis depends not only on base pairing between sense leader TRS and antisense body TRS, but also on the primary sequence of the body TRS. While the leader TRS merely plays a targeting role for strand transfer, the body TRS fulfils multiple functions. The sequences of mRNA leader–body junctions of TRS mutants strongly suggested that the discontinuous step occurs during minus strand synthesis. url: http://europepmc.org/articles/pmc125340?pdf=render doi: 10.1093/emboj/20.24.7220 id: cord-010680-lc1onm53 author: Patel, Ami title: In Vivo Delivery of Nucleic Acid-Encoded Monoclonal Antibodies date: 2020-03-10 words: 13044.0 sentences: 659.0 pages: flesch: 41.0 cache: ./cache/cord-010680-lc1onm53.txt txt: ./txt/cord-010680-lc1onm53.txt summary: Some of these hurdles may be overcome through transient in vivo gene delivery platforms, such as non-viral synthetic plasmid DNA and messenger RNA vectors that are engineered to encode optimized mAb genes. In this review, we focus on nucleic acid delivery of antibody employing synthetic plasmid DNA vector platforms, and RNA delivery, these being important approaches that are advancing simple, rapid, in vivo expression and having an impact in animal models of infectious diseases and cancer, among others. The original studies surrounding in vivo antibody gene delivery focused primarily on gene delivery using recombinant viral vectors such as AAV and adenovirus (Ad), which were advanced clinically, building on work in the traditional gene therapy-based field. Additional studies to help evaluate fully human pDNA-mAbs in mouse models would be highly informative for both non-viral and viral delivery and provide an important path forward for preclinical evaluation of in vivo-delivered antibodies [109] . abstract: Antibody immunotherapy is revolutionizing modern medicine. The field has advanced dramatically over the past 40 years, driven in part by major advances in isolation and manufacturing technologies that have brought these important biologics to the forefront of modern medicine. However, the global uptake of monoclonal antibody (mAb) biologics is impeded by biophysical and biochemical liabilities, production limitations, the need for cold-chain storage and transport, as well as high costs of manufacturing and distribution. Some of these hurdles may be overcome through transient in vivo gene delivery platforms, such as non-viral synthetic plasmid DNA and messenger RNA vectors that are engineered to encode optimized mAb genes. These approaches turn the body into a biological factory for antibody production, eliminating many of the steps involved in bioprocesses and providing several other significant advantages, and differ from traditional gene therapy (permanent delivery) approaches. In this review, we focus on nucleic acid delivery of antibody employing synthetic plasmid DNA vector platforms, and RNA delivery, these being important approaches that are advancing simple, rapid, in vivo expression and having an impact in animal models of infectious diseases and cancer, among others. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211204/ doi: 10.1007/s40259-020-00412-3 id: cord-284076-087oltss author: Patel, Deendayal title: Peptide-conjugated morpholino oligomers inhibit porcine reproductive and respiratory syndrome virus replication date: 2007-10-04 words: 7761.0 sentences: 411.0 pages: flesch: 56.0 cache: ./cache/cord-284076-087oltss.txt txt: ./txt/cord-284076-087oltss.txt summary: Of 12 peptide-conjugated PMO (PPMO), four were found to be highly effective at inhibiting PRRSV replication in cell culture in a dose-dependant and sequence-specific manner. In a previous study (Zhang et al., 2006) , we tested six PPMO and found one of them (5UP1), designed to target the 5 terminal region of the PRRSV genome, to be a highly effective inhibitor of PRRSV replication in a sequence-specific and dose-dependent manner. Confirmation of the CPE observations and PRRSV yield titration was obtained by IFA on CRL11171 cells after virus inoculation and PPMO treatment (Fig. 2B ). demonstrated that PPMO generated little cytotoxicity in both CRL11171 and PAM cells, further indicating that the suppression of virus replication observed in the antiviral experiments above was due to sequence-specific effects. Treatment of cells with PPMO 5UP2 or 5HP led to suppression of PRRSV replication of all North American strains, producing virus yields not detectable (ND) in this assay. abstract: Porcine reproductive and respiratory syndrome (PRRS) has been devastating the global swine industry for more than a decade, and current strategies to control PRRS are inadequate. In this study we characterized the inhibition of PRRS virus (PRRSV) replication by antisense phosphorodiamidate morpholino oligomers (PMO). Of 12 peptide-conjugated PMO (PPMO), four were found to be highly effective at inhibiting PRRSV replication in cell culture in a dose-dependant and sequence-specific manner. PPMO 5UP2 and 5HP are complementary to sequence in the 5′ end of the PRRSV genome, and 6P1 and 7P1 to sequence in the translation initiation regions of ORF6 and ORF7, respectively. Treatment of cells with 5UP2 or 5HP caused a 4.5 log(10) reduction in PRRSV yield, compared to a control PPMO. Combination of 6P1 and 7P1 led to higher level reduction than 6P1 or 7P1 alone. 5UP2, 5HP, and a combination of 6P1 and 7P1 inhibited PRRSV replication in porcine alveolar macrophages and protected the cells from PRRSV-induced cytopathic effect. Northern blot and real-time RT-PCR results demonstrated that the effective PPMO led to a reduction of PRRSV RNA level. 5UP2 and 5HP inhibited virus replication of 10 other strains of PRRSV. Results from this study suggest potential applications of PPMO for PRRS control. url: https://www.ncbi.nlm.nih.gov/pubmed/17959259/ doi: 10.1016/j.antiviral.2007.09.002 id: cord-271781-cfv0ta10 author: Patel, Kishan P. title: Transmission of SARS-CoV-2: an update of current literature date: 2020-07-07 words: 4469.0 sentences: 232.0 pages: flesch: 47.0 cache: ./cache/cord-271781-cfv0ta10.txt txt: ./txt/cord-271781-cfv0ta10.txt summary: To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Additionally, studies have noted that its fecal-oral transmission potential may lie in the fact that prolonged viral shedding can occur in fecal matter-one case reported an asymptomatic COVID-19 patient experiencing viral detection in the stool for up to 42 days, while nasopharyngeal sampling was negative [31] . To oppose, in a retrospective review of nine COVID-19 pregnant mothers who underwent cesarean section, six patients had samples of amniotic fluid, cord blood, neonatal throat swab, and breastmilk samples tested for SARS-CoV-2, and all were negative [43] . abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent for the 2019 coronavirus disease (COVID-19) pandemic, has caused a public health emergency. The need for additional research in viral pathogenesis is essential as the number of cases and deaths rise. Understanding the virus and its ability to cause disease has been the main focus of current literature; however, there is much unknown. Studies have revealed new findings related to the full transmission potential of SARS-CoV-2 and its subsequent ability to cause infection by different means. The virus is hypothesized to be of increased virulence compared with previous coronavirus that caused epidemics, in part due to its overall structural integrity and resilience to inactivation. To date, many studies have discussed that the rationale behind its transmission potential is that viral RNA has unexpectedly been detected in multiple bodily fluids, with some samples having remained positive for extended periods of time. Additionally, the receptor by which the virus gains cellular entry, ACE2, has been found to be expressed in different human body systems, thereby potentiating its infection in those locations. In this evidence-based comprehensive review, we discuss various potential routes of transmission of SARS-CoV-2—respiratory/droplet, indirect, fecal-oral, vertical, sexual, and ocular. Understanding these different routes is important as they pertain to clinical practice, especially in taking preventative measures to mitigate the spread of SARS-CoV-2. url: https://doi.org/10.1007/s10096-020-03961-1 doi: 10.1007/s10096-020-03961-1 id: cord-280001-y7pvj2l1 author: Patel, Robin title: Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19 date: 2020-03-26 words: 1785.0 sentences: 77.0 pages: flesch: 46.0 cache: ./cache/cord-280001-y7pvj2l1.txt txt: ./txt/cord-280001-y7pvj2l1.txt summary: If the test is positive though, the result is most likely correct, although stray viral RNA that makes its way into the testing process (for example, as the specimen is being collected or as a result of specimen cross-contamination or testing performed by a laboratory worker who is infected with SARS-CoV-2 [these are just some examples]) could conceivably result in a falsely positive result. Testing patients for SARS-CoV-2 helps identify those who are infected, which is useful for individual patient management, as well as for implementation of mitigation strategies to prevent spread in health care facilities and in the community alike (Fig. 1) . Given that SARS-CoV-2 can infect anyone and result in transmission prior to the onset of symptoms or even possibly without individuals ever developing symptoms, testing asymptomatic patients could even be considered. Finally, serologic testing can possibly be used diagnostically to test viral RNA-negative individuals presenting late in their illness. abstract: nan url: https://doi.org/10.1128/mbio.00722-20 doi: 10.1128/mbio.00722-20 id: cord-000018-amvlm09p author: Pauli, Eva-K. title: Influenza A Virus Inhibits Type I IFN Signaling via NF-κB-Dependent Induction of SOCS-3 Expression date: 2008-11-07 words: 9011.0 sentences: 515.0 pages: flesch: 53.0 cache: ./cache/cord-000018-amvlm09p.txt txt: ./txt/cord-000018-amvlm09p.txt summary: Our study was based on the observation that in cells that were infected with influenza A virus and subsequently stimulated with IFNα/β, phosphorylation of the signal transducer and activator of transcription protein 1 (STAT1) was strongly reduced. This direct viral induction of SOCS-3 mRNA and protein expression appears to be relevant for suppression of the antiviral response since in SOCS-3 deficient cells a sustained phosphorylation of STAT1 correlated with elevated expression of type I IFN-dependent genes. These results are consistent with data gained from previous experiments in Vero cells ( Figure 1E ) and indicate that neither induction of SOCS-3 mRNA nor inhibition of STAT phosphorylation is dependent on virus-induced type I IFN expression. To answer the question whether enhanced STAT phosphorylation in SOCS-3 deficient cells would also lead to enhanced expression of ISGs, total RNA was isolated at different time points p.i. from infected wild type and knock out cells and monitored for induction of SP110, IRF-1 and OAS1 ( Figure 7E, 7F and 7G ). abstract: The type I interferon (IFN) system is a first line of defense against viral infections. Viruses have developed various mechanisms to counteract this response. So far, the interferon antagonistic activity of influenza A viruses was mainly observed on the level of IFNβ gene induction via action of the viral non-structural protein 1 (NS1). Here we present data indicating that influenza A viruses not only suppress IFNβ gene induction but also inhibit type I IFN signaling through a mechanism involving induction of the suppressor of cytokine signaling-3 (SOCS-3) protein. Our study was based on the observation that in cells that were infected with influenza A virus and subsequently stimulated with IFNα/β, phosphorylation of the signal transducer and activator of transcription protein 1 (STAT1) was strongly reduced. This impaired STAT1 activation was not due to the action of viral proteins but rather appeared to be induced by accumulation of viral 5′ triphosphate RNA in the cell. SOCS proteins are potent endogenous inhibitors of Janus kinase (JAK)/STAT signaling. Closer examination revealed that SOCS-3 but not SOCS-1 mRNA levels increase in an RNA- and nuclear factor kappa B (NF-κB)-dependent but type I IFN-independent manner early in the viral replication cycle. This direct viral induction of SOCS-3 mRNA and protein expression appears to be relevant for suppression of the antiviral response since in SOCS-3 deficient cells a sustained phosphorylation of STAT1 correlated with elevated expression of type I IFN-dependent genes. As a consequence, progeny virus titers were reduced in SOCS-3 deficient cells or in cells were SOCS-3 expression was knocked-down by siRNA. These data provide the first evidence that influenza A viruses suppress type I IFN signaling on the level of JAK/STAT activation. The inhibitory effect is at least in part due to the induction of SOCS-3 gene expression, which results in an impaired antiviral response. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572141/ doi: 10.1371/journal.ppat.1000196 id: cord-002651-9r384oxd author: Pauly, Matthew D. title: Epistatic Interactions within the Influenza A Virus Polymerase Complex Mediate Mutagen Resistance and Replication Fidelity date: 2017-08-16 words: 8111.0 sentences: 429.0 pages: flesch: 50.0 cache: ./cache/cord-002651-9r384oxd.txt txt: ./txt/cord-002651-9r384oxd.txt summary: Studies of mutagen-resistant viruses have identified determinants of replicative fidelity and the importance of mutation rate to viral population dynamics. Consistent with the importance of epistatic interactions in the influenza virus polymerase, our data suggest that nucleoside analog resistance and replication fidelity are strain dependent. To this end, we identified variants within the polymerase complex of influenza virus that are able to tolerate drug-mediated increases in viral mutation rates. In most cases, mutagen-resistant variants encode polymerases that exhibit increased replication fidelity, and characterization of these mutants has elucidated the molecular mechanisms governing mutation rate. We tested each of the variant polymerases for reduced nucleoside sensitivity by comparing titers after replication of the corresponding virus populations in mock-or drug-treated cell cultures 24 h postinfection (Fig. 1A) . We used a serial passage competition assay (15) to measure the replicative fitness of each mutant virus relative to the WT PR8 and also performed growth curves to quantify RNA genome production. abstract: Lethal mutagenesis is a broad-spectrum antiviral strategy that employs mutagenic nucleoside analogs to exploit the high mutation rate and low mutational tolerance of many RNA viruses. Studies of mutagen-resistant viruses have identified determinants of replicative fidelity and the importance of mutation rate to viral population dynamics. We have previously demonstrated the effective lethal mutagenesis of influenza A virus using three nucleoside analogs as well as the virus’s high genetic barrier to mutagen resistance. Here, we investigate the mutagen-resistant phenotypes of mutations that were enriched in drug-treated populations. We find that PB1 T123A has higher replicative fitness than the wild type, PR8, and maintains its level of genome production during 5-fluorouracil (2,4-dihydroxy-5-fluoropyrimidine) treatment. Surprisingly, this mutagen-resistant variant also has an increased baseline rate of C-to-U and G-to-A mutations. A second drug-selected mutation, PA T97I, interacts epistatically with PB1 T123A to mediate high-level mutagen resistance, predominantly by limiting the inhibitory effect of nucleosides on polymerase activity. Consistent with the importance of epistatic interactions in the influenza virus polymerase, our data suggest that nucleoside analog resistance and replication fidelity are strain dependent. Two previously identified ribavirin {1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-1,2,4-triazole-3-carboxamide} resistance mutations, PB1 V43I and PB1 D27N, do not confer drug resistance in the PR8 background, and the PR8-PB1 V43I polymerase exhibits a normal baseline mutation rate. Our results highlight the genetic complexity of the influenza A virus polymerase and demonstrate that increased replicative capacity is a mechanism by which an RNA virus can counter the negative effects of elevated mutation rates. IMPORTANCE RNA viruses exist as genetically diverse populations. This standing genetic diversity gives them the potential to adapt rapidly, evolve resistance to antiviral therapeutics, and evade immune responses. Viral mutants with altered mutation rates or mutational tolerance have provided insights into how genetic diversity arises and how it affects the behavior of RNA viruses. To this end, we identified variants within the polymerase complex of influenza virus that are able to tolerate drug-mediated increases in viral mutation rates. We find that drug resistance is highly dependent on interactions among mutations in the polymerase complex. In contrast to other viruses, influenza virus counters the effect of higher mutation rates primarily by maintaining high levels of genome replication. These findings suggest the importance of maintaining large population sizes for viruses with high mutation rates and show that multiple proteins can affect both mutation rate and genome synthesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557677/ doi: 10.1128/msphere.00323-17 id: cord-329107-43e2lkht author: Pawlicka, Kamila title: Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics date: 2020-03-24 words: 6690.0 sentences: 377.0 pages: flesch: 44.0 cache: ./cache/cord-329107-43e2lkht.txt txt: ./txt/cord-329107-43e2lkht.txt summary: Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a surveillance pathway used by cells to control the quality mRNAs and to fine-tune transcript abundance. Disturbance of this control mechanism caused by genetic mutations or dys-regulation of the NMD pathway can lead to pathologies, including neurological disorders, immune diseases and cancers. Nonsense-mediated mRNA decay (NMD) is a critical cellular surveillance mechanism that recognizes and eliminates aberrant RNAs containing premature termination codons (PTC) or abnormally long 3 untranslated regions (UTRs). Nonsense-mediated mRNA decay is a critical RNA quality control and plays a vital role in the recognition of PTCs in transcripts, as well as in the regular homeostasis of the transcriptome. Understanding the mechanism of nonsense-mediated mRNA decay might lead to new ways to use surveillance in cancer therapy or other PTC-associated genetic diseases. Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon Hypoxic Inhibition of Nonsense-Mediated RNA Decay Regulates Gene Expression and the Integrated Stress Response abstract: Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a surveillance pathway used by cells to control the quality mRNAs and to fine-tune transcript abundance. NMD plays an important role in cell cycle regulation, cell viability, DNA damage response, while also serving as a barrier to virus infection. Disturbance of this control mechanism caused by genetic mutations or dys-regulation of the NMD pathway can lead to pathologies, including neurological disorders, immune diseases and cancers. The role of NMD in cancer development is complex, acting as both a promoter and a barrier to tumour progression. Cancer cells can exploit NMD for the downregulation of key tumour suppressor genes, or tumours adjust NMD activity to adapt to an aggressive immune microenvironment. The latter case might provide an avenue for therapeutic intervention as NMD inhibition has been shown to lead to the production of neoantigens that stimulate an immune system attack on tumours. For this reason, understanding the biology and co-option pathways of NMD is important for the development of novel therapeutic agents. Inhibitors, whose design can make use of the many structures available for NMD study, will play a crucial role in characterizing and providing diverse therapeutic options for this pathway in cancer and other diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/32213869/ doi: 10.3390/cancers12030765 id: cord-319781-6thdg2up author: Payne, Kelly title: Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications in Men date: 2020-07-24 words: 8233.0 sentences: 454.0 pages: flesch: 51.0 cache: ./cache/cord-319781-6thdg2up.txt txt: ./txt/cord-319781-6thdg2up.txt summary: To understand factors that may contribute to viral spread and address long-term health sequelae for survivors, it is important to review evidence regarding viral presence in semen, sexual transmission potential, and possible effects on fertility. We review evidence for the following viruses: Ebola, Zika, West Nile, pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-corona virus-2 (SARS-CoV-2). Then, we present the state of current research regarding presence in semen, sexual transmission, and fertility effects for the Zika virus (ZIKV), Ebola virus (EBOV), West Nile virus (WNV), pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-coronavirus-2 (SARS-CoV-2) ( Table 1) . In this article, we have reviewed the presence in semen, possibility of sexual transmission, and fertility implications of each of the major recent viral pandemics: Zika, Ebola, West Nile, pandemic influenza, SARS, and SARS-CoV-2. abstract: INTRODUCTION: The 21st century has seen a series of viral pandemics that have collectively infected millions of individuals. To understand factors that may contribute to viral spread and address long-term health sequelae for survivors, it is important to review evidence regarding viral presence in semen, sexual transmission potential, and possible effects on fertility. AIM: To review the current literature regarding the sexual transmissibility of recent viral pandemics and their effects on semen parameters and fertility. We review evidence for the following viruses: Ebola, Zika, West Nile, pandemic influenza, severe acute respiratory syndrome (SARS), and SARS-corona virus-2 (SARS-CoV-2). METHODS: A literature search was conducted to identify relevant studies. Titles and abstracts were reviewed for relevance. References from identified articles were searched and included, if appropriate. MAIN OUTCOME MEASURES: The main outcome measure of this study was reviewing of peer-reviewed literature. RESULTS: Both the Ebola virus and Zika virus are present in semen, but only the Zika virus shows consistent evidence of sexual transmission. Current evidence does not support the presence of the West Nile virus, pandemic influenza, SARS, and SARS-CoV-2 in semen. The Zika virus appears to alter semen parameters in a way that diminishes fertility, but the effect is likely time limited. The West Nile virus and SARS have been associated with orchitis in a small number of case reports. Viruses that cause febrile illness, such as pandemic influenza, SARS, and SARS-CoV-2, are associated with decreased sperm count and motility and abnormal morphology. SARS and SARS-CoV-2 may interact with angiotensin-converting enzyme 2 receptors present in the testes, which could impact spermatogenesis. CONCLUSIONS: We have reported the presence in semen, sexual transmission potential, and fertility side effects of recent viral pandemics. Overall, semen studies and fertility effects are highly understudied in viral pandemics, and rigorous study on these topics should be undertaken as novel pandemics emerge. Payne K, Kenny P, Scovell JM, et al. Twenty-First Century Viral Pandemics: A Literature Review of Sexual Transmission and Fertility Implications for Men. Sex Med Rev 2020;XX:XXX–XXX. url: https://doi.org/10.1016/j.sxmr.2020.06.003 doi: 10.1016/j.sxmr.2020.06.003 id: cord-354051-ro3o27pv author: Peccia, J. title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics date: 2020-05-22 words: 1244.0 sentences: 101.0 pages: flesch: 57.0 cache: ./cache/cord-354051-ro3o27pv.txt txt: ./txt/cord-354051-ro3o27pv.txt summary: title: SARS-CoV-2 RNA concentrations in primary municipal sewage sludge as a leading indicator of COVID-19 outbreak dynamics We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. As viral shedding can occur before cases are detected, we hypothesize that the time course of SARS-CoV-2 RNA concentrations in primary sewage sludge is a leading indicator of outbreak dynamics within a community served by the treatment plant. SARS-CoV-2 viral RNA concentrations were quantitatively compared with local hospital admission data and community COVID-19 compiled testing data. SARS-CoV-2 RNA sludge concentrations were quantitatively compared with data that are commonly used to track the community progression of COVID-19 including hospital admissions (Figure 2A This study uniquely utilized primary sewage sludge instead of raw wastewater for virus RNA measurements. abstract: We report a time course of SARS-CoV-2 RNA concentrations in primary sewage sludge during the Spring COVID-19 outbreak in a northeastern U.S. metropolitan area. SARS-CoV-2 RNA was detected in all environmental samples and, when adjusted for the time lag, the virus RNA concentrations were highly correlated with the COVID-19 epidemiological curve (R2=0.99) and local hospital admissions (R2=0.99). SARS-CoV-2 RNA concentrations were a seven-day leading indicator ahead of compiled COVID-19 testing data and led local hospital admissions data by three days. Decisions to implement or relax public health measures and restrictions require timely information on outbreak dynamics in a community. url: http://medrxiv.org/cgi/content/short/2020.05.19.20105999v1?rss=1 doi: 10.1101/2020.05.19.20105999 id: cord-259246-azt5sr9w author: Peng, Qi title: Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir date: 2020-10-19 words: 3216.0 sentences: 158.0 pages: flesch: 50.0 cache: ./cache/cord-259246-azt5sr9w.txt txt: ./txt/cord-259246-azt5sr9w.txt summary: This structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase, and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues which may explain its capacity for mimicking both adenine and guanine nucleotides. Recently, we and other groups have determined the structures of SARS-CoV-2 core polymerase complex in both apo and RNA-bound states 26-30 , providing important information for structure-based antiviral drug design. Similar observations were also reported recently that SARS-CoV-2 polymerase is more tolerant for mismatches between template and product residues than other viral RdRps 5 , which further highlights the requirement for the proofreading nuclease nsp14 to maintain the integrity of viral genome. Interestingly, Favipiravir could be incorporated into the RNA product with similar efficiencies to those of ATP or GTP substrates guided by U or C template residues, respectively (Fig. 1c) . abstract: The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has developed into an unprecedented global pandemic. Nucleoside analogues, such as Remdesivir and Favipiravir, can serve as the first-line broad-spectrum antiviral drugs against the newly emerging viral diseases. Recent clinical trials of these two drugs for SARS-CoV-2 treatment revealed antiviral efficacies as well as side effects with different extents1–4. As a pyrazine derivative, Favipiravir could be incorporated into the viral RNA products by mimicking both adenine and guanine nucleotides, which may further lead to mutations in progeny RNA copies due to the non-conserved base-pairing capacity5. Here, we determined the cryo-EM structure of Favipiravir bound to the replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state. This structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase, and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues which may explain its capacity for mimicking both adenine and guanine nucleotides. These findings shed lights on the mechanism of coronavirus polymerase catalysis and provide a rational basis for developing antiviral drugs to combat the SARS-CoV-2 pandemic. url: https://doi.org/10.1101/2020.10.19.345470 doi: 10.1101/2020.10.19.345470 id: cord-280994-w8dtfjel author: Peng, Qi title: Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus date: 2020-04-23 words: 2105.0 sentences: 135.0 pages: flesch: 55.0 cache: ./cache/cord-280994-w8dtfjel.txt txt: ./txt/cord-280994-w8dtfjel.txt summary: Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. Simultaneous 193 replacement of the nsp7 and nsp8 cofactors further enhanced the efficiency for RNA synthesis 194 to ~2.2 times of that for the SARS-CoV-2 homologous complex ( Figure 4B ). After 3 rounds of extensive 2D classification, ~924,000 particles 437 were selected for 3D classification with the density map of SARS-CoV nsp12-nsp7-nsp8 438 complex (EMDB-0520) as the reference which was low-pass filtered to 60 Å resolution. One severe acute respiratory syndrome 631 coronavirus protein complex integrates processive RNA polymerase and exonuclease activities abstract: The ongoing global pandemic of coronavirus disease 2019 (COVID-19) has caused huge number of human deaths. Currently, there are no specific drugs or vaccines available for this virus. The viral polymerase is a promising antiviral target. However, the structure of COVID-19 virus polymerase is yet unknown. Here, we describe the near-atomic resolution structure of its core polymerase complex, consisting of nsp12 catalytic subunit and nsp7-nsp8 cofactors. This structure highly resembles the counterpart of SARS-CoV with conserved motifs for all viral RNA-dependent RNA polymerases, and suggests the mechanism for activation by cofactors. Biochemical studies revealed reduced activity of the core polymerase complex and lower thermostability of individual subunits of COVID-19 virus as compared to that of SARS-CoV. These findings provide important insights into RNA synthesis by coronavirus polymerase and indicate a well adaptation of COVID-19 virus towards humans with relatively lower body temperatures than the natural bat hosts. url: https://doi.org/10.1101/2020.04.23.057265 doi: 10.1101/2020.04.23.057265 id: cord-351482-hzh5tyoo author: Peng, Xinxia title: Integrative Deep Sequencing of the Mouse Lung Transcriptome Reveals Differential Expression of Diverse Classes of Small RNAs in Response to Respiratory Virus Infection date: 2011-11-15 words: 7697.0 sentences: 348.0 pages: flesch: 49.0 cache: ./cache/cord-351482-hzh5tyoo.txt txt: ./txt/cord-351482-hzh5tyoo.txt summary: The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16). abstract: We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22086488/ doi: 10.1128/mbio.00198-11 id: cord-335231-617e5dcy author: Pettersson, Lisa title: Hantavirus RNA in Saliva from Patients with Hemorrhagic Fever with Renal Syndrome date: 2008-03-17 words: 3332.0 sentences: 178.0 pages: flesch: 54.0 cache: ./cache/cord-335231-617e5dcy.txt txt: ./txt/cord-335231-617e5dcy.txt summary: During an outbreak in northern Sweden of nephropathia epidemica (NE), a milder form of hemorrhagic fever with renal syndrome, we collected saliva and plasma from 14 hospitalized NE patients with verifi ed Puumala virus (PUUV) infection. During an outbreak in northern Sweden of nephropathia epidemica (NE), a milder form of hemorrhagic fever with renal syndrome, we collected saliva and plasma from 14 hospitalized NE patients with verifi ed Puumala virus (PUUV) infection. For this reason, we collected saliva from patients during an NE outbreak in northern Sweden and analyzed the samples for the presence and levels of PUUV RNA by using a real-time reverse transcription-PCR (RT-PCR) assay. Furthermore, we detected no inhibition of real-time RT-PCR in saliva or plasma when we analyzed our patient samples by using an internal positive control (data not shown). abstract: Hantaviruses cause 2 zoonotic diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome. Infection is usually initiated after inhalation of virus-contaminated rodent excreta. In addition to the zoonotic infection route, growing evidence suggests person-to-person transmission of Andes virus. For this reason, we studied whether saliva from HFRS patients contained hantavirus. During an outbreak in northern Sweden of nephropathia epidemica (NE), a milder form of hemorrhagic fever with renal syndrome, we collected saliva and plasma from 14 hospitalized NE patients with verified Puumala virus (PUUV) infection. PUUV RNA was detected in saliva from 10 patients (range 1,530–121,323 PUUV RNA copies/mL) by quantitative reverse transcription–PCR. The PUUV S-segment sequences from saliva and plasma of the same patients were identical. Our data show that hantavirus RNA could be detected in human saliva several days after onset of disease symptoms and raise the question whether interhuman transmission of hantavirus may occur through saliva. url: https://doi.org/10.3201/eid1403.071242 doi: 10.3201/eid1403.071242 id: cord-349684-2tioh80m author: Pezzotti, Giuseppe title: Rapid Inactivation of SARS-CoV-2 by Silicon Nitride, Copper, and Aluminum Nitride date: 2020-06-20 words: 5388.0 sentences: 338.0 pages: flesch: 51.0 cache: ./cache/cord-349684-2tioh80m.txt txt: ./txt/cord-349684-2tioh80m.txt summary: The present study compared the effects of exposing SARS-CoV-2 to aqueous suspensions of Si3N4 and aluminum nitride (AlN) particles and two controls, (i.e., a suspension of copper (Cu) particles (positive control) and a sham treatment (negative control)). In (c) and (d), results of RT-PCR tests for supernatants after 10 min exposure of virus suspension to Cu, AlN, and Si3N4 powders for viral N gene "set 1" and "set 2" primers are shown, respectively. The present work is the first to show that compounds capable of endogenous nitrogen-release, such as Si3N4 and AlN, can inactivate the SARS-CoV-2 virus at least as effectively as Cu. These results suggest that multiple antiviral mechanisms may be operative, such as RNA fragmentation, and in the case of Cu, direct metal ion toxicity; but while Cu and AlN supernatants demonstrated strong and partial cellular lysis, respectively, Si3N4 provoked no metabolic alterations. abstract: Introduction Viral disease spread by contaminated commonly touched surfaces is a global concern. Silicon nitride, an industrial ceramic that is also used as an implant in spine surgery, has known antibacterial activity. The mechanism of antibacterial action relates to the hydrolytic release of surface disinfectants. It is hypothesized that silicon nitride can also inactivate the coronavirus SARS-CoV-2. Methods SARS-CoV-2 virions were exposed to 15 wt.% aqueous suspensions of silicon nitride, aluminum nitride, and copper particles. The virus was titrated by the TCD50 method using VeroE6/TMPRSS2 cells, while viral RNA was evaluated by real-time RT-PCR. Immunostaining and Raman spectroscopy were used as additional probes to investigate the cellular responses to virions exposed to the respective materials. Results All three tested materials showed >99% viral inactivation at one and ten minutes of exposure. Degradation of viral RNA was also observed with all materials. Immunofluorescence testing showed that silicon nitride-treated virus failed to infect VeroE6/TMPRSS2 cells without damaging them. In contrast, the copper-treated virus suspension severely damaged the cells due to copper ion toxicity. Raman spectroscopy indicated differential biochemical cellular changes due to infection and metal toxicity for two of the three materials tested. Conclusions Silicon nitride successfully inactivated the SARS-CoV-2 in this study. The mechanism of action was the hydrolysis-mediated surface release of nitrogen-containing disinfectants. Both aluminum nitride and copper were also effective in the inactivation of the virus. However, while the former compound affected the cells, the latter compound had a cytopathic effect. Further studies are needed to validate these findings and investigate whether silicon nitride can be incorporated into personal protective equipment and commonly touched surfaces, as a strategy to discourage viral persistence and disease spread. url: https://doi.org/10.1101/2020.06.19.159970 doi: 10.1101/2020.06.19.159970 id: cord-314254-9ye8tfvz author: Pfaender, Stephanie title: Natural reservoirs for homologs of hepatitis C virus date: 2014-03-26 words: 6841.0 sentences: 322.0 pages: flesch: 47.0 cache: ./cache/cord-314254-9ye8tfvz.txt txt: ./txt/cord-314254-9ye8tfvz.txt summary: To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaciand pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Non-primate hepaciviruses (NPHV) were initially discovered in domestic dogs and subsequently in horses 12, 13 and other diverse and widespread HCV-like viruses have been reported in wild populations of rodents and bats. Furthermore, liver function analyses revealed no indication for hepatic inflammation as c-glutamyl transferase and glutamate dehydrogenase values were within reference range, with the exception of a mildly elevated c-glutamyl transferase New HCV-like viruses in different mammalian hosts Pfaender et al 4 level in one horse. abstract: Hepatitis C virus is considered a major public health problem, infecting 2%–3% of the human population. Hepatitis C virus infection causes acute and chronic liver disease, including chronic hepatitis, cirrhosis and hepatocellular carcinoma. In fact, hepatitis C virus infection is the most frequent indication for liver transplantation and a vaccine is not available. Hepatitis C virus displays a narrow host species tropism, naturally infecting only humans, although chimpanzees are also susceptible to experimental infection. To date, there is no evidence for an animal reservoir of viruses closely related to hepatitis C virus which may have crossed the species barrier to cause disease in humans and resulted in the current pandemic. In fact, due to this restricted host range, a robust immunocompetent small animal model is still lacking, hampering mechanistic analysis of virus pathogenesis, immune control and prophylactic vaccine development. Recently, several studies discovered new viruses related to hepatitis C virus, belonging to the hepaci- and pegivirus genera, in small wild mammals (rodents and bats) and domesticated animals which live in close contact with humans (dogs and horses). Genetic and biological characterization of these newly discovered hepatitis C virus-like viruses infecting different mammals will contribute to our understanding of the origins of hepatitis C virus in humans and enhance our ability to study pathogenesis and immune responses using tractable animal models. In this review article, we start with an introduction on the genetic diversity of hepatitis C virus and then focus on the newly discovered viruses closely related to hepatitis C virus. Finally, we discuss possible theories about the origin of this important viral human pathogen. url: https://doi.org/10.1038/emi.2014.19 doi: 10.1038/emi.2014.19 id: cord-291965-9r9ll83m author: Pfefferle, Susanne title: Distant Relatives of Severe Acute Respiratory Syndrome Coronavirus and Close Relatives of Human Coronavirus 229E in Bats, Ghana date: 2009-09-17 words: 4306.0 sentences: 245.0 pages: flesch: 56.0 cache: ./cache/cord-291965-9r9ll83m.txt txt: ./txt/cord-291965-9r9ll83m.txt summary: Studies conducted in China in the aftermath of the SARS epidemic have identified CoVs in bats (Chiroptera) and implicated this speciose mammalian order as the most likely reservoir of all known coronaviruses (3) (4) (5) (6) (7) . Bayesian phylogenetic inference with different substitution models and parallel analysis using Metropolis coupling now placed the virus reliably next to a common ancestor with the 2b group of CoV (SARS-like viruses, Figure 3 ). These fragments could be combined into contig*MRCA, most recent common ancestor; CI, confidence interval; HPD, high population density; SARS, severe acute respiratory syndrome; hCoV, human coronavirus; GTR + + I, general time reversible gamma-shaped rate distribution across sites and an invariant site assumption. One of our Hipposideros CoVs was in a basal phylogenetic relationship with the SARS-like clade (group 2b); their most recent common ancestors date back to ≈400 bc. abstract: We tested 12 bat species in Ghana for coronavirus (CoV) RNA. The virus prevalence in insectivorous bats (n = 123) was 9.76%. CoV was not detected in 212 fecal samples from Eidolon helvum fruit bats. Leaf-nosed bats pertaining to Hipposideros ruber by morphology had group 1 and group 2 CoVs. Virus concentrations were <45,000 copies/100 mg of bat feces. The diversified group 1 CoV shared a common ancestor with the human common cold virus hCoV-229E but not with hCoV-NL63, disputing hypotheses of common human descent. The most recent common ancestor of hCoV-229E and GhanaBt-CoVGrp1 existed in ≈1686–1800 ad. The GhanaBt-CoVGrp2 shared an old ancestor (≈2,400 years) with the severe acute respiratory syndrome–like group of CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/19788804/ doi: 10.3201/eid1509.090224 id: cord-304058-i8cywew0 author: Pfefferle, Susanne title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo date: 2009-08-24 words: 9548.0 sentences: 514.0 pages: flesch: 53.0 cache: ./cache/cord-304058-i8cywew0.txt txt: ./txt/cord-304058-i8cywew0.txt summary: title: Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. In the context of viral host switching, it is interesting that several SARS-CoV proteins encoded on subgenomic (sg) RNAs seem to be dispensable for virus replication in cultured cells of primate or rodent origin, as well as in rodent models [17] [18] [19] . Both BACs were sequenced, confirming presence of all marker mutations and absence of any further mutations (refer to Influence on apoptosis and type I interferon induction by overexpression of ORF 7a, ORF 7b, and ORF 7b with the Frankfurt-1-specific deletion Interferon beta promoter-specific reporter gene expression (y-axis), shown as the factor of induction as compared to the mock-transfected, non-superinfected control (see below). abstract: During the outbreak of SARS in 2002/3, a prototype virus was isolated from a patient in Frankfurt/Germany (strain Frankfurt-1). As opposed to all other SARS-Coronavirus strains, Frankfurt-1 has a 45-nucleotide deletion in the transmembrane domain of its ORF 7b protein. When over-expressed in HEK 293 cells, the full-length protein but not the variant with the deletion caused interferon beta induction and cleavage of procaspase 3. To study the role of ORF 7b in the context of virus replication, we cloned a full genome cDNA copy of Frankfurt-1 in a bacterial artificial chromosome downstream of a T7 RNA polymerase promoter. Transfection of capped RNA transcribed from this construct yielded infectious virus that was indistinguishable from the original virus isolate. The presumed Frankfurt-1 ancestor with an intact ORF 7b was reconstructed. In CaCo-2 and HUH7 cells, but not in Vero cells, the variant carrying the ORF 7b deletion had a replicative advantage against the parental virus (4- and 6-fold increase of virus RNA in supernatant, respectively). This effect was neither associated with changes in the induction or secretion of type I interferon, nor with altered induction of apoptosis in cell culture. However, pretreatment of cells with interferon beta caused the deleted virus to replicate to higher titers than the parental strain (3.4-fold in Vero cells, 7.9-fold in CaCo-2 cells). In Syrian Golden Hamsters inoculated intranasally with 10e4 plaque forming units of either virus, mean titers of infectious virus and viral RNA in the lungs after 24 h were increased 23- and 94.8-fold, respectively, with the deleted virus. This difference could explain earlier observations of enhanced virulence of Frankfurt-1 in Hamsters as compared to other SARS-Coronavirus reference strains and identifies the SARS-CoV 7b protein as an attenuating factor with the SARS-Coronavirus genome. Because attenuation was focused on the early phase of infection in-vivo, ORF 7b might have contributed to the delayed accumulation of virus in patients that was suggested to have limited the spread of the SARS epidemic. url: https://www.ncbi.nlm.nih.gov/pubmed/19698190/ doi: 10.1186/1743-422x-6-131 id: cord-000866-dr2uow4m author: Picard-Jean, Frédéric title: The Immunosuppressive Agent Mizoribine Monophosphate Is an Inhibitor of the Human RNA Capping Enzyme date: 2013-01-17 words: 7046.0 sentences: 368.0 pages: flesch: 50.0 cache: ./cache/cord-000866-dr2uow4m.txt txt: ./txt/cord-000866-dr2uow4m.txt summary: In the present study, we investigated the ability of MZP to directly inhibit the human RNA capping enzyme (HCE), a protein harboring both RNA 5′-triphosphatase and RNA guanylyltransferase activities. An RNA guanylyltransferase (GTase) then catalyzes a two-step reaction in which it initially utilizes GTP as a substrate to form a covalent enzyme-GMP (EpG) intermediate, with the concomitant release of pyrophosphate (PPi). Since ribavirin triphosphate and MZP share functional similarities, we investigated the attractive possibility that MZP could also inhibit the GTase activity of the human RNA capping enzyme (HCE). The enzyme-GMP complex formation assays were carried out for 3 min at 37uC in a buffer containing 1 mM [a-32 P]GTP, 4 mM HCE, 50 mM Tris-HCl, pH 7.5, 5 mM MgCl 2 , 500 mM DTT, 0.5 ng/ml pyrophosphatase (Roche), and various concentration of MZP (as indicated). abstract: Mizoribine monophosphate (MZP) is a specific inhibitor of the cellular inosine-5′-monophosphate dehydrogenase (IMPDH), the enzyme catalyzing the rate-limiting step of de novo guanine nucleotide biosynthesis. MZP is a highly potent antagonistic inhibitor of IMPDH that blocks the proliferation of T and B lymphocytes that use the de novo pathway of guanine nucleotide synthesis almost exclusively. In the present study, we investigated the ability of MZP to directly inhibit the human RNA capping enzyme (HCE), a protein harboring both RNA 5′-triphosphatase and RNA guanylyltransferase activities. HCE is involved in the synthesis of the cap structure found at the 5′ end of eukaryotic mRNAs, which is critical for the splicing of the cap-proximal intron, the transport of mRNAs from the nucleus to the cytoplasm, and for both the stability and translation of mRNAs. Our biochemical studies provide the first insight that MZP can inhibit the formation of the RNA cap structure catalyzed by HCE. In the presence of MZP, the RNA 5′-triphosphatase activity appears to be relatively unaffected while the RNA guanylyltransferase activity is inhibited, indicating that the RNA guanylyltransferase activity is the main target of MZP inhibition. Kinetic studies reveal that MZP is a non-competitive inhibitor that likely targets an allosteric site on HCE. Mizoribine also impairs mRNA capping in living cells, which could account for the global mechanism of action of this therapeutic agent. Together, our study clearly demonstrates that mizoribine monophosphate inhibits the human RNA guanylyltransferase in vitro and impair mRNA capping in cellulo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547949/ doi: 10.1371/journal.pone.0054621 id: cord-332484-qy8vj6uu author: Pierini, Roberto title: Modulation of membrane traffic between endoplasmic reticulum, ERGIC and Golgi to generate compartments for the replication of bacteria and viruses date: 2009-04-01 words: 4247.0 sentences: 239.0 pages: flesch: 42.0 cache: ./cache/cord-332484-qy8vj6uu.txt txt: ./txt/cord-332484-qy8vj6uu.txt summary: This review describes examples where both intracellular bacteria (Salmonella, Chlamydia and Legionella) and viruses (picornaviruses and hepatitis C) recruit membrane vesicles to sites of replication by modulating proteins that control the secretory pathway. Intracellular bacteria remain within membrane-bound vacuoles to avoid delivery to lysosomes and then recruit vesicles from the secretory pathway to provide nutrients necessary for microbial growth and cell division. Many viruses generate densely packed membrane vesicles to shield them from recognition by cellular defence pathways that recognise double-stranded RNA, and at the same time the membranes provide a platform to recruit viral and host proteins required for replication [3] [4] [5] . This review describes how recent work on intracellular bacteria such as Salmonella, Chlamydia and Leigionella draws parallels with studies on (+) strand RNA viruses where microbial proteins recruit membranes by modulating proteins that control the secretory pathway. abstract: Several bacteria and viruses remodel cellular membranes to form compartments specialised for replication. Bacteria replicate within inclusions which recruit membrane vesicles from the secretory pathway to provide nutrients for microbial growth and division. Viruses generate densely packed membrane vesicles called viroplasm which provide a platform to recruit host and viral proteins necessary for replication. This review describes examples where both intracellular bacteria (Salmonella, Chlamydia and Legionella) and viruses (picornaviruses and hepatitis C) recruit membrane vesicles to sites of replication by modulating proteins that control the secretory pathway. In many cases this involves modulation of Rab and Arf GTPases. url: https://doi.org/10.1016/j.semcdb.2009.03.015 doi: 10.1016/j.semcdb.2009.03.015 id: cord-265381-ppjohov8 author: Pillai-Nair, Neeta title: Cis-acting Regulatory Elements in the Potato Virus X 3′ Non-translated Region Differentially Affect Minus-strand and Plus-strand RNA Accumulation date: 2003-02-21 words: 10016.0 sentences: 521.0 pages: flesch: 57.0 cache: ./cache/cord-265381-ppjohov8.txt txt: ./txt/cord-265381-ppjohov8.txt summary: 6 -13 Cis-acting elements required for minus-strand RNA accumulation in vivo or RNA synthesis in vitro have been well studied for the plant plus-strand RNA viruses that contain tRNA-like structures in the 3 0 NTR 2 such as brome mosaic virus (BMV), 14 -16 cucumber mosaic virus (CMV), 17 tobacco mosaic virus (TMV) 18 and turnip yellow mosaic virus (TYMV), 19, 20 and for several other viruses such as alfalfa mosaic virus (AlMV), 21, 22 barley stripe mosaic virus (BSMV), 23 cymbidium ringspot virus (CymRSV), 24 red clover necrotic mosaic virus (RCNMV) 25 and turnip crinkle virus (TCV). The role of the 3 0 NTR cis-acting sequences and/ or structures in PVX RNA accumulation was studied by solution structure probing and by introducing wild-type (w.t.) and mutant transcripts into tobacco protoplasts for analysis of minus and plusstrand RNA accumulation by S 1 nuclease protection assays. abstract: The 72 nt 3′ non-translated region (NTR) of potato virus X (PVX) RNA is identical in all sequenced PVX strains and contains sequences that are conserved among all potexviruses. Computer folding of the 3′ NTR sequence predicted three stem-loop structures (SL1, SL2, and SL3 in the 3′ to 5′ direction), which generally were supported by solution structure analyses. The importance of these sequence and/or structural elements to PVX RNA accumulation was further analyzed by inoculation of Nicotiana tabacum (NT-1) protoplasts with PVX transcripts containing mutations in the 3′ NTR. Analyses of RNA accumulation by S(1) nuclease protection indicated that multiple sequence elements throughout the 3′ NTR were important for minus-strand RNA accumulation. Formation of SL3 was required for accumulation of minus-strand RNA, whereas SL1 and SL2 formation were less important. However, sequences within all of these predicted structures were required for minus-strand RNA accumulation, including a conserved hexanucleotide sequence element in the loop of SL3, and the CU nucleotide in a U-rich sequence within SL2. In contrast, 13 nucleotides that were predicted to reside in SL1 could be deleted without any significant reduction in minus or plus-strand RNA levels. Potential polyadenylation signals (near upstream elements; NUEs) in the 3′ NTR of PVX RNA were more important for plus-strand RNA accumulation than for minus-strand RNA accumulation. In addition, one of these NUEs overlapped with other sequence required for optimal minus-strand RNA levels. These data indicate that the PVX 3′ NTR contains multiple, overlapping elements that influence accumulation of both minus and plus-strand RNA. url: https://www.sciencedirect.com/science/article/pii/S0022283602013694 doi: 10.1016/s0022-2836(02)01369-4 id: cord-300023-2dg7njki author: Pillet, S. title: Contamination of healthcare workers' mobile phones by epidemic viruses() date: 2015-12-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Mobile phones (MPs) are potential reservoirs of nosocomial bacteria, but few data are available concerning viruses. We aimed to evaluate the presence of virus RNA from epidemic viruses including metapneumovirus, respiratory syncytial virus, influenza viruses, rotavirus (RV) and norovirus on the MPs used by healthcare workers (HCWs) and to relate it to hygiene measures. An anonymous behavioural questionnaire about MP use at hospital was administered to the HCWs of four adult and paediatric departments of a university hospital. After sampling personal (PMP) and/or professional MPs (digital enhanced cordless telephone, DECT), virus RNAs were extracted and amplified by one-step real-time reverse transcription–quantitative PCR. The molecular results were analysed in a masked manner in relation to the behavioural survey. Questionnaires from 114 HCWs (35 senior physicians, 30 residents, 32 nurses, 27 nurses' assistants) working either in adult (n = 58) or paediatric (n = 56) departments were analysed. Medical personnel used their PMP more frequently than paramedical HCWs (33/65 vs. 10/59, p <0.001). MPs were used during care more frequently in adult wards than in paediatric ones (46/58 vs. 27/56, p <0.001). Virus RNA was detected on 42/109 (38.5%) collected MPs, with RV found on 39, respiratory syncytial virus on three and metapneumovirus on one. The presence of virus RNA was significantly associated with MPs from the paediatric HCWs (p <0.001). MPs routinely used in hospital, even during care, can host virus RNA, especially RV. Promotion of frequent hand hygiene before and after MP use, along with frequent cleaning of MPs, should be encouraged. url: https://www.sciencedirect.com/science/article/pii/S1198743X15010344 doi: 10.1016/j.cmi.2015.12.008 id: cord-005865-7lohh5ty author: Pipper, Juergen title: Catching bird flu in a droplet date: 2007-09-23 words: 4167.0 sentences: 207.0 pages: flesch: 52.0 cache: ./cache/cord-005865-7lohh5ty.txt txt: ./txt/cord-005865-7lohh5ty.txt summary: Here we present a microfluidic platform that can detect the highly pathogenic avian influenza virus H5N1 in a throat swab sample by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. Here we present a microfluidic platform that can detect the highly pathogenic avian influenza virus H5N1 in a throat swab sample by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. Starting from a throat swab sample, we show how HPAI H5N1 can be detected by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. (h) After SPE, the immobilized viral RNA is magnetically pulled out of the raw sample solution, washed four times to remove residual contaminants, and desorbed into an RT-PCR solution positioned on top of a miniaturized real-time thermocycler (see also Supplementary Fig. 1 ). abstract: It is assumed that a timely mass administration of antiviral drugs, backed by quarantines and social distancing, could contain a nascent influenza epidemic at its source, provided that the first clusters of cases were localized within a short time. However, effective routine surveillance may be impossible in countries lacking basic public health resources. For a global containment strategy to be successful, low-cost, easy-to-use handheld units that permit decentralized testing would be vital. Here we present a microfluidic platform that can detect the highly pathogenic avian influenza virus H5N1 in a throat swab sample by using magnetic forces to manipulate a free droplet containing superparamagnetic particles. In a sequential process, the viral RNA is isolated, purified, preconcentrated by 50,000% and subjected to ultrafast real-time RT-PCR. Compared to commercially available tests, the bioassay is equally sensitive and is 440% faster and 2,000–5,000% cheaper. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nm1634) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095864/ doi: 10.1038/nm1634 id: cord-336447-hpnkou41 author: Pitlik, Silvio Daniel title: COVID-19 Compared to Other Pandemic Diseases date: 2020-07-31 words: 6148.0 sentences: 396.0 pages: flesch: 49.0 cache: ./cache/cord-336447-hpnkou41.txt txt: ./txt/cord-336447-hpnkou41.txt summary: Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. 7, 8 This paper reviews the microbiological, clinical, and epidemiological characteristics of the coronavirus disease 2019 (COVID-19) pandemic, as well as its socio-economic impact. In the early days of the pandemic great effort was invested into understanding the life cycle of SARS-CoV-2, 9 so as to provide a basis for discovery of an effective vaccine to prevent COVID-19 and/or a safe and efficacious drug to cure it, or at the least, to ameliorate its symptoms, shorten its duration, and/ or block its mechanism of transmission. 59 Unfortunately, to date, no human genetic markers predisposing to SARS-CoV-2 infection, nor the severity of COVID-19, have been found-although recent isolated exceptions to this statement can be found. abstract: In December 2019, the first cases of a new contagious disease were diagnosed in the city of Wuhan, the capital of Hubei province in China. Within a short period of time the outbreak developed exponentially into a pandemic that infected millions of people, with a global death toll of more than 500,000 during its first 6 months. Eventually, the novel disease was named coronavirus disease 2019 (COVID-19), and the new virus was identified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Similar to all known pandemics throughout history, COVID-19 has been accompanied by a large degree of fear, anxiety, uncertainty, and economic disaster worldwide. Despite multiple publications and increasing knowledge regarding the biological secrets of SARS-CoV-2, as of the writing of this paper, there is neither an approved vaccine nor medication to prevent infection or cure for this highly infectious disease. Past pandemics were caused by a wide range of microbes, primarily viruses, but also bacteria. Characteristically, a significant proportion of them originated in different animal species (zoonoses). Since an understanding of the microbial cause of these diseases was unveiled relatively late in human history, past pandemics were often attributed to strange causes including punishment from God, demonic activity, or volatile unspecified substances. Although a high case fatality ratio was common to all pandemic diseases, some striking clinical characteristics of each disease allowed contemporaneous people to clinically diagnose the infection despite null microbiological information. In comparison to past pandemics, SARS-CoV-2 has tricky and complex mechanisms that have facilitated its rapid and catastrophic spread worldwide. url: https://doi.org/10.5041/rmmj.10418 doi: 10.5041/rmmj.10418 id: cord-347221-g98q9cga author: Piyush, Ravikant title: Nucleic acid-based therapy for coronavirus disease 2019 date: 2020-09-19 words: 4217.0 sentences: 246.0 pages: flesch: 50.0 cache: ./cache/cord-347221-g98q9cga.txt txt: ./txt/cord-347221-g98q9cga.txt summary: This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. This phenomenon of producing an effective immunity is particularly important in their use against the development of nucleic acid based therapeutic drugs for the treatment of SARS-CoV-2. Nucleic acid-based therapies, especially, RNA therapies including RNAi (RNA interference), siRNAs (small interfering RNA) and RNA aptamers, Ribozymes and ASOs (antisense oligonucleotides) target and neutralize the crucial components of the virus-like specific mRNA molecules, viral proteins like E (envelope), M (membrane), or N (nucleocapsid), or SARS helicase, etc. The nucleic acid-based vaccination technologies involve the use of RNA (mRNA) [34] or plasmid DNA, which encodes for antigen. abstract: The coronavirus disease 2019 (COVID-19), the pandemic that originated in China has already spread into more than 190 countries, resulting in huge loss of human life and many more are at the stake of losing it; if not intervened with the best therapeutics to contain the disease. For that aspect, various scientific groups are continuously involved in the development of an effective line of treatment to control the novel coronavirus from spreading rapidly. Worldwide scientists are evaluating various biomolecules and synthetic inhibitors against COVID-19; where the nucleic acid-based molecules may be considered as potential drug candidates. These molecules have been proved potentially effective against SARS-CoV, which shares high sequence similarity with SARS-CoV-2. Recent advancements in nucleic acid-based therapeutics are helpful in targeted drug delivery, safely and effectively. The use of nucleic acid-based molecules also known to regulate the level of gene expression inside the target cells. This review mainly focuses on various nucleic acid-based biologically active molecules and their therapeutic potentials in developing vaccines for SARS-CoV-2. url: https://doi.org/10.1016/j.heliyon.2020.e05007 doi: 10.1016/j.heliyon.2020.e05007 id: cord-004851-h9ppa064 author: Plagemann, P. G. W. title: Hepatitis C virus date: 1991 words: 6835.0 sentences: 320.0 pages: flesch: 48.0 cache: ./cache/cord-004851-h9ppa064.txt txt: ./txt/cord-004851-h9ppa064.txt summary: The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pestiand flaviviruses, the following genome organization has been predicted. A recent study of stored blood samples from prospective studies of 15 U.S.A. patients with transfusion-associated chronic hepatitis documented by liver biopsies indicated that the time course of changes in plasma ALT activity and of the formation of anti-HepCV antibodies can vary considerably between patients [4] . The putative nucleocapsid protein sequence derived from PCR products of RNA extracted from healthy Japanese carrier plasma exhibited a 97.4% amino acid identity with the sequence determined for the original chimpanzee HepCV isolate (HepCV-1) but only a 90.5 % identity at the nucleotide level [45] [46] [47] . abstract: HepCV is the major cause of NANB PT hepatitis and is also implicated as the cause in a large proportion of sporadic cases of NANBH. Chronic infection with HepCV has also been linked to the development of hepatocellular carcinoma. Chimpanzees and marmosets are the only animals found to be experimentally infectable and the virus has not been propagated in any cell culture system. HepCV is an enveloped virus with a diameter of 30–60 nm and a 10-kb positive-stranded RNA genome. Its genome organization resembles that of the flaviviruses and pestiviruses. A 5′-untranslated segment of 341 nucleotides precedes a continuous ORF of 9030/9033 nucleotides which is followed by a 54 nucleotides long 3′-non-coding segment. Further work is required to resolve the question of whether the genomic RNA possesses a 3′-poly(U) or poly(A) tail. The genome also carries an internal poly(A) segment towards the 5′-end of its ORF. Genomic RNA is probably translated into a single polyprotein of 3010/3011 amino acids which is processed into functional proteins. The viral proteins have not been identified, but on the basis of the predicted amino acid sequences, hydrophobicity plots, location of potential glycosylation sites and similarities of these properties to those of pesti- and flaviviruses, the following genome organization has been predicted. The predicted viral structural proteins, a nucleocapsid protein and two envelope glycoproteins are located at the aminoterminal end of the polyprotein. They are followed by a highly hydrophobic protein and proteins that exhibit proteinase, helicase and replicase domains and thus are probably involved in RNA replication and protein processing. The replicase domain is located close to the carboxy terminus of the polyprotein. Although the overall nucleotide and amino acid homologies between HepCV and pestiviruses are low, a number of similarities exist that point to a closer ancestral relationship to the latter than the flaviviruses. First, the 5′-untranslated segment of the HepCV genome resembles that of the pestivirus genomes in size and presence of several short ORFs and it contains several segments with high nucleotide homology. Second, the two putative envelope glycoproteins of HepCV resemble two of the three putative envelope glycoproteins of the pestiviruses. Because its genome organization and predicted virion structure closely resemble those of the flaviviruses and pestiviruses, HepCV has been proposed to be placed in the familyFlaviviridae. It has been suggested to be classified as a new third genus in this family because it is only remotely related to the pestiviruses and flaviviruses in nucleotide sequence of its genome and the amino acid sequences of the predicted viral proteins. On the basis of genomic sequence information, an immunoprobe has been devised for screening blood supplies and donors for anti-HepCV antibodies to a non-structural protein of HepCV. The immuno-assay exhibits a high efficiency in detecting infected donors, though one caveat is that antibodies to the test antigen develop in infected individuals only between 2 and 8 months post infection. On the other hand, viral RNA can be detected in plasma by reverse transcription and amplification of the cDNA by PCR within a few days post infection. Thus the latter technique may become more important in the detection of HepCV in blood and tissues once the technique becomes more widely established as a diagnostic tool. The untranslated 5′-segment has been found to be highly conserved in the genomes of different HepCV isolates from various parts of the world. The replicase domain is also highly conserved, but considerable amino acid and nucleotide differences exist in other segments of the long ORFs of various HepCV isolates. Divergence among different isolates is particularly great (up to 30%) in the segment encoding the two putative envelope glycoproteins and the upstream hydrophobic protein. The variability in envelope glycoproteins needs to be considered in the development of immuno-probes and of vaccines for HepCV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087296/ doi: 10.1007/bf01310473 id: cord-253282-zwl0safn author: Plant, Ewan P. title: Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production date: 2013-01-18 words: 5007.0 sentences: 266.0 pages: flesch: 55.0 cache: ./cache/cord-253282-zwl0safn.txt txt: ./txt/cord-253282-zwl0safn.txt summary: In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. Here, analyses using synonymous protein coding mutations demonstrate that the region of the genome that harbors the frameshift signal affects the regulation of genomic and subgenomic RNA production without altering protein sequence. Here we describe deletion and mutagenesis experiments with a dual luciferase reporter to show that the effect the sequence between stems 1 and 2 has on frameshifting efficiency is due to structural changes those mutations cause in the pseudoknot. Similar to previously described viruses containing mutations in the slippery site of the frameshift signal [7] , here we show that mutations to the SARS-CoV frameshift stimulating mRNA pseudoknot can also affect the production of viral genomic RNA. abstract: In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. It was not clear if these differences were due to changes in genomic sequence, the protein sequence or the frequency of frameshifting. Here, viruses with synonymous codon changes are shown to produce different ratios of genomic and subgenomic RNA. These findings demonstrate that the protein sequence is not the primary cause of altered genomic and subgenomic RNA production. The synonymous codon changes affect both the structure of the frameshift signal and frameshifting efficiency. Small differences in frameshifting efficiency result in dramatic differences in genomic RNA production and TCID(50) suggesting that the frameshifting frequency must stay above a certain threshold for optimal virus production. The data suggest that either the RNA sequence or the ratio of viral proteins resulting from different levels of frameshifting affects viral replication. url: https://doi.org/10.3390/v5010279 doi: 10.3390/v5010279 id: cord-286842-04cuk2cn author: Plyusnina, Angelina title: Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture date: 2005-02-22 words: 2147.0 sentences: 115.0 pages: flesch: 51.0 cache: ./cache/cord-286842-04cuk2cn.txt txt: ./txt/cord-286842-04cuk2cn.txt summary: title: Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture Tula hantavirus carrying recombinant S RNA segment (recTULV) grew in a cell culture to the same titers as the original cell adapted variant but presented no real match to the parental virus. Using the two specific RT-PCR conditions, the presence of V-type and REC-type S RNA was monitored on ten sequential passages of the mixture of TULV02 and RecTULV5 variants (Fig. 2 ). Although relatively short, the observed survival time of the recTULV in the presence of the original variant TUL02 seems to be sufficient for transmission of a recombinant virus, in a hypothetical in vivo situation, from one rodent to another. The data presented in this paper show that the recTULV presents no real match to the original cell adapted variant and that the lower fitness of the recombinant virus can not be increased by pre-passaging in cell culture. abstract: Tula hantavirus carrying recombinant S RNA segment (recTULV) grew in a cell culture to the same titers as the original cell adapted variant but presented no real match to the parental virus. Our data showed that the lower competitiveness of recTULV could not be increased by pre-passaging in the cell culture. Nevertheless, the recombinant virus was able to survive in the presence of the parental virus during five consecutive passages. The observed survival time seems to be sufficient for transmission of newly formed recombinant hantaviruses in nature. url: https://www.ncbi.nlm.nih.gov/pubmed/15725355/ doi: 10.1186/1743-422x-2-12 id: cord-007463-8g0zklzy author: Pocock, D.H. title: Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis date: 2002-11-13 words: 1932.0 sentences: 91.0 pages: flesch: 49.0 cache: ./cache/cord-007463-8g0zklzy.txt txt: ./txt/cord-007463-8g0zklzy.txt summary: The 3′ terminal labelling method for the analysis of genome profiles used in this study required only 1 ng of viral RNA, an increase of 1000-fold in sensitivity over ethidium bromide staining for detecting all rotavirus genome segments. To investigate the latter, mixtures containing known amounts of ds-RNA from two rotavirus isolates with disparate genome profiles (UK strain and a C7 type) were used to simulate the type of samples that might be recovered from calves concurrently infected with these two viruses. After 3'' terminal labelling the RNA segments were analysed by electrophoresis (Fig. 3) profiles, and meant that in a faecal sample containing two rotaviruses if one virus was present at a concentration 10-fold less than the other, i.e. 1 log10 dilution, it would not be detected. Rotaviruses isolated from 43 sub-clinically infected calves were characterised by genome profile analysis. abstract: Rotaviruses isolated from 43 sub-clinically infected calves from a single farm were analysed by genome profile analysis. The isolates showed genomic variation and eight different profiles were observed, including one which was atypical for Group A rotaviruses. The 3′ terminal labelling method for the analysis of genome profiles used in this study required only 1 ng of viral RNA, an increase of 1000-fold in sensitivity over ethidium bromide staining for detecting all rotavirus genome segments. However, dual infections involving two rotaviruses with distinct profiles could not be detected if the concentrations of the viruses differed by > 10-fold. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7117224/ doi: 10.1016/0378-1135(87)90095-2 id: cord-342681-pqzcy9wu author: Pongpirul, Wannarat A. title: Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand date: 2020-07-17 words: 1740.0 sentences: 117.0 pages: flesch: 41.0 cache: ./cache/cord-342681-pqzcy9wu.txt txt: ./txt/cord-342681-pqzcy9wu.txt summary: Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. During the study period, Thailand''s discharge criteria for hospitalized COV-ID-19 patients required resolution of clinical signs and symptoms and 2 respiratory specimens without detectable SARS-CoV-2 RNA collected >24 hours apart. Clinical resolution occurred a median of 12 (9-13.5 ) days after illness onset, and these patients had detectable SARS-CoV-2 RNA in upper respiratory tract specimens for a median of 14 (9-26) days after illness onset (Table 2) . However, patients became afebrile 6 days after illness onset, with a median of 9 (3-19.75 ) additional days of detectable SARS-CoV-2 RNA in respiratory specimens after resolution of fever ( Table 2 ). Other studies have described asymptomatic patients with upper respiratory specimens positive for SARS-CoV-2 (9), and evidence suggests such cases pose a risk for transmission (10) (11) (12) . abstract: Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. We identified viral co-infections and an asymptomatic person with detectable virus RNA in serial tests. We describe implications for surveillance. url: https://www.ncbi.nlm.nih.gov/pubmed/32267826/ doi: 10.3201/eid2607.200598 id: cord-315616-pvt0amth author: Poole, Anthony title: Methyl-RNA: an evolutionary bridge between RNA and DNA? date: 2004-06-17 words: 5623.0 sentences: 281.0 pages: flesch: 54.0 cache: ./cache/cord-315616-pvt0amth.txt txt: ./txt/cord-315616-pvt0amth.txt summary: Ribonucleotide reductase itself, which synthesises deoxyribonucleotides from ribonucleotides, requires complex protein radical chemistry, and RNA world genomes may have reached their limits of coding capacity well before such complex enzymes had evolved. Even with this gap in the RNA world model, current knowledge suggests the RNA organism that evolved protein synthesis was likely to have been dangerously close to the Eigen limit for RNA, and probably emIn the ¢rst step, a radical is generated at some distance from the active site. By virtue of its non-speci¢c dsRNA methylating activity, this enzyme is hypothesised to have been recruited into methylation of genomic RNA, improving the stability of the genetic material prior to the origin of DNA. The predicted stabilising effect of 2P-O-methylation on genomic RNA argues that the coding capacity of the genome would have increased suf¢ciently for genuinely catalytic proteins such as RNA polymerase, and later ribonucleotide reductase, to arise, paving the way to the DNA world (Figure 4) . abstract: Given the apparent limitation of double-stranded RNA (dsRNA) genomes to about 30 kb, together with the complexity of DNA synthesis, it appears difficult for a dsRNA genome to encode all the information required before the transition from an RNA to a DNA genome. Ribonucleotide reductase itself, which synthesises deoxyribonucleotides from ribonucleotides, requires complex protein radical chemistry, and RNA world genomes may have reached their limits of coding capacity well before such complex enzymes had evolved. The transition from RNA to DNA thus appears to require intermediate steps, and we suggest that the naturally occurring 2′-O-methylated RNA, with chemical properties intermediate between RNA and DNA, is a suitable candidate. url: https://www.ncbi.nlm.nih.gov/pubmed/11137821/ doi: 10.1016/s1074-5521(00)00042-9 id: cord-297078-pxggjaby author: Poole, Anthony M. title: Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome? date: 2005-03-16 words: 8279.0 sentences: 391.0 pages: flesch: 50.0 cache: ./cache/cord-297078-pxggjaby.txt txt: ./txt/cord-297078-pxggjaby.txt summary: Leipe, Aravind, and Koonin (1999) suggest that LUCA possessed a hybrid DNA/RNA genome, thereby providing an explanation for the universal distribution of certain components of the DNA replication/repair apparatus. We argue from structural and functional data that the second of these, RNA polymerase-dependent proofreading and repair, is likely to have been a feature of LUCA rather than a recent innovation as part of selection for improved messenger RNA (mRNA) quality control, though this is no doubt the current function of this phenomenon. In this scenario, cleavage-stimulatory factors evolved twice independently (GreA/GreB in bacteria and transcription factor S/TFIIS in archaea/eukaryotes) with an initial function in RNA genome repair. This implies that the LUCA possessed an RNA genome, and in this scenario, bacterial RNA polymerase-associated cleavage-stimulatory factors (GreA/GreB) and their archaeal/eukaryotic equivalents (TFS/TFIIS) were originally involved in proofreading and repair of the genome, as indicated by [Gen] . abstract: RNA repair has now been demonstrated to be a genuine biological process and appears to be present in all three domains of life. In this article, we consider what this might mean for the transition from an early RNA-dominated world to modern cells possessing genetically encoded proteins and DNA. There are significant gaps in our understanding of how the modern protein-DNA world could have evolved from a simpler system, and it is currently uncertain whether DNA genomes evolved once or twice. Against this backdrop, the discovery of RNA repair in modern cells is timely food for thought and brings us conceptually one step closer to understanding how RNA genomes were replaced by DNA genomes. We have examined the available literature on multisubunit RNA polymerase structure and function and conclude that a strong case can be made that the Last Universal Common Ancestor (LUCA) possessed a repair-competent RNA polymerase, which would have been capable of acting on an RNA genome. However, while this lends credibility to the proposal that the LUCA had an RNA genome, the alternative, that LUCA had a DNA genome, cannot be completely ruled out. url: https://www.ncbi.nlm.nih.gov/pubmed/15774424/ doi: 10.1093/molbev/msi132 id: cord-300685-bcjnujlj author: Poon, Leo L M title: Rapid Diagnosis of a Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) date: 2003-06-01 words: 2425.0 sentences: 115.0 pages: flesch: 54.0 cache: ./cache/cord-300685-bcjnujlj.txt txt: ./txt/cord-300685-bcjnujlj.txt summary: The detection of live virus (4 ) and the detection of high copy numbers of viral sequence from NPA samples in the current study clearly support that the concept that cough and sneeze droplets from SARS patients are a major route of spread of this infectious agent. Interestingly, two of four available stool samples from the SARS patients in this study were positive in the assay (data not shown). RNA samples from this study were subjected to nested reverse transcription-PCR (4 ), and no evidence of metapneumovirus infection was detected in any of the patients in this study (data not shown), suggesting that the novel coronavirus is the key player in the pathogenesis of SARS. The PCR products from all 23 positive cases in this study had the same melting point, strongly suggesting that there was no viral sequence variation in the target region of samples collected at the two Hong Kong hospitals during the 1-month period of patient accrual. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/12765993/ doi: 10.1373/49.6.953 id: cord-260695-qwepi0we author: Postler, Thomas S. title: Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection date: 2017-11-01 words: 6315.0 sentences: 377.0 pages: flesch: 55.0 cache: ./cache/cord-260695-qwepi0we.txt txt: ./txt/cord-260695-qwepi0we.txt summary: Of the host-encoded lncRNAs reported to be differentially expressed upon HIV-1 infection, only nuclear enriched abundant transcript 1 (NEAT1) and noncoding repressor of nuclear factor of activated T cells (NRON) have been functionally characterized (Lazar et al., 2016) . In this report, we describe a meta-analysis of two independent RNA-seq studies of HIV-1-infected cells and show that, unexpectedly, only three lncRNAs are differentially expressed in both of these datasets (Chang et al., 2011; Mohammadi et al., 2013) . To obtain an unbiased understanding of any changes in lncRNA expression during HIV-1 infection, we performed a meta-analysis of two independent RNA-seq studies conducted by two different groups using two different virus strains ( Supplementary Fig. S1 ) (Chang et al., 2011; Mohammadi et al., 2013) . To validate the results of the in silico analysis of lnc173 expression, we isolated RNA from 4 human cell lines and probed for the presence of both transcript variants by quantitative RT-PCR (qRT-PCR; Fig. 3A -D). abstract: Long non-coding RNAs (lncRNAs) are rapidly emerging as important regulators of a diverse array of cellular functions. Here, we describe a meta-analysis of two independent RNA-seq studies to identify lncRNAs that are differentially expressed upon HIV-1 infection. Only three lncRNA genes exhibited altered expression of ≥2-fold in HIV-1-infected cells. Of these, the uncharacterized lncRNA LINC00173 was chosen for further study. Both transcript variants of LINC00173 (lnc173 TSV1 and 2) could be detected by qPCR, localized predominantly to the nucleus and were reproducibly up-regulated during infection. Knock-out of the LINC00173 locus did not have detectable effects on HIV-1 replication. Interestingly, however, stimulation of Jurkat T cells with PMA/ionomycin resulted in a decrease of lnc173 expression, and Jurkat cells deficient for lnc173 on average expressed higher levels of specific cytokines than control cells. These data suggest that lnc173 may have a role in the regulation of cytokines in T cells. url: https://doi.org/10.1016/j.virol.2017.08.006 doi: 10.1016/j.virol.2017.08.006 id: cord-006960-9pho3hk6 author: Prakash, R. title: Droplet Microfluidic Chip Based Nucleic Acid Amplification and Real-Time Detection of Influenza Viruses date: 2013-12-27 words: 6279.0 sentences: 286.0 pages: flesch: 51.0 cache: ./cache/cord-006960-9pho3hk6.txt txt: ./txt/cord-006960-9pho3hk6.txt summary: In this work, we have utilized electro-actuation based DMF technology, integrated with suitably tailored resistive micro-heaters and temperature sensors, to achieve chip based real-time, quantitative PCR (qRT-PCR). Performance of the integrated DMF device was analyzed in real-time chip based qRT-PCR detection of in-vitro synthesized influenza A and C virus RNAs during 30-35 PCR cycles. Among the contact temperature control methods, the micro-fabricated resistive heaters/RTDs have smaller power requirement, faster thermal response and higher heating ramp rates and are therefore preferred for the proposed qRT-PCR micro-device. Mixing of the influenza C RNA sample and the off-chip prepared PCR reagents, followed by the RT reaction and thermal cycling over Micro-electrode 1, is shown in Figure 7 . This article demonstrates the design and micro-fabrication of integrated droplet microfluidic device, with nano-textured superhydrophobic top surface, that is capable of electro-handling of PCR samples/reagents, facilitating chip based mixing/sample preparation and chip based qRT-PCR amplification and detection of influenza viruses. abstract: Miniaturized bio-diagnostic devices have the potential to allow for rapid pathogen screening in clinical patient samples, as a low cost and portable alternative to conventional bench-top equipment. Miniaturization of key bio-diagnostic techniques, such as: nucleic acid detection and quantification, polymerase chain reaction (PCR), DNA fingerprinting, enzyme linked immunosorbent assay (ELISA), results in substantial reduction of reaction volumes (expensive samples/reagents) and shorter reaction times. Droplet microfluidics (DMF) is one of several miniaturized bio-sample handling techniques available for manipulating clinical samples and reagents in microliter (10(−6) L) to picoliter (10(−12) L) volume regime. Electro-actuation of sample and reagent in the form of droplets in the aforementioned volume regime, using dielectrophoresis (DEP) and/or Electrowetting (EW) are achieved by means of patterned, insulated metal electrodes on one or more substrates. In this work, we have utilized electro-actuation based DMF technology, integrated with suitably tailored resistive micro-heaters and temperature sensors, to achieve chip based real-time, quantitative PCR (qRT-PCR). This qRT-PCR micro-device was utilized to detect and quantify the presence of influenza A and C virus nucleic acids, using in-vitro synthesized viral RNA segments. The experimental analysis of the DMF micro-device confirms its capabilities in qRT-PCR based detection and quantification of pathogen samples, with accuracy levels comparable to established commercial bench-top equipment (PCR efficiency ∼95%). The limit of detection (LOD) of the chip based qRT-PCR technique was estimated to be ∼5 copies of template RNA per PCR reaction. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105149/ doi: 10.1149/2.013402jes id: cord-329311-p68kr4ga author: Prebensen, Christian title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 date: 2020-09-05 words: 1454.0 sentences: 111.0 pages: flesch: 61.0 cache: ./cache/cord-329311-p68kr4ga.txt txt: ./txt/cord-329311-p68kr4ga.txt summary: title: SARS-CoV-2 RNA in plasma is associated with ICU admission and mortality in patients hospitalized with COVID-19 Routine biochemistry was taken at admission and study-specific samples of EDTA plasma and serum were taken at three time points; baseline (enrollment), day 3 (1 day) and day 9 ( 2 days) in patients who were still hospitalized (details in Supplementary Figure 1) . SARS-CoV-2 RNAemia was detected in at least one sample in 58/123 (47%) patients, and in a significantly higher proportion of patients who were admitted to the ICU or died (80% vs. RNAemia was significantly more frequent at all time points in patients who reached the primary endpoint, whereas RNA loads were significantly higher at baseline and day 3 ( Table 1 , Supplementary Figure 2A ). In this prospective study of patients hospitalized with COVID-19 we detected SARS-CoV-2 RNAemia in 47% of included patients, and a significantly higher frequency of RNAemia and higher RNA loads in and similarly found that RNAemia was associated with ICU admission and hospital mortality [3] . abstract: The clinical significance of SARS-CoV-2 RNA in the circulation is unknown. In this prospective cohort study, we detected viral RNA in the plasma of 58/123 (47%) patients hospitalized with COVID-19. RNA was detected more frequently, and levels were higher, in patients who were admitted to the ICU and/or died. url: https://www.ncbi.nlm.nih.gov/pubmed/32888003/ doi: 10.1093/cid/ciaa1338 id: cord-000736-6f8vyziv author: Pripuzova, Natalia title: Development of Real-Time PCR Array for Simultaneous Detection of Eight Human Blood-Borne Viral Pathogens date: 2012-08-17 words: 6818.0 sentences: 328.0 pages: flesch: 54.0 cache: ./cache/cord-000736-6f8vyziv.txt txt: ./txt/cord-000736-6f8vyziv.txt summary: FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). The analytical sensitivity of each primer set was determined in the single virus testing using FDA/CBER panels (kindly provided by Dr. Stephen Kerby, FDA/CBER) consisting of various amounts of the viruses (0-1,000 genome copies/ml) spiked into the ''''normal'''' human plasma. The results of sensitivity testing of the real-time PCR array primer sets specific for HIV-1, HIV-2, HBV, HCV, and WNV the with FDA/CBER analytical plasma panels. Tm and C(t) values obtained with primer sets specific for HIV-1, HCV, or HBV in testing of 17 human clinical samples in the format of PCR array targeting eight different viruses. abstract: BACKGROUND: Real-time PCR array for rapid detection of multiple viral pathogens should be highly useful in cases where the sample volume and the time of testing are limited, i.e. in the eligibility testing of tissue and organ donors. FINDINGS: We developed a real-time PCR array capable of simultaneously detecting eight human viral pathogens: human immunodeficiency virus types 1 and 2 (HIV-1 and -2), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-cell leukemia virus-1 and -2 (HTLV-1 and -2), vaccinia virus (VACV) and West Nile virus (WNV). One hundred twenty (120) primers were designed using a combination of bioinformatics approaches, and, after experimental testing, 24 primer sets targeting eight viral pathogens were selected to set up the array with SYBR Green chemistry. The specificity and sensitivity of the virus-specific primer sets selected for the array were evaluated using analytical panels with known amounts of viruses spiked into human plasma. The array detected: 10 genome equivalents (geq)/ml of HIV-2 and HCV, 50 geq of HIV-1 (subtype B), HBV (genotype A) and WNV. It detected 100–1,000 geq/ml of plasma of HIV-1 subtypes (A – G), group N and CRF (AE and AG) isolates. Further evaluation with a panel consisting of 28 HIV-1 and HIV-2 clinical isolates revealed no cross-reactivity of HIV-1 or HIV-2 specific primers with another type of HIV. All 28 viral isolates were identified with specific primer sets targeting the most conserved genome areas. The PCR array correctly identified viral infections in a panel of 17 previously quantified clinical plasma samples positive for HIV-1, HCV or HBV at as low as several geq per PCR reaction. CONCLUSIONS: The viral array described here demonstrated adequate performance in the testing of donors’ clinical samples. Further improvement in its sensitivity for the broad spectrum of HIV-1 subtypes is under development. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422334/ doi: 10.1371/journal.pone.0043246 id: cord-103807-x4hrwhkz author: Prokop, J. W. title: Viral Induced Genetics Revealed by Multi-Dimensional Precision Medicine Transcriptional Workflow date: 2020-04-06 words: 6843.0 sentences: 375.0 pages: flesch: 50.0 cache: ./cache/cord-103807-x4hrwhkz.txt txt: ./txt/cord-103807-x4hrwhkz.txt summary: Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Using multi-time point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology vs. The power of RNA generated data likely is in its potential to effect therapeutic changes in individual patients with diverse clinical presentations, such as Multiple Organ Dysfunction Syndrome (MODS). Additional insights from the top mapped bacteria include normal flora elevation of Polynucleobacter necessarius and Bordetella parapertussis in patient 24 suggested to have issues in antigen processing and presentation (case study presented below for RNASEH2B), multiple Streptococcus strains (including pyogenes) identified in patients 11 and 5 that were culture positive, Pandoraea faecigallinarum in patient 10, and Cryobacterium arcticum in patient 10 day 0. abstract: Precision medicine requires the translation of basic biological understanding to medical insights, mainly applied to characterization of each unique patient. In many clinical settings, this requires tools that can be broadly used to identify pathology and risks. Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Etiology and outcomes are unique to individuals, making it difficult to cohort patients with MODS, but presenting a prime target for testing/developing tools for precision medicine. Using multi-time point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology vs. environmental response, and unique biological insights in each patient using a single platform measurement. Integration of a transcriptome workflow yielded unexpected insights into the complex interplay between host genetics and viral/bacterial specific mechanisms, highlighted by a unique case of virally induced genetics (VIG) within one of these 27 patients. The power of RNAseq to study unique patient biology while investigating environmental contributions can be a critical tool moving forward for translational sciences applied to precision medicine. url: http://medrxiv.org/cgi/content/short/2020.04.01.20050054v1?rss=1 doi: 10.1101/2020.04.01.20050054 id: cord-253480-qchrw337 author: Pu, Jieying title: Antiviral activity of Carbenoxolone disodium against dengue virus infection date: 2016-12-23 words: 5289.0 sentences: 287.0 pages: flesch: 52.0 cache: ./cache/cord-253480-qchrw337.txt txt: ./txt/cord-253480-qchrw337.txt summary: Here, we found that the production of infectious DENV particles was significantly decreased by CBX treatment in DENV‐permissive cells, while the viral RNA and viral protein synthesis were not affected. Moreover, results from time-of-addition study showed that the inhibitory effect of CBX on DENV was exhibited by targeting the virus itself, not the host cells. In this study, we investigated whether CBX treatment inhibits dengue infection by measuring the production of progeny virions and viral RNA as well as viral protein expression. To determine whether CBX inhibits the production of infectious progeny DENV in other dengue-permissive cells, TCID 50 assay was performed to measure the virus titer in CBX-treated THP-1 and HUVEC cells, both of which are widely used in DENV studies [Halstead, 1988; Wu et al., 2000] . CBX treatment did not inhibit DENV-1 or DENV-2 RNA synthesis and protein expression in one replication cycle, but markedly reduced progeny virus The total RNA was isolated from the infected cells and analyzed by quantitative RT-PCR. abstract: As one of the most important mosquito‐borne viral diseases, dengue infection is now becoming a global concern due to its rapid spread and rise in incidence. Currently, there is no approved vaccine or effective antiviral drug for dengue virus (DENV) infection. Glycyrrhetinic acid (GNa) and its related derivatives have been reported to inhibit a broad spectrum of viruses. However, it is unknown whether Carbenoxolone disodium (CBX), one of the GNa derivatives, affects DENV infection. Here, we found that the production of infectious DENV particles was significantly decreased by CBX treatment in DENV‐permissive cells, while the viral RNA and viral protein synthesis were not affected. Moreover, results from time‐of‐addition study showed that the inhibitory effect of CBX on DENV was exhibited by targeting the virus itself, not the host cells. Directly incubating DENV with CBX resulted in a remarkable reduction of virus titer and virus infectivity. Furthermore, DENV RNA from progeny virions in the supernatants was significantly decreased by CBX treatment in a dose‐dependent manner. Taken together, these data indicate that the antiviral activity of CBX against DENV may be mainly due to a virucidal effect exerted by the compound itself. Our work, for the first time, demonstrates that CBX has antiviral activity against DENV infection, providing useful information for development of potential therapeutic interventions against dengue. J. Med. Virol. 89:571–581, 2017. © 2016 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/27155198/ doi: 10.1002/jmv.24571 id: cord-263580-zxnmylkw author: Pyle, Anna Marie title: RNA helicases and remodeling proteins date: 2011-08-20 words: 2650.0 sentences: 131.0 pages: flesch: 50.0 cache: ./cache/cord-263580-zxnmylkw.txt txt: ./txt/cord-263580-zxnmylkw.txt summary: New studies have revealed molecular mechanisms for coupling between ATP hydrolysis and unwinding, the physical basis for regulatory control by cofactors, and novel functions for RNA remodeling proteins. For DEAD-box proteins where the mechanochemical cycle has been studied, ATP hydrolysis (specifically, at the stage of Pi release) stimulates the dissociation of bound RNA molecules [46 ,47] , allowing recycling of these ''single-use'' proteins [7] . Like many DEAD-box proteins, Mss116 is capable of unwinding short RNA duplexes [46 ,52,53] , however, studies of Mss116 mutants in vivo and in vitro show that its role in splicing is not necessarily dependent on helicase activity [52, 54 ] . This structure reveals the Dbp5 export motor imbedded within the complex containing other proteins involved in its function, revealing roles for small molecule activators and a conserved mechanism for ATP hydrolysis in RNA release abstract: It is becoming increasingly clear that RNA molecules play a major role in all aspects of metabolism. The conformational state and stability of RNA are controlled by RNA remodeling proteins, which are ubiquitous motor proteins in the cell. Here, we review advances in our understanding of the structure and function of three major structural families of RNA remodeling proteins, the hexameric ring proteins, the processive monomeric RNA translocase/helicases, and the functionally diverse DEAD-box remodeling proteins. New studies have revealed molecular mechanisms for coupling between ATP hydrolysis and unwinding, the physical basis for regulatory control by cofactors, and novel functions for RNA remodeling proteins. url: https://api.elsevier.com/content/article/pii/S1367593111001268 doi: 10.1016/j.cbpa.2011.07.019 id: cord-345157-fhmhpobi author: Qi, Dan title: Virus infection-induced host mRNA degradation and potential application of live cell imaging date: 2018-12-12 words: 2619.0 sentences: 158.0 pages: flesch: 49.0 cache: ./cache/cord-345157-fhmhpobi.txt txt: ./txt/cord-345157-fhmhpobi.txt summary: Herein, we focus on several possible mechanisms of infection-induced host RNA turnover, which seems to be a common strategy for both prokaryotic and eukaryotic viruses during the very early stage of infection and a potential application of live cell imaging on its visualization. Many viruses also impair the translation of cellular mRNA [1e3], one of the mechanisms during the shift of gene expression from host to virus, a process termed "host shutoff", in order to prevent the production of anti-viral, host protecting proteins [4] . Moreover, Gaglia et al.''s work showed that viral encoded proteins trigger host mRNA degradation by a primary endonucleolytic cleavage causing shutoff of host gene expression and a host exonuclease such as Xrn1, an important 5 0 to 3 0 exonuclease in human cells, were required in subsequent completion of host mRNA turnover [5] . abstract: Viruses exist wherever there is life. They can cause allergy, immune response, inflammation, and even fatal diseases directly or indirectly. Accumulating evidence shows that host RNA undergoes rapid degradation during virus infection. Herein, we focus on several possible mechanisms of infection-induced host RNA turnover, which seems to be a common strategy for both prokaryotic and eukaryotic viruses during the very early stage of infection and a potential application of live cell imaging on its visualization. url: https://doi.org/10.1016/j.jrid.2018.12.002 doi: 10.1016/j.jrid.2018.12.002 id: cord-259593-shrd1s7r author: Qin, Zhao-ling title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA date: 2007-06-27 words: 4603.0 sentences: 255.0 pages: flesch: 56.0 cache: ./cache/cord-259593-shrd1s7r.txt txt: ./txt/cord-259593-shrd1s7r.txt summary: title: siRNAs targeting terminal sequences of the SARS-associated coronavirus membrane gene inhibit M protein expression through degradation of M mRNA To study M protein function, three candidate small interfering RNAs (siRNAs) corresponding to M gene sequences were designed, transcribed in vitro, and then tested for their ability to silence M protein expression. The results showed that the mean green fluorescence intensity and M RNA transcripts were significantly reduced, and that the expression of M glycoprotein was strongly inhibited in those cells co-transfected with M-specific siRNAs. These findings demonstrated that the three M-specific siRNAs were able to specifically and effectively inhibit M glycoprotein expression in cultured cells by blocking the accumulation of mRNA, which provides an approach for studies on the functions of M protein and for the development of novel prophylactic or therapeutic agents for SCoV infection. abstract: SARS-associated coronavirus (SCoV) M protein plays a key role in viral assembly and budding. Recent studies revealed that M protein could interact with N protein in the Golgi complex. In this study, we showed that SCoV M protein co-localized in the Golgi apparatus with a Golgi vector marker. To study M protein function, three candidate small interfering RNAs (siRNAs) corresponding to M gene sequences were designed, transcribed in vitro, and then tested for their ability to silence M protein expression. The plasmid, pEGFP-M, encoding SCoV M protein as a fusion protein with EGFP, was used for silencing and for reporter gene detection in HEK 293T cells transfected with siRNA constructs. The results showed that the mean green fluorescence intensity and M RNA transcripts were significantly reduced, and that the expression of M glycoprotein was strongly inhibited in those cells co-transfected with M-specific siRNAs. These findings demonstrated that the three M-specific siRNAs were able to specifically and effectively inhibit M glycoprotein expression in cultured cells by blocking the accumulation of mRNA, which provides an approach for studies on the functions of M protein and for the development of novel prophylactic or therapeutic agents for SCoV infection. url: https://www.sciencedirect.com/science/article/pii/S016609340700198X doi: 10.1016/j.jviromet.2007.05.017 id: cord-303403-9th2jiq6 author: Qing, Jie title: Cyclophilin A Associates with Enterovirus-71 Virus Capsid and Plays an Essential Role in Viral Infection as an Uncoating Regulator date: 2014-10-02 words: 10095.0 sentences: 479.0 pages: flesch: 56.0 cache: ./cache/cord-303403-9th2jiq6.txt txt: ./txt/cord-303403-9th2jiq6.txt summary: CypA is also known to play critical roles in the proliferation of a number of viruses, including human immunodeficiency virus type 1 (HIV-1), influenza virus, hepatitis C virus (HCV), vesicular stomatitis virus (VSV), vaccinia virus, severe acute respiratory syndrome coronavirus (SARS-CoV), rotavirus (RV) and human papillomavirus (HPV), by interacting with viral proteins or facilitating IFN-b production [2, 3] . CypA was further revealed to interact with extracellular CD147, which is the main receptor for CypA on the cell membrane of human leukocytes, and this interaction can induce the phosphorylation of HIV-1 matrix protein to regulate the liberation of the reverse transcriptase complex into cytoplasm during an early stage of HIV-1 infection or can function in HIV-1 attachment to host cells [8] . The results we report here demonstrate that the CypA host factor played a crucial role in the uncoating process during the entry step of EV71 infection, and the action site of CypA was mapped to the H-I loop of capsid protein VP1. abstract: Viruses utilize host factors for their efficient proliferation. By evaluating the inhibitory effects of compounds in our library, we identified inhibitors of cyclophilin A (CypA), a known immunosuppressor with peptidyl-prolyl cis-trans isomerase activity, can significantly attenuate EV71 proliferation. We demonstrated that CypA played an essential role in EV71 entry and that the RNA interference-mediated reduction of endogenous CypA expression led to decreased EV71 multiplication. We further revealed that CypA directly interacted with and modified the conformation of H-I loop of the VP1 protein in EV71 capsid, and thus regulated the uncoating process of EV71 entry step in a pH-dependent manner. Our results aid in the understanding of how host factors influence EV71 life cycle and provide new potential targets for developing antiviral agents against EV71 infection. url: https://www.ncbi.nlm.nih.gov/pubmed/25275585/ doi: 10.1371/journal.ppat.1004422 id: cord-309722-04pp3lv0 author: Qiu, Yingshan title: Delivery of RNAi Therapeutics to the Airways—From Bench to Bedside date: 2016-09-20 words: 13203.0 sentences: 800.0 pages: flesch: 42.0 cache: ./cache/cord-309722-04pp3lv0.txt txt: ./txt/cord-309722-04pp3lv0.txt summary: Notes: AHR, airway hyperresponsiveness; ALI, Acute lung injury; BALF, bronchoalveolar lavage fluid; CD86, cluster of differentiation 86; C-kit, a stem cell factor receptor; DCs, dendritic cells; HMGB1A, high mobility group box-1 A peptide; IFU, infectious unit; LPS, lipopolysaccharide; Mpl, myeloproliferative leukemia virus oncogene; OVA, ovalbumin; R3V6, an arginine-rich peptide; Rip2, receptor-interacting protein 2; RSV, respiratory syncytial virus; S1Plyase, sphingosine-1-phosphate lyase, SOCS, Suppressors of cytokine signaling protein 3; STAT6, signal transducer and activator of transcription factor 6; Syk, spleen tyrosine kinase; Tf-PEI, transferrin polyethylenimine; T h 2, T helper 2 cells; TNF-α, tumor necrosis factor-α; VEGFR, Vascular endothelial growth factor. After siRNA targeting, SOCS3 was intranasally administered to the lungs of chronic asthmatic mouse model [12] , the silencing of SOCS3 down-regulated the expression of T h 2 cell associated cytokines, IL-4, IL-5 and IL-13, leading to substantial reduction of airway inflammation, AHR as well as IgE production. abstract: RNA interference (RNAi) is a potent and specific post-transcriptional gene silencing process. Since its discovery, tremendous efforts have been made to translate RNAi technology into therapeutic applications for the treatment of different human diseases including respiratory diseases, by manipulating the expression of disease-associated gene(s). Similar to other nucleic acid-based therapeutics, the major hurdle of RNAi therapy is delivery. Pulmonary delivery is a promising approach of delivering RNAi therapeutics directly to the airways for treating local conditions and minimizing systemic side effects. It is a non-invasive route of administration that is generally well accepted by patients. However, pulmonary drug delivery is a challenge as the lungs pose a series of anatomical, physiological and immunological barriers to drug delivery. Understanding these barriers is essential for the development an effective RNA delivery system. In this review, the different barriers to pulmonary drug delivery are introduced. The potential of RNAi molecules as new class of therapeutics, and the latest preclinical and clinical studies of using RNAi therapeutics in different respiratory conditions are discussed in details. We hope this review can provide some useful insights for moving inhaled RNAi therapeutics from bench to bedside. url: https://www.ncbi.nlm.nih.gov/pubmed/27657028/ doi: 10.3390/molecules21091249 id: cord-287324-ecpicv5v author: Qiu, Yuan title: Detection of viromes of RNA viruses using the next generation sequencing libraries prepared by three methods date: 2017-06-02 words: 3736.0 sentences: 194.0 pages: flesch: 55.0 cache: ./cache/cord-287324-ecpicv5v.txt txt: ./txt/cord-287324-ecpicv5v.txt summary: In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. In this study, we detected the viromes of RNA viruses of one mock sample and two pooled authentic samples, using the libraries prepared by the three methods on the Personal Genome Machine (PGM) platform, with the aim to generate data of significance for virome detection of RNA viruses and characterize the viromes of RNA viruses in ducks and minks. In the future, it is of significance to compare methods 2 and 3 in detecting viromes of RNA viruses in some clinical samples containing limited viral RNA. Detection of viromes of ducks and minks increases our understanding of the viral diversity in the animals, and provides novel clues for further studies regarding diagnosis of infectious diseases, identification of novel viruses and research of host-virus relationships. abstract: Virome (viral megagenomics) detection using next generation sequencing has been widely applied in virology, but its methods remain complicated and need optimization. In this study, we detected the viromes of RNA viruses of one mock sample, one pooled duck feces sample and one pooled mink feces sample on the Personal Genome Machine platform using the sequencing libraries prepared by three methods. The sequencing primers were added through random hybridization and ligation to fragmented viral RNA using a RNA-Seq kit in method 1, through random reverse transcription (RT) and polymerase chain reaction (PCR) in method 2 which was developed in our laboratory, and through hybridization and ligation to fragmented amplicons of random RT-PCR using a single primer in method 3. Although the results of these three samples (nine libraries) all showed that more classified viral families and genera were identified using methods 2 and 3 than using method 1, and more classified viral families and genera were identified using method 2 than using method 3, most of the differences were of no statistical significance. Moreover, 11 mammalian viral genera in minks were possibly identified for the first time through this study. url: https://api.elsevier.com/content/article/pii/S0168170217302150 doi: 10.1016/j.virusres.2017.05.003 id: cord-310141-2jofy8fo author: Qureshi, Abid title: A review on current status of antiviral siRNA date: 2018-04-15 words: 3380.0 sentences: 254.0 pages: flesch: 42.0 cache: ./cache/cord-310141-2jofy8fo.txt txt: ./txt/cord-310141-2jofy8fo.txt summary: Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. For example, siRNAs directed against different genes of deadly viruses like human immunodeficiency virus (HIV), 9, 10 influenza virus (INFV), 11, 12 hepatitis B virus (HBV), 13 SARS coronavirus (SARS-CoV), 14, 15 human papillomavirus (HPV), 16 and West Nile virus (WNV) 17 in infected cells displayed encouraging results in inhibiting viral replication. 18, 19 Short interfering RNAs for various human viruses like respiratory syncytial virus (RSV), hepatitis C virus (HCV), HBV, and HIV are also appearing in clinical trials, which further elucidate their importance in inhibiting viral infections. Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice abstract: Viral diseases like influenza, AIDS, hepatitis, and Ebola cause severe epidemics worldwide. Along with their resistant strains, new pathogenic viruses continue to be discovered so creating an ongoing need for new antiviral treatments. RNA interference is a cellular gene‐silencing phenomenon in which sequence‐specific degradation of target mRNA is achieved by means of complementary short interfering RNA (siRNA) molecules. Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions. In this review, we briefly summarize the current status of siRNA therapy for representative examples from different virus families. In addition, other aspects like their design, delivery, medical significance, bioinformatics resources, and limitations are also discussed. url: https://doi.org/10.1002/rmv.1976 doi: 10.1002/rmv.1976 id: cord-275252-4e3cn50u author: Rad SM, Ali Hosseini title: Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting date: 2020-05-16 words: 4368.0 sentences: 302.0 pages: flesch: 53.0 cache: ./cache/cord-275252-4e3cn50u.txt txt: ./txt/cord-275252-4e3cn50u.txt summary: In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. A common primary focus of mutational analysis of emerging viruses is the alteration in amino acid sequence of viral proteins that may provide enhanced or new functions for virus replication, immune avoidance, or spread. However, the potential of these mutations to impact upon RNA structure and miRNA recognition provides a basis for ongoing monitoring of viral evolution at these sites in the SARS-CoV-2 genome. abstract: The SARS-CoV-2 virus is a recently-emerged zoonotic pathogen already well adapted to transmission and replication in humans. Although the mutation rate is limited, recently introduced mutations in SARS-CoV-2 have the potential to alter viral fitness. In addition to amino acid changes, mutations could affect RNA secondary structure critical to viral life cycle, or interfere with sequences targeted by host miRNAs. We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary structure. Filtering to targets matching miRNAs expressed in SARS-CoV-2 permissive host cells, we identified twelve separate target sequences in the SARS-CoV-2 genome; eight of these targets have been lost through conserved mutations. A genomic site targeted by the highly abundant miR-197-5p, overexpressed in patients with cardiovascular disease, is lost by a conserved mutation. Our results are compatible with a model that SARS-CoV-2 replication within the human host could be constrained by host miRNA defence. The impact of these and further mutations on secondary structures, miRNA targets or potential splice sites offers a new context in which to view future SARS-CoV-2 evolution, and a potential platform for engineered viral attenuation and antigen presentation. url: https://doi.org/10.1101/2020.05.15.098947 doi: 10.1101/2020.05.15.098947 id: cord-290550-u8x9drva author: Radford, Alan D. title: Application of next-generation sequencing technologies in virology date: 2012-09-17 words: 7931.0 sentences: 382.0 pages: flesch: 43.0 cache: ./cache/cord-290550-u8x9drva.txt txt: ./txt/cord-290550-u8x9drva.txt summary: Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. Although this review has concentrated on the use of NGS to study viral sequences directly, it is clear that these approaches provide new opportunities to explore the interaction of replicating viruses with their host, particularly their transcriptome, in a non-targeted, hypothesis-generating mode. Viral transcriptome analysis of feline immunodeficiency virus infected cells using second generation sequencing technology abstract: The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health. url: https://doi.org/10.1099/vir.0.043182-0 doi: 10.1099/vir.0.043182-0 id: cord-283439-hqdq2qrh author: Rahman, Mohammad Tariqur title: Can Zn Be a Critical Element in COVID-19 Treatment? date: 2020-05-26 words: 5248.0 sentences: 315.0 pages: flesch: 50.0 cache: ./cache/cord-283439-hqdq2qrh.txt txt: ./txt/cord-283439-hqdq2qrh.txt summary: The suggested treatments for COVID-19 are, but not limited to, the use of (i) convalescent plasma for COVID-19 treatment [63] [64] [65] ; (ii) ribavirin, a nucleoside analogue in combination with recombinant interferon showed inhibition of MERS-CoV replication [66] ; (iii) lopinavir/ritonavir-a combination of a protease inhibitor and a booster used for the treatment of human immunodeficiency virus infection [67] ; (iv) remdesivir, a nucleotide analogue that inhibit RNA polymerase with a broad spectrum of anti-viral activities; in inhibition of human and zoonotic coronavirus [15, 68, 69] ; (v) favipiravir (also known as T-705, Avigan or favilavir) is a pyrazinecarboxamide derivative known to inhibit RNA polymerase [70] . In the current pandemic of SARS-CoV-2, Zn supplement could play an important role to treat COVID-19 patients such as (i) added immune boosting effects with anti-viral drugs and (ii) stopping SARS-CoV-2 replication in infected cells, if combined with chloroquine. abstract: The current COVID-19 pandemic caused by SARS-CoV-2 has prompted investigators worldwide to search for an effective anti-viral treatment. A number of anti-viral drugs such as ribavirin, remdesivir, lopinavir/ritonavir, antibiotics such as azithromycin and doxycycline, and anti-parasite such as ivermectin have been recommended for COVID-19 treatment. In addition, sufficient pre-clinical rationale and evidence have been presented to use chloroquine for the treatment of COVID-19. Furthermore, Zn has the ability to enhance innate and adaptive immunity in the course of a viral infection. Besides, Zn supplement can favour COVID-19 treatment using those suggested and/or recommended drugs. Again, the effectiveness of Zn can be enhanced by using chloroquine as an ionophore while Zn inside the infected cell can stop SARS-CoV-2 replication. Given those benefits, this perspective paper describes how and why Zn could be given due consideration as a complement to the prescribed treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32458149/ doi: 10.1007/s12011-020-02194-9 id: cord-003382-v3w1wi5c author: Rahmatpanah, Farah title: Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors date: 2018-10-02 words: 5543.0 sentences: 342.0 pages: flesch: 56.0 cache: ./cache/cord-003382-v3w1wi5c.txt txt: ./txt/cord-003382-v3w1wi5c.txt summary: We examined the effect of human primary bronchial epithelial cells (PBECs) on PDC functions by performing RNA-sequencing of PDCs after co-culture with air liquid interface differentiated PBECs. Functional analysis revealed that PDCs co-cultured with PBECs displayed upregulation of type I IFN production and response genes. In keeping with the RNA-seq data, we observe increased secretion of type I IFN and other cytokines in response to influenza in PDCs co-cultured with PBECs. The PDCs also primed Th1 responses in T cells. PDCs exposed to PBECs secreted significantly higher levels of type I IFNs (p = 0.0001) on stimulation with influenza as compared to PDCs cultured alone (Fig. 3a) , which is in keeping with the RNA-seq data. In keeping with the activation genes in RNA-seq, we also observed increased secretion of type I IFN from influenza stimulated PDCs co-cultured with PBECs. The expression of TLR9 and ZBP1 was upregulated. abstract: Plasmacytoid dendritic cells (PDCs) are critical for defense against respiratory viruses because of their propensity to secrete high levels of type I interferons (IFN). The functions of PDCs in the lung can be influenced by airway epithelial cells. We examined the effect of human primary bronchial epithelial cells (PBECs) on PDC functions by performing RNA-sequencing of PDCs after co-culture with air liquid interface differentiated PBECs. Functional analysis revealed that PDCs co-cultured with PBECs displayed upregulation of type I IFN production and response genes. Upregulated transcripts included those encoding cytosolic sensors of DNA, ZBP-1,IRF-3, and NFkB as well as genes involved in amplification of the IFN response, such as IFNAR1, JAK/STAT, ISG15. In keeping with the RNA-seq data, we observe increased secretion of type I IFN and other cytokines in response to influenza in PDCs co-cultured with PBECs. The PDCs also primed Th1 responses in T cells. The enhanced response of PDCs co-cultured with PBECs was due to the action of growth factors, GMCSF, GCSF, and VEGF, which were secreted by PBECs on differentiation. These data highlight possible mechanisms to enhance the production of type-I IFN in the airways, which is critical for host defense against respiratory infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301110/ doi: 10.1038/s41385-018-0097-1 id: cord-017297-q3qtgrfc author: Rajagopal, Vaishnavi title: Viral Helicases date: 2008-11-01 words: 11546.0 sentences: 654.0 pages: flesch: 52.0 cache: ./cache/cord-017297-q3qtgrfc.txt txt: ./txt/cord-017297-q3qtgrfc.txt summary: In a recent study on HSV-1 UL9 helicase, mutational analysis of the residues in the Ia motif implicated in DNA binding resulted in moderate to severe defects in single-stranded nucleic-acids binding and ssNA stimulated ATPase activity, while retaining the intrinsic ATPase activity similar to that of wildtype enzyme (Marintcheva and Weller 2003) . Thus, in order to understand the mechanism of helicase catalyzed unwinding reactions, it is important to understand all the individual steps to it, namely: nucleic-acid binding, NTP binding and hydrolysis, single-stranded translocation, and then finally the strand-separation function. Two early genes of bacteriophage T5 encode proteins containing an NTP-binding sequence motif and probably involved in DNA replication, recombination and repair Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases A functional interaction of ICP8, the herpes simplex virus single-stranded DNA-binding protein, and the helicase-primase complex that is dependent on the presence of the UL8 subunit abstract: Helicases are motor proteins that use the free energy of NTP hydrolysis to catalyze the unwinding of duplex nucleic acids. Helicases participate in almost all processes involving nucleic acids. Their action is critical for replication, recombination, repair, transcription, translation, splicing, mRNA editing, chromatin remodeling, transport, and degradation (Matson and Kaiser-Rogers 1990; Matson et al. 1994; Mendonca et al. 1995; Luking et al. 1998). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7121818/ doi: 10.1007/b135974_20 id: cord-326911-va3x6au2 author: Ramos-Mandujano, G. title: A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples date: 2020-06-29 words: 4424.0 sentences: 288.0 pages: flesch: 55.0 cache: ./cache/cord-326911-va3x6au2.txt txt: ./txt/cord-326911-va3x6au2.txt summary: We developed an open-source method called Magneticnanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. To date, molecular diagnosis of COVID-19 predominantly relies on detection of SARS-CoV-2 RNA using real-time reverse transcription polymerase chain reaction (rRT-PCR) assays, such as those approved by the US Centers for Disease Control and Prevention (US CDC) 1 . MAVRICS performed on par or better than commercial RNA extraction kits in rRT-PCR detection of SARS-CoV-2, influenza viruses and respiratory syncytial virus in various clinical and environmental samples. . https://doi.org/10.1101/2020.06.28.20141945 doi: medRxiv preprint Next, we aimed to develop an efficient SiMNP-based RNA extraction protocol using the contrived SARS-CoV-2 samples and US CDC 2019-nCoV_N1 and N3 rRT-PCR assays. abstract: Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method called Magnetic- nanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. MAVRICS is scalable and thus could become an enabling technology for widespread community testing and wastewater monitoring in the current and future pandemics. url: https://doi.org/10.1101/2020.06.28.20141945 doi: 10.1101/2020.06.28.20141945 id: cord-301226-hmc2wmst author: Randazzo, Walter title: Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance date: 2020-04-27 words: 2158.0 sentences: 127.0 pages: flesch: 52.0 cache: ./cache/cord-301226-hmc2wmst.txt txt: ./txt/cord-301226-hmc2wmst.txt summary: Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Here, we show that SARS-CoV-2 can be reproducibly detected by RT-qPCR in longitudinal samples from sewage treatment plants that receive wastewaters from over one million inhabitants in the metropolitan area of Valencia, Spain. Following concentration of viral content by flocculation, a standard RT-qPCR procedure allowed us to detect SARS-CoV-2 RNA in 12/12 samples collected from March 9 to April 14, 2020, with Ct values ranging between 34•00 and 37•84, correspondingly revealing between 5•22 and 5•99 log 10 genomic copies (gc)/L (Table 1) . Interestingly, we consistently detected SARS-CoV-2 RNA in samples collected on March 9 and March 11, when only 50 and 76 cumulative cases were declared in the entire Region of Valencia. abstract: Background: The COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a rapidly emerging pandemic which has enforced extreme containment measures worldwide. In the absence of a vaccine or efficient treatment, cost-effective epidemiological surveillance strategies are urgently needed. Methods: Here, we have used RT-qPCR for SARS-CoV-2 detection in a series of longitudinal metropolitan wastewaters samples collected during the earliest stages of the epidemic in the Region of Valencia, Spain. Results: We were able to consistently detect SARS-CoV-2 RNA in samples taken when communicated cases in that region were only incipient. We also find that the wastewater viral RNA context increased rapidly and anticipated the subsequent ascent in the number of declared cases. Interpretation: Our results strongly suggest that the virus was undergoing community transmission earlier than previously believed, and show that wastewater analysis is a sensitive and cost-effective strategy for COVID-19 epidemiological surveillance. Routine implementation of this surveillance tool would significantly improve our preparedness against new or re-occurring viral outbreaks. url: http://medrxiv.org/cgi/content/short/2020.04.23.20076679v1?rss=1 doi: 10.1101/2020.04.23.20076679 id: cord-346978-ubkqny8j author: Ranoa, Diana Rose E. title: Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction date: 2020-06-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Convenient, repeatable, large-scale molecular testing for SARS-CoV-2 would be a key weapon to help control the COVID-19 pandemic. Unfortunately, standard SARS-CoV-2 testing protocols are invasive and rely on numerous items that can be subject to supply chain bottlenecks, and as such are not suitable for frequent repeat testing. Specifically, personal protective equipment (PPE), nasopharyngeal (NP) swabs, the associated viral transport media (VTM), and kits for RNA isolation and purification have all been in short supply at various times during the COVID-19 pandemic. Moreover, SARS-CoV-2 is spread through droplets and aerosols transmitted through person-to-person contact, and thus saliva may be a relevant medium for diagnosing SARS-CoV-2 infection status. Here we describe a saliva-based testing method that bypasses the need for RNA isolation/purification. In experiments with inactivated SARS-CoV-2 virus spiked into saliva, this method has a limit of detection of 500-1000 viral particles per mL, rivalling the standard NP swab method, and initial studies also show excellent performance with 100 clinical samples. This saliva-based process is operationally simple, utilizes readily available materials, and can be easily implemented by existing testing sites, thus allowing for high-throughput, rapid, and repeat testing of large populations. Graphical Abstract url: https://doi.org/10.1101/2020.06.18.159434 doi: 10.1101/2020.06.18.159434 id: cord-334771-uy3s6443 author: Rao, BL title: A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus date: 2004-09-09 words: 3672.0 sentences: 187.0 pages: flesch: 49.0 cache: ./cache/cord-334771-uy3s6443.txt txt: ./txt/cord-334771-uy3s6443.txt summary: Samples obtained were: 54 blood samples, 22 throat swabs, ten CSF samples, and one brain aspirate from 55 patients with encephalitis; five blood samples and nine throat swabs from 13 fever cases; and ten blood samples and one throat swab from ten family contacts (including specimens from the brother and mother of a patient who Methods Cell lines and peripheral blood lymphocyte co-cultures were used to isolate the causative agent from clinical samples. The confirmed Chandipura virus encephalitis group consisted of individuals from whose samples we isolated the virus, viral RNA, or reactive IgM antibodies. The viruses isolated in different cell lines from clinical samples from patients with encephalitis were confirmed as Chandipura virus with various techniques including complement fixation, neutralisation test, and immunofluorescence assay. Moreover, the presence of Chandipura virus RNA in nine patients with encephalitis, all from samples obtained before day 4 after onset of illness, suggests an early viraemic phase of the infection process. abstract: BACKGROUND: An outbreak of acute encephalitis of unknown origin with high case fatality (183 of 329 cases) was reported in children from Andhra Pradesh state in southern India during 2003. We investigated the causative agent. METHODS: Cell lines and peripheral blood lymphocyte co-cultures were used to isolate the causative agent from clinical samples. Identity of the agent was established by electron microscopy and serological and molecular assays. FINDINGS: Clinical samples tested negative for IgM antibodies to Japanese encephalitis, West Nile, dengue, and measles viruses, and for RNA of coronavirus, paramyxovirus, enterovirus, and influenza viruses. Virus was isolated from six patients with encephalitis and was identified as Chandipura virus by electron microscopy, complement fixation, and neutralisation tests. Chandipura virus RNA was detected in clinical samples from nine patients. Sequencing of five of these RNA samples showed 96·7–97·5% identity with the reference strain of 1965. Chandipura viral antigen and RNA were detected in brain tissue of a deceased child by immunofluorescent antibody test and PCR. Neutralising, IgG, and IgM antibodies to Chandipura virus were present in some patients' serum samples. Serum samples obtained after 4 days of illness were more frequently positive for IgM to Chandipura virus than were those obtained earlier (p<0·001). A similar trend was noted for neutralising antibodies. INTERPRETATION: Our findings suggest that this outbreak of acute encephalitis in Andhra Pradesh was associated with Chandipura virus, adding to the evidence suggesting that this virus should be considered as an important emerging pathogen. url: https://www.sciencedirect.com/science/article/pii/S0140673604169821 doi: 10.1016/s0140-6736(04)16982-1 id: cord-002102-0zbp3uqf author: Rasche, Andrea title: Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015 date: 2016-07-17 words: 1697.0 sentences: 106.0 pages: flesch: 54.0 cache: ./cache/cord-002102-0zbp3uqf.txt txt: ./txt/cord-002102-0zbp3uqf.txt summary: title: Hepatitis E Virus Infection in Dromedaries, North and East Africa, United Arab Emirates, and Pakistan, 1983–2015 A new hepatitis E virus (HEV-7) was recently found in dromedaries and 1 human from the United Arab Emirates. Recently, HEV sequences were reported from 3 dromedaries sampled in the United Arab Emirates (UAE) in 2013 and were classified as a new orthohepevirus A genotype, HEV-7 (2, 3) . To determine the geographic distribution of HEV-7, we conducted a geographically comprehensive study of HEV-7 prevalence in dromedaries by testing 2,438 specimens sampled in 6 countries during the past 3 decades. Serum and fecal samples were collected from dromedary camels in the UAE, Somalia, Sudan, Egypt, Kenya, and Pakistan during 1983-2015 (5-7). Detections of HEV-7 RNA in feces in this and a previous study (2) point at feces or feces-contaminated camel products, such as milk, as putative additional sources of human infection. abstract: A new hepatitis E virus (HEV-7) was recently found in dromedaries and 1 human from the United Arab Emirates. We screened 2,438 dromedary samples from Pakistan, the United Arab Emirates, and 4 African countries. HEV-7 is long established, diversified and geographically widespread. Dromedaries may constitute a neglected source of zoonotic HEV infections. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918144/ doi: 10.3201/eid2207.160168 id: cord-000364-ikq38rm1 author: Rasmuson, J. title: Time to revise the paradigm of hantavirus syndromes? Hantavirus pulmonary syndrome caused by European hantavirus date: 2011-01-15 words: 2839.0 sentences: 178.0 pages: flesch: 43.0 cache: ./cache/cord-000364-ikq38rm1.txt txt: ./txt/cord-000364-ikq38rm1.txt summary: Lung computer tomography (CT) on admission revealed pronounced diffuse bilateral interstitial infiltrates with pulmonary oedema, dependant atelectasis, and moderate pleural effusions (Fig. 1 ) which were later drained (>800 ml). Hantavirus infection was verified with the detection of PUUV RNA in plasma (630,000 copies/ml) on the day of admission, while IgM and IgG were negative. Consecutive plasma samples were analysed for PUUV RNA with declining viral copy numbers until negative 16 days post onset of Fig. 1 Chest CT-scans of two European patients with hantavirus pulmonary syndrome. Concerning the cases of European hantavirus infection in our present report, there was only mild or no renal impairment at the time of admission, whereas the respiratory involvement was early and severe, consistent with acute respiratory distress syndrome (ARDS), fulfilling criteria of HPS according to CDC case definition [19] . abstract: Hantaviruses have previously been recognised to cause two separate syndromes: hemorrhagic fever with renal syndrome in Eurasia, and hantavirus pulmonary syndrome (HPS) in the Americas. However, increasing evidence suggests that this dichotomy is no longer fruitful when recognising human hantavirus disease and understanding the pathogenesis. Herein are presented three cases of severe European Puumala hantavirus infection that meet the HPS case definition. The clinical and pathological findings were similar to those found in American hantavirus patients. Consequently, hantavirus infection should be considered as a cause of acute respiratory distress in all endemic areas worldwide. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3075397/ doi: 10.1007/s10096-010-1141-6 id: cord-348860-zaimorg0 author: Ratra, Ruchi title: Functional genomics as a tool in virus research date: 2008-06-01 words: 3379.0 sentences: 171.0 pages: flesch: 39.0 cache: ./cache/cord-348860-zaimorg0.txt txt: ./txt/cord-348860-zaimorg0.txt summary: The genomics era has revolutionized the biological sciences and has heralded the emergence of new ''omics'' methodologies such as transcriptomics (study of the gene expression and expression levels of mRNAs at a given time and condition), proteomics (study of the entire protein content of a cell/tissue under various conditions, their structure and functions), metabolomics (study of the metabolite profi le of different cellular processes), phosphoproteomics (a branch of proteomics that characterizes proteins that are phosphorylated), interactomics/system biology (a science that unifi es transcriptomics, proteomics and metabolomics to look at the organism as a whole) and so on. DNA microarrays, proteomics and bioinformatic analysis are routinely used to analyze changes in host and viral gene and protein expression that occur in a virus infected cell [25] . abstract: Genomics is the study of an organism’s entire genome. It started out as a great scientific endeavor in the 1990s which aimed to sequence the complete genomes of certain biological species. However viruses are not new to this field as complete viral genomes have routinely been sequenced since the past thirty years. The ‘genomic era’ has been said to have revolutionized biology. This knowledge of full genomes has created the field of functional genomics in today’s post-genomic era, which, is in most part concerned with the studies on the expression of the organism’s genome under different conditions. This article is an attempt to introduce its readers to the application of functional genomics to address and answer several complex biological issues in virus research. url: https://www.ncbi.nlm.nih.gov/pubmed/23100713/ doi: 10.1007/s12088-008-0032-3 id: cord-354096-x2skguz8 author: Ray, Pradipta R. title: A pharmacological interactome between COVID-19 patient samples and human sensory neurons reveals potential drivers of neurogenic pulmonary dysfunction date: 2020-06-01 words: 6354.0 sentences: 328.0 pages: flesch: 46.0 cache: ./cache/cord-354096-x2skguz8.txt txt: ./txt/cord-354096-x2skguz8.txt summary: We hypothesized that SARS-CoV-2 infection drives changes in immune cell-derived factors that then interact with receptors expressed by the sensory neuronal innervation of the lung to further promote important aspects of disease severity, including ARDS. We sought to quantify how immune cells might interact with sensory innervation of the lung in COVID-19 using published data from patients, existing RNA sequencing datasets from human dorsal root ganglion neurons and other sources, and a genome-wide ligand-receptor pair database curated for pharmacological interactions relevant for neuro-immune interactions. Additionally, we found that upregulation of transcription factor genes in COVID-19 samples identifies transcription factors associated with alveolar cell types (EHF, PAX9, ELF3, GHRL2) and immune cells (RFX3, SOX5, TP63, HOPX) with functions including regulation of antiviral pathways (NR3C2), based on ARCHS4 database (Lachmann et al., 2018) and the Enrichr gene set enrichment analysis tool (Kuleshov et al., 2016) (Supplementary Table 2 ). abstract: The SARS-CoV-2 virus infects cells of the airway and lungs in humans causing the disease COVID-19. This disease is characterized by cough, shortness of breath, and in severe cases causes pneumonia and acute respiratory distress syndrome (ARDS) which can be fatal. Bronchial alveolar lavage fluid (BALF) and plasma from mild and severe cases of COVID-19 have been profiled using protein measurements and bulk and single cell RNA sequencing. Onset of pneumonia and ARDS can be rapid in COVID-19, suggesting a potential neuronal involvement in pathology and mortality. We hypothesized that SARS-CoV-2 infection drives changes in immune cell-derived factors that then interact with receptors expressed by the sensory neuronal innervation of the lung to further promote important aspects of disease severity, including ARDS. We sought to quantify how immune cells might interact with sensory innervation of the lung in COVID-19 using published data from patients, existing RNA sequencing datasets from human dorsal root ganglion neurons and other sources, and a genome-wide ligand-receptor pair database curated for pharmacological interactions relevant for neuro-immune interactions. Our findings reveal a landscape of ligand-receptor interactions in the lung caused by SARS-CoV-2 viral infection and point to potential interventions to reduce the burden of neurogenic inflammation in COVID-19 pulmonary disease. In particular, our work highlights opportunities for clinical trials with existing or under development rheumatoid arthritis and other (e.g. CCL2, CCR5 or EGFR inhibitors) drugs to treat high risk or severe COVID-19 cases. url: https://api.elsevier.com/content/article/pii/S088915912030670X doi: 10.1016/j.bbi.2020.05.078 id: cord-006826-vnmg0zid author: Rayaprolu, Vamseedhar title: Length of encapsidated cargo impacts stability and structure of in vitro assembled alphavirus core-like particles date: 2017-12-06 words: 6543.0 sentences: 338.0 pages: flesch: 56.0 cache: ./cache/cord-006826-vnmg0zid.txt txt: ./txt/cord-006826-vnmg0zid.txt summary: In this work, we wanted to determine how the length of the cargo impacts the stability and structure of the assembled CLPs. We hypothesized that cargo neutralizes the basic region of the alphavirus capsid protein and if the cargo is long enough, it will also act to scaffold the CP monomers together. Modest differences in particle size on DLS and EM suggest that changes in light scattering intensity indicate that similar amounts of CLPs were formed using 48hp, 48lin, and 90mer oligos than with the shorter 27mer ( figure 1(B) ). From our ionic strength stability results (figure 1(B)), we postulated that longer cargo that functioned to both neutralize charge and scaffold CP would favor the formation of complete, closed, spherical cores. This model provides an explanation for the structural defects observed in the cryo-EM classification, but does not account for the possible role of longer cargo in scaffolding or bridging between CP monomers to promote CLP assembly. abstract: In vitro assembly of alphavirus nucleocapsid cores, called core-like particles (CLPs), requires a polyanionic cargo. There are no sequence or structure requirements to encapsidate single-stranded nucleic acid cargo. In this work, we wanted to determine how the length of the cargo impacts the stability and structure of the assembled CLPs. We hypothesized that cargo neutralizes the basic region of the alphavirus capsid protein and if the cargo is long enough, it will also act to scaffold the CP monomers together. Experimentally we found that CLPs encapsidating short 27mer oligonucleotides were less stable than CLPs encapsidating 48mer or 90mer oligonucleotides under different chemical and thermal conditions. Furthermore, cryo-EM studies showed there were structural differences between CLPs assembled with 27mer and 48mer cargo. To mimic the role of the cargo in CLP assembly we made a mutant (4D) where we substituted a cluster of four Lys residues in the CP with four Asp residues. We found that these few amino acid substitutions were enough to initiate CLP assembly in the absence of cargo. The cargo-free 4D CLPs show higher resistance to ionic strength and increased temperature compared to wild-type cargo containing CLPs suggesting their CLP assembly mechanism might also be different. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103146/ doi: 10.1088/1361-648x/aa90d0 id: cord-254713-ghcwfcx2 author: Razanajatovo, Norosoa H title: Detection of new genetic variants of Betacoronaviruses in Endemic Frugivorous Bats of Madagascar date: 2015-03-12 words: 4163.0 sentences: 200.0 pages: flesch: 49.0 cache: ./cache/cord-254713-ghcwfcx2.txt txt: ./txt/cord-254713-ghcwfcx2.txt summary: RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species. abstract: BACKGROUND: Bats are amongst the natural reservoirs of many coronaviruses (CoVs) of which some can lead to severe infection in human. African bats are known to harbor a range of pathogens (e.g., Ebola and Marburg viruses) that can infect humans and cause disease outbreaks. A recent study in South Africa isolated a genetic variant closely related to MERS-CoV from an insectivorous bat. Though Madagascar is home to 44 bat species (41 insectivorous and 3 frugivorous) of which 34 are endemic, no data exists concerning the circulation of CoVs in the island’s chiropteran fauna. Certain Malagasy bats can be frequently found in close contact with humans and frugivorous bats feed in the same trees where people collect and consume fruits and are hunted and consumed as bush meat. The purpose of our study is to detect and identify CoVs from frugivorous bats in Madagascar to evaluate the risk of human infection from infected bats. METHODS: Frugivorous bats belonging to three species were captured in four different regions of Madagascar. We analyzed fecal and throat swabs to detect the presence of virus through amplification of the RNA-dependent RNA polymerase (RdRp) gene, which is highly conserved in all known coronaviruses. Phylogenetic analyses were performed from positive specimens. RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Phylogenetic analysis revealed that the Malagasy strains belong to the genus Betacoronavirus but form three distinct clusters, which seem to represent previously undescribed genetic lineages. CONCLUSIONS: Our findings suggest that CoVs circulate in frugivorous bats of Madagascar, demonstrating the needs to evaluate spillover risk to human populations especially for individuals that hunt and consume infected bats. Possible dispersal mechanisms as to how coronaviruses arrived on Madagascar are discussed. url: https://doi.org/10.1186/s12985-015-0271-y doi: 10.1186/s12985-015-0271-y id: cord-305737-bnzd7b25 author: Rehwinkel, Jan title: Targeting the viral Achilles’ heel: recognition of 5′-triphosphate RNA in innate anti-viral defence date: 2013-05-23 words: 4133.0 sentences: 246.0 pages: flesch: 55.0 cache: ./cache/cord-305737-bnzd7b25.txt txt: ./txt/cord-305737-bnzd7b25.txt summary: Targeting the viral Achilles'' heel: recognition of 5 0 -triphosphate RNA in innate anti-viral defence Jan Rehwinkel 1 and Caetano Reis e Sousa 2 Some RNA virus genomes bear 5 0 -triphosphates, which can be recognized in the cytoplasm of infected cells by host proteins that mediate anti-viral immunity. Both the innate sensor RIG-I and the interferon-induced IFIT proteins bind to 5 0 -triphosphate viral RNAs. RIG-I signals for induction of interferons during RNA virus infection while IFITs sequester viral RNAs to exert an antiviral effect. Recent work shows that the IFN system targets 5PPP RNAs during both phases: both RIG-I, a virus sensor that induces IFN expression, and IFITs, effector molecules that execute anti-viral activities, can specifically recognize 5PPP RNAs. As such, 5PPP RNAs appear to be Achilles'' heel of many RNA viruses in their interaction with the innate immune system (Figure 3a ). abstract: Some RNA virus genomes bear 5′-triphosphates, which can be recognized in the cytoplasm of infected cells by host proteins that mediate anti-viral immunity. Both the innate sensor RIG-I and the interferon-induced IFIT proteins bind to 5′-triphosphate viral RNAs. RIG-I signals for induction of interferons during RNA virus infection while IFITs sequester viral RNAs to exert an anti-viral effect. Notably, the structures of these proteins reveal both similarities and differences, which are suggestive of independent evolution towards ligand binding. 5′-triphosphates, which are absent from most RNAs in the cytosol of uninfected cells, are thus a marker of virus infection that is targeted by the innate immune system for both induction and execution of the anti-viral response. url: https://doi.org/10.1016/j.mib.2013.04.009 doi: 10.1016/j.mib.2013.04.009 id: cord-345898-a6vt8kso author: Ren, Linzhu title: Live Cell Reporter Systems for Positive-Sense Single Strand RNA Viruses date: 2016-01-04 words: 6000.0 sentences: 289.0 pages: flesch: 38.0 cache: ./cache/cord-345898-a6vt8kso.txt txt: ./txt/cord-345898-a6vt8kso.txt summary: There are three types of cell-based reporter systems that express certain reporter protein for positive-sense single strand RNA virus infections. An RVP is a type of virus-like particle (VLP) composed of viral structural proteins and a self-replicating replicon RNA containing a reporter gene [17, 63] . However, when the cells were infected with the specific virus, the viral RdRp was provided by the virus and the defective replicon was activated, resulting in high-level expression of the reporter gene, which could be easily examined [44] . However, when the cells were infected with the specific virus, the viral RdRp was provided by the virus and the defective replicon was activated, resulting in high-level expression of the reporter gene, which could be easily examined [44] . Development of Dengue type-2 virus replicons expressing GFP reporter gene in study of viral RNA replication abstract: Cell-based reporter systems have facilitated studies of viral replication and pathogenesis, virus detection, and drug susceptibility testing. There are three types of cell-based reporter systems that express certain reporter protein for positive-sense single strand RNA virus infections. The first type is classical reporter system, which relies on recombinant virus, reporter virus particle, or subgenomic replicon. During infection with the recombinant virus or reporter virus particle, the reporter protein is expressed and can be detected in real time in a dose-dependent manner. Using subgenomic replicon, which are genetically engineered viral RNA molecules that are capable of replication but incapable of producing virions, the translation and replication of the replicon could be tracked by the accumulation of reporter protein. The second type of reporter system involves genetically engineered cells bearing virus-specific protease cleavage sequences, which can sense the incoming viral protease. The third type is based on viral replicase, which can report the specific virus infection via detection of the incoming viral replicase. This review specifically focuses on the major technical breakthroughs in the design of cell-based reporter systems and the application of these systems to the further understanding and control of viruses over the past few decades. url: https://doi.org/10.1007/s12010-015-1968-5 doi: 10.1007/s12010-015-1968-5 id: cord-271127-l9bxqtqs author: Renault, Sylvaine title: Commensal and mutualistic relationships of reoviruses with their parasitoid wasp hosts date: 2005-02-28 words: 6784.0 sentences: 376.0 pages: flesch: 54.0 cache: ./cache/cord-271127-l9bxqtqs.txt txt: ./txt/cord-271127-l9bxqtqs.txt summary: (2) Putative mutualistic virus: a reovirus present routinely in a wasp population in association with others viruses, but which does not appear to play a major role in the host/parasitoid relationship. DpAV-4 has been shown to be essential in the host/parasitoid relationship, as it is able to inhibit melanization, and to interfere with the cytolysis of host tissues in lepidopteran pupae parasitized by the wasp (Bigot et al., 1997b; Renault et al., 2002) . The occurrence of this domain in the protein coded by the DpRV-1 4.3 kb genomic fragment might be correlated with a possible role of this virus in its interaction with the ascovirus DpAV-4 in its lepidopteran and wasp hosts. Owing to the apparent absence of DpAV-1 virions or RNA within the egg, the transmission of DpRV-1 to the wasp larva during their development in host pupae was investigated. abstract: Abstract During evolution, certain endoparasitoid wasps have developed mechanisms to suppress the defence systems of their hosts. For this purpose, these species, all of which belong to the families Ichneumonidae and Braconidae, inject various kinds of virus-like particles. The most studied of these particles are classified as polydnaviruses (family Polydnaviridae) which are symbiotic viruses. Over the past decade, it has also been shown that several wasp species harbour reoviruses (family Reoviridae), and that two of these suppress host defence, allowing the development of the parasitoid eggs. In this paper, we summarize the key features of these viruses and their relationships with their wasp hosts. Five reoviruses are known that appear to be non-pathogenic for the wasps. Three of these, McRVLP, HeRV, OpRVLP, use their wasp hosts as vectors, and do not appear to be involved in host defence suppression. The fourth, DpRV-1, is a commensal reovirus detected in most field populations of the wasp, Diadromus pulchellus. This reovirus is always found associated with an ascovirus, DpAV-4a, which is indispensable for host immune suppression. Although DpRV-1 has not been shown to directly increase D. pulchellus parasitic success, it may contribute to this success by retarding DpAV-4a replication in the wasp. The fifth reovirus, DpRV-2, occurs in a specific population of D. pulchellus in which DpRV-1 and DpAV-4 are absent. This virus has a mutualistic relationship with its wasp host, as its injection by females during oviposition is essential for host immunosuppression. Interestingly, these viruses belong to several different reovirus genera. url: https://api.elsevier.com/content/article/pii/S0022191004001441 doi: 10.1016/j.jinsphys.2004.08.002 id: cord-330800-s91zfzfi author: Reta, Daniel Hussien title: Molecular and Immunological Diagnostic Techniques of Medical Viruses date: 2020-09-04 words: 10548.0 sentences: 574.0 pages: flesch: 43.0 cache: ./cache/cord-330800-s91zfzfi.txt txt: ./txt/cord-330800-s91zfzfi.txt summary: e nucleic acid amplification tests are very popular in the diagnosis of viral infections caused by several viruses, including hepatitis C virus (HCV), human immunodeficiency virus (HIV), dengue virus, Epstein-Barr virus (EBV), influenza viruses, Zika virus (ZIKV), Ebola virus, and coronavirus [26] [27] [28] [29] [30] [31] [32] . Owing to high sensitivity and specificity, short turnaround time for results, and ease of performance [33, 61] , most laboratories across the globe employ real-time PCR for the detection and quantification of medical DNA and RNA viruses in clinical specimens. For example, Co-Diagnostics (Salt Lake City, USA) has developed real-time RT-PCR kit (Logix Smart COVID-19 test) for qualitative detection of nucleic acid from the SARS-CoV-2 in lower respiratory samples (e.g., bronchoalveolar lavage, sputum, and tracheal aspirate) and upper respiratory specimens (e.g., oropharyngeal swabs, nasal swabs, and nasopharyngeal swabs). LAMP is another isothermal nucleic acid amplification method that is extensively utilized for sensitive, specific, rapid, and cost-effective detection of both DNA and RNA viruses in human specimens. abstract: Viral infections are causing serious problems in human population worldwide. The recent outbreak of coronavirus disease 2019 caused by SARS-CoV-2 is a perfect example how viral infection could pose a great threat to global public health and economic sectors. Therefore, the first step in combating viral pathogens is to get a timely and accurate diagnosis. Early and accurate detection of the viral presence in patient sample is crucial for appropriate treatment, control, and prevention of epidemics. Here, we summarize some of the molecular and immunological diagnostic approaches available for the detection of viral infections of humans. Molecular diagnostic techniques provide rapid viral detection in patient sample. They are also relatively inexpensive and highly sensitive and specific diagnostic methods. Immunological-based techniques have been extensively utilized for the detection and epidemiological studies of human viral infections. They can detect antiviral antibodies or viral antigens in clinical samples. There are several commercially available molecular and immunological diagnostic kits that facilitate the use of these methods in the majority of clinical laboratories worldwide. In developing countries including Ethiopia where most of viral infections are endemic, exposure to improved or new methods is highly limited as these methods are very costly to use and also require technical skills. Since researchers and clinicians in all corners of the globe are working hard, it is hoped that in the near future, they will develop good quality tests that can be accessible in low-income countries. url: https://www.ncbi.nlm.nih.gov/pubmed/32908530/ doi: 10.1155/2020/8832728 id: cord-310771-tnwfp1je author: Revilla-Fernández, Sandra title: The use of endogenous and exogenous reference RNAs for qualitative and quantitative detection of PRRSV in porcine semen date: 2005-02-23 words: 5933.0 sentences: 297.0 pages: flesch: 51.0 cache: ./cache/cord-310771-tnwfp1je.txt txt: ./txt/cord-310771-tnwfp1je.txt summary: A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. As endogenous control for one-step real-time reverse transcription (RT)-PCR UBE2D2 mRNA was selected. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36). For the development of one-step real-time RT-PCR for four endogenous reference RNAs (HPRT, UBE2D2, PPIA, and HMBS) appropriate target regions were selected and the assay conditions were optimised for amplification efficiency. One-step real-time RT-PCR assays for PRRSV-1 and -2 RNA allowed quantitation with optimal efficiency (Fig. 1a ; standard curves for two additional viremic pigs infected with PRRSV-1 (data not shown)) as achieved for endogenous and Fig. 1 . abstract: Semen is known to be a route of porcine reproductive and respiratory syndrome virus (PRRSV) transmission. A method was developed for qualitative and quantitative detection of the seminal cell-associated PRRSV RNA in relation to endogenous and exogenous reference RNAs. As endogenous control for one-step real-time reverse transcription (RT)-PCR UBE2D2 mRNA was selected. Particularly for the analysis of persistent infections associated with low copy numbers of PRRSV RNA, UBE2D2 mRNA is an ideal control due to its low expression in seminal cells and its detection in all samples analysed (n = 36). However, the amount of UBE2D2 mRNA in porcine semen varied (up to 106-fold), thus its use is limited to qualitative detection of PRRSV RNA. For quantitation, a synthetic, non-metazoan RNA was added to the RNA isolation reaction at an exact copy number. The photosynthesis gene ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) from Arabidopsis thaliana was used as an exogenous spike. Unexpectedly, PRRSV RNA was detected in a herd of specific pathogen-free (SPF) boars which were tested ELISA-negative for anti-PRRSV antibodies. Therefore, RT-PCR for seminal cell-associated PRRSV is a powerful tool for managing the SPF status during quarantine programs and for routine outbreak investigations. url: https://www.ncbi.nlm.nih.gov/pubmed/15847915/ doi: 10.1016/j.jviromet.2005.01.018 id: cord-343448-xhm97wy2 author: Rinaldi, Andrea title: RNA to the rescue: RNA is one of the most promising targets for drug development given its wide variety of uses date: 2020-06-26 words: 2934.0 sentences: 167.0 pages: flesch: 49.0 cache: ./cache/cord-343448-xhm97wy2.txt txt: ./txt/cord-343448-xhm97wy2.txt summary: In brief, RNAi works through gene silencing, degrading the mRNA for a specific protein through the coordinated action of double-stranded RNA and a complex biochemical machinery it activates (Fig 1) . The spearhead is mRNA-1273, which encodes a prefusion-stabilized form of the spike (S) protein of SARS-CoV-2, developed at an unusually fast rate (first volunteer injected on Mach 16, only 65 days after the publication of the virus sequence) by Moderna, a biotech based in Cambridge, Massachusetts (https://www.modernatx.c om/). Multi-component proteins that would be impossible to target with other systems are accessible with RNA technology, as recently demonstrated by the generation of a multi-antigenic mRNA vaccine encoding human cytomegalovirus glycoproteins gB and pentameric complex (John et al, 2018) . CV9202, for example, is a mRNA encoding six antigens usually expressed in non-small-cell lung cancer (NSCLC), developed by CureVac, a biotech based in Tübingen, Germany (https://www.curevac.com/), in collaboration with Boehringer Ingelheim. abstract: The race for a vaccine against SARS‐CoV‐2 has accelerated research on RNA‐based therapeutics. Beyond vaccines, RNA also shows great potential for cancer therapies.[Image: see text] url: https://www.ncbi.nlm.nih.gov/pubmed/32588530/ doi: 10.15252/embr.202051013 id: cord-102898-eyyd7ent author: Rizvi, Vaseef A. title: Translation regulation of Japanese encephalitis virus revealed by ribosome profiling date: 2020-07-17 words: 3048.0 sentences: 159.0 pages: flesch: 44.0 cache: ./cache/cord-102898-eyyd7ent.txt txt: ./txt/cord-102898-eyyd7ent.txt summary: Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. downstream polyprotein, 2) Significant modulation in levels of a distinct subset of ribosome-bound tRNAs 48 that cannot be explained by virtue of codon usage and 3) Translation from an upstream ORF (uORF) using 49 a non-canonical initiation codon in the 5 UTR region of JEV. However, these sites do not represent commonly associated Studies on RNA viruses have suggested adaptations in codon usage of viral genes to the host translation [30] . Interestingly, JEV infection appears to stimulate 251 expression from UUG start site by almost 67% suggesting viral or virus-induced host trans-regulatory factors 252 promoting uORF translation (Fig.4D) . We also identify a subset of ribosome associated 286 tRNAs whose levels are modulated globally upon JEV infection (Fig.3) . abstract: Japanese encephalitis virus (JEV), a neurotropic flavivirus, is the leading cause of viral encephalitis in endemic regions of Asia. Although the mechanisms modulating JEV virulence and neuroinvasiveness are poorly understood, several acquired mutations in the live attenuated vaccine strain (SA14-14-2) point towards translation regulation as a key strategy. Using ribosome profiling, we identify multiple mechanisms including frameshifting, tRNA dysregulation and alternate translation initiation sites that regulate viral protein synthesis. A significant fraction (~ 40%) of ribosomes undergo frameshifting on NS1 coding sequence leading to early termination, translation of NS1′ protein and modulation of viral protein stoichiometry. Separately, a tRNA subset (glutamate, serine, leucine and histidine) was found to be associated in high levels with the ribosomes upon JEV infection. We also report a previously uncharacterised translational initiation event from an upstream UUG initiation codon in JEV 5′ UTR. A silent mutation at this start site in the vaccine strain has been shown to abrogate neuroinvasiveness suggesting the potential role of translation from this region. Together, our study sheds light on distinct mechanisms that modulate JEV translation with likely consequences for viral pathogenesis. url: https://doi.org/10.1101/2020.07.16.206920 doi: 10.1101/2020.07.16.206920 id: cord-320713-b37c8aye author: Roberts, Lisa O. title: Chapter 9 Viral Strategies to Subvert the Mammalian Translation Machinery date: 2009-10-27 words: 20205.0 sentences: 1067.0 pages: flesch: 48.0 cache: ./cache/cord-320713-b37c8aye.txt txt: ./txt/cord-320713-b37c8aye.txt summary: 6 The rate of translation initiation in mammalian cells is also controlled by sequence elements within the 5 0 -and 3 0 -UTRs of mRNAs which regulate this process by providing sites for interaction of regulatory proteins and RNAs. These include upstream open reading frames (uORFs), microRNA (miRNA) target sites, and polyadenylation elements. 5 It was suggested that alternative eIF4F complexes lacking PABP could selectively promote the synthesis of viral, but not host, proteins, so that KSHV-encoded mRNAs would compete more effectively for host translation machinery in infected cells. Picornavirus translation is directed by internal ribosome entry sites (IRESs) within the 5 0 -UTRs of the viral RNAs. The central one-third of eIF4G, containing the eIF3 and one eIF4A-binding domain, is sufficient to support translation initiation from these IRESs. 43 This allows picornavirus RNAs to compete effectively for the host translation machinery following infection, although the situation appears to be more complicated than this (see Section III). abstract: Viruses do not carry their own protein biosynthesis machinery and the translation of viral proteins therefore requires that the virus usurps the machinery of the host cell. To allow optimal translation of viral proteins at the expense of cellular proteins, virus families have evolved a variety of methods to repress the host translation machinery, while allowing effective viral protein synthesis. Many viruses use noncanonical mechanisms that permit translation of their own RNAs under these conditions. Viruses have also developed mechanisms to evade host innate immune responses that would repress translation under conditions of viral infection, in particular PKR activation in response to double-stranded RNA (dsRNA). Importantly, the study of viral translation mechanisms has enormously enhanced our understanding of many aspects of the cellular protein biosynthesis pathway and its components. A number of unusual mechanisms of translation initiation that were first discovered in viruses have since been observed in cellular mRNAs, and it has become apparent that a diverse range of translation mechanisms operates in eukaryotes, allowing subtle regulation of this essential process. url: https://api.elsevier.com/content/article/pii/S1877117309900096 doi: 10.1016/s1877-1173(09)90009-6 id: cord-022336-zqnczjpp author: Robertson, Hugh D. title: Virus Origins: Conjoined RNA Genomes as Precursors to DNA Genomes date: 2007-09-02 words: 6163.0 sentences: 229.0 pages: flesch: 47.0 cache: ./cache/cord-022336-zqnczjpp.txt txt: ./txt/cord-022336-zqnczjpp.txt summary: The chapter also outlines the significance of work on viroid-like pathogens, circular RNA replication, and their potential relation to early RNA; and relates the early emergence of RNA mosaics to developments leading to today''s DNA-based systems of viral gene expression. Recent work to be reviewed below shows that there is one class of primitive life forms-the viroid-like pathogens -whose properties today could help us to understand how primitive RNA-based self-replication may have been compatible with expansion to produce more complex RNAs. In summary, the causative agent for human hepatitis delta contains two specialized domains, one concerned with replication and the other encoding a single protein (Branch et al., 1989; Purcell and Gerin, 1996; Taylor, 1996) . It is evident that if RNA conjunction leading to delta-like RNA mosaics with both replicating and functionally translatable protein-coding domains has taken place, we need to consider the consequences both for the evolution of primitive RNA systems, yielding today''s DNA-based cellular information system, and for presentday RNA-level events. abstract: RNA's unprecedented ability to act both as a template for information storage and as an enzymatic molecule has led to the proposal that primitive living systems were based on RNA, with protein synthesis and DNA templates for information storage added later. This chapter reviews the current knowledge about RNA rearrangement and recombination in viruses, and cites evidence for various mechanisms catalyzing these events. RNA recombination can occur in a spontaneous manner, and such a potential, even at low frequency, would expand opportunities for RNA conjunction. The chapter also outlines the significance of work on viroid-like pathogens, circular RNA replication, and their potential relation to early RNA; and relates the early emergence of RNA mosaics to developments leading to today's DNA-based systems of viral gene expression. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155586/ doi: 10.1016/b978-012220360-2/50003-9 id: cord-306535-j26eqmxt author: Robertson, Matthew J. title: Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets date: 2020-08-19 words: 16758.0 sentences: 846.0 pages: flesch: 49.0 cache: ./cache/cord-306535-j26eqmxt.txt txt: ./txt/cord-306535-j26eqmxt.txt summary: The majority of candidate genes identified in our screen that were testis-specific were already identified by the Human Protein Atlas [9] and/or our reanalysis of (See figure on previous page.) Fig. 1 Summary of the human and mouse RNA-seq samples used in the identification of novel male reproductive tract-specific drug targets. Additional file 14: Fig. S6 shows the complete list of male reproductive tract-specific human genes for which a previously generated mouse model shows male infertility phenotype, as identified in each of the respective cell and/or tissue datasets. Through the integration of hundreds of published and newly acquired human and mouse reproductive and non-reproductive tissue and cell RNA-seq datasets, we have generated a list of novel genes expressed predominantly or exclusively in the male reproductive tract that are worthy of consideration for functional validation in an animal model and potential targeting for a male contraceptive. abstract: BACKGROUND: The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the function of key proteins involved in reproduction, understanding male reproductive physiology is limited by incomplete information on the genes expressed in reproductive tissues, and no contraceptive targets have so far reached clinical trials. To advance product development, further identification of novel reproductive tract-specific genes leading to potentially druggable protein targets is imperative. RESULTS: In this study, we expand on previous single tissue, single species studies by integrating analysis of publicly available human and mouse RNA-seq datasets whose initial published purpose was not focused on identifying male reproductive tract-specific targets. We also incorporate analysis of additional newly acquired human and mouse testis and epididymis samples to increase the number of targets identified. We detected a combined total of 1178 genes for which no previous evidence of male reproductive tract-specific expression was annotated, many of which are potentially druggable targets. Through RT-PCR, we confirmed the reproductive tract-specific expression of 51 novel orthologous human and mouse genes without a reported mouse model. Of these, we ablated four epididymis-specific genes (Spint3, Spint4, Spint5, and Ces5a) and two testis-specific genes (Pp2d1 and Saxo1) in individual or double knockout mice generated through the CRISPR/Cas9 system. Our results validate a functional requirement for Spint4/5 and Ces5a in male mouse fertility, while demonstrating that Spint3, Pp2d1, and Saxo1 are each individually dispensable for male mouse fertility. CONCLUSIONS: Our work provides a plethora of novel testis- and epididymis-specific genes and elucidates the functional requirement of several of these genes, which is essential towards understanding the etiology of male infertility and the development of male contraceptives. url: https://www.ncbi.nlm.nih.gov/pubmed/32814578/ doi: 10.1186/s12915-020-00826-z id: cord-350019-4nlbu54e author: Robinson, Elektra K. title: The how and why of lncRNA function: An innate immune perspective() date: 2019-09-02 words: 13173.0 sentences: 715.0 pages: flesch: 44.0 cache: ./cache/cord-350019-4nlbu54e.txt txt: ./txt/cord-350019-4nlbu54e.txt summary: Using this extensively studied biological system, we identified the first example of a TLR-stimulated lncRNA, lincRNA-Cox2, which was capable of positively and negatively regulating distinct types of innate immune genes [42] [43] [44] [45] [46] . The majority of lncRNAs studied in immunity were initially identified following RNA-sequencing to examine their expression profiles in specific cell lines or tissues during inflammatory activation. Hence future studies may opt to target TF binding sites, secondary structure and/or polyadenylation sites as a way to more finely dissect the functional portions of lncRNAs. The ease in which Cas9 can be targeted to specific genomic regions sparked the development of a modified (catalytically inactivated) version of the protein fused to the KRAB (Krüppel associated box) chromatin-silencing domain termed CRISPRi [174, 175] (Fig. 3C) . Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites abstract: Next-generation sequencing has provided a more complete picture of the composition of the human transcriptome indicating that much of the “blueprint” is a vastness of poorly understood non-protein-coding transcripts. This includes a newly identified class of genes called long noncoding RNAs (lncRNAs). The lack of sequence conservation for lncRNAs across species meant that their biological importance was initially met with some skepticism. LncRNAs mediate their functions through interactions with proteins, RNA, DNA, or a combination of these. Their functions can often be dictated by their localization, sequence, and/or secondary structure. Here we provide a review of the approaches typically adopted to study the complexity of these genes with an emphasis on recent discoveries within the innate immune field. Finally, we discuss the challenges, as well as the emergence of new technologies that will continue to move this field forward and provide greater insight into the biological importance of this class of genes. This article is part of a Special Issue entitled: ncRNA in control of gene expression edited by Kotb Abdelmohsen. url: https://www.ncbi.nlm.nih.gov/pubmed/31487549/ doi: 10.1016/j.bbagrm.2019.194419 id: cord-261735-03hvi4el author: Rodrigues, R. title: Development of a one step real time RT-PCR assay to detect and quantify Dugbe virus date: 2011-06-14 words: 2637.0 sentences: 159.0 pages: flesch: 60.0 cache: ./cache/cord-261735-03hvi4el.txt txt: ./txt/cord-261735-03hvi4el.txt summary: A one-step real time quantitative RT-PCR (qRT-PCR) assay was developed to detect all published Dugbe virus (DUGV) genomes of the Nairovirus genus. Frequently detected in tick-borne virus surveys in Africa (Guilherme et al., 1996) , DUGV is a tri-segmented single-stranded negative RNA enveloped virus and is considered endemic in arid regions (Burt et al., 1996) . The aim of this study was to develop a sensitive, specific and rapid one-step quantitative real time RT-PCR assay (qRT-PCR) to detect DUGV in infected cell supernatants, ticks or serum samples. The specificity was evaluated by using RNA extracted from supernatants from CCHFV, Hazara virus, Coronavirus and Influenza A virus infected cells. Among the 498 captured ticks, one Dugbe virus RNA was detected in one tick using the qRT-PCR assay (0.2%). In conclusion, a sensitive and specific qRT-PCR assay was developed to detect and quantify DUGV RNAs in infected cell supernatants, extracts from ticks and potentially sera. abstract: A one-step real time quantitative RT-PCR (qRT-PCR) assay was developed to detect all published Dugbe virus (DUGV) genomes of the Nairovirus genus. Primers and probes were designed to detect specific sequences on the most conserved regions of the S segment. The limit of detection of the assay was 10 copies per reaction which is an improvement of 3 log(10) FFU/mL over the sensitivity of conventional RT-PCR. The specificity of the primers and probe was confirmed with the closely related Nairoviruses CCHFV and Hazara virus, and on the non-related viruses Coronavirus and Influenza A virus. This qRT-PCR assay was used to screen nucleic acids extracted from 498 ticks collected in the Republic of Chad. One sample was found positive suggesting that DUGV is present in this part of the world. The molecular assay developed in this study is sensitive, specific and rapid and can be used for research and epidemiological studies. url: https://www.ncbi.nlm.nih.gov/pubmed/21703306/ doi: 10.1016/j.jviromet.2011.06.003 id: cord-324697-c0dv1zmi author: Rodriguez, William title: Fated for decay: RNA elements targeted by viral endonucleases date: 2020-06-07 words: 6407.0 sentences: 336.0 pages: flesch: 50.0 cache: ./cache/cord-324697-c0dv1zmi.txt txt: ./txt/cord-324697-c0dv1zmi.txt summary: Consequently, viruses have evolved an arsenal of strategies to target these RNA features and ultimately take control of the pathways they influence, and these strategies contribute to the global shutdown of the host gene expression machinery known as "Host Shutoff". Throughout this section we will discuss how each of these RNA features render mRNA susceptible toand in many cases directviral endonuclease cleavage or similar strategies aimed at degradation of the host transcriptome during viral infection. Nsp1 thus emerges as a thorough RNA decay trigger that uses diverse and non-overlapping strategies to widely target host mRNAs. How the viral transcripts escape nsp-1 mediated is still under investigation. Overall, SARS coronavirus nsp1 is an interesting regulator of RNA stability: currently, nsp1 does not appear to have any endonucleolytic activity of its own, and instead binds to the 40 s subunit exploiting the host''s RNA quality control pathways to trigger mRNA degradation. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression abstract: For over a decade, studies of messenger RNA regulation have revealed an unprecedented level of connectivity between the RNA pool and global gene expression. These connections are underpinned by a vast array of RNA elements that coordinate RNA-protein and RNA-RNA interactions, each directing mRNA fate from transcription to translation. Consequently, viruses have evolved an arsenal of strategies to target these RNA features and ultimately take control of the pathways they influence, and these strategies contribute to the global shutdown of the host gene expression machinery known as “Host Shutoff”. This takeover of the host cell is mechanistically orchestrated by a number of non-homologous virally encoded endoribonucleases. Recent large-scale screens estimate that over 70 % of the host transcriptome is decimated by the expression of these viral nucleases. While this takeover strategy seems extraordinarily well conserved, each viral endonuclease has evolved to target distinct mRNA elements. Herein, we will explore each of these RNA structures/sequence features that render messenger RNA susceptible or resistant to viral endonuclease cleavage. By further understanding these targeting and escape mechanisms we will continue to unravel untold depths of cellular RNA regulation that further underscores the integral relationship between RNA fate and the fate of the cell. url: https://doi.org/10.1016/j.semcdb.2020.05.010 doi: 10.1016/j.semcdb.2020.05.010 id: cord-290254-m9l8ntur author: Rodriguez-Manzano, J. title: A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes date: 2020-06-30 words: 5622.0 sentences: 340.0 pages: flesch: 54.0 cache: ./cache/cord-290254-m9l8ntur.txt txt: ./txt/cord-290254-m9l8ntur.txt summary: In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 {+/-} 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Currently, reverse transcriptase polymerase chain reaction using real-time benchtop platform (RT-qPCR) is considered the gold standard for COVID-19 diagnosis due to its capability to detect the presence of SARS-CoV-2 RNA close to the onset of symptomatic illness which is critical for isolation. In this paper, we combined LAMP with an in-house LoC device to develop a rapid PoC diagnostic test (< 20 min) for the detection of SARS-CoV-2 RNA from extracted samples. abstract: The COVID-19 pandemic is a global health emergency characterized by the high rate of transmission and ongoing increase of cases globally. Rapid point-of-care (PoC) diagnostics to detect the causative virus, SARS-CoV-2, are urgently needed to identify and isolate patients, contain its spread and guide clinical management. In this work, we report the development of a rapid PoC diagnostic test (< 20 min) based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and semiconductor technology for the detection of SARS-CoV-2 from extracted RNA samples. The developed LAMP assay was tested on a real-time benchtop instrument (RT-qLAMP) showing a lower limit of detection of 10 RNA copies per reaction. It was validated against 183 clinical samples including 127 positive samples (screened by the CDC RT-qPCR assay). Results showed 90.55% sensitivity and 100% specificity when compared to RT-qPCR and average positive detection times of 15.45 {+/-} 4.43 min. For validating the incorporation of the RT-LAMP assay onto our PoC platform (RT-eLAMP), a subset of samples was tested (n=40), showing average detection times of 12.89 {+/-} 2.59 min for positive samples (n=34), demonstrating a comparable performance to a benchtop commercial instrument. Paired with a smartphone for results visualization and geo-localization, this portable diagnostic platform with secure cloud connectivity will enable real-time case identification and epidemiological surveillance. url: http://medrxiv.org/cgi/content/short/2020.06.29.20142349v1?rss=1 doi: 10.1101/2020.06.29.20142349 id: cord-335040-1qa6pe4v author: Rogstam, Annika title: Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 date: 2020-10-06 words: 7408.0 sentences: 385.0 pages: flesch: 59.0 cache: ./cache/cord-335040-1qa6pe4v.txt txt: ./txt/cord-335040-1qa6pe4v.txt summary: The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication. observed SARS nsp10 in the same space group as reported here, I213, reporting a monomer in the asymmetric unit but a dimer in solution, as was determined by size exclusion Residues shaded in red are fully conserved, while residues with text in red indicate a change to a similar residue. We determined the crystal structure and behaviour in solution of SARS-CoV-2 nsp10 in its unbound form. abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), causing Coronavirus Disease 19 (COVID-19), emerged at the end of 2019 and quickly spread to cause a global pandemic with severe socio-economic consequences. The early sequencing of its RNA genome revealed its high similarity to SARS, likely to have originated from bats. The SARS-CoV-2 non-structural protein 10 (nsp10) displays high sequence similarity with its SARS homologue, which binds to and stimulates the 3′-to-5′ exoribonuclease and the 2′-O-methlytransferase activities of nsps 14 and 16, respectively. Here, we report the biophysical characterization and 1.6 Å resolution structure of the unbound form of nsp10 from SARS-CoV-2 and compare it to the structures of its SARS homologue and the complex-bound form with nsp16 from SARS-CoV-2. The crystal structure and solution behaviour of nsp10 will not only form the basis for understanding the role of SARS-CoV-2 nsp10 as a central player of the viral RNA capping apparatus, but will also serve as a basis for the development of inhibitors of nsp10, interfering with crucial functions of the replication–transcription complex and virus replication. url: https://www.ncbi.nlm.nih.gov/pubmed/33036230/ doi: 10.3390/ijms21197375 id: cord-287501-7it4kh0e author: Roh, Changhyun title: A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide date: 2012-05-03 words: 2964.0 sentences: 153.0 pages: flesch: 45.0 cache: ./cache/cord-287501-7it4kh0e.txt txt: ./txt/cord-287501-7it4kh0e.txt summary: We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. 33 In this study, we report a novel approach for the inhibitor screening of SARS-CoV N protein using a quantum dots (QDs)-conjugated oligonucleotide system with wide applicability for facile and sensitive imaging analysis on a biochip. To the best of our knowledge, this is the first report on the inhibition effects of (-)-catechin gallate and (-)-gallocatechin gallate on SARS-CoV N protein using an optical nanoparticle-based RNA oligonucleotide platform. Among the polyphenolic compounds screened, (-)-catechin gallate and (-)-gallocatechin gallate showed high anti-SARS-CoV N protein activity. At a concentration of 0.05 µg mL -1 , (-)-catechin gallate and (-)-gallocatechin gallate showed more than 40% inhibition activity on a QDs-RNA oligonucleotide biochip platform. abstract: Hundreds of million people worldwide have been infected with severe acute respiratory syndrome (SARS), and the rate of global death from SARS has remarkably increased. Hence, the development of efficient drug treatments for the biological effects of SARS is highly needed. We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV) nucleocapsid (N) protein. In this study, we found that a designed biochip could analyze inhibitors of the SARS-CoV N protein using nanoparticle-based RNA oligonucleotide. Among the polyphenolic compounds examined, (−)-catechin gallate and (−)-gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. (−)-catechin gallate and (−)-gallocatechin gallate attenuated the binding affinity in a concentrated manner as evidenced by QDs-conjugated RNA oligonucleotide on a designed biochip. At a concentration of 0.05 μg mL(−1), (−)-catechin gallate and (−)-gallocatechin gallate showed more than 40% inhibition activity on a nanoparticle-based RNA oligonucleotide biochip system. url: https://doi.org/10.2147/ijn.s31379 doi: 10.2147/ijn.s31379 id: cord-341324-f9g9gitn author: Rojas, José M. title: Viral pathogen-induced mechanisms to antagonize mammalian interferon (IFN) signaling pathway date: 2020-10-21 words: 10837.0 sentences: 595.0 pages: flesch: 42.0 cache: ./cache/cord-341324-f9g9gitn.txt txt: ./txt/cord-341324-f9g9gitn.txt summary: This includes for instance cooperating in PRR recognition of viral PAMPs, stabilizing signaling complexes to improve their resistance to degradation, stopping virus entry, blocking viral capsid formation, impairing trafficking and budding of virions from the infected cells, but also modulating the IFN response to avoid the toxicity of these potent immune mediators. The phosphorylated STAT1/STAT2 heterodimer associates with interferon regulatory factor 9 (IRF9) to form the transcriptional factor complex ISGF3, which translocate to the nucleus and binds the IFN-response elements (ISRE) in ISG promoters leading to the expression of ISG products [36] (Fig. 2 The oligoadenylate synthetase (OAS)-latent RNase (RNase L) pathway is another IFN-inducible pathway that provides the cell with an effector mechanism upon recognition of viral dsRNA (reviewed in [44] ). abstract: Antiviral responses of interferons (IFNs) are crucial in the host immune response, playing a relevant role in controlling viralw infections. Three types of IFNs, type I (IFN-α, IFN-β), II (IFN-γ) and III (IFN-λ), are classified according to their receptor usage, mode of induction, biological activity and amino acid sequence. Here, we provide a comprehensive review of type I IFN responses and different mechanisms that viruses employ to circumvent this response. In the first part, we will give an overview of the different induction and signaling cascades induced in the cell by IFN-I after virus encounter. Next, highlights of some of the mechanisms used by viruses to counteract the IFN induction will be described. And finally, we will address different mechanism used by viruses to interference with the IFN signaling cascade and the blockade of IFN induced antiviral activities. url: https://www.ncbi.nlm.nih.gov/pubmed/33084946/ doi: 10.1007/s00018-020-03671-z id: cord-270892-ycc3csyh author: Rollinger, Judith M. title: The human rhinovirus: human‐pathological impact, mechanisms of antirhinoviral agents, and strategies for their discovery date: 2010-12-13 words: 19628.0 sentences: 1166.0 pages: flesch: 41.0 cache: ./cache/cord-270892-ycc3csyh.txt txt: ./txt/cord-270892-ycc3csyh.txt summary: [79] [80] [81] [82] Taken together, the results of natural cold studies as well as of experimental infection in human volunteers clearly demonstrate that HRV are able to replicate in the upper as well as in the lower airways. Such an anti-HRV drug would have to be (i) with broad spectrum activity because of the high number of HRV serotypes, (ii) administered very early in infection to demonstrate a good antiviral effect because of the fast infection kinetics, (iii) very safe because of the broad application by millions of people, and (iv) directed against a highly conserved target with low risk of resistance development. The HRV-induced CPE, infectious virus titers, viral protein expression, and RNA synthesis can be chosen as parameters to evaluate the anti-HRV activity of compounds in cell-culture based assays. Due to the lack of a small-animal model for HRV infection until 2008, the experimental human challenge model has to be used to approve effects of potential antiviral drugs under controlled conditions in preclinical studies. abstract: As the major etiological agent of the common cold, human rhinoviruses (HRV) cause millions of lost working and school days annually. Moreover, clinical studies proved an association between harmless upper respiratory tract infections and more severe diseases e.g. sinusitis, asthma, and chronic obstructive pulmonary disease. Both the medicinal and socio‐economic impact of HRV infections and the lack of antiviral drugs substantiate the need for intensive antiviral research. A common structural feature of the approximately 100 HRV serotypes is the icosahedrally shaped capsid formed by 60 identical copies of viral capsid proteins VP1‐4. The capsid protects the single‐stranded, positive sense RNA genome of about 7,400 bases in length. Both structural as well as nonstructural proteins produced during the viral life cycle have been identified as potential targets for blocking viral replication at the step of attachment, entry, uncoating, RNA and protein synthesis by synthetic or natural compounds. Moreover, interferon and phytoceuticals were shown to protect host cells. Most of the known inhibitors of HRV replication were discovered as a result of empirical or semi‐empirical screening in cell culture. Structure–activity relationship studies are used for hit optimization and lead structure discovery. The increasing structural insight and molecular understanding of viral proteins on the one hand and the advent of innovative computer‐assisted technologies on the other hand have facilitated a rationalized access for the discovery of small chemical entities with antirhinoviral (anti‐HRV) activity. This review will (i) summarize existing structural knowledge about HRV, (ii) focus on mechanisms of anti‐HRV agents from synthetic and natural origin, and (iii) demonstrate strategies for efficient lead structure discovery. © 2009 Wiley Periodicals, Inc. Med Res Rev, 31, No. 1, 42–92, 2010 url: https://doi.org/10.1002/med.20176 doi: 10.1002/med.20176 id: cord-294842-aesiff1f author: Romero-Brey, Inés title: Membranous Replication Factories Induced by Plus-Strand RNA Viruses date: 2014-07-22 words: 11038.0 sentences: 520.0 pages: flesch: 40.0 cache: ./cache/cord-294842-aesiff1f.txt txt: ./txt/cord-294842-aesiff1f.txt summary: Three-dimensional reconstructions of the WNV KUN replication sites revealed an intimate association of the rough ER (rER) with the bounding membrane of the VPs [20] (Figure 2B ), resembling the vesicles observed in DENV-infected cells. In cells infected with TBEV, one of the most important tick-transmitted viruses in Europe and Asia, virus particles and membrane-connected vesicles were also observed inside the ER [25] , similar to what was described for DENV and WNV KUN . Importantly, pulse-radiolabeling experiments localized sites of active RNA replication to the outer surface of single-membrane tubules [71] and isolation of the membranous replication factories and their subsequent visualization by EM revealed that they form rosette-like structures composed of virus-induced cytoplasmic vesicles [124] . Formation of plant RNA virus replication complexes on membranes: Role of an endoplasmic reticulum-targeted viral protein abstract: In this review, we summarize the current knowledge about the membranous replication factories of members of plus-strand (+) RNA viruses. We discuss primarily the architecture of these complex membrane rearrangements, because this topic emerged in the last few years as electron tomography has become more widely available. A general denominator is that two “morphotypes” of membrane alterations can be found that are exemplified by flaviviruses and hepaciviruses: membrane invaginations towards the lumen of the endoplasmatic reticulum (ER) and double membrane vesicles, representing extrusions also originating from the ER, respectively. We hypothesize that either morphotype might reflect common pathways and principles that are used by these viruses to form their membranous replication compartments. url: https://doi.org/10.3390/v6072826 doi: 10.3390/v6072826 id: cord-347472-n6811ens author: Rosebrock, Adam P. title: Patient DNA cross-reactivity of the CDC SARS-CoV-2 extraction control leads to an inherent potential for false negative results date: 2020-05-15 words: 6252.0 sentences: 344.0 pages: flesch: 51.0 cache: ./cache/cord-347472-n6811ens.txt txt: ./txt/cord-347472-n6811ens.txt summary: The US Centers for Disease Control and Prevention (CDC) have specified and given emergency use authorization (EUA) for a SARS-CoV-2 molecular diagnostic used to detect viral RNA in clinical samples (2) . Genomic DNA is co-purified in quantities sufficient to generate strong positive signals for the CDC-specified extraction control during work-up of clinical RNA specimens. To test for the presence of control-affecting DNA, qPCR reactions lacking reverse transcriptase were performed on SARS-CoV-2-positive clinical samples using the CDC-specified RP primer and probe. All clinical samples tested generated unambiguous extraction control positive signals in the absence of reverse transcription, a reaction context that could not have detected virus an RNA virus ( Fig. 2A) Single-digit copies of genomic DNA are sufficient to generate a positive control signal using the CDC-designed assay. Due to the presence of co-purifying genomic DNA in clinical samples, loss of RNA integrity leads to false-negative results using the CDC-specified control. abstract: Testing for RNA viruses such as SARS-CoV-2 requires careful handling of inherently labile RNA during sample collection, clinical processing, and molecular analysis. Tests must include fail-safe controls that affirmatively report the presence of intact RNA and demonstrate success of all steps of the assay. A result of “no virus signal” is insufficient for clinical interpretation: controls must also say “The reaction worked as intended and would have found virus if present.” Unfortunately, a widely used test specified by the US Centers for Disease Control and Prevention (CDC) incorporates a control that does not perform as intended and claimed. Detecting SARS-CoV-2 with this assay requires both intact RNA and successful reverse transcription. The CDC-specified control does not require either of these, due to its inability to differentiate human genomic DNA from reverse-transcribed RNA. Patient DNA is copurified from nasopharyngeal swabs during clinically-approved RNA extraction and is sufficient to return an “extraction control success” signal using the CDC design. As such, this assay fails-unsafe: truly positive patient samples return a false-negative result of “no virus detected, control succeeded” following any of several readily-encountered mishaps. This problem affects tens-of-millions of patients worth of shipped assays, but many of these flawed reagents have not yet been used. There is an opportunity to improve this important diagnostic tool. As demonstrated here, a re-designed transcript-specific control correctly monitors sample collection, extraction, reverse transcription, and qPCR detection. This approach can be rapidly implemented and will help reduce truly positive patients from being incorrectly given the all-clear. One Sentence Summary A widely-used COVID-19 diagnostic is mis-designed and generates false-negative results, dangerously confusing “No” with “Don’t know” – but it’s fixable url: https://doi.org/10.1101/2020.05.13.094839 doi: 10.1101/2020.05.13.094839 id: cord-256615-gvq8uyfk author: Rosenberg, Ronald title: Detecting the emergence of novel, zoonotic viruses pathogenic to humans date: 2014-11-22 words: 6688.0 sentences: 306.0 pages: flesch: 45.0 cache: ./cache/cord-256615-gvq8uyfk.txt txt: ./txt/cord-256615-gvq8uyfk.txt summary: RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. Despite the differences in clinical presentation and geographical location, these three pathogens share three characteristics: all were unknown before found infecting humans, all are RNA viruses, and all have proven or putative non-human, animal sources. A single subtropical bat species hardly represents all mammal species and indeed many viruses are known to infect more than one species; they tested for only 9 of the 25 virus families pathogenic to humans. abstract: RNA viruses, with their high potential for mutation and epidemic spread, are the most common class of pathogens found as new causes of human illness. Despite great advances made in diagnostic technology since the 1950s, the annual rate at which novel virulent viruses have been found has remained at 2–3. Most emerging viruses are zoonoses; they have jumped from mammal or bird hosts to humans. An analysis of virus discovery indicates that the small number of novel viruses discovered annually is an artifact of inadequate surveillance in tropical and subtropical countries, where even established endemic pathogens are often misdiagnosed. Many of the emerging viruses of the future are already infecting humans but remain to be uncovered by a strategy of disease surveillance in selected populations. url: https://doi.org/10.1007/s00018-014-1785-y doi: 10.1007/s00018-014-1785-y id: cord-356009-emn2w8if author: Roshandel, M. R. title: What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis date: 2020-10-13 words: 4687.0 sentences: 292.0 pages: flesch: 49.0 cache: ./cache/cord-356009-emn2w8if.txt txt: ./txt/cord-356009-emn2w8if.txt summary: Conclusions: Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight ?percent of patients but also its incidence may have associations with the severity of the ?systemic disease, ICU admission, and fatality rates. The searches included medical subject headings (MeSH) and keywords for SARS-CoV-2, COVID, Corona, together with shedding, persistence, urine, urinary, specimen, viral load, or RNA body fluids. We completed the data abstraction process using created forms to record study characteristics, clinical data, and laboratory data including study year and design, country of study origin, total initial population size, test type for disease diagnosis, test type for samples (urine/stool/rectal swab/blood), patients age (including mean and range), number of positive and total patients and/or (wherever applicable) number of positive and total specimens collected for each test category, disease severity, ICU admission, and fatality rate. abstract: Objective:Investigating the infectivity of body fluid can be useful for preventative measures in the community and ensuring safety in the operating rooms and on the laboratory practices. Methods:We performed a literature search of clinical trials, cohorts, and case series using PubMed/MEDLINE, Google Scholar, and Cochrane library, and downloadable database of CDC. We excluded case reports and searched all language articles for review and repeated until the final drafting. The search protocol was registered in the PROSPERO database. Results: Thirty studies with urinary sampling for viral shedding were included. A total number of 1,271 patients were enrolled initially, among which 569 patients had undergone urinary testing. Nine studies observed urinary viral shedding in urine from 41 patients. The total incidence of urinary SARS-CoV-2 shedding was 8%, compared to 21.3% and 39.5 % for blood and stool, respectively. The summarized risk ratio (RR) estimates for urine positive rates compared to the pharyngeal rate was 0.08. The pertaining RR urine compared to blood and stool positive rates were 0.20 and 0.33 respectively. Conclusions: Our review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight ?percent of patients but also its incidence may have associations with the severity of the ?systemic disease, ICU admission, and fatality rates. Moreover, the findings in our review ?suggest that a larger population size may reveal more positive urinary cases possibly by ?minimizing biases. However, it is important to notice that it is the naso-pharyngeal specimens, ?stool, and serum that show more possibilities to became positive, respectively. url: https://doi.org/10.1101/2020.10.08.20209544 doi: 10.1101/2020.10.08.20209544 id: cord-308331-55ge7kmr author: Routh, Andrew title: Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data date: 2013-10-09 words: 6014.0 sentences: 285.0 pages: flesch: 52.0 cache: ./cache/cord-308331-55ge7kmr.txt txt: ./txt/cord-308331-55ge7kmr.txt summary: Using ViReMa, we demonstrate that by mapping the distribution and frequency of recombination events in the genome of flock house virus (FHV), we can discover de novo functional genomic motifs required for viral replication and encapsidation. Here, segments at the 5 0 and the 3 0 end of a complex recombination event have been mapped to nt 500-550 and nt 1040-1080 of FHV RNA 1, but there remain a small number of trimmed nucleotides in the middle. We generated 5 043 791 synthetic reads containing 99 033 unique recombination events and aligned these reads to the FHV genome with ViReMa using a seed length of 20 nt. Our analysis of FHV demonstrates that by isolating a small number of virus particles, deep sequencing the encapsidated RNA and mapping the positions of recombination events, functional RNA motifs can be discovered. abstract: We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5′ end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3′ end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome. url: https://doi.org/10.1093/nar/gkt916 doi: 10.1093/nar/gkt916 id: cord-275683-1qj9ri18 author: Roux, Simon title: Metagenomics in Virology date: 2019-06-12 words: 5891.0 sentences: 225.0 pages: flesch: 37.0 cache: ./cache/cord-275683-1qj9ri18.txt txt: ./txt/cord-275683-1qj9ri18.txt summary: Against the background of an extensive viral diversity revealed by metagenomics across many environments, new sequence assembly approaches that reconstruct complete genome sequences from metagenomes have recently revealed surprisingly cosmopolitan viruses in specific ecological niches. However, these techniques can only detect previously known viruses, and often require Box 1 Use of complementary methods to target different types of viruses A number of approaches have been developed to specifically select and survey the genetic material contained by virus particles in a given sample. Virus sequences obtained from "bulk" metagenomes will typically reflect viruses infecting their host cell at the time of sampling, either actively replicating or not, while viromes enables a deeper and more focused exploration of the virus diversity in a specific site or sample. With viral metagenomics being applied to a larger set of samples and environments, and with bioinformatic analyses including genome assembly and interpretation constantly improving, novel groups of dominant and widespread viruses may thus be progressively revealed across many environments. abstract: Metagenomics, i.e., the sequencing and analysis of genomic information extracted directly from clinical or environmental samples, has become a fundamental tool to explore the viral world. Against the background of an extensive viral diversity revealed by metagenomics across many environments, new sequence assembly approaches that reconstruct complete genome sequences from metagenomes have recently revealed surprisingly cosmopolitan viruses in specific ecological niches. Metagenomics is also applied to clinical samples as a non-targeted diagnostic and surveillance tool. By enabling the study of these uncultivated viruses, metagenomics provides invaluable insights into the virus-host interactions, epidemiology, ecology, and evolution of viruses across all ecosystems. url: https://api.elsevier.com/content/article/pii/B9780128096338209576 doi: 10.1016/b978-0-12-809633-8.20957-6 id: cord-340422-8f5xe4zc author: Rowland, R. R. R. title: Inhibition of porcine reproductive and respiratory syndrome virus by interferon-gamma and recovery of virus replication with 2-aminopurine date: 2001 words: 4715.0 sentences: 283.0 pages: flesch: 50.0 cache: ./cache/cord-340422-8f5xe4zc.txt txt: ./txt/cord-340422-8f5xe4zc.txt summary: Porcine reproductive and respiratory syndrome virus (PRRSV) belongs to a group of RNA viruses that establish persistent infections. IFN-γ mRNA expression was observed in the lymph nodes and lungs of pigs infected with wild-type PRRSV strain SDSU-23983. The purpose of this study was to evaluate the production of IFN-␥ in pigs following infection with PRRSV and to characterize the mechanism of IFN-␥ action following infection of MARC-145 cells with wild-type and culture adapted PRRSV isolates. The results show that IFN-␥ efficiently inhibits PRRSV replication in MARC-145 cells, and at least part of the antiviral activity may be through PKR. IFN-␥ mRNA expression was detected in the lymph nodes from two of the 3 pigs infected with the wild-type P6 virus (Fig. 1) . Consistent with other reports describing the presence of cell-mediated immunity during PRRSV infection [4, 31] , we observed IFN-␥ mRNA expression in lymph nodes and lungs of PRRSV-infected pigs (Fig. 1) . IFN gamma inhibits porcine reproductive and respiratory syndrome virus replication in macrophages abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) belongs to a group of RNA viruses that establish persistent infections. A proposed strategy for evading immunity during persistent PRRSV infection is by preventing the induction of IFN activity in pigs and/or by blocking the activation of antiviral proteins in permissive cells. IFN-γ mRNA expression was observed in the lymph nodes and lungs of pigs infected with wild-type PRRSV strain SDSU-23983. Pretreatment of MARC-145 cells with IFN-γ inhibited wild-type (SDSU-23983 P6) and culture-adapted (SDSU-23983 P136) PRRS viruses in a dose-dependent manner and at relatively low concentrations. The effect of IFN-γ on virus replication included reductions in the number of infected cells, virus yield, and RNA content in single cells. Virus replication was partially restored by the addition of 2-aminopurine (2-AP), an inhibitor of dsRNA inducible protein kinase (PKR). The addition of 2-AP also restored the viral RNA content per cell to near normal levels, suggesting that inhibition of viral RNA synthesis was through PKR. The principal difference between P6 and P136 isolates was the recovery of P136 replication with lower concentrations of 2-AP. Immunostaining with anti-PKR antibody showed a redistribution of PKR from the cytoplasm into nucleoli of infected cells. url: https://www.ncbi.nlm.nih.gov/pubmed/11338389/ doi: 10.1007/s007050170161 id: cord-261160-g92zhv19 author: Rowland, Raymond R.R title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero date: 2003-10-30 words: 6383.0 sentences: 322.0 pages: flesch: 48.0 cache: ./cache/cord-261160-g92zhv19.txt txt: ./txt/cord-261160-g92zhv19.txt summary: title: Lymphoid tissue tropism of porcine reproductive and respiratory syndrome virus replication during persistent infection of pigs originally exposed to virus in utero Even though PRRSV-specific antibody appears as early as 5 days post-infection and is followed by serum neutralizing activity and cell-mediated immunity Molitor, 1997, 1999; Rowland et al., 1999 Rowland et al., , 2001 persistently infected pigs can continue to shed virus. The purpose of this study was to further understand persistent infection in congenitally infected pigs by characterizing the course of clinical disease, sites of virus replication and the capacity to transmit virus in a group of pigs exposed to PRRSV in utero. Analysis of virus and antibody in blood and/or umbilical cords from the 28 live neonates showed that at least 20 or 74% were virus isolation (VI) or RT-PCR positive for PRRSV at the time of farrowing indicating that in utero infection was successful. abstract: The ability of porcine reproductive and respiratory syndrome virus (PRRSV) to establish a persistent infection is the principal contributing factor to the world-wide spread of the disease. Several studies have documented the course of viral infection in postnatally infected pigs; however, very little is known regarding sites of virus replication during persistent infection of pigs exposed to PRRSV in utero. In this study, virus replication and PRRSV-specific antibody were followed for several hundred days in a group of pigs derived from three sows infected at 90 days of gestation with PRRSV isolate VR-2332. Eighty-four percent of pigs were born viremic with a mortality of 54% within 21 days after birth. At approximately 60 days sera from pigs were negative for virus by virus isolation. Analysis of virus replication in the tissues of pigs randomly sacrificed between 63 and 132 days showed no evidence of virus in lung and other non-lymphoid organs. However, virus was easily recovered from tonsil and lymph nodes and in situ hybridization identified these tissues as sites of virus replication. Even though replication was at a low level, virus was easily transmitted to sentinel pigs. By 260 days pigs became seronegative and did not transmit virus to sentinel pigs. Sacrifice of remaining pigs after 300 days showed no evidence of virus in blood and tissues. This study shows that congenital PRRSV-infected pigs can support virus replication for an extended period during which virus replication is primarily restricted to tonsil and lymph nodes. url: https://www.ncbi.nlm.nih.gov/pubmed/14559170/ doi: 10.1016/j.vetmic.2003.07.006 id: cord-350697-u032yk0z author: Roy, Anupam title: Can concomitant use of zinc and curcumin with other immunity‐boosting nutraceuticals be the arsenal against COVID‐19? date: 2020-06-02 words: 1110.0 sentences: 68.0 pages: flesch: 44.0 cache: ./cache/cord-350697-u032yk0z.txt txt: ./txt/cord-350697-u032yk0z.txt summary: Lack of effective prophylaxis against COVID-19 has prompted regulatory authorities to propose boosting of immunity of individuals via nutritional supplements. While modern medicine directly confronts an antigen (via vaccination or antibiotic), in comparison nutraceuticals, food supplements, and traditional medicines activate the overall immunity of the human body. Both molecules have a proven history of antiviral activity in both in vitro and in vivo trials thus could be leadings in developing new prophylactic candidates against COVID-19. Thus, these supplements as a part of the food, nutraceutical, or traditional medicines may pave the way towards developing a therapeutic strategy against the COVID-19 pandemic. The success story of TCM is continuously inspiring us to test food supplements and raise individual immunity. Potential mechanisms by which Curcumin and Zinc can exert therapeutic effects against COVID-19. Curcumin inhibits SARS-CoV-2 entry by binding directly to the receptorbinding domain (RBD) of Spike (S) protein of the virus. abstract: nan url: https://doi.org/10.1002/ptr.6766 doi: 10.1002/ptr.6766 id: cord-334947-pa0p5dif author: Rozen-Gagnon, Kathryn title: Alphavirus Mutator Variants Present Host-Specific Defects and Attenuation in Mammalian and Insect Models date: 2014-01-16 words: 8887.0 sentences: 415.0 pages: flesch: 44.0 cache: ./cache/cord-334947-pa0p5dif.txt txt: ./txt/cord-334947-pa0p5dif.txt summary: Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. To estimate the population diversity of variants by deep sequencing, cDNA libraries were prepared by Superscript III from RNA extracted from virus generated in BHK-21 or C6/36 cells, and the viral genome was amplified using a high fidelity polymerase (Phusion) to generate 5 overlapping amplicons 2-3 kb in length. To address the possibility that the fitness cost of defective replication, observed in mosquito cell culture, would favor the reversion of these mutant polymerases to wildtype, we deep sequenced virus from the body of an individual mosquito that presented the median titer from each group. abstract: Arboviruses cycle through both vertebrates and invertebrates, which requires them to adapt to disparate hosts while maintaining genetic integrity during genome replication. To study the genetic mechanisms and determinants of these processes, we use chikungunya virus (CHIKV), a re-emerging human pathogen transmitted by the Aedes mosquito. We previously isolated a high fidelity (or antimutator) polymerase variant, C483Y, which had decreased fitness in both mammalian and mosquito hosts, suggesting this residue may be a key molecular determinant. To further investigate effects of position 483 on RNA-dependent RNA-polymerase (RdRp) fidelity, we substituted every amino acid at this position. We isolated novel mutators with decreased replication fidelity and higher mutation frequencies, allowing us to examine the fitness of error-prone arbovirus variants. Although CHIKV mutators displayed no major replication defects in mammalian cell culture, they had reduced specific infectivity and were attenuated in vivo. Unexpectedly, mutator phenotypes were suppressed in mosquito cells and the variants exhibited significant defects in RNA synthesis. Consequently, these replication defects resulted in strong selection for reversion during infection of mosquitoes. Since residue 483 is conserved among alphaviruses, we examined the analogous mutations in Sindbis virus (SINV), which also reduced polymerase fidelity and generated replication defects in mosquito cells. However, replication defects were mosquito cell-specific and were not observed in Drosophila S2 cells, allowing us to evaluate the potential attenuation of mutators in insect models where pressure for reversion was absent. Indeed, the SINV mutator variant was attenuated in fruit flies. These findings confirm that residue 483 is a determinant regulating alphavirus polymerase fidelity and demonstrate proof of principle that arboviruses can be attenuated in mammalian and insect hosts by reducing fidelity. url: https://www.ncbi.nlm.nih.gov/pubmed/24453971/ doi: 10.1371/journal.ppat.1003877 id: cord-030028-s6sxi8uj author: Rubio, Luis title: Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution date: 2020-07-17 words: 14687.0 sentences: 698.0 pages: flesch: 40.0 cache: ./cache/cord-030028-s6sxi8uj.txt txt: ./txt/cord-030028-s6sxi8uj.txt summary: This technique has been used to differentiate isolates of some plant viruses, such as prunus necrotic ringspot virus (PNRSV), TYLCV and CTV (Gillings et al., 1993; Hammond et al., 1998; Font et al., 2007) ; iii) Single-strand conformation polymorphism (SSCP) analysis is based on electrophoresis of denatured dsDNA in non-denaturing gels so migration of single-stranded DNA depends on its conformation determined by its nucleotide sequence and the electrophoretic conditions. This technique followed by sequencing of the different haplotypes detected has been used to evaluate the genetic variation of some plant viruses, such as cucumber mosaic virus (CMV), citrus psorosis virus (CPsV) and CTV (Rubio et al., 1996; Rubio et al., 1999; Vives et al., 2002; Lin et al., 2003; Martıń et al., 2006) . Procedures to detect and identify various viruses or virus strains in a single assay simultaneously reduce time and cost of the analysis (see Pallaś et al., 2018 for a comprehensive review), and are especially suitable for evaluating mixed infections in individual plants. abstract: Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380168/ doi: 10.3389/fpls.2020.01092 id: cord-271241-w1q46y63 author: Ruggiero, Emanuela title: Viral G-quadruplexes: New frontiers in virus pathogenesis and antiviral therapy date: 2020-05-18 words: 8912.0 sentences: 495.0 pages: flesch: 45.0 cache: ./cache/cord-271241-w1q46y63.txt txt: ./txt/cord-271241-w1q46y63.txt summary: Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. 1 In the past few decades, pharmaceutical and biotechnological advance has succeeded in developing new therapeutics for the management of different viral diseases: for example, anti-retroviral therapy against the human immunodeficiency virus (HIV), or the pan-genotypic direct-acting antiviral drugs used for hepatitis C (HCV) management. In addition, such PQSs are highly conserved, despite the high recombination rates that characterize viruses, suggesting a crucial role for G4s in viral evolution and replication, and corroborating their targeting as a valid pharmacological approach for antiviral therapy. abstract: Viruses are the most abundant organisms on our planet, affecting all living beings: some of them are responsible for massive epidemics that concern health, national economies and the overall welfare of societies. Although advances in antiviral research have led to successful therapies against several human viruses, still some of them cannot be eradicated from the host and most of them do not have any treatment available. Consequently, innovative antiviral therapies are urgently needed. In the past few years, research on G-quadruplexes (G4s) in viruses has boomed, providing powerful evidence for the regulatory role of G4s in key viral steps. Comprehensive bioinformatics analyses have traced putative G4-forming sequences in the genome of almost all human viruses, showing that their distribution is statistically significant and their presence highly conserved. Since the genomes of viruses are remarkably variable, high conservation rates strongly suggest a crucial role of G4s in the viral replication cycle and evolution, emphasizing the possibility of targeting viral G4s as a new pharmacological approach in antiviral therapy. Recent studies have demonstrated the formation and function of G4s in pathogens responsible for serious diseases, such as HIV-1, Hepatitis B and C, Ebola viruses, to cite a few. In this chapter, we present the state of the art on the structural and functional characterization of viral G4s in RNA viruses, DNA viruses and retroviruses. We also present the G4 ligands that provide further details on the viral G4 role and which, showing promising antiviral activity, which could be exploited for the development of innovative antiviral agents. url: https://api.elsevier.com/content/article/pii/S0065774320300142 doi: 10.1016/bs.armc.2020.04.001 id: cord-319116-2ts6zpdb author: Ruggiero, Emanuela title: G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy date: 2018-04-20 words: 9124.0 sentences: 410.0 pages: flesch: 42.0 cache: ./cache/cord-319116-2ts6zpdb.txt txt: ./txt/cord-319116-2ts6zpdb.txt summary: Since the number of reports describing the presence of G4s in virus genomes has boomed in the past 2 years and treatment with several G4 ligands has shown potentially interesting therapeutic activity, we here aim at presenting, organizing and discussing an up-to-date close-up of the literature on G4s in viruses and the classes of molecules that have shown antiviral activity by viral G4 targeting. The research of G4s in the HIV-1 genome has been quite productive, concerning not only the two RNA viral genome copies, but also the integrated proviral genome, specifically For each virus the following information is shown: virion structure and dimension, genome size and organization; schematic representation of the G4 (red dots) location in the viral genomes or in the mRNA and G4 binding proteins; number of G4s assessed through bioinformatics analysis, according to the corresponding references; G4 ligands reported to date to display antiviral effect and corresponding references. abstract: G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing interest. Indeed, G4s have been reported in several viruses, including those involved in recent epidemics, such as the Zika and Ebola viruses. Viral G4s are usually located in regulatory regions of the genome and implicated in the control of key viral processes; in some cases, they have been involved also in viral latency. In this context, G4 ligands have been developed and tested both as tools to study the complexity of G4-mediated mechanisms in the viral life cycle, and as therapeutic agents. In general, G4 ligands showed promising antiviral activity, with G4-mediated mechanisms of action both at the genome and transcript level. This review aims to provide an updated close-up of the literature on G4s in viruses. The current state of the art of G4 ligands in antiviral research is also reported, with particular focus on the structural and physicochemical requirements for optimal biological activity. The achievements and the to-dos in the field are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/29554280/ doi: 10.1093/nar/gky187 id: cord-274080-884x48on author: Rumlová, Michaela title: In vitro methods for testing antiviral drugs date: 2018-06-30 words: 17989.0 sentences: 941.0 pages: flesch: 41.0 cache: ./cache/cord-274080-884x48on.txt txt: ./txt/cord-274080-884x48on.txt summary: For the majority of animal viruses, the activation of these fusion or penetration mechanisms occurs through conformational changes and structural rearrangements in viral surface proteins and/or the whole virion shell that may destabilize the capsid core. D: Three mechanisms (I.-III.) of DNA viruses replication are shown: (I): Following entry and uncoating, the DNA genome is transported to the nucleus; products of early genes (regulatory proteins, transcription factors) regulate the synthesis of viral enzymes (e.g. DNA polymerase) required for genome replication; expression of late genes encoding structural capsid proteins in the cytosol, they are then transported into nucleus where packaging and pre-assembly take place; preassembled procapsids exit the nucleus and leave the cell (e.g. Herpesviruses). Here, we provide an overview of in vitro methods, including cell-based assays, that may be suitable for screening of antivirotics that interfere with the key steps of viral life cycles and target either virus or cell-encoded proteins required for the infectivity. abstract: Abstract Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/29292156/ doi: 10.1016/j.biotechadv.2017.12.016 id: cord-003707-fbe47bgi author: Russo, Alice G title: Novel insights into endogenous RNA viral elements in Ixodes scapularis and other arbovirus vector genomes date: 2019-06-18 words: 9010.0 sentences: 611.0 pages: flesch: 55.0 cache: ./cache/cord-003707-fbe47bgi.txt txt: ./txt/cord-003707-fbe47bgi.txt summary: I. scapularis NIRVS are enriched in bunyaand orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. NIRVS arise from the reverse transcription of viral RNA into cDNA and its integration into the genome of a host germ cell, followed by vertical transmission to offspring (Katzourakis and Gifford 2010) . Yet recent evidence has highlighted the abundance of NIRVS in some arthropod genomes-e.g., Ae. aegypti and Ae. albopictus contain >100 NIRVS from over eight RNA virus families encompassing þssRNA, ÀssRNA, and dsRNA viral groups (Palatini et al. Using the well-studied genomes of Aedes mosquitoes to validate our analysis, we employed a bioinformatic pipeline to characterise NIRVS in seven non-Aedes arbovirus vectors that have representative genomic sequences (Table 1 and Fig. 1 ). scapularis lacked NIRVS from positive-sense RNA viruses, which comprise about one tenth of NIRVS in Aedes mosquitoes ( Fig. 3; Supplementary Table S2 ). abstract: Many emerging arboviruses are not transmitted by traditional mosquito vectors, but by lesser-studied arthropods such as ticks, midges, and sand flies. Small RNA (sRNA) silencing pathways are the main antiviral defence mechanism for arthropods, which lack adaptive immunity. Non-retroviral integrated RNA virus sequences (NIRVS) are one potential source of sRNAs which comprise these pathways. NIRVS are remnants of past germline RNA viral infections, where viral cDNA integrates into the host genome and is vertically transmitted. In Aedes mosquitoes, NIRVS are widespread and produce PIWI-interacting RNAs (piRNAs). These are hypothesised to target incoming viral transcripts to modulate viral titre, perhaps rendering the organism a more efficient arbovirus vector. To explore the NIRVS landscape in alternative arbovirus vectors, we validated the NIRVS landscape in Aedes spp. and then identified novel NIRVS in six medically relevant arthropods and also in Drosophila melanogaster. We identified novel NIRVS in Phlebotomus papatasi, Culicoides sonorensis, Rhipicephalus microplus, Anopheles gambiae, Culex quinquefasciatus, and Ixodes scapularis. Due to their unexpected abundance, we further characterised NIRVS in the blacklegged tick I. scapularis (n = 143). Interestingly, NIRVS are not enriched in R. microplus, another hard tick, suggesting this is an Ixodes-specific adaptation. I. scapularis NIRVS are enriched in bunya- and orthomyxo-like sequences, reflecting that ticks are a dominant host for these virus groups. Unlike in mosquitoes, I. scapularis NIRVS are more commonly derived from the non-structural region (replicase) of negative-sense viruses, as opposed to structural regions (e.g. glycoprotein). Like other arthropods, I. scapularis NIRVS preferentially integrate into genomic piRNA clusters, and serve as a template for primary piRNA production in the commonly used embryonic I. scapularis ISE6 cell line. Interestingly, we identified a two-fold enrichment of non-long terminal repeat (non-LTR) retrotransposons, in genomic proximity to NIRVS, contrasting with studeis in Ae. aegypti, where LTR retrotransposons are instead associated with NIRVS formation. We characterised NIRVS phylogeny and integration patterns in the important vector, I. scapularis, revealing they are distinct from those in Aedes spp. Future studies will explore the possible antiviral mechanism conferred by NIRVS to I. scapularis,which may help the transmission of pathogenic arboviruses. Finally, this study explored NIRVS as an untapped wealth of viral diversity in arthropods. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580184/ doi: 10.1093/ve/vez010 id: cord-344714-0cam9ipf author: Russo, Maria title: Roles of flavonoids against coronavirus infection date: 2020-07-28 words: 8395.0 sentences: 394.0 pages: flesch: 46.0 cache: ./cache/cord-344714-0cam9ipf.txt txt: ./txt/cord-344714-0cam9ipf.txt summary: Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL(pro), 3CL(pro), NTPase/helicase. Inhibition of TMPRSS2 and Furin protease activities can be considered an interesting therapeutic option against coronavirus infection, especially COVID-19, allowing the block and/or prevention of SARS-CoV-2 infection, as recently reported [28] . Based on these observations, it is not surprising that molecular docking approach, summarized in Fig. 3 , supports the role of flavonoids in the inhibition of SARS-CoV 3CL pro by binding His41 and Cys145 of the catalytic site and other active site residues (e.g., Met49, Gly143, His163, His164, Glu166, Pro168, and Gln89), stimulating their validation by in vitro and in vivo studies. abstract: In terms of public health, the 21st century has been characterized by coronavirus pandemics: in 2002-03 the virus SARS-CoV caused SARS; in 2012 MERS-CoV emerged and in 2019 a new human betacoronavirus strain, called SARS-CoV-2, caused the unprecedented COVID-19 outbreak. During the course of the current epidemic, medical challenges to save lives and scientific research aimed to reveal the genetic evolution and the biochemistry of the vital cycle of the new pathogen could lead to new preventive and therapeutic strategies against SARS-CoV-2. Up to now, there is no cure for COVID-19 and waiting for an efficacious vaccine, the development of “savage” protocols, based on “old” anti-inflammatory and anti-viral drugs represents a valid and alternative therapeutic approach. As an alternative or additional therapeutic/preventive option, different in silico and in vitro studies demonstrated that small natural molecules, belonging to polyphenols family, can interfere with various stages of coronavirus entry and replication cycle. Here, we reviewed the capacity of well-known (e.g. quercetin, baicalin, luteolin, hesperetin, gallocatechin gallate, epigallocatechin gallate) and uncommon (e.g. scutellarein, amentoflavone, papyriflavonol A) flavonoids, secondary metabolites widely present in plant tissues with antioxidant and anti-microbial functions, to inhibit key proteins involved in coronavirus infective cycle, such as PL(pro), 3CL(pro), NTPase/helicase. Due to their pleiotropic activities and lack of systemic toxicity, flavonoids and their derivative may represent target compounds to be tested in future clinical trials to enrich the drug arsenal against coronavirus infections. url: https://doi.org/10.1016/j.cbi.2020.109211 doi: 10.1016/j.cbi.2020.109211 id: cord-355477-7xd93aqv author: SATIJA, NAMITA title: The Molecular Biology of SARS Coronavirus date: 2007-04-23 words: 4946.0 sentences: 279.0 pages: flesch: 52.0 cache: ./cache/cord-355477-7xd93aqv.txt txt: ./txt/cord-355477-7xd93aqv.txt summary: abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). Organ distribution of severe acute respiratory syndrome (SARS) associated coronavirus (SARS-CoV) in SARS patients: implications for pathogenesis and virus transmission pathways Assembly of severe acute respiratory syndrome coronavirus RNA packaging signal into virus-like particles is nucleocapsid dependent Recombinant severe acute respiratory syndrome (SARS) coronavirus nucleocapsid protein forms a dimer through its C-terminal domain Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells The 3a protein of severe acute respiratory syndrome-associated coronavirus induces apoptosis in Vero E6 cells abstract: abstract: Severe acute respiratory syndrome (SARS) is the first emerging infectious disease of the 21st century that has been highly transmissible and fatal and was caused by a previously unknown coronavirus (SARS‐CoV). The SARS epidemic in 2003 resulted in more than 8400 SARS cases and approximately 800 deaths. Existing in non‐identified animal reservoirs, SARS‐CoV continues to represent a threat to humans although more than four years have passed since a large outbreak of SARS, and no new cases have been reported. However, we cannot exclude the possibility of reemergence of SARS. It is hence necessary to understand the biology of the SARS‐CoV to deal adequately with the next outbreak, whenever it happens. The SARS‐CoV is a novel coronavirus with a large (∼30 thousand nucleotides) positive‐sense, single‐stranded RNA containing 14 functional open reading frames (ORFs) of which 2 large ORFs constitute the replicase gene which encodes proteins required for viral RNA syntheses. The remaining 12 ORFs encode the 4 structural proteins: spike, membrane, nucleocapsid and envelope; and eight accessory proteins. The viral genome and its expression within the host cell undergoes extensive translational and enzymatic processing to form the 4 structural, 8 accessory and 16 nonstructural proteins. In an effort to understand the molecular mechanisms or capsid assembly and viral pathogenesis, laboratories around the world have adopted a variety of approaches to answering these trivial questions. It has been our effort to consolidate all information known to date about the molecular mechanisms of the SARS‐CoV into this chapter to update our readership on the current status of research. url: https://www.ncbi.nlm.nih.gov/pubmed/17470909/ doi: 10.1196/annals.1408.002 id: cord-288651-bgo8istm author: SHI, Yi title: Inhibition of genes expression of SARS coronavirus by synthetic small interfering RNAs date: 2005-03-17 words: 3062.0 sentences: 242.0 pages: flesch: 62.0 cache: ./cache/cord-288651-bgo8istm.txt txt: ./txt/cord-288651-bgo8istm.txt summary: RNA interference (RNAi) is triggered by the presence of a double-stranded RNA (dsRNA), and results in the silencing of homologous gene expression through the specific degradation of an mRNA containing the same sequence. Here, we studied the effects of synthetic siRNA duplexes targeted to SARS coronavirus structural proteins E, M, and N in a cell culture system. Specific inhibition of cellular mRNA by RNAi can be triggered in mammalian cells by the introduction of synthetic 21-to 23-nucleotide duplexes of RNA N genes of SARS-CoV and evaluated their effects on viral genes expression in Vero E6 cells. The results show that all siRNA duplexes specifically reduced SARS-CoV genes expression to different extents compared with the control (Fig. 1) . Kinetic study results (Fig. 2B ) revealed a continuous increase in the specific inhibition of SARS-CoV genes expression by No. 5, No. 6, and No. 16 siRNA from 24 to 72 h after transfection. abstract: RNA interference (RNAi) is triggered by the presence of a double-stranded RNA (dsRNA), and results in the silencing of homologous gene expression through the specific degradation of an mRNA containing the same sequence. dsRNA-mediated RNAi can be used in a wide variety of eucaryotes to induce the sequence-specific inhibition of gene expression. Synthetic 21-23 nucleotide (nt) small interfering RNA (siRNA) with 2 nt 3′ overhangs was recently found to mediate efficient sequence-specific mRNA degradation in mammalian cells. Here, we studied the effects of synthetic siRNA duplexes targeted to SARS coronavirus structural proteins E, M, and N in a cell culture system. Among total 26 siRNA duplexes, we obtained 3 siRNA duplexes which could sequence-specifically reduce target genes expression over 80% at the concentration of 60 nM in Vero E6 cells. The downregulation effect was in correlation with the concentrations of the siRNA duplexes in a range of 0∼60 nM. Our results also showed that many inactive siRNA duplexes may be brought to life simply by unpairing the 5' end of the antisense strands. Results suggest that siRNA is capable of inhibiting SARS coronavirus genes expression and thus may be a new therapeutic strategy for treatment of SARS. url: https://www.ncbi.nlm.nih.gov/pubmed/15780182/ doi: 10.1038/sj.cr.7290286 id: cord-020969-lh2ergpm author: STRAUSS, JAMES H. title: Gene Therapy date: 2012-07-27 words: 11793.0 sentences: 597.0 pages: flesch: 52.0 cache: ./cache/cord-020969-lh2ergpm.txt txt: ./txt/cord-020969-lh2ergpm.txt summary: Together with methods for cloning and manipulating viral genomes, this information has made possible the use of viruses as vectors to express foreign genes. The use of minus-strand RNA viruses as vectors was delayed because the virion RNA itself is not infectious, but recent developments has made it possible to rescue virus from cloned DNA by using coexpression of the appropriate viral proteins in a transfected cell. It is also possible to transfect cells with the E1 or E3 expression cassette together with DNA clones encoding the rest of the adenovirus genome, in which case homologous recombination results in the production of virus. Because the poliovirus replicon lacks a full complement of the structural genes (it is a suicide vector), packaging to produce particles requires infection of a cell that expresses the polioviral structural proteins by some mechanism. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7148746/ doi: 10.1016/b978-0-12-373741-0.50014-3 id: cord-021568-tdfn6up8 author: STRAUSS, JAMES H. title: Subviral Agents date: 2012-07-27 words: 10937.0 sentences: 588.0 pages: flesch: 59.0 cache: ./cache/cord-021568-tdfn6up8.txt txt: ./txt/cord-021568-tdfn6up8.txt summary: The conserved domains highlighted in the figure are thought to be important for the replication of the viroid (i.e., to form promoters recognized by RNA polymerase II) and for its cleavage to produce unit-length molecules. GSS, most FFI, and some cases of CJD occur as dominant inherited diseases, associated with mutations in the gene for the prion protein. The pattern of symptoms associated with a particular TSE may vary, however, depending in part on how the disease was contracted; on the source of the infecting agent; and on the nature of mutations in the prion protein. Studies in mice and other animals, as well as the finding that mutations in the prion protein are associated with inherited TSEs in humans, have made clear that the prion protein, abbreviated PrP, is intimately involved in the transmission of TSE and in the disease process. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7150261/ doi: 10.1016/b978-0-12-373741-0.50012-x id: cord-023726-2fduzqyb author: STRAUSS, JAMES H. title: The Structure of Viruses date: 2012-07-27 words: 10614.0 sentences: 633.0 pages: flesch: 57.0 cache: ./cache/cord-023726-2fduzqyb.txt txt: ./txt/cord-023726-2fduzqyb.txt summary: Also shown for each family is the presence or absence of an envelope in the virion, the triangulation number (defined later) if the virus is icosahedral, the morphology of the nucleocapsid or core, and figure numbers where the structures of members of a family are illustrated. Structural studies of viruses have shown that the capsid proteins that form the virions of many plant and animal icosahedral viruses have a common fold. The largest particle is the nucleocapsid of herpes simplex virus, which is 1250 Å in diameter and has T=16 symmetry (the virion is enveloped but only the nucleocapsid is regular FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. For most RNA viruses, nucleocapsids can be recognized as distinct structures within the infected cell and can be isolated from virions by treatment with detergents that dissolve the envelope. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173534/ doi: 10.1016/b978-0-12-373741-0.50005-2 id: cord-328768-2qk884x2 author: Sabatier, Marina title: Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses date: 2020-10-06 words: 5361.0 sentences: 293.0 pages: flesch: 45.0 cache: ./cache/cord-328768-2qk884x2.txt txt: ./txt/cord-328768-2qk884x2.txt summary: Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). The development of metagenomics next-generation sequencing (mNGS) has enabled the exploration of whole viral nucleic acids within a clinical sample (human virome) in order to detect pathogens not targeted by conventional PCR and to identify emerging viruses [1] [2] [3] [4] [5] [6] [7] [8] . The aim of this study was to compare two automated extraction platforms commonly used in diagnostic laboratories, the eMAG (bioMérieux, Marcy-l Étoile, France) and the MagNA Pure 24 (MP24) (Roche, Basel, Switzerland), and one manual QIAamp Viral RNA Mini Kit extraction (Qiagen, Hilden, Germany), which is among one of the most popular methods used in research laboratories. abstract: Viral metagenomics next-generation sequencing (mNGS) is increasingly being used to characterize the human virome. The impact of viral nucleic extraction on virome profiling has been poorly studied. Here, we aimed to compare the sensitivity and sample and reagent contamination of three extraction methods used for viral mNGS: two automated platforms (eMAG; MagNA Pure 24, MP24) and the manual QIAamp Viral RNA Mini Kit (QIAamp). Clinical respiratory samples (positive for Respiratory Syncytial Virus or Herpes Simplex Virus), one mock sample (including five viruses isolated from respiratory samples), and a no-template control (NTC) were extracted and processed through an mNGS workflow. QIAamp yielded a lower proportion of viral reads for both clinical and mock samples. The sample cross-contamination was higher when using MP24, with up to 36.09% of the viral reads mapping to mock viruses in the NTC (vs. 1.53% and 1.45% for eMAG and QIAamp, respectively). The highest number of viral reads mapping to bacteriophages in the NTC was found with QIAamp, suggesting reagent contamination. Our results highlight the importance of the extraction method choice for accurate virome characterization. url: https://www.ncbi.nlm.nih.gov/pubmed/33036303/ doi: 10.3390/microorganisms8101539 id: cord-277830-6fsz9iy7 author: Saikatendu, Kumar Singh title: Structural Basis of Severe Acute Respiratory Syndrome Coronavirus ADP-Ribose-1″-Phosphate Dephosphorylation by a Conserved Domain of nsP3 date: 2005-11-08 words: 6555.0 sentences: 344.0 pages: flesch: 56.0 cache: ./cache/cord-277830-6fsz9iy7.txt txt: ./txt/cord-277830-6fsz9iy7.txt summary: The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p. One of its sequence homologs, Poa1p (YBR022) from Saccharomyces cerevisiae, was recently functionally characterized as a highly specific phosphatase that removes the 1 00 phosphate group of ADP-ribose-1 00 -phosphate (Appr-1 00 -p) in the latter half of the tRNA splicing pathway in yeast (Shull et al., 2005) , hinting at a similar substrate specificity for SARS ADRP. A view of the proposed active site of SARS ADRP along with the superimposed structures of AF1521 and yeast Ymx7 are shown in Figure 4B , highlighting the interactions that are likely between residues of the protein with the ligand. abstract: The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 Å resolution. The structure of this “X” domain, seen in many single-stranded RNA viruses, reveals a three-layered α/β/α core with a macro-H2A-like fold. The putative active site is a solvent-exposed cleft that is conserved in its three structural homologs, yeast Ymx7, Archeoglobus fulgidus AF1521, and Er58 from E. coli. Its sequence is similar to yeast YBR022W (also known as Poa1P), a known phosphatase that acts on ADP-ribose-1″-phosphate (Appr-1″-p). The SARS nsP3 domain readily removes the 1″ phosphate group from Appr-1″-p in in vitro assays, confirming its phosphatase activity. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1″-p. url: https://api.elsevier.com/content/article/pii/S0969212605003138 doi: 10.1016/j.str.2005.07.022 id: cord-015850-ef6svn8f author: Saitou, Naruya title: Eukaryote Genomes date: 2013-08-22 words: 7424.0 sentences: 484.0 pages: flesch: 53.0 cache: ./cache/cord-015850-ef6svn8f.txt txt: ./txt/cord-015850-ef6svn8f.txt summary: General overviews of eukaryote genomes are first discussed, including organelle genomes, introns, and junk DNAs. We then discuss the evolutionary features of eukaryote genomes, such as genome duplication, C-value paradox, and the relationship between genome size and mutation rates. Most of the protein coding genes of melon mitochondrial DNAs are highly similar to those of its congeneric species, which are watermelon and squash whose mitochondrial genome sizes are 119 kb and 125 kb, respectively. There are various genomic features that are specifi c to eukaryotes other than existence of introns and junk DNAs, such as genome duplication, RNA editing, C-value paradox, and the relationship between genome size and mutation rates. The Perigord black truffl e ( Tuber melanosporum ), shown as A i n Fig. 8.9 , has the largest genome size (~125 Mb) among the 88 fungi species whose genome sequences were so far determined, yet the number of genes is only ~7,500 [ 81 ] . abstract: General overviews of eukaryote genomes are first discussed, including organelle genomes, introns, and junk DNAs. We then discuss the evolutionary features of eukaryote genomes, such as genome duplication, C-value paradox, and the relationship between genome size and mutation rates. Genomes of multicellular organisms, plants, fungi, and animals are then briefly discussed. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119937/ doi: 10.1007/978-1-4471-5304-7_8 id: cord-273326-gmw8gl2r author: Saiz, Juan-Carlos title: Host-Directed Antivirals: A Realistic Alternative to Fight Zika Virus date: 2018-08-24 words: 7111.0 sentences: 293.0 pages: flesch: 34.0 cache: ./cache/cord-273326-gmw8gl2r.txt txt: ./txt/cord-273326-gmw8gl2r.txt summary: In this line, and contrary to above mentioned report [73] , CQ, an FDA-approved anti-inflammatory 4-aminoquinoline and an autophagy inhibitor widely used as an anti-malaria drug that is administered to pregnant women at risk of exposure to Plasmodium parasites, was shown to have anti-ZIKV activity in different cell types (Vero cells, human brain microvascular endothelial cells (hBMECs), and human neural stem cells (NSCs)), affecting early stages of the viral life cycle, possibly by raising the endosomal pH and inhibiting the fusion of the envelope protein to the endosomal membrane [74, 75] . Similarly, by using a drug repurposing screening of over 6000 molecules, it was found that emricasan, a pan-caspase inhibitor that restrains ZIKV-induced increases in caspase-3 activity and is currently in phase 2 clinical trials in chronic hepatitis C virus (HCV)-infected patients, protected human cortical neural progenitor cells (NPC) in both monolayer and three-dimensional organoid cultures, showing neuroprotective activity without suppression of viral replication [82] . abstract: Zika virus (ZIKV), a mosquito-borne flavivirus, was an almost neglected pathogen until its introduction in the Americas in 2015, where it has been responsible for a threat to global health, causing a great social and sanitary alarm due to its increased virulence, rapid spread, and an association with severe neurological and ophthalmological complications. Currently, no specific antiviral therapy against ZIKV is available, and treatments are palliative and mainly directed toward the relief of symptoms, such as fever and rash, by administering antipyretics, anti-histamines, and fluids for dehydration. Nevertheless, lately, search for antivirals has been a major aim in ZIKV investigations. To do so, screening of libraries from different sources, testing of natural compounds, and repurposing of drugs with known antiviral activity have allowed the identification of several antiviral candidates directed to both viral (structural proteins and enzymes) and cellular elements. Here, we present an updated review of current knowledge about anti-ZIKV strategies, focusing on host-directed antivirals as a realistic alternative to combat ZIKV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/30149598/ doi: 10.3390/v10090453 id: cord-352088-9k01ej6l author: Saiz, Juan-Carlos title: Vaccines against RNA Viruses date: 2020-08-27 words: 2330.0 sentences: 94.0 pages: flesch: 39.0 cache: ./cache/cord-352088-9k01ej6l.txt txt: ./txt/cord-352088-9k01ej6l.txt summary: The authors show that vaccination with the GP5-Mosaic-based vaccines resulted in cellular reactivity and higher levels of neutralizing antibodies to both VR2332 and MN184C PRRSV strains, whilst vaccination with the GP5-WT vaccines only induced response against the heterologous challenging virus (VR2332). Another important disease in pigs is that caused by the porcine epidemic diarrhea virus (PEDV), a coronavirus responsible of highly contagious intestinal infections that may result in the death of newborn piglets and weight loss in pigs of all ages, and that seriously damages the swine industry. López-Gil and coworkers [7] , by using an approach based on the modified vaccinia Ankara (MVA) encoding the RVFV glycoproteins (rMVAGnGc), extend their previous observations that a single inoculation was sufficient to induce a protective immune response in mice after a lethal viral challenge, which was related to the presence of glycoprotein specific CD8+ cells and a low-level detection of in vitro neutralizing antibodies. abstract: RNA viruses cause animal, human, and zoonotic diseases that affect millions of individuals, as is being exemplified by the devastating ongoing epidemic of the recently identified SARS-Cov-2 [...]. url: https://doi.org/10.3390/vaccines8030479 doi: 10.3390/vaccines8030479 id: cord-321505-m40s6uw9 author: Sakamoto, Naoya title: Inhibition of hepatitis C virus infection and expression in vitro and in vivo by recombinant adenovirus expressing short hairpin RNA date: 2007-08-07 words: 4424.0 sentences: 253.0 pages: flesch: 45.0 cache: ./cache/cord-321505-m40s6uw9.txt txt: ./txt/cord-321505-m40s6uw9.txt summary: Background and Aim: We have reported previously that synthetic small interfering RNA (siRNA) and DNA‐based siRNA expression vectors efficiently and specifically suppress hepatitis C virus (HCV) replication in vitro. Intravenous delivery of the adenovirus expressing shRNA into transgenic mice that can be induced to express HCV structural proteins by the Cre/loxP switching system resulted in specific suppression of virus protein synthesis in the liver. Here, we report that HCV replication was suppressed in vitro by recombinant retrovirus and adenovirus vectors expressing short hairpin RNA (shRNA) and that the delivery of the adenovirus vector to mice in vivo specifically inhibited viral protein synthesis in the liver. These results indicated that the decrease in luciferase activities was due to specific suppressive effects of shRNA on expression of HCV genomic RNA and the viral proteins, and not due to non-specific effects caused by the delivery of shRNA or to toxicity of the adenovirus vectors. abstract: Background and Aim: We have reported previously that synthetic small interfering RNA (siRNA) and DNA‐based siRNA expression vectors efficiently and specifically suppress hepatitis C virus (HCV) replication in vitro. In this study, we investigated the effects of the siRNA targeting HCV‐RNA in vivo. Methods: We constructed recombinant retrovirus and adenovirus expressing short hairpin RNA (shRNA), and transfected into replicon‐expressing cells in vitro and transgenic mice in vivo. Results: Retroviral transduction of Huh7 cells to express shRNA and subsequent transfection of an HCV replicon into the cells showed that the cells had acquired resistance to HCV replication. Infection of cells expressing the HCV replicon with an adenovirus expressing shRNA resulted in efficient vector delivery and expression of shRNA, leading to suppression of the replicon in the cells by ∼10(−3). Intravenous delivery of the adenovirus expressing shRNA into transgenic mice that can be induced to express HCV structural proteins by the Cre/loxP switching system resulted in specific suppression of virus protein synthesis in the liver. Conclusion: Taken together, our results support the feasibility of utilizing gene targeting therapy based on siRNA and/or shRNA expression to counteract HCV replication, which might prove valuable in the treatment of hepatitis C. url: https://www.ncbi.nlm.nih.gov/pubmed/17683479/ doi: 10.1111/j.1440-1746.2007.05076.x id: cord-276739-84vf5bts author: Sakurai, Akira title: Rapid typing of influenza viruses using super high-speed quantitative real-time PCR date: 2011-08-22 words: 3311.0 sentences: 182.0 pages: flesch: 54.0 cache: ./cache/cord-276739-84vf5bts.txt txt: ./txt/cord-276739-84vf5bts.txt summary: Using SHRT-PCR, 86 strains of influenza viruses isolated by the Tokyo Metropolitan Institute of Public Health were tested; the results showed 100% sensitivity and specificity for each influenza A and B virus, and swine-origin influenza virus. This method offers high sensitivity and selectivity, but generally requires approximately 2 h per run; therefore, qRT-PCR is not appropriate for rapid virus detection or subtyping in outbreaks of fast-spreading and/or highly pathogenic viruses at public health centers, hospitals, airports, and other public transportation hubs. The commercial reaction mixture was from the qRT-PCR kit, RNA-Direct TM SYBR ® Green Real-time PCR Master Mix (Toyobo, Osaka, Japan; http://www.toyobo.co.jp/e/). The SHRT-PCR system detects the highly conserved sequence of the corresponding viral genome, and the newly designed primer sets targeted for typing MP segments do not exhibit any cross reactions among other influenza viruses (Table 5 ). abstract: The development of a rapid and sensitive system for detecting influenza viruses is a high priority for controlling future epidemics and pandemics. Quantitative real-time PCR is often used for detecting various kinds of viruses; however, it requires more than 2 h per run. Detection assays were performed with super high-speed RT-PCR (SHRT-PCR) developed according to a newly designed heating system. The new method uses a high-speed reaction (18 s/cycle; 40 cycles in less than 20 min) for typing influenza viruses. The detection limit of SHRT-PCR was 1 copy/reaction and 10(−1) plaque-forming unit/reaction for viruses in culture supernatants during 20 min. Using SHRT-PCR, 86 strains of influenza viruses isolated by the Tokyo Metropolitan Institute of Public Health were tested; the results showed 100% sensitivity and specificity for each influenza A and B virus, and swine-origin influenza virus. Twenty-seven swabs collected from the pharyngeal mucosa of outpatients were also tested, showing positive signs for influenza virus on an immunochromatographic assay; the results between SHRT-PCR and immunochromatography exhibited 100% agreement for both positive and negative results. The rapid reaction time and high sensitivity of SHRT-PCR makes this technique well suited for monitoring epidemics and pre-pandemic influenza outbreaks. url: https://api.elsevier.com/content/article/pii/S0166093411003491 doi: 10.1016/j.jviromet.2011.08.015 id: cord-293525-c7nwygl1 author: Saldanha, I. F. title: Extension of the known distribution of a novel clade C betacoronavirus in a wildlife host date: 2019-04-03 words: 5041.0 sentences: 235.0 pages: flesch: 46.0 cache: ./cache/cord-293525-c7nwygl1.txt txt: ./txt/cord-293525-c7nwygl1.txt summary: An EriCoV-specific BRYT-Green(®) real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Characterisation of these Erinaceus coronavirus (EriCoV) nucleotide sequences revealed high nucleotide identity to MERS-CoV [3] , the cause of an acute respiratory syndrome in humans with high case fatality rates [5, 6] . Many animal species seem to have the capacity for coronavirus infection in the absence of apparent disease, including bats [15] , aquatic birds [16] and rabbits when inoculated with MERS-CoV [17] . Whole genome sequencing was performed on RNA extracted from one faecal sample collected in 2014 (R618/14) which was identified as EriCoV-positive by real-time RT-PCR. The highest proportion of EriCoV-positive hedgehog samples were submitted from the South of England (34/217, 16%); however, BLR showed no significant association (P = 0.678) between EriCoV infection status and wider region when other factors including age and year were included. abstract: Disease surveillance in wildlife populations presents a logistical challenge, yet is critical in gaining a deeper understanding of the presence and impact of wildlife pathogens. Erinaceus coronavirus (EriCoV), a clade C Betacoronavirus, was first described in Western European hedgehogs (Erinaceus europaeus) in Germany. Here, our objective was to determine whether EriCoV is present, and if it is associated with disease, in Great Britain (GB). An EriCoV-specific BRYT-Green(®) real-time reverse transcription PCR assay was used to test 351 samples of faeces or distal large intestinal tract contents collected from casualty or dead hedgehogs from a wide area across GB. Viral RNA was detected in 10.8% (38) samples; however, the virus was not detected in any of the 61 samples tested from Scotland. The full genome sequence of the British EriCoV strain was determined using next generation sequencing; it shared 94% identity with a German EriCoV sequence. Multivariate statistical models using hedgehog case history data, faecal specimen descriptions and post-mortem examination findings found no significant associations indicative of disease associated with EriCoV in hedgehogs. These findings indicate that the Western European hedgehog is a reservoir host of EriCoV in the absence of apparent disease. url: https://www.ncbi.nlm.nih.gov/pubmed/31063092/ doi: 10.1017/s0950268819000207 id: cord-326217-ji0njeha author: Saleh, Maged title: Glycogen Synthase Kinase 3β Enhances Hepatitis C Virus Replication by Supporting miR-122 date: 2018-11-27 words: 4731.0 sentences: 262.0 pages: flesch: 48.0 cache: ./cache/cord-326217-ji0njeha.txt txt: ./txt/cord-326217-ji0njeha.txt summary: We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. To assess whether both GSK3 isoforms are required for HCV replication, we silenced GSK3α and / or GSK3β gene expression by transfecting siRNAs and quantified HCV RNA in Huh-7.5 cells harboring HCV subgenomic replicon (Con1) or infectious HCV (Jc1). Given the well-known dependency of HCV on miR-122 (Jopling et al., 2005 (Jopling et al., , 2008 Machlin et al., 2011) and the regulatory circuit between insulin-like growth factor 1 receptor, GSK3β, and miR-122 identified previously (Zeng et al., 2010) , we assessed the effect of GSK3 inhibition on miR-122 expression in Huh-7.5 cells harboring a subgenomic HCV replicon. abstract: Hepatitis C virus (HCV) infection is associated with alterations in host lipid and insulin signaling cascades, which are partially explained by a dependence of the HCV life cycle on key molecules in these metabolic pathways. Yet, little is known on the role in the HCV life cycle of glycogen synthase kinase 3 (GSK3), one of the most important kinases in cellular metabolism. Therefore, the impact of GSK3 on the HCV life cycle was assessed in human hepatoma cell lines harboring subgenomic genotype 1b and 2a replicons or producing cell culture-derived HCV genotype 2a by exposure to synthetic GSK3 inhibitors, GSK3 gene silencing, overexpression of GSK3 constructs and immunofluorescence analyses. In addition, the role of GSK3 in hepatitis E virus (HEV) replication was investigated to assess virus specificity of the observed findings. We found that both inhibition of GSK3 function by synthetic inhibitors as well as silencing of GSK3β gene expression resulted in a decrease of HCV replication and infectious particle production, whereas silencing of the GSK3α isoform had no relevant effect on the HCV life cycle. Conversely, overexpression of GSK3β resulted in enhanced HCV replication. In contrast, GSK3β had no effect on replication of subgenomic HEV replicon. The pro-viral effect of GSK3β on HCV replication was mediated by supporting expression of microRNA-122 (miR-122), a micro-RNA which is mandatory for wild-type HCV replication, as GSK3 inhibitors suppressed miR-122 levels and as inhibitors of GSK3 had no antiviral effect on a miR-122-independent HCV mutant. In conclusion, we have identified GSK3β is a novel host factor supporting HCV replication by maintaining high levels of hepatic miR-122 expression. url: https://www.ncbi.nlm.nih.gov/pubmed/30542341/ doi: 10.3389/fmicb.2018.02949 id: cord-048471-7jszm1nd author: Salim, Omar title: Functional Analysis of the 5′ Genomic Sequence of a Bovine Norovirus date: 2008-05-14 words: 5646.0 sentences: 246.0 pages: flesch: 49.0 cache: ./cache/cord-048471-7jszm1nd.txt txt: ./txt/cord-048471-7jszm1nd.txt summary: Although slightly larger than predicted the N-term protein was detected in a processed form in vivo, thus not only demonstrating initial translation of the ORF1 polyprotein but also activity of the viral protease. Previous studies of norovirus polyprotein processing have yielded three major products following in vitro transcription and translation, representing the uncleaved 3ABCD, N-term and 2C proteins. In addition, this important observation also confirms for the first time that the JV 3C protease was active in cells transfected with capped RNA as the size of the V5/N-term indicated successful cleavage of the protein from the ORF1 polyprotein. Unlike similarly studied human noroviruses JV initially did not appear to express the N-terminal protein, presenting the possibility that the encoding RNA sequence had a regulatory function itself, most likely involved in translation initiation in an IRES-like manner. abstract: BACKGROUND: Jena Virus (JV), a bovine Norovirus, causes enteric disease in cattle and represents a potential model for the study of enteric norovirus infection and pathogenesis. The positive sense RNA genome of JV is organised into ORF1 (non-structural proteins), ORF2 (major capsid protein) and ORF3 (minor capsid protein). The lack of a cell culture system for studying JV replication has meant that work to date has relied upon in vitro systems to study non-structural protein synthesis and processing. PRINCIPAL FINDINGS: Only two of the three major ORF1 proteins were identified (p110 and 2C) following in vitro translation of JV RNA, the N-term protein was not detected. The N-term encoding genomic sequence (5′GS) was tested for IRES-like function in a bi-cistronic system and displayed no evidence of IRES-like activity. The site of translation initiation in JV was determined to be at the predicted nucleotide 22. Following the insertion of an epitope within the 5′GS the JV N-term protein was identified in vitro and within RNA transfected cells. CONCLUSIONS: The in vitro transcription/translation system is currently the best system for analysing protein synthesis and processing in JV. Unlike similarly studied human noroviruses JV initially did not appear to express the N-terminal protein, presenting the possibility that the encoding RNA sequence had a regulatory function, most likely involved in translation initiation in an IRES-like manner. This was not the case and, following determination of the site of translation initiation the N-term protein was detected using an epitope tag, both in vitro and in vivo. Although slightly larger than predicted the N-term protein was detected in a processed form in vivo, thus not only demonstrating initial translation of the ORF1 polyprotein but also activity of the viral protease. These findings indicate that the block to noroviral replication in cultured cells lies elsewhere. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2364642/ doi: 10.1371/journal.pone.0002169 id: cord-318853-mxyxwkhx author: Sallie, Richard title: Replicative homeostasis II: Influence of polymerase fidelity on RNA virus quasispecies biology: Implications for immune recognition, viral autoimmunity and other "virus receptor" diseases date: 2005-08-22 words: 10541.0 sentences: 396.0 pages: flesch: 25.0 cache: ./cache/cord-318853-mxyxwkhx.txt txt: ./txt/cord-318853-mxyxwkhx.txt summary: Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. Hence, as relative concentrations of wild-type and variant viral proteins vary, alteration of both processivity and fidelity of RNA pol results, permitting viruses to adaptively respond to environmental changes, including immune recognition and reaction to evolving cell receptors. As clear evidence exists for viral disruption of leptin function [106] and virus-associated weight gain in humans [107] and monkeys [108] , is it possible the global epidemics of type II diabetes mellitus, insulin resistance, hyperlipidaemia and obesity now prevalent [109] [110] [111] [112] [113] [114] [115] [116] , are just that; epidemics fundamentally caused by viruses that co-opt insulin or leptin or other associated receptors for cell access and generate protein quasispecies that disrupt receptor function? abstract: Much of the worlds' population is in active or imminent danger from established infectious pathogens, while sporadic and pandemic infections by these and emerging agents threaten everyone. RNA polymerases (RNA(pol)) generate enormous genetic and consequent antigenic heterogeneity permitting both viruses and cellular pathogens to evade host defences. Thus, RNA(pol )causes more morbidity and premature mortality than any other molecule. The extraordinary genetic heterogeneity defining viral quasispecies results from RNA(pol )infidelity causing rapid cumulative genomic RNA mutation a process that, if uncontrolled, would cause catastrophic loss of sequence integrity and inexorable quasispecies extinction. Selective replication and replicative homeostasis, an epicyclical regulatory mechanism dynamically linking RNApol fidelity and processivity with quasispecies phenotypic diversity, modulating polymerase fidelity and, hence, controlling quasispecies behaviour, prevents this happening and also mediates immune escape. Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. This mechanism – "Viral Receptor Disease (VRD)" – may explain so-called "viral autoimmunity", some classical autoimmune disorders and other diseases, including type II diabetes mellitus, and some forms of obesity. Viral receptor disease is a unifying hypothesis that may also explain some diseases with well-established, but multi-factorial and apparently unrelated aetiologies – like coronary artery and other vascular diseases – in addition to diseases like schizophrenia that are poorly understood and lack plausible, coherent, pathogenic explanations. url: https://www.ncbi.nlm.nih.gov/pubmed/16115320/ doi: 10.1186/1743-422x-2-70 id: cord-313684-61hkogdh author: Samaddar, Arghadip title: Pathophysiology and Potential Therapeutic Candidates for COVID-19: A Poorly Understood Arena date: 2020-09-17 words: 11700.0 sentences: 585.0 pages: flesch: 42.0 cache: ./cache/cord-313684-61hkogdh.txt txt: ./txt/cord-313684-61hkogdh.txt summary: Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. abstract: Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. To date, there are no proven drugs or vaccines against this virus. Hence, the situation demands an urgent need to explore all potential therapeutic strategies that can be made available to prevent the disease progression and improve patient outcomes. In absence of clinically proven treatment guidelines, several repurposed drugs and investigational agents are currently being evaluated in clinical trials for their probable benefits in the treatment of COVID-19. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. Moreover, there is a need to clearly define the patient populations who warrant therapy and also the timing of initiation of treatment. Understanding the disease pathology responsible for the clinical manifestations of COVID-19 is imperative to identify the potential targets for drug development. This review explains the pathophysiology of COVID-19 and summarizes the potential treatment candidates, which can provide guidance in developing effective therapeutic strategies. url: https://doi.org/10.3389/fphar.2020.585888 doi: 10.3389/fphar.2020.585888 id: cord-284941-wfn0pnev author: Samal, S.K. title: Paramyxoviruses of Animals date: 2008-07-30 words: 4948.0 sentences: 251.0 pages: flesch: 41.0 cache: ./cache/cord-284941-wfn0pnev.txt txt: ./txt/cord-284941-wfn0pnev.txt summary: The members of this virus family are enveloped and have genomes consisting of a single segment of negative-sense RNA that contains 6–10 genes encoding up to 12 proteins. The family Paramyxoviridae contains a large number of viruses of animals (Table 1) , including a number of major animal pathogens (such as Newcastle disease virus (NDV), canine distemper virus, and rinderpest virus), zoonotic pathogens (such as Hendra and Nipah viruses), and a number of somewhat obscure viruses whose natural histories are poorly understood. A number of animal paramyxoviruses have been recovered from cDNAs using reverse genetics, including simian virus 5, NDV, bovine parainfluenza virus 3, Sendai virus, canine distemper virus, rinderpest virus, bovine respiratory syncytial virus, and avian metapneumovirus. Infection occurs by several different routes, including aerosols (NDV, bovine respiratory syncytial virus, avian metapneumovirus) and contaminated feed and water (Newcastle disease, canine distemper, and rinderpest viruses). abstract: Paramyxoviruses (some of which are also called parainfluenza viruses) cause a wide variety of diseases in animals. Many paramyxoviruses cause primarily respiratory disease, while others cause serious systemic disease. Many diseases caused by animal paramyxoviruses also have a neurological component or a reproductive disease component. Several of the most devastating diseases of animals, such as rinderpest, Newcastle disease, and canine distemper, are caused by paramyxoviruses. Some of the animal paramyxoviruses, such as the Hendra and Nipah viruses, are emerging zoonotic pathogens of major public health concern. New paramyxoviruses are being isolated on a continuing basis from a wide variety of animals. All animal paramyxoviruses belong to the family Paramyxoviridae. The members of this virus family are enveloped and have genomes consisting of a single segment of negative-sense RNA that contains 6–10 genes encoding up to 12 proteins. Although there are many animal paramyxoviruses, only a few effective vaccines are currently available. In the last decade, methods of producing many animal paramyxoviruses entirely from cDNA clones (reverse genetics) have been developed. This has not only greatly improved our understanding of the molecular biology and pathogenesis of these viruses, but has also made it possible to engineer improved vaccines for them. url: https://api.elsevier.com/content/article/pii/B978012374410400460X doi: 10.1016/b978-012374410-4.00460-x id: cord-256036-gd53s4dv author: Sandmann, Lisa title: Barriers of hepatitis C virus interspecies transmission date: 2013-01-01 words: 7894.0 sentences: 373.0 pages: flesch: 40.0 cache: ./cache/cord-256036-gd53s4dv.txt txt: ./txt/cord-256036-gd53s4dv.txt summary: In contrast to human hepatocytes, murine cells do not support HCV entry thereby creating a first and important barrier for a broader host tropism of the virus. Utilizing blocking antibodies specific to CD81 or the viral envelope protein E2, expression of entry factor mutants and mice with a targeted disruption of the SCARB1 gene validated uptake of HCV into murine hepatocytes in an HCV glycoprotein-mediated fashion. Taking advantage of the high mutational plasticity of HCV, three adaptive mutations in the viral glycoproteins E1 and E2 were identified that allowed the virus to enter cells expressing human SCARB1, CLDN1, OCLN and mouse CD81. Recently, a genetically humanized mouse model was constructed utilizing cell culture produced recombinant hepatitis C virus to activate a cellular encoded reporter (Dorner et al., 2011, in press ). Human occludin is a hepatitis C virus entry factor required for infection of mouse cells A humanized mouse model to study Hepatitis C virus infection, immune response, and liver disease abstract: Hepatitis C virus (HCV) is a major causative agent of severe liver disease including fibrosis, cirrhosis and liver cancer. Therapy has improved over the years, but continues to be associated with adverse side effects and variable success rates. Furthermore, a vaccine protecting against HCV infection remains elusive. Development of more effective intervention measures has been delayed by the lack of a suitable animal model. Naturally, HCV infects only humans and chimpanzees. The determinants of this limited host range are poorly understood in part due to difficulties of studying HCV in cell culture. Some progress has been made elucidating the barriers for the HCV lifecycle in non-permissive species which will help in the future to construct animal models for HCV infection, immunity and pathogenesis. url: https://doi.org/10.1016/j.virol.2012.09.044 doi: 10.1016/j.virol.2012.09.044 id: cord-315483-l6dm82pp author: Santhakumar, Diwakar title: Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses date: 2018-05-01 words: 10776.0 sentences: 579.0 pages: flesch: 47.0 cache: ./cache/cord-315483-l6dm82pp.txt txt: ./txt/cord-315483-l6dm82pp.txt summary: To confirm the sequence of the cDNA and to identify the genomic structure of the identified IFIT gene, the transcript was amplified from RNA extracted from NDV-infected CEFs. Complete sequence analysis of the gene revealed an open reading frame (ORF) of 1440 bps (479 amino acids excluding stop codon) with high sequence identity (48% and 67%) with the human and duck IFIT5 proteins, respectively ( Supplementary Fig. 1B) . The levels of chIFN-β gene induction was proportional to the NDV replication (Fig. 2D) , therefore, it can be inferred that the virus-induced expression of chicken IFIT5 is IFN-dependent and that chIFIT5 is an early-ISG with capacity to modulate initial steps of virus life cycle. To compare anti-viral effects of chIFIT5 (only IFIT gene identified in chickens so far) with its orthologous and homologous human proteins, huIFIT1, huIFIT2, huIFIT3 and huIFIT5 were expressed in chicken cells and antiviral affect was monitored (Fig. 5A ). abstract: The intracellular actions of interferon (IFN)-regulated proteins, including IFN-induced proteins with tetratricopeptide repeats (IFITs), attribute a major component of the protective antiviral host defense. Here we applied genomics approaches to annotate the chicken IFIT locus and currently identified a single IFIT (chIFIT5) gene. The profound transcriptional level of this effector of innate immunity was mapped within its unique cis-acting elements. This highly virus- and IFN-responsive chIFIT5 protein interacted with negative sense viral RNA structures that carried a triphosphate group on its 5′ terminus (ppp-RNA). This interaction reduced the replication of RNA viruses in lentivirus-mediated IFIT5-stable chicken fibroblasts whereas CRISPR/Cas9-edited chIFIT5 gene knockout fibroblasts supported the replication of RNA viruses. Finally, we generated mosaic transgenic chicken embryos stably expressing chIFIT5 protein or knocked-down for endogenous chIFIT5 gene. Replication kinetics of RNA viruses in these transgenic chicken embryos demonstrated the antiviral potential of chIFIT5 in ovo. Taken together, these findings propose that IFIT5 specifically antagonize RNA viruses by sequestering viral nucleic acids in chickens, which are unique in innate immune sensing and responses to viruses of both poultry and human health significance. url: https://www.ncbi.nlm.nih.gov/pubmed/29717152/ doi: 10.1038/s41598-018-24905-y id: cord-299943-wzkh04dv author: Santhanam, Manikandan title: DNA/RNA Electrochemical Biosensing Devices a Future Replacement of PCR Methods for a Fast Epidemic Containment date: 2020-08-18 words: 7350.0 sentences: 438.0 pages: flesch: 41.0 cache: ./cache/cord-299943-wzkh04dv.txt txt: ./txt/cord-299943-wzkh04dv.txt summary: In a sensor detection scheme, ssDNA(s) specifically hybridizes with a target DNA sequence that is being employed as a probe(s): a capture probe used to attach the target DNA to the surface of materials and/or a reporter probe labeled with signaling molecules, e.g., redox-active molecules. To make a quantitative measurement, the DNA hybridization event is coupled with electrochemical reactions, in a way that a probe-target complex increases/decreases a coupled redox reaction at the electrode surface. DPV-Differential pulse voltammetry, CV-Cyclic Voltammetry, EIS-Electrochemical Impedance spectroscopy, CSD-Circular strand displacement, RCA-Rolling circle amplification, EXPAR-Isothermal exponential amplification, HCR-Hybridization chain reaction, HDA-Helicase dependent amplification, TMB-3,3 ,5,5 -tetramethylbenzidine, N,S-GQDs@AuNP-Nitrogen, sulfur codoped graphene quantum, CNT-PANI-Carbon nanotube-polyanilline, NA-Not applicable, * If limit of detection is not reported, lowest detected value is provided. Different methods have been employed in signal amplification approaches to detect a low copy number of target DNA on the electrode surface. abstract: Pandemics require a fast and immediate response to contain potential infectious carriers. In the recent 2020 Covid-19 worldwide pandemic, authorities all around the world have failed to identify potential carriers and contain it on time. Hence, a rapid and very sensitive testing method is required. Current diagnostic tools, reverse transcription PCR (RT-PCR) and real-time PCR (qPCR), have its pitfalls for quick pandemic containment such as the requirement for specialized professionals and instrumentation. Versatile electrochemical DNA/RNA sensors are a promising technological alternative for PCR based diagnosis. In an electrochemical DNA sensor, a nucleic acid hybridization event is converted into a quantifiable electrochemical signal. A critical challenge of electrochemical DNA sensors is sensitive detection of a low copy number of DNA/RNA in samples such as is the case for early onset of a disease. Signal amplification approaches are an important tool to overcome this sensitivity issue. In this review, the authors discuss the most recent signal amplification strategies employed in the electrochemical DNA/RNA diagnosis of pathogens. url: https://www.ncbi.nlm.nih.gov/pubmed/32824787/ doi: 10.3390/s20164648 id: cord-253307-4bpdfgau author: Sanz, Miguel A. title: Inhibition of host protein synthesis by Sindbis virus: correlation with viral RNA replication and release of nuclear proteins to the cytoplasm date: 2014-11-19 words: 10157.0 sentences: 537.0 pages: flesch: 49.0 cache: ./cache/cord-253307-4bpdfgau.txt txt: ./txt/cord-253307-4bpdfgau.txt summary: Analysis of a SINV variant with a point mutation in nsP2, exhibiting defects in the shut‐off of host protein synthesis, indicates that both viral RNA replication and the release of nuclear proteins to the cytoplasm are greatly inhibited. Furthermore, nucleoside analogues that inhibit cellular and viral RNA synthesis impede the blockade of host mRNA translation, in addition to the release of nuclear proteins. Therefore, in SINV nsP2 (P726G)-replicating BHK cells, a correlation exists between the inhibition of viral RNA replication and the release of nuclear proteins, in addition to the failure to completely block cellular mRNA translation. Thus, in agreement with previous results, these findings indicate that the shutoff of host translation after SINV infection is restricted when viral RNA synthesis is blocked and nuclear proteins are not released to the cytoplasm. Indeed, in cells co-transfected with rep C+luc(ΔnsPs) and EMCV(IRES)-nsP1-4 mRNA, there is low-level RNA replication, no release of nuclear proteins and the synthesis of cellular proteins is not blocked. abstract: Infection of mammalian cells by Sindbis virus (SINV) profoundly blocks cellular mRNA translation. Experimental evidence points to viral non‐structural proteins (nsPs), in particular nsP2, as the mediator of this inhibition. However, individual expression of nsP1, nsP2, nsP3 or nsP1‐4 does not block cellular protein synthesis in BHK cells. Trans‐complementation of a defective SINV replicon lacking most of the coding region for nsPs by the co‐expression of nsP1‐4 propitiates viral RNA replication at low levels, and inhibition of cellular translation is not observed. Exit of nuclear proteins including T‐cell intracellular antigen and polypyrimidine tract‐binding protein is clearly detected in SINV‐infected cells, but not upon the expression of nsPs, even when the defective replicon was complemented. Analysis of a SINV variant with a point mutation in nsP2, exhibiting defects in the shut‐off of host protein synthesis, indicates that both viral RNA replication and the release of nuclear proteins to the cytoplasm are greatly inhibited. Furthermore, nucleoside analogues that inhibit cellular and viral RNA synthesis impede the blockade of host mRNA translation, in addition to the release of nuclear proteins. Prevention of the shut‐off of host mRNA translation by nucleoside analogues is not due to the inhibition of eIF2α phosphorylation, as this prevention is also observed in PKR (−/−) mouse embryonic fibroblasts that do not phosphorylate eIF2α after SINV infection. Collectively, our observations are consistent with the concept that for the inhibition of cellular protein synthesis to occur, viral RNA replication must take place at control levels, leading to the release of nuclear proteins to the cytoplasm. url: https://www.ncbi.nlm.nih.gov/pubmed/25329362/ doi: 10.1111/cmi.12381 id: cord-324137-nau83mjv author: Saranathan, Nandhini title: G-Quadruplexes: More Than Just a Kink in Microbial Genomes date: 2018-09-14 words: 6722.0 sentences: 379.0 pages: flesch: 42.0 cache: ./cache/cord-324137-nau83mjv.txt txt: ./txt/cord-324137-nau83mjv.txt summary: Several reports convincingly demonstrate antimicrobial activity of quadruplex-binding ligands against clinically challenging pathogens, including HIV-1, HCV, Ebola virus, Plasmodium falciparum, and Mycobacterium tuberculosis. An earlier study reports that, following concatemeric replication of HHV-1, the cleavage of unit length genomes and their encapsidation is achieved by the binding of virus proteins to a DNA secondary structure formed by a DNA packaging sequence (pac-1) [50] . G4s have been shown to inhibit the transcription or translation of structural and nonstructural proteins in viruses, deleteriously affecting the virus loads and their pathogenicity; the stabilization of these quadruplexes with ligands has been investigated as a potential mechanism for targeting viruses. Negative regulation of virus transcription, translation or replication by quadruplex motifs in virus genomes forms the basis of using G4-binding ligands as antiviral agents. G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions abstract: G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein–Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy. url: https://api.elsevier.com/content/article/pii/S0966842X18301951 doi: 10.1016/j.tim.2018.08.011 id: cord-292416-3hhi4wps author: Sarid, Ronit title: Investigating an Emerging Virus During a Sudden Pandemic Outbreak date: 2020-07-31 words: 4869.0 sentences: 230.0 pages: flesch: 41.0 cache: ./cache/cord-292416-3hhi4wps.txt txt: ./txt/cord-292416-3hhi4wps.txt summary: Five years later, in 2020, when the World Health Organization declared the coronavirus disease 2019 (COVID-19)-caused by the newly emerging SARS-CoV-2 virus-to be a pandemic, this talk was widely acknowledged to be almost prophetic. 24, 25 All four reportedly mild pathogenic coronaviruses are associated with 10%-30% of cases of the common cold, 26 -28 yet they have the potential to cause severe lower respiratory tract infection in infants, in the elderly, and in patients with other underlying illness, 29 while hCoV-OC43, like SARS-CoV-2, has been associated with neurologic dysfunction as well. Development of animal models for SARS-CoV-2 infection is vital in providing comprehensive understanding of the pathogenic mechanisms involved but may also serve for screening anti-viral drugs and vaccines. Accordingly, transfusion of convalescent plasma is likely to be beneficial to SARS-CoV-2, 45 ,46 yet its effect on virus shedding and disease outcome must be evaluated when given to healthy individuals and patients at different stages and severity of the disease. abstract: At the time of writing, in July 2020, the recently emerging SARS-CoV-2 pandemic has attracted major attention to viral diseases, in particular coronaviruses. In spite of alarming molecular evidence, documentation of interspecies transmission in livestock, and the emergence of two new and relatively virulent human coronaviruses within a 10-year period, many gaps remain in the study and understanding of this family of viruses. This paper provides an overview of our knowledge regarding the coronavirus family, while highlighting their key biological properties in the context of our overall understanding of viral diseases. url: https://doi.org/10.5041/rmmj.10414 doi: 10.5041/rmmj.10414 id: cord-341330-31ngknq4 author: Sarma, Phulen title: In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain) date: 2020-05-18 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: The N terminal domain (NTD) of Nucleocapsid protein (N protein) of coronavirus (CoV) binds to the viral (+) sense RNA and results in CoV ribonucleoprotien (CoV RNP) complex, essential for the virus replication. In this study, the RNA-binding N terminal domain (NTD) of the N protein was targeted for the identification of possible inhibitors of RNA binding. Two NTD structures of N proteins were selected (2OFZ and 1SSK, 92% homology) for virtual screening of 56,079 compounds from Asinex and Maybridge library to identify top 15 hits for each of the targets based on ‘docking score’. These top-hits were further screened for MM-GBSA binding free energy, pharmacokinetic properties (QikProp) and drug-likeness (SwissADME) and subjected to molecular dynamics (MD) studies. Two suitable binders (ZINC00003118440 and ZINC0000146942) against the target 2OFZ were identified. ZINC00003118440 is a theophylline derivative under the drug class ‘bronchodilators’ and further screening with approved bronchodilators was also studied to identify their ability to bind to the RNA binding region on the N protein. The other identified top hit is ZINC0000146942, which is a 3,4dihydropyrimidone class molecule. Hence this study suggests two important class of compounds, theophylline and pyrimidone derivaties as possible inhibitors of RNA binding to the N terminal domain of N protein of coronavirus, thus opening new avenues for in vitro validations. Communicated by Ramaswamy H. Sarma url: https://www.ncbi.nlm.nih.gov/pubmed/32266867/ doi: 10.1080/07391102.2020.1753580 id: cord-259500-ndjbrtrv author: Satyanarayana, Tatineni title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli date: 2003-09-01 words: 6465.0 sentences: 322.0 pages: flesch: 60.0 cache: ./cache/cord-259500-ndjbrtrv.txt txt: ./txt/cord-259500-ndjbrtrv.txt summary: title: Frameshift mutations in infectious cDNA clones of Citrus tristeza virus: a strategy to minimize the toxicity of viral sequences to Escherichia coli These data demonstrate that, when hosts are sufficiently susceptible for infection by transcripts of reduced specific infectivity, introduction of frameshift mutations at "slippery sequences" near toxic regions of viral cDNAs can be used as an additional strategy to clone recalcitrant viral sequences in high-copy-number plasmids for reverse genetics. A similar frameshift mutation was also found in the derivative replicon pCTV-⌬Cla. However, the sequence of the progeny virion RNA of CTV9 from infected protoplasts or citrus plants did not contain the additional nt at position 3732 that occurred in the cDNA clones, suggesting that the frameshift mutation present in the original cDNA clone was repaired either during the in vitro transcription or during replication in the protoplasts. abstract: The advent of reverse genetics revolutionized the study of positive-stranded RNA viruses that were amenable for cloning as cDNAs into high-copy-number plasmids of Escherichia coli. However, some viruses are inherently refractory to cloning in high-copy-number plasmids due to toxicity of viral sequences to E. coli. We report a strategy that is a compromise between infectivity of the RNA transcripts and toxicity to E. coli effected by introducing frameshift mutations into “slippery sequences” near the viral “toxicity sequences” in the viral cDNA. Citrus tristeza virus (CTV) has cDNA sequences that are toxic to E. coli. The original full-length infectious cDNA of CTV and a derivative replicon, CTV-ΔCla, cloned into pUC119, resulted in unusually limited E. coli growth. However, upon sequencing of these cDNAs, an additional uridinylate (U) was found in a stretch of U’s between nts 3726 and 3731 that resulted in a change to a reading frame with a stop codon at nt 3734. Yet, in vitro produced RNA transcripts from these clones infected protoplasts, and the resulting progeny virus was repaired. Correction of the frameshift mutation in the CTV cDNA constructs resulted in increased infectivity of in vitro produced RNA transcripts, but also caused a substantial increase of toxicity to E. coli, now requiring 3 days to develop visible colonies. Frameshift mutations created in sequences not suspected to facilitate reading frame shifting and silent mutations introduced into oligo(U) regions resulted in complete loss of infectivity, suggesting that the oligo(U) region facilitated the repair of the frameshift mutation. Additional frameshift mutations introduced into other oligo(U) regions also resulted in transcripts with reduced infectivity similarly to the original clones with the +1 insertion. However, only the frameshift mutations introduced into oligo(U) regions that were near and before the toxicity region improved growth and stability in E. coli. These data demonstrate that, when hosts are sufficiently susceptible for infection by transcripts of reduced specific infectivity, introduction of frameshift mutations at “slippery sequences” near toxic regions of viral cDNAs can be used as an additional strategy to clone recalcitrant viral sequences in high-copy-number plasmids for reverse genetics. url: https://www.sciencedirect.com/science/article/pii/S0042682203003878 doi: 10.1016/s0042-6822(03)00387-8 id: cord-015376-z739ifu5 author: Savarino, Andrea title: Potential therapies for coronaviruses date: 2006-08-31 words: 6361.0 sentences: 313.0 pages: flesch: 48.0 cache: ./cache/cord-015376-z739ifu5.txt txt: ./txt/cord-015376-z739ifu5.txt summary: These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. The potential usefulness of 3CLpro as a drug target is supported by: i) its fundamental role in coronavirus replication; ii) its well defined 3D structure; and iii) preliminary clinical observation indicating that drugs cross-targeting this enzyme, that is, the HIV-1 protease inhibitors (HIV-1 PIs; 2 -6) produced some clinical benefits in patients treated with IFNs and ribavirin. abstract: Coronavirus replication offers several attractive targets for chemotherapy. These include: viral entry (inhibited by chloroquine and peptides); viral RNA (targeted by antisense approaches/RNAi); the main protease 3CLpro (inhibited by peptidic molecules such as HIV-1 protease inhibitors and miscellaneous compounds); the accessory protease(s) PLpro(s) (inhibited by zinc ions); RNA-dependent RNA polymerase (inhibited by aurintricarboxylic acid and antisense approaches); and helicase (inhibited by bananins). Chloroquine and HIV-1 protease inhibitors (with well-known toxicity profiles) should be considered for clinical tests if severe acute respiratory syndrome (SARS) re-emerges; however, there are other attractive compounds. Lessons should be learnt from AIDS research for choosing the best strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103690/ doi: 10.1517/13543776.16.9.1269 id: cord-356115-vblgotjn author: Sawicki, Stanley G title: Functional and Genetic Analysis of Coronavirus Replicase-Transcriptase Proteins date: 2005-12-09 words: 10631.0 sentences: 458.0 pages: flesch: 52.0 cache: ./cache/cord-356115-vblgotjn.txt txt: ./txt/cord-356115-vblgotjn.txt summary: The coronavirus replicase-transcriptase complex is an assembly of viral and cellular proteins that mediate the synthesis of genome and subgenome-sized mRNAs in the virus-infected cell. Here, we report a genetic and functional analysis of 19 temperature-sensitive (ts) mutants of Murine hepatitis virus MHV-A59 that are unable to synthesize viral RNA when the infection is initiated and maintained at the non-permissive temperature. We focused our phenotypic analysis on the eight MHV-A59 ts mutants that had been genotyped and began by measuring ''''total'''' viral RNA synthesis in infected cells prior to and following shift from the permissive to the non-permissive temperature. This phenotype resembled that seen with MHV-A59-infected cells treated with CH, and we conclude that the complementation group I mutants are defective in their ability to form active replicase-transcriptase complexes at 40 8C but retain the positive-strand synthesis activity of the complexes formed at the permissive temperature. abstract: The coronavirus replicase-transcriptase complex is an assembly of viral and cellular proteins that mediate the synthesis of genome and subgenome-sized mRNAs in the virus-infected cell. Here, we report a genetic and functional analysis of 19 temperature-sensitive (ts) mutants of Murine hepatitis virus MHV-A59 that are unable to synthesize viral RNA when the infection is initiated and maintained at the non-permissive temperature. Both classical and biochemical complementation analysis leads us to predict that the majority of MHV-A59 ORF1a replicase gene products (non-structural proteins nsp1–nsp11) form a single complementation group (cistron1) while the replicase gene products encoded in ORF1b (non-structural proteins nsp12–nsp16) are able to function in trans and comprise at least three, and possibly five, further complementation groups (cistrons II–VI). Also, we have identified mutations in the non-structural proteins nsp 4, nsp5, nsp10, nsp12, nsp14, and nsp16 that are responsible for the ts phenotype of eight MHV-A59 mutants, which allows us to conclude that these proteins are essential for the assembly of a functional replicase-transcriptase complex. Finally, our analysis of viral RNA synthesis in ts mutant virus-infected cells allows us to discriminate three phenotypes with regard to the inability of specific mutants to synthesize viral RNA at the non-permissive temperature. Mutant LA ts6 appeared to be defective in continuing negative-strand synthesis, mutant Alb ts16 appeared to form negative strands but these were not utilized for positive-strand RNA synthesis, and mutant Alb ts22 was defective in the elongation of both positive- and negative-strand RNA. On the basis of these results, we propose a model that describes a pathway for viral RNA synthesis in MHV-A59-infected cells. Further biochemical analysis of these mutants should allow us to identify intermediates in this pathway and elucidate the precise function(s) of the viral replicase proteins involved. url: https://www.ncbi.nlm.nih.gov/pubmed/16341254/ doi: 10.1371/journal.ppat.0010039 id: cord-352178-irjhmxsg author: Saxton-Shaw, Kali D. title: O''nyong nyong Virus Molecular Determinants of Unique Vector Specificity Reside in Non-Structural Protein 3 date: 2013-01-24 words: 5953.0 sentences: 299.0 pages: flesch: 49.0 cache: ./cache/cord-352178-irjhmxsg.txt txt: ./txt/cord-352178-irjhmxsg.txt summary: Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Our study analyzed both structural and non-structural regions of the ONNV genome using chimeric viruses and artificially infected Anopheles gambiae mosquitoes. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from chikungunya virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. Six additional non-structural chimeric viruses were also constructed using a novel type II restriction enzyme cloning strategy to examine the broader genome with respect to ONNV''s unique vector specificity for An. gambiae mosquitoes (Figure 2) . abstract: O'nyong nyong virus (ONNV) and Chikungunya virus (CHIKV) are two closely related alphaviruses with very different infection patterns in the mosquito, Anopheles gambiae. ONNV is the only alphavirus transmitted by anopheline mosquitoes, but specific molecular determinants of infection of this unique vector specificity remain unidentified. Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. Only one region, non-structural protein 3 (nsP3), was sufficient to up-regulate infection to rates similar to those seen with parental ONNV. When ONNV non-structural protein 3 (nsP3) replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. No other single gene or viral region addition was able to restore infection rates. Thus, we have shown that a non-structural genome element involved in viral replication is a major element involved in ONNV's unique vector specificity. url: https://www.ncbi.nlm.nih.gov/pubmed/23359824/ doi: 10.1371/journal.pntd.0001931 id: cord-339431-kyr5lv15 author: Saçar Demirci, Müşerref Duygu title: Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection date: 2020-03-17 words: 2323.0 sentences: 163.0 pages: flesch: 52.0 cache: ./cache/cord-339431-kyr5lv15.txt txt: ./txt/cord-339431-kyr5lv15.txt summary: In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Although there are studies regarding to the viral replication and their interaction with host innate immune system, the role of miRNA-mediated RNA-silencing in SARS-CoV-2 infection has not been enlightened yet. In this study, SARS-CoV-2 genome was searched for miRNA-like sequences and potential host-virus interactions based on miRNA actions were analyzed. In our study, we have also identified possible miRNA like small RNAs from SARS-CoV-2 genome which target important human genes. abstract: MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that have been found in more than 200 diverse organisms. Although it is still not fully established if RNA viruses could generate miRNAs that would target their own genes or alter the host gene expression, there are examples of miRNAs functioning as an antiviral defense mechanism. In the case of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there are several mechanisms that would make miRNAs impact the virus, like interfering with replication, translation and even modulating the host expression. In this study, we performed a machine learning based miRNA prediction analysis for the SARS-CoV-2 genome to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAs and viral genes. Our PANTHER gene function analysis results indicate that viral derived miRNA candidates could target various human genes involved in crucial cellular processes including transcription. For instance, a transcriptional regulator, STAT1 and transcription machinery might be targeted by virus-derived miRNAs. In addition, many known human miRNAs appear to be able to target viral genes. Considering the fact that miRNA-based therapies have been successful before, comprehending mode of actions of miRNAs and their possible roles during SARS-CoV-2 infections could create new opportunities for the development and improvement of new therapeutics. url: https://doi.org/10.1101/2020.03.15.992438 doi: 10.1101/2020.03.15.992438 id: cord-342649-ysossker author: Scagnolari, Carolina title: Evaluation of viral load in infants hospitalized with bronchiolitis caused by respiratory syncytial virus date: 2012-03-10 words: 3759.0 sentences: 161.0 pages: flesch: 42.0 cache: ./cache/cord-342649-ysossker.txt txt: ./txt/cord-342649-ysossker.txt summary: The relationship between viral load, disease severity and antiviral immune activation in infants suffering from respiratory syncytial virus (RSV)-associated bronchiolitis has not been well identified. The main objective of this study was to determine the existence of a correlation between RSV load and disease severity and also between different clinical markers and mRNA levels of the interferon stimulated gene (ISG)56 in infants hospitalized for bronchiolitis. Results indicated that viral load was positively related to the clinical severity of bronchiolitis, the length of hospital stay, the levels of glycemia and the relative gene expression of ISG56, whereas an inverse correlation was observed with the levels of hemoglobin. In the framework of a study aimed at understanding the pathogenesis of RSV infection and at further characterizing viral and host factors involved in determining the severity of bronchiolitis, we addressed whether any diVerences in RSV-RNA levels in the airway tracts of infants with bronchiolitis might explain the broad clinical spectrum of RSVassociated bronchiolitis. abstract: The relationship between viral load, disease severity and antiviral immune activation in infants suffering from respiratory syncytial virus (RSV)-associated bronchiolitis has not been well identified. The main objective of this study was to determine the existence of a correlation between RSV load and disease severity and also between different clinical markers and mRNA levels of the interferon stimulated gene (ISG)56 in infants hospitalized for bronchiolitis. We also evaluated whether viral load tended to be persistent over the course of the RSV infection. The levels of RSV-RNA were quantified in nasopharyngeal washings, collected from 132 infants infected with RSV as a single (90.15%) or as a dual infection with other respiratory viruses (9.85%). Results indicated that viral load was positively related to the clinical severity of bronchiolitis, the length of hospital stay, the levels of glycemia and the relative gene expression of ISG56, whereas an inverse correlation was observed with the levels of hemoglobin. We also found that the RSV load significantly decreased between the first and second nasopharingeal washings sample in most subjects. These results suggest that infants with high RSV load on hospital admission are more likely to have both more severe bronchiolitis and a higher airway activation of antiviral immune response. url: https://www.ncbi.nlm.nih.gov/pubmed/22406873/ doi: 10.1007/s00430-012-0233-6 id: cord-345204-ch0e6lzl author: Scarlata, S. title: Design Of A Rapid And Reversible Fluorescence Assay To Detect COVID-19 And Other Pathogens date: 2020-10-05 words: 2917.0 sentences: 172.0 pages: flesch: 59.0 cache: ./cache/cord-345204-ch0e6lzl.txt txt: ./txt/cord-345204-ch0e6lzl.txt summary: The method uses fluorescent sensors (i.e. molecular beacons) designed to detect COVID-19 RNA or any RNA of interest, concurrent with an internal control without the need for amplification. The molecular beacons are stem-loop structures in which a ~10 nucleotide loop region has the complementary sequence of a region of the target RNA, and a fluorophore and quencher are placed on the 5'' and 3'' ends of the stem. Here, we designed a COVID-19 beacon that is completely quenched in its native form and undergoes a 50-fold increase in fluorescence when exposed to nanomolar amounts of synthetic viral oligonucleotide. Fluorescence increases from beacon responses signals are rapid and can be reversed by the addition of inexpensive ssDNA with a sequence identical to the loop region, or high salt if attached to a matrix. abstract: We describe a rapid and reusable biophysical method to assay COVID-19. The method uses fluorescent sensors (i.e. molecular beacons) designed to detect COVID-19 RNA or any RNA of interest, concurrent with an internal control without the need for amplification. The molecular beacons are stem-loop structures in which a ~10 nucleotide loop region has the complementary sequence of a region of the target RNA, and a fluorophore and quencher are placed on the 5' and 3' ends of the stem. The energy of hybridization of the loop with its target is designed to be greater than the hybridization energy of the energy of the stem so that when the beacon encounters its target RNA, the structure opens resulting in dequenching of the fluorophore. Here, we designed a COVID-19 beacon that is completely quenched in its native form and undergoes a 50-fold increase in fluorescence when exposed to nanomolar amounts of synthetic viral oligonucleotide. No changes in intensity are seen when control RNA is added. A control beacon to a human GAPDH RNA, chosen for its high levels in saliva, behaved similar to the COVID-19 beacon. This increase in fluorescence with beacon opening can be completely reversed upon addition of single stranded DNA complementary to COVID-19 beacon loop region. Beacons can be attached to an insert matrix allowing their use in concentrated form and can be made from morphilino oligonucleotides that are resistant to RNases. We present an analysis of the parameters that will allow the development of test strips to detect virus in aerosol, body fluids and community waste. url: http://medrxiv.org/cgi/content/short/2020.10.02.20196113v1?rss=1 doi: 10.1101/2020.10.02.20196113 id: cord-354003-ko45l1qv author: Scarpin, M Regina title: Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation date: 2020-10-15 words: 16822.0 sentences: 829.0 pages: flesch: 46.0 cache: ./cache/cord-354003-ko45l1qv.txt txt: ./txt/cord-354003-ko45l1qv.txt summary: Pioneering efforts to identify the mechanisms regulating translation of 5 0 TOP mRNAs, however, did show that wheat germ extracts contain a repressor that specifically limits translation of 5 0 TOP mRNAs in cell-free translation assays (Biberman and Meyuhas, 1999; Shama and Meyuhas, 1996) , suggesting that plants also discriminately regulate translation of 5 0 TOP mRNAs. Here, we show that the TOR-LARP1-5 0 TOP signaling axis regulates translation in Arabidopsis, impacting expression of a set of deeply conserved 5 0 TOP genes, including translation elongation factors, polyA-binding proteins, karyopherins/importins, and the translationally-controlled tumor protein. TOR-LARP1-5 0 TOP signaling in Arabidopsis seedlings regulates translation of mRNAs that encode deeply conserved eukaryotic proteins, plant lineage-specific proteins, and diverse proteins involved in ribosome biogenesis. abstract: Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5′ oligopyrimidine tract motifs (5′TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5′TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5′TOP mRNAs, as well as new, plant-specific 5′TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5′TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1. url: https://www.ncbi.nlm.nih.gov/pubmed/33054972/ doi: 10.7554/elife.58795 id: cord-288879-rj03dsib author: Schein, Catherine H. title: Polyglutamine Repeats in Viruses date: 2018-09-04 words: 6195.0 sentences: 301.0 pages: flesch: 45.0 cache: ./cache/cord-288879-rj03dsib.txt txt: ./txt/cord-288879-rj03dsib.txt summary: While the mechanisms for the function and toxicity of extended polyQ segments (or the nucleic regions that encode them) in eukaryotic proteins continue to be actively studied [16] , there has been little exploration of their occurrence and possible roles, even in neurovirulent viruses. At the start of this work, the ViPR database [29] , which allows rapid access to the published sequences of over 75,000 viral genomes or genome segments, was used to determine which RNA and DNA viruses contain polyQ repeats. As discussed below, the longest repeats were found in DNA virus proteins that function in enhancing transmissibility (cowpox ATI) or contribute to viral latency (herpes viruses). Under growth conditions allowing the virus to resume lytic growth, where the enzyme activity is required to ensure efficient replication, the region Fig. 2 Soluble polyQ segments (of cell or viral origin) may prevent beclin-1-induced autophagy, which depends on the DNA binding ability of the polyQ segment of wt-ataxin-3 (based on [2, 67] ). abstract: This review explores the presence and functions of polyglutamine (polyQ) in viral proteins. In mammals, mutations in polyQ segments (and CAG repeats at the nucleotide level) have been linked to neural disorders and ataxias. PolyQ regions in normal human proteins have documented functional roles, in transcription factors and, more recently, in regulating autophagy. Despite the high frequency of polyQ repeats in eukaryotic genomes, little attention has been given to the presence or possible role of polyQ sequences in virus genomes. A survey described here revealed that polyQ repeats occur rarely in RNA viruses, suggesting that they have detrimental effects on virus replication at the nucleotide or protein level. However, there have been sporadic reports of polyQ segments in potyviruses and in reptilian nidoviruses (among the largest RNA viruses known). Conserved polyQ segments are found in the regulatory control proteins of many DNA viruses. Variable length polyQ tracts are found in proteins that contribute to transmissibility (cowpox A-type inclusion protein (ATI)) and control of latency (herpes viruses). New longer-read sequencing methods, using original biological samples, should reveal more details on the presence and functional role of polyQ in viruses, as well as the nucleotide regions that encode them. Given the known toxic effects of polyQ repeats, the role of these segments in neurovirulent and tumorigenic viruses should be further explored. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12035-018-1269-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30182336/ doi: 10.1007/s12035-018-1269-4 id: cord-348243-e5tdb08v author: Schermer, Bernhard title: Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay date: 2020-11-02 words: 3958.0 sentences: 236.0 pages: flesch: 56.0 cache: ./cache/cord-348243-e5tdb08v.txt txt: ./txt/cord-348243-e5tdb08v.txt summary: METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). To allow for the comparison of different nucleic acid detection methods for SARS-CoV-2 we collected redundant material from nasopharyngeal swabs obtained for qPCR testing in clinical routine due to suspected COVID-19. We first tested two recently described assays for SARS-CoV-2 detection on isolated RNA from patient samples. In summary, our multiplex RT-LAMP protocol is a simple and sensitive way to detect SARS-CoV-2 RNA from clinical samples. Currently, a test based on our multiplexed RT-LAMP assay would-in contrast to a good specificity-most likely miss to identify those infected patients with very low amounts of viral RNA in the nose or throat and would not yet reach the sensitivity of the gold-standard qPCR assays. abstract: BACKGROUND: Rapid and extensive testing of large parts of the population and specific subgroups is crucial for proper management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and decision-making in times of a pandemic outbreak. However, point-of-care (POC) testing in places such as emergency units, outpatient clinics, airport security points or the entrance of any public building is a major challenge. The need for thermal cycling and nucleic acid isolation hampers the use of standard PCR-based methods for this purpose. METHODS: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK). RESULTS: Whilst specificity of standard RT-LAMP assays appears to be satisfactory, sensitivity does not reach the current gold-standard quantitative real-time polymerase chain reaction (qPCR) assays yet. We describe a novel multiplexed RT-LAMP approach and validate its sensitivity on primary samples. This approach allows for fast and reliable identification of infected individuals. Primer optimization and multiplexing helps to increase sensitivity significantly. In addition, we directly compare and combine our novel RT-LAMP assays with SHERLOCK. CONCLUSION: In summary, this approach reveals one-step multiplexed RT-LAMP assays as a prime-option for the development of easy and cheap POC test kits. url: https://doi.org/10.1371/journal.pone.0238612 doi: 10.1371/journal.pone.0238612 id: cord-334123-wb45ww7f author: Schimmel, Paul title: RNA pseudoknots that interact with components of the translation apparatus date: 1989-07-14 words: 3334.0 sentences: 169.0 pages: flesch: 60.0 cache: ./cache/cord-334123-wb45ww7f.txt txt: ./txt/cord-334123-wb45ww7f.txt summary: A third and earlier study proposed that an RNA pseudoknot is recognized by a DNA binding protein that autogenously regulates translation of its mRNA (McPheeters et al., 1988) . The tRNA-like structures at the 3'' ends of plant viral RNAs provide one example where the pseudoknot format may be necessary to form a substrate that is specifically recognized by an enzyme. Previous structural mapping experiments by Draper and co-workers suggested a model for the 5'' region of the mRNA which constitutes the S4 binding site; it envisions a hairpin helix and loop that encompasses nucleotides 19 to 72. The second study provides evidence that pseudoknot formation in a viral mRNA is required for frameshift suppression of a termination codon that, in turn, allows a fusion protein to be synthesized from two overlapping reading frames. This element encodes a stem-loop structure that starts six nucleotides downstream from the proposed site of frameshifting, near the end of the first reading frame. abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/2473840/ doi: 10.1016/0092-8674(89)90395-4 id: cord-312240-0k8y86pf author: Schlaberg, Robert title: Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology date: 2017-05-01 words: 4837.0 sentences: 239.0 pages: flesch: 46.0 cache: ./cache/cord-312240-0k8y86pf.txt txt: ./txt/cord-312240-0k8y86pf.txt summary: Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. We first assessed the ability of RNA-seq and PVG PCR to detect known respiratory pathogens using specimens from children with CAP (n = 63) and asymptomatic control (n = 52) subjects in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. We validated RNA-seq and PVG PCR methods to detect known respiratory pathogens by testing specimens using both methods from children with CAP (n = 63) and asymptomatic control subjects (n = 52) in whom viral or atypical bacterial pathogens had been detected using the EPIC study protocol. Using RNA-seq and PVG PCR, we identified additional viruses from upper respiratory tract specimens in >30% children hospitalized with clinical and radiographic pneumonia but in whom no pathogen was identified despite extensive testing by culture, molecular, and serologic methods. abstract: BACKGROUND. Community-acquired pneumonia (CAP) is a leading cause of pediatric hospitalization. Pathogen identification fails in approximately 20% of children but is critical for optimal treatment and prevention of hospital-acquired infections. We used two broad-spectrum detection strategies to identify pathogens in test-negative children with CAP and asymptomatic controls. METHODS. Nasopharyngeal/oropharyngeal (NP/OP) swabs from 70 children <5 years with CAP of unknown etiology and 90 asymptomatic controls were tested by next-generation sequencing (RNA-seq) and pan viral group (PVG) PCR for 19 viral families. Association of viruses with CAP was assessed by adjusted odds ratios (aOR) and 95% confidence intervals controlling for season and age group. RESULTS. RNA-seq/PVG PCR detected previously missed, putative pathogens in 34% of patients. Putative viral pathogens included human parainfluenza virus 4 (aOR 9.3, P = .12), human bocavirus (aOR 9.1, P < .01), Coxsackieviruses (aOR 5.1, P = .09), rhinovirus A (aOR 3.5, P = .34), and rhinovirus C (aOR 2.9, P = .57). RNA-seq was more sensitive for RNA viruses whereas PVG PCR detected more DNA viruses. CONCLUSIONS. RNA-seq and PVG PCR identified additional viruses, some known to be pathogenic, in NP/OP specimens from one-third of children hospitalized with CAP without a previously identified etiology. Both broad-range methods could be useful tools in future epidemiologic and diagnostic studies. url: https://academic.oup.com/jid/article-pdf/215/9/1407/24262313/jix148.pdf doi: 10.1093/infdis/jix148 id: cord-003435-ke0az7nf author: Schlake, Thomas title: mRNA as novel technology for passive immunotherapy date: 2018-10-17 words: 15190.0 sentences: 850.0 pages: flesch: 40.0 cache: ./cache/cord-003435-ke0az7nf.txt txt: ./txt/cord-003435-ke0az7nf.txt summary: Recombinant technologies further expanded the available therapies based on mAbs. In vitro antibody selection technologies like phage or ribosome display were developed to enable the generation of highly specific human mAbs out of libraries that may even be naïve for the specific antigens [31] [32] [33] [34] [35] [36] 1 Schematic illustration comparing active immunization and passive antibody immunotherapies. While T cell engineering for adoptive transfer inevitably requires the use of nucleic acids encoding a target-specific receptor, antibody immunotherapy can deploy recombinant proteins. However, the effects of mRNA modifications on translation, immunostimulation and resulting protein expression appear to be variable, for instance dependent on the type of target cells. In comparison to a single transfer of cells with retroviral CAR expression, an mRNA-encoded receptor required three consecutive lymphocyte infusions to obtain a comparable antitumor effect [262] . abstract: While active immunization elicits a lasting immune response by the body, passive immunotherapy transiently equips the body with exogenously generated immunological effectors in the form of either target-specific antibodies or lymphocytes functionalized with target-specific receptors. In either case, administration or expression of recombinant proteins plays a fundamental role. mRNA prepared by in vitro transcription (IVT) is increasingly appreciated as a drug substance for delivery of recombinant proteins. With its biological role as transient carrier of genetic information translated into protein in the cytoplasm, therapeutic application of mRNA combines several advantages. For example, compared to transfected DNA, mRNA harbors inherent safety features. It is not associated with the risk of inducing genomic changes and potential adverse effects are only temporary due to its transient nature. Compared to the administration of recombinant proteins produced in bioreactors, mRNA allows supplying proteins that are difficult to manufacture and offers extended pharmacokinetics for short-lived proteins. Based on great progress in understanding and manipulating mRNA properties, efficacy data in various models have now demonstrated that IVT mRNA constitutes a potent and flexible platform technology. Starting with an introduction into passive immunotherapy, this review summarizes the current status of IVT mRNA technology and its application to such immunological interventions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339677/ doi: 10.1007/s00018-018-2935-4 id: cord-007689-0vpp3xdl author: Schlee, M. title: Beyond Double-Stranded RNA-Type I IFN Induction by 3pRNA and Other Viral Nucleic Acids date: 2007 words: 7735.0 sentences: 488.0 pages: flesch: 53.0 cache: ./cache/cord-007689-0vpp3xdl.txt txt: ./txt/cord-007689-0vpp3xdl.txt summary: Since the discovery of type I IFNs in 1957, long double-stranded RNA formed during replication of many viruses was thought to be responsible for type I IFN induction, and for decades double-stranded RNA-activated protein kinase (PKR) was thought to be the receptor. It now became evident that not PKR but two members of the Toll-like receptor (TLR) family, TLR7 and TLR9, and two cytosolic helicases, RIG-I and MDA-5, are responsible for the majority of type I IFNs induced upon recognition of viral nucleic acids. Based on the recent progress in the field, we now know that TLR7, TLR9, and RIG-I do not require long double-stranded RNA for type I IFN induction. These two cytosolic receptors are then responsible for the second and prolonged wave of type I IFN production and for the induction of apoptosis of virally infected cells. Small interfering RNAs mediate sequence-independent gene suppression and induce immune activation by signaling through toll-like receptor 3 abstract: Production of type I IFN is the key response to viral infection. Since the discovery of type I IFNs in 1957, long double-stranded RNA formed during replication of many viruses was thought to be responsible for type I IFN induction, and for decades double-stranded RNA-activated protein kinase (PKR) was thought to be the receptor. Recently, this picture has dramatically changed. It now became evident that not PKR but two members of the Toll-like receptor (TLR) family, TLR7 and TLR9, and two cytosolic helicases, RIG-I and MDA-5, are responsible for the majority of type I IFNs induced upon recognition of viral nucleic acids. In this review, we focus on the molecular mechanisms by which those innate immune receptors detect viral infection. Based on the recent progress in the field, we now know that TLR7, TLR9, and RIG-I do not require long double-stranded RNA for type I IFN induction. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120510/ doi: 10.1007/978-3-540-71329-6_11 id: cord-307598-p54p7enk author: Schlee, Martin title: Master sensors of pathogenic RNA – RIG-I like receptors date: 2013-07-01 words: 12853.0 sentences: 779.0 pages: flesch: 56.0 cache: ./cache/cord-307598-p54p7enk.txt txt: ./txt/cord-307598-p54p7enk.txt summary: Similar to TLRs, RIG-I and MDA5 induce type I IFN and chemokines (but no IL12) upon activation by viral but also bacterial RNA. Since type I IFN induction by this RNA required RNase L, the authors concluded that RNase L recognizes and processes viral mRNA into a MDA5 activating structure. Before 5 triphosphate was identified as the crucial RNA modification to induce RIG-I activation, Marques and colleagues observed that synthetic blunt ended dsRNA oligonucleotides can stimulate RIG-I ( Fig. 3 ) (Marques et al. (2010b) confirmed the requirement of a base paired 5 -ppp end of dsRNA for RIG-I activation and suggested that some arenaviruses and bunyaviruses use a prime and realign mechanism for genome synthesis, leading to 5 overhangs in order to evade RIG-I recognition (Marq et al. pneumophilae did not induce type I IFN in HEK293 cells, thus excluding RIG-I-mediated recognition of RNA polymerase-III transcripts in the host cell, as previously suggested (Chiu et al. abstract: Initiating the immune response to invading pathogens, the innate immune system is constituted of immune receptors (pattern recognition receptors, PRR) that sense microbe-associated molecular patterns (MAMPs). Detection of pathogens triggers intracellular defense mechanisms, such as the secretion of cytokines or chemokines to alarm neighboring cells and attract or activate immune cells. The innate immune response to viruses is mostly based on PRRs that detect the unusual structure, modification or location of viral nucleic acids. Most of the highly pathogenic and emerging viruses are RNA genome-based viruses, which can give rise to zoonotic and epidemic diseases or cause viral hemorrhagic fever. As viral RNA is located in the same compartment as host RNA, PRRs in the cytosol have to discriminate between viral and endogenous RNA by virtue of their structure or modification. This challenging task is taken on by the homologous cytosolic DExD/H-box family helicases RIG-I and MDA5, which control the innate immune response to most RNA viruses. This review focuses on the molecular basis for RIG-I like receptor (RLR) activation by synthetic and natural ligands and will discuss controversial ligand definitions. url: https://api.elsevier.com/content/article/pii/S0171298513001204 doi: 10.1016/j.imbio.2013.06.007 id: cord-010188-884d196k author: Schlesinger, Sondra title: Alphaviruses — vectors for the expression of heterologous genes date: 2004-08-26 words: 3049.0 sentences: 140.0 pages: flesch: 47.0 cache: ./cache/cord-010188-884d196k.txt txt: ./txt/cord-010188-884d196k.txt summary: Sindbis virus and Semliki Forest vires are best known as valuable models for molecular and cell biology, and it is these two viruses that are presently being developed as vectors for the expression of heterologous genes. The basic strategy for using alphaviruses as vectors for the expression of heterologous genes has been to construct cDNAs of the alphavirus genome, in which the heterologous gene is placed downstream from the promoter used to transcribe a subgenomic RNA 13 (Fig. 2a) . A second potential problem is recombination between the packaging helper virus RNA and vector RNAs. The two Sindbis RNAs can undergo recombination to produce a single molecule of RNA containing the genes that encode both the nonstructural and structural proteins m. The initial studies with Sindbis and Semliki Forest virus suggest that both viruses are promising as vectors for heterologous gene expression. abstract: DNA viruses and retroviruses are well established as vectors for the expression of heterologous genes, but there is increasing interest in the possibilities of using RNA viruses, which do not replicate through a DNA intermediate, for this purpose. This article summarizes some of the general properties of RNA viruses and concentrates on one class of RNA viruses — the alphaviruses — and their potential as expression vectors. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172487/ doi: 10.1016/0167-7799(93)90070-p id: cord-003254-yiqdsf9z author: Schlub, Timothy E title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences date: 2018-08-07 words: 6313.0 sentences: 292.0 pages: flesch: 49.0 cache: ./cache/cord-003254-yiqdsf9z.txt txt: ./txt/cord-003254-yiqdsf9z.txt summary: Herein, we present a new statistical method for detecting overlapping genes in different reading frames that relies on only a single nucleotide sequence of a gene or genome. For the synonymous mutation test (C), codons that preserve the original amino acid sequence are randomly generated and the length of ORFs on alternative reading frames subsequently measured (note that codon replacement is not restricted to the example mutations shown in the figure, all of which occur in the third nucleotide positions, and that codon replacement with the original codon is also possible). Accordingly, whole genome sequences were downloaded from 2548 reference linear RNA viruses available on GenBank; this produced a total of 6408 coding regions that were used to estimate the sensitivity and false discovery rate of each test. where C is the empirical cumulative distribution function of the theoretical distribution of lengths calculated by permuting codons in the original coding sequence: that is, C(L) is the Simple Method to Detect Candidate Overlapping Genes . abstract: Overlapping genes in viruses maximize the coding capacity of their genomes and allow the generation of new genes without major increases in genome size. Despite their importance, the evolution and function of overlapping genes are often not well understood, in part due to difficulties in their detection. In addition, most bioinformatic approaches for the detection of overlapping genes require the comparison of multiple genome sequences that may not be available in metagenomic surveys of virus biodiversity. We introduce a simple new method for identifying candidate functional overlapping genes using single virus genome sequences. Our method uses randomization tests to estimate the expected length of open reading frames and then identifies overlapping open reading frames that significantly exceed this length and are thus predicted to be functional. We applied this method to 2548 reference RNA virus genomes and find that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides. Notably, this analysis provided evidence for 29 previously undiscovered functional overlapping genes, some of which are coded in the antisense direction suggesting there are limitations in our current understanding of RNA virus replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6188560/ doi: 10.1093/molbev/msy155 id: cord-255545-nycdhdsd author: Schoenike, Barry title: Quantitative sense-specific determination of murine coronavirus RNA by reverse transcription polymerase chain reaction date: 1999-03-10 words: 6170.0 sentences: 265.0 pages: flesch: 48.0 cache: ./cache/cord-255545-nycdhdsd.txt txt: ./txt/cord-255545-nycdhdsd.txt summary: In theory, sense-specific measurement of viral RNAs may be achieved by reverse transcription polymerase chain reaction (RT-PCR) assays which utilize primers of defined polarity during the RT step. Key RT-PCR parameters which were optimized include the design of tagged primers, DNase treatment of in vitro transcribed RNA standards, specification of temperature differences between RT and PCR annealing steps, and use of competitive RNA templates for quantitative assays. In fact, several studies have demonstrated that RT-PCR assays based on specific RNA template recognition by RT primers of defined polarity will not reliably distinguish between viral RNAs of positive or negative sense. Despite the findings above, many published research reports are based on conventional RT-PCR assays, relying on the polarity of primers added to the RT step in putative sense-specific measurements of viral RNAs; rarely are control reactions performed to rigorously show that this method is in fact sense-specific. abstract: In many applications, it is useful to know the sense and amount of viral RNAs present in a sample. In theory, sense-specific measurement of viral RNAs may be achieved by reverse transcription polymerase chain reaction (RT-PCR) assays which utilize primers of defined polarity during the RT step. However, in practice, it has been shown that such assays are prone to artifacts, such as non-specific priming, which drastically diminish their reliability. Using murine coronavirus MHV-4 as a model, we describe and validate several modifications of the RT-PCR procedure which eliminate these artifacts. Key RT-PCR parameters which were optimized include the design of tagged primers, DNase treatment of in vitro transcribed RNA standards, specification of temperature differences between RT and PCR annealing steps, and use of competitive RNA templates for quantitative assays. The assays described may be used to determine the sense and abundance of any viral or host RNA of interest in complex biological specimens. url: https://www.ncbi.nlm.nih.gov/pubmed/10204695/ doi: 10.1016/s0166-0934(98)00167-0 id: cord-299509-7xjdryoq author: Scholte, Florine E. M. title: Characterization of Synthetic Chikungunya Viruses Based on the Consensus Sequence of Recent E1-226V Isolates date: 2013-08-01 words: 9607.0 sentences: 442.0 pages: flesch: 48.0 cache: ./cache/cord-299509-7xjdryoq.txt txt: ./txt/cord-299509-7xjdryoq.txt summary: Infectious cDNA clones of viruses have become invaluable tools that allow reverse genetics studies to elucidate the contribution of specific amino acids or RNA structures to viraemia, virulence, antigenicity, replication kinetics, interactions with host factors, adaptation to new vectors, and many other aspects of the viral life cycle. To obtain a virus that -in terms of virulence, sensitivity to antiviral compounds, and CHIKV-host interactions -is expected to have the general characteristics of the E1-226V CHIKV strains that were circulating during the 2005-2009 outbreaks, we have constructed a completely synthetic CHIKV cDNA clone based on the consensus sequence of the aligned genomes of these recent isolates. Indirect immunofluorescence analysis of Vero E6 cells infected with CHIKV LS3, LS3-GFP, or ITA07-RA1 at various time points showed that the localization and expression kinetics of E2 and dsRNA were similar for the natural isolate and the synthetic viruses (Fig. 6) . abstract: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that re-emerged in 2004 and has caused massive outbreaks in recent years. The lack of a licensed vaccine or treatment options emphasize the need to obtain more insight into the viral life cycle and CHIKV-host interactions. Infectious cDNA clones are important tools for such studies, and for mechanism of action studies on antiviral compounds. Existing CHIKV cDNA clones are based on a single genome from an individual clinical isolate, which is expected to have evolved specific characteristics in response to the host environment, and possibly also during subsequent cell culture passaging. To obtain a virus expected to have the general characteristics of the recent E1-226V CHIKV isolates, we have constructed a new CHIKV full-length cDNA clone, CHIKV LS3, based on the consensus sequence of their aligned genomes. Here we report the characterization of this synthetic virus and a green fluorescent protein-expressing variant (CHIKV LS3-GFP). Their characteristics were compared to those of natural strain ITA07-RA1, which was isolated during the 2007 outbreak in Italy. In cell culture the synthetic viruses displayed phenotypes comparable to the natural isolate, and in a mouse model they caused lethal infections that were indistinguishable from infections with a natural strain. Compared to ITA07-RA1 and clinical isolate NL10/152, the synthetic viruses displayed similar sensitivities to several antiviral compounds. 3-deaza-adenosine was identified as a new inhibitor of CHIKV replication. Cyclosporin A had no effect on CHIKV replication, suggesting that cyclophilins -opposite to what was found for other +RNA viruses- do not play an essential role in CHIKV replication. The characterization of the consensus sequence-based synthetic viruses and their comparison to natural isolates demonstrated that CHIKV LS3 and LS3-GFP are suitable and representative tools to study CHIKV-host interactions, screen for antiviral compounds and unravel their mode of action. url: https://www.ncbi.nlm.nih.gov/pubmed/23936484/ doi: 10.1371/journal.pone.0071047 id: cord-018564-3igg5s57 author: Schomburg, Dietmar title: RNA helicase 3.6.4.13 date: 2013 words: 12324.0 sentences: 1241.0 pages: flesch: 67.0 cache: ./cache/cord-018564-3igg5s57.txt txt: ./txt/cord-018564-3igg5s57.txt summary: Driven by the energy of ATP hydrolysis, this movement allows the protein to displace complementary strands of DNA or RNA [13] ; <38> the DEAD-box protein DED1 has the ability to balance RNA unwinding with a profound strand annealing activity in a highly dynamic fashion [11] ; <10,20> RNA helicase activity [2, 4] ; <12> multifunctional enzyme possessing serine protease, NTPase, and RNA unwinding activities [42] ; <12> NTPase activity analyzed, ambiguous helicase activity, enzyme capable for unwinding RNA and DNA [38] ; <39> RNA-stimulated ATPase activities determined, interaction between the replicative component nonstructural protein 3 (NS3) with the nonstructural protein 4A (NS4A) [44] ; <12> the Arg-rich amino acid motif HCV1487-1500, a fragment of domain 2 NS3 of Hepatitis C virus, as well as the complete domain 2, and domain 2 lacking the flexible loop localized between Val1458 and Thr1476, mediate competitive inhibition of diverse protein kinase C functions, inhibition of rat brain PKC, overview [39] ; <17> the West Nile virus RNA helicase uses the energy derived from the hydrolysis of nucleotides to separate complementary strands of RNA [62] ; <13> translation of HIV-1 gag mRNA is reliant on the ATP-dependent helicase activity of RNA helicase A [61] ) (Reversibility: ?) [2, 4, 5, 6, 11, 12, 13, 21, 22, 28, 30, 31, 32, 37, 38, 39, 41, 42, 43, 44, 45, 46, 61, 62 ] P ADP + phosphate S RNA + H 2 O <2,5,10,42> (<5> helicase/unwinding activity [43] ; <42> helicase/unwinding activity, either ATP or dATP is required for the unwinding activity [32] ; <2> RNA unwinding activity, the enzyme contains two RecA-like domains, opening and closing of the interdomain cleft during RNA unwinding [45] ) (Reversibility: ?) [32, 41, 43, 45 ] P ? abstract: EC number 3.6.4.13 Systematic name ATP phosphohydrolase (RNA helix unwinding) Recommended name RNA helicase Synonyms 1a NTPase/helicase <16> [5] ATP/dATP-dependent RNA helicase <1,42> [32] ATPase <10,12> [1,36] ATPase/RNA helicase <1,42> [32] ATPase/helicase <10> [36,41] BMV 1a protein <16> [5] BmL3-helicase <1,42> [32] Brr2p <6> [50] DBP2 <24> [30] DDX17 <33> [12] DDX19 <43> [56] DDX25 <23,34,35> [12,21] DDX3 <25> [8] DDX3X <25> (<25> the gene is localized to the X chromosome [12]) [12] DDX3Y <29> (<29> the gene is localized to the Y chromosome [12]) [12] DDX4 <30> [12] DDX5 <32> [12] DEAD box RNA helicase <1,2,3> [32,45,52] DEAD box helicase <2> [45] DEAD-box RNA helicase <4,5,7,38,47,48> [9,14,16,25,53,55] DEAD-box protein DED1 <38> [11] DEAD-box rRNA helicase <5> [26] DEAH-box RNA helicase <24> [30] DEAH-box protein 2 <24> [30] DED1 <38> [11,14] DENV NS3H <10> [41] DEXD/H-box RNA helicase <43> [56] DEx(H/D)RNA helicase <12> [23] DHX9 <44> [58] DbpA <5> [10,25,26] Dhx9/RNA helicase A <13> [61] EhDEAD1 <7> [16] EhDEAD1 RNA helicase <7> [16] FRH <9> [54] FRQ-interacting RNA helicase <9> [54] GRTH <3> [57] GRTH/DDX25 <3,35> [21,51] HCV NS3 helicase <12> [48] KOKV helicase <27> [7] Mtr4p <31> [22] NPH-II <8> [18,28] NS3 <10,12,17,20,39,41> (<12,39> ambiguous [27,42,44]) [1,2,4,27,35,36,39, 42,44,46] NS3 ATPase/helicase <10> [41] NS3 NTPase/helicase <17> (<17> ambiguous [46]) [46] NS3 helicase <10,12,17> [15,44,46] NS3 protein <10,12,17,18> (<12> ambiguous [39]) [15,39,40,41,62] NTPase/helicase <12> (<12> ambiguous [37]) [37,39] RHA <6> [31,49] RNA helicase <2> [45] RNA helicase A <6,44> [31,49,58] RNA helicase CrhR <14> [59] RNA helicase DDX3 <25> [8] RNA helicase Ddx39 <47> [53] RNA helicase Hera <4> [9] RNA-dependent ATPase <37> [34] RNA-dependent NTPase/helicase <12> [1] RTPase <10> [36] RhlB <5> [43] SpolvlgA <48> [55] Supv3L1 <46> [64] TGBp1 NTPase/helicase domain <22,28> [24] Tk-DeaD <15> [47] VRH1 <26> [33] YxiN <2> [45] eIF4A <36> [20] eIF4A helicase <36> [20] eIF4AIII <37> [34] eukaryotic initiation factor eIF 4A <36> [20] gonadotropin-regulated testicular RNA helicase <3> [51,57] helicase <10> [41] helicase B <5> [43] helicase/nucleoside triphosphatase <10> [4] non structural protein 3 <12> (<12> ambiguous [37,38]) [37,38] non-structural 3 <10> [36] non-structural protein 3 <17> [46] non-structural protein 3 protein <18> [40] nonstructural protein 3 <12,17,20,39,40,41> (<12,17,39,40> ambiguous [6,27, 39,42,44,46]) [1,2,6,27,35,39,42,44,46] nucleoside 5’-triphosphatase <10> [4] nucleoside triphosphatase/RNA helicase and 5’-RNA triphosphatase <20> [2] nucleoside triphosphatase/helicase <16> [5] p54 RNA helicase <45> [60] p68 RNA helicase <3,6> [52,63] protein NS3 <12> (<12> ambiguous [38]) [38] url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123474/ doi: 10.1007/978-3-642-36260-6_25 id: cord-007819-51h2jrsy author: Schommer, Susan K. title: Use of a PRRSV Infectious Clone to Evaluate in Vitro Quasispecies Evolution date: 2006 words: 1393.0 sentences: 82.0 pages: flesch: 52.0 cache: ./cache/cord-007819-51h2jrsy.txt txt: ./txt/cord-007819-51h2jrsy.txt summary: Use of the infectious clone also allows us to begin with a single DNA sequence, providing a well-defined starting point for studying PRRSV evolution. 8 The ORF3 protein has the greatest percentage of amino acid changes between the modified live vaccine (Ingelvac) and its parent strain, VR-2332, the isolate from which the infectious clone used in this study was derived. These sequences were then compared to a low passage VR-2332 cell culture propagated stock to determine if the use of an infectious clone was able to decrease the quasispecies variation as compared to a viral stock. The master sequence for each sample derived from the infectious clone was the same as the original plasmid for all genetic regions investigated. Generation of an infectious clone of VR-2332, a highly virulent North American-type isolate of porcine reproductive and respiratory syndrome virus abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124123/ doi: 10.1007/978-0-387-33012-9_78 id: cord-297834-me1ajoyb author: Schountz, Tony title: Hantavirus Immunology of Rodent Reservoirs: Current Status and Future Directions date: 2014-03-14 words: 6425.0 sentences: 334.0 pages: flesch: 38.0 cache: ./cache/cord-297834-me1ajoyb.txt txt: ./txt/cord-297834-me1ajoyb.txt summary: The immune response is energetically expensive for wild animals, thus the findings of experimental studies will be critical for understanding the ecoimmunology of reservoir hosts of hantaviruses [6, 7] , and experiments using wild rodents in natural or semi-natural environments [8, 9] will be required to validate laboratory findings. Currently, three laboratory infection systems have been developed to study hantavirus infections of reservoir hosts: Seoul virus (SEOV) infection of the Norway rat (Rattus norvegicus), Puumala virus (PUUV) infection of the bank vole (Myodes glareolus), and Sin Nombre virus (SNV) infection of the deer mouse (Peromyscus maniculatus) [12, 14, 16] . Experimental data have also shown that patterns of the expression of genes related to the immune response are different in infected males and females [32] , and it is likely these differences have important roles in hantavirus ecology. abstract: Hantaviruses are hosted by rodents, insectivores and bats. Several rodent-borne hantaviruses cause two diseases that share many features in humans, hemorrhagic fever with renal syndrome in Eurasia or hantavirus cardiopulmonary syndrome in the Americas. It is thought that the immune response plays a significant contributory role in these diseases. However, in reservoir hosts that have been closely examined, little or no pathology occurs and infection is persistent despite evidence of adaptive immune responses. Because most hantavirus reservoirs are not model organisms, it is difficult to conduct meaningful experiments that might shed light on how the viruses evade sterilizing immune responses and why immunopathology does not occur. Despite these limitations, recent advances in instrumentation and bioinformatics will have a dramatic impact on understanding reservoir host responses to hantaviruses by employing a systems biology approach to identify important pathways that mediate virus/reservoir relationships. url: https://www.ncbi.nlm.nih.gov/pubmed/24638205/ doi: 10.3390/v6031317 id: cord-268467-btfz6ye8 author: Schreiber, Steven S. title: Sequence analysis of the nucleocapsid protein gene of human coronavirus 229E date: 1989-03-31 words: 5035.0 sentences: 343.0 pages: flesch: 59.0 cache: ./cache/cord-268467-btfz6ye8.txt txt: ./txt/cord-268467-btfz6ye8.txt summary: The 3′-noncoding region of the genome contains an 11-nucleotide sequence, which is relatively conserved throughout the Coronavirus family and lends support to the theory that this region is important for the replication of negative-strand RNA. This result suggested that the HCV229E subgenomic mRNAs possess a nested-set structure similar to other coronaviruses and that A34 represented a cDNA clone of either the 3''-end of the genomic RNA or the leader sequence. The 3''-noncoding region contains the sequence TGGAAGAGCCA, 75 nucleotides from the 3''-end (Fig. 4) which is relatively conserved among coronaviruses and is found at approximately the same location in all of these viral genomes (Kapke and Brian, 1986; Skinner and Siddell, 1984; Armstrong et a/., 1983; Lapps et al., 1987; Kamahora et a/., 1988; Boursnell et al., 1985) ( Table 1) . Three intergenic regions of coronavirus mouse hepatitis virus strain A59 genome RNA contain a common nucleotide sequence that is homologous to the 3''end of the viral mRNA leader sequence abstract: Abstract Human coronaviruses are important human pathogens and have also been implicated in multiple sclerosis. To further understand the molecular biology of human coronavirus 229E (HCV-229E), molecular cloning and sequence analysis of the viral RNA have been initiated. Following established protocols, the 3′-terminal 1732 nucleotides of the genome were sequenced. A large open reading frame encodes a 389 amino acid protein of 43,366 Da, which is presumably the nucleocapsid protein. The predicted protein is similar in size, chemical properties, and amino acid sequence to the nucleocapsid proteins of other coronaviruses. This is especially evident when the sequence is compared with that of the antigenically related porcine transmissible gastroenteritis virus (TGEV), with which a region of 46% amino acid sequence homology was found. Hydropathy profiles revealed the existence of several conserved domains which could have functional significance. An intergenic consensus sequence precedes the 5′-end of the proposed nucleocapsid protein gene. The consensus sequence is present in other coronaviruses and has been proposed as the site of binding of the leader sequence for mRNA transcriptional start. This region was also examined by primer extension analysis of mRNAs, which identified a 60-nucleotide leader sequence. The 3′-noncoding region of the genome contains an 11-nucleotide sequence, which is relatively conserved throughout the Coronavirus family and lends support to the theory that this region is important for the replication of negative-strand RNA. url: https://api.elsevier.com/content/article/pii/0042682289900500 doi: 10.1016/0042-6822(89)90050-0 id: cord-287396-18p171nr author: Schroyen, Martine title: Current transcriptomics in pig immunity research date: 2014-11-15 words: 9824.0 sentences: 467.0 pages: flesch: 44.0 cache: ./cache/cord-287396-18p171nr.txt txt: ./txt/cord-287396-18p171nr.txt summary: Other meta-analysis studies, examining the immune response to Salmonella typhimurium, combine microarray information with data such as serum cytokine measurements or microbiota differences. typhimurium will be discussed in the section ''''Overall value of transcriptomics in important infectious swine diseases.'''' In addition, whole genome microarrays were used to study pig response to Haemophilus parasuis infection by Zhao et al. In 2010, Xiao and collaborators performed a 3'' tag digital gene expression (DGE) analysis of the porcine lung transcriptome on pigs infected with the PRRS virus (Xiao et al. Most pig immune studies conducted to identify host response to common porcine pathogens or to immune response stimulators such as LPS or PMA/ionomycin described in this review provide gene expression data from a single tissue or isolated cell type, and this at a limited number of times post-infection/stimulation. Recently, such a meta-analysis was performed by combining results of several microarray-based pig immune studies to find PRRS-specific responses (Badaoui et al. abstract: Swine performance in the face of disease challenge is becoming progressively more important. To improve the pig’s robustness and resilience against pathogens through selection, a better understanding of the genetic and epigenetic factors in the immune response is required. This review highlights results from the most recent transcriptome research, and the meta-analyses performed, in the context of pig immunity. A technological overview is given including wholegenome microarrays, immune-specific arrays, small-scale high-throughput expression methods, high-density tiling arrays, and next generation sequencing (NGS). Although whole genome microarray techniques will remain complementary to NGS for some time in domestic species, research will transition to sequencing-based methods due to cost-effectiveness and the extra information that such methods provide. Furthermore, upcoming high-throughput epigenomic studies, which will add greatly to our knowledge concerning the impact of epigenetic modifications on pig immune response, are listed in this review. With emphasis on the insights obtained from transcriptomic analyses for porcine immunity, we also discuss the experimental design in pig immunity research and the value of the newly published porcine genome assembly in using the pig as a model for human immune response. We conclude by discussing the importance of establishing community standards to maximize the possibility of integrative computational analyses, such as was clearly beneficial for the human ENCODE project. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00335-014-9549-4) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s00335-014-9549-4 doi: 10.1007/s00335-014-9549-4 id: cord-301904-mjfbvl5n author: Schultz-Cherry, S. title: Astroviruses date: 2014-11-28 words: 5493.0 sentences: 270.0 pages: flesch: 39.0 cache: ./cache/cord-301904-mjfbvl5n.txt txt: ./txt/cord-301904-mjfbvl5n.txt summary: Astrovirus as a cause of hospital-acquired viral diarrhea in young children is second only to rotavirus and norovirus, occurring at rates of 4.5-6%, and, in some studies, surpasses rotavirus in rates of nosocomial infections. Recent studies reported that an HAstV-VA1-like strain was detected in a patient with new-onset celiac disease and associated with extra-intestinal dissemination (including neural tissue) in immunocompromised children. Given the susceptibility of different cell lines for HAstV infection (depending on the serotype and genotype) it is possible that astroviruses use a variety of attachment proteins or receptors including carbohydrate moieties. The immunological response to astrovirus infection is poorly defined; however, observations in humans and animal models suggest that both the adaptive and innate responses play important roles in controlling and eliminating the virus. While astrovirus antibodies protected individuals from symptoms associated with infection, virus was identified in the feces, suggesting that such antibodies do not necessarily prevent viral replication. abstract: Astroviruses are positive-sense, single-stranded RNA viruses. Their genomes contain three open reading frames, but the exact number of encoded proteins remains unknown. Astroviruses were originally identified in association with childhood diarrhea; subsequently, they have been identified as a common enteric virus infecting children under the age of 2. Infection is not restricted to humans, however, and astroviruses have been found in widespread mammalian and avian species. Generally, infection causes a mild, self-limiting gastroenteritis, although infection can result in nephritis, hepatitis, and encephalitis in certain host species. Astrovirus pathogenicity and immune response is only poorly characterized and may differ between mammalian and avian species. In this article, the current knowledge of astroviruses is reviewed, including their molecular virology, viral evolution, pathogenesis, and immune response. url: https://api.elsevier.com/content/article/pii/B9780128012383025393 doi: 10.1016/b978-0-12-801238-3.02539-3 id: cord-311007-0i1abjfa author: Schwarz, Megan C. title: Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone date: 2016-09-28 words: 4857.0 sentences: 241.0 pages: flesch: 50.0 cache: ./cache/cord-311007-0i1abjfa.txt txt: ./txt/cord-311007-0i1abjfa.txt summary: High levels of infectious virus were produced following transfection of the plasmid bearing the wild-type MR766 ZIKV genome, but not one with a disruption to the viral nonstructural protein 5 (NS5) polymerase active site. Multicycle growth curve and plaque assay experiments indicated that the MR766 virus resulting from plasmid transfection exhibited growth characteristics that were more similar to its parental isolate than previously published 2010 Cambodia and 2015 Brazil cDNA-rescued ZIKV. Indeed, sequence analysis of bacterial plasmid clones of these RT-PCRs demonstrated that all products from wild-type plasmid-transfected cell RNA lacked the inserted intron (Fig. 3B) . In contrast to parental virus RT-PCR products (Fig. 3B) , these sequences carried a single silent G3127A mutation that was inserted during intron cloning, which indicated that these RNAs were generated from the MR766 plasmid. The addition of supernatants from wild-type plasmid-transfected or parental virus-infected 293T cells resulted in readily detectable levels of viral proteins. abstract: The recent Zika virus (ZIKV) outbreak has been linked to severe pathogenesis. Here, we report the construction of a plasmid carrying a cytomegalovirus (CMV) promoter-expressed prototype 1947 Uganda MR766 ZIKV cDNA that can initiate infection following direct plasmid DNA transfection of mammalian cells. Incorporation of a synthetic intron in the nonstructural protein 1 (NS1) region of the ZIKV polyprotein reduced viral cDNA-associated toxicity in bacteria. High levels of infectious virus were produced following transfection of the plasmid bearing the wild-type MR766 ZIKV genome, but not one with a disruption to the viral nonstructural protein 5 (NS5) polymerase active site. Multicycle growth curve and plaque assay experiments indicated that the MR766 virus resulting from plasmid transfection exhibited growth characteristics that were more similar to its parental isolate than previously published 2010 Cambodia and 2015 Brazil cDNA-rescued ZIKV. This ZIKV infectious clone will be useful for investigating the genetic determinants of ZIKV infection and pathogenesis and should be amenable to construction of diverse infectious clones expressing reporter proteins and representing a range of ZIKV isolates. IMPORTANCE The study of ZIKV, which has become increasingly important with the recent association of this virus with microcephaly and Guillain-Barré syndrome, would benefit from an efficient strategy to genetically manipulate the virus. This work describes a model system to produce infectious virus in cell culture. We created a plasmid carrying the prototype 1947 Uganda MR766 ZIKV genome that both was stable in bacteria and could produce high levels of infectious virus in mammalian cells through direct delivery of this DNA. Furthermore, growth properties of this rescued virus closely resembled those of the viral isolate from which it was derived. This model system will provide a simple and effective means to study how ZIKV genetics impact viral replication and pathogenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/27704051/ doi: 10.1128/msphere.00246-16 id: cord-301997-63160t7f author: Schwer, Beate title: Discontinuous transcription or RNA processing of vaccinia virus late messengers results in a 5′ poly(A) leader date: 1987-07-17 words: 4743.0 sentences: 236.0 pages: flesch: 55.0 cache: ./cache/cord-301997-63160t7f.txt txt: ./txt/cord-301997-63160t7f.txt summary: We have shown that RNA transcripts from a translocated 11K and from the authentic 11K and 4b late promoters are extended by approximately 35 nucleotides beyond the "start site" determined by Sl mapping using vaccinia genomic DNA as a probe. We have shown that RNA transcripts from a translocated 11K and from the authentic 11K and 4b late promoters are extended by approximately 35 nucleotides beyond the "start site" determined by Sl mapping using vaccinia genomic DNA as a probe. As a negative control, we have performed primer extension with a dhfr primer and wild-type mRNA that does not contain dhfr sequences ( Figure 1, cDNA-RNA hybrids were incubated in the presence or absence of RNAase A at a final concentration of 10 Kg/ml and the hybrids were cap-selected by immunoprecipitation using a rabbit anti-m7G antiserum as described. After RNAase treatment-cap selection of the cDNA-RNA hybrids, we obtained the same results as for the wild-type translocated promoter-dhfr messengers (data not shown). abstract: Abstract We have demonstrated by primer elongation and cap analysis that mature vaccinia virus late transcripts are discontinuously synthesized. We have shown that RNA transcripts from a translocated 11K and from the authentic 11K and 4b late promoters are extended by approximately 35 nucleotides beyond the “start site” determined by S1 mapping using vaccinia genomic DNA as a probe. Sequencing of the RNA and of the first strand cDNA reveal that a homopolymeric poly(A) sequence is linked to the 5′ terminus of the RNA transcripts. S1 mapping of RNA transcripts with a DNA probe containing an A-stretch, replacing promoter sequences upstream of position −1, confirms the existence of a poly(A) leader of approximately 35 A-residues. url: https://www.ncbi.nlm.nih.gov/pubmed/3594569/ doi: 10.1016/0092-8674(87)90212-1 id: cord-306424-gf0bglm0 author: Scutigliani, Enzo Maxim title: Interaction of the innate immune system with positive-strand RNA virus replication organelles date: 2017-06-27 words: 8320.0 sentences: 382.0 pages: flesch: 36.0 cache: ./cache/cord-306424-gf0bglm0.txt txt: ./txt/cord-306424-gf0bglm0.txt summary: Thus, these data indicate that MAMs are critical locations for antiviral signaling and have an important role in expression of type I and III IFNs. Moreover, increasing evidence suggests that at least some +RNA viruses in fact occupy or hijack MAM-membranes during infection, as MAMs of HCV-infected cells were found to contain proteins involved in virus assembly and fully assembled virions [111] . At last, based on recent studies that demonstrated how IFN-g inducible GTPases are capable of disrupting PVs, we discussed the possibility of a general function of IFN-inducible GTPases in the targeting of viral ROs. In summary, upon infection, +RNA viruses hamper IFN and ISG induction at multiple levels to decelerate antiviral innate immune signaling. Antiviral innate immune response interferes with the formation of replication-associated membrane structures induced by a +RNA virus abstract: The potential health risks associated with (re-)emerging positive-strand RNA (+RNA) viruses emphasizes the need for understanding host-pathogen interactions for these viruses. The innate immune system forms the first line of defense against pathogenic organisms like these and is responsible for detecting pathogen-associated molecular patterns (PAMPs). Viral RNA is a potent inducer of antiviral innate immune signaling, provoking an antiviral state by directing expression of interferons (IFNs) and pro-inflammatory cytokines. However, +RNA viruses developed various methods to avoid detection and downstream signaling, including isolation of viral RNA replication in membranous viral replication organelles (ROs). These structures therefore play a central role in infection, and consequently, loss of RO integrity might simultaneously result in impaired viral replication and enhanced antiviral signaling. This review summarizes the first indications that the innate immune system indeed has tools to disrupt viral ROs and other non- or aberrant-self membrane structures, and may do this by marking these membranes with proteins such as microtubule-associated protein 1A/1B-light chain 3 (LC3) and ubiquitin, resulting in the recruitment of IFN-inducible GTPases. Further studies should evaluate whether this process forms a general effector mechanism in +RNA virus infection, thereby creating the opportunity for development of novel antiviral therapies. url: https://api.elsevier.com/content/article/pii/S1359610117300667 doi: 10.1016/j.cytogfr.2017.05.007 id: cord-291029-oldket3n author: Sefers, Susan E. title: QIAamp MinElute Virus kit effectively extracts viral nucleic acids from cerebrospinal fluids and nasopharyngeal swabs() date: 2005-07-21 words: 3532.0 sentences: 182.0 pages: flesch: 53.0 cache: ./cache/cord-291029-oldket3n.txt txt: ./txt/cord-291029-oldket3n.txt summary: The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. In this study, we have chosen both nasopharyngeal swab (NPS) and cerebrospinal fluid (CSF) specimens submitted for influenza A virus, enterovirus and herpesvirus testing to validate the MinElute nucleic acid extraction system. Nucleic acid recovery rates between the MinElute and RNAzol B were further determined by quantitating HIV-1 or CMV viral loads in extracted RNA or DNA specimens using a real-time TaqMan PCR. The MinElute kits possessed an equivalent sensitivity in nucleic acid recovery and detection, in comparison to the IsoQuick and RNAzol B, for both DNA and RNA extraction. abstract: BACKGROUND: Nucleic acid preparation from a variety of clinical specimens requires efficient target recovery and amplification inhibitor removal and is critical for successful molecular diagnosis. The QIAamp MinElute Virus kit (Qiagen Inc., Valencia, CA) was compared to the two existing methods currently used in our laboratory, IsoQuick (Orca Research Inc., Bothell, WA) for DNA extraction and RNAzol B (Leedo Laboratories Inc., Houston, TX) for RNA extraction, of viral nucleic acids. STUDY DESIGN: A total of 150 clinical specimens, including cerebrospinal fluid (CSF) and nasopharyngeal swabs (NPS), were used to determine the extraction efficiency of the MinElute compared to the other two methods. Nucleic acid recovery, hands-on time, turn-around-time and cost were compared across all kits. RESULTS: There was complete concordance between the MinElute and IsoQuick/RNAzol kits when herpes simplex virus (HSV), Epstein–Barr virus (EBV), varicella-zoster virus (VZV), influenza A virus or enteroviruses were detected using a colorimetric microtiter plate PCR system. The kits were equivalent in their ability to detect either DNA or RNA with superior ability to recover a high quality and quantity of RNA. With the potential to process larger specimen volumes, the MinElute kit can significantly shorten processing time from 2 h to 50–55 min. CONCLUSIONS: Although relatively high test kit costs were noted, the MinElute kit provides another rapid and user-friendly specimen processing tool in the diagnostic molecular microbiology laboratory. url: https://www.sciencedirect.com/science/article/pii/S1386653205001526 doi: 10.1016/j.jcv.2005.05.011 id: cord-315085-rucfowvv author: Sekulic, Miroslav title: Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases date: 2020-05-26 words: 5025.0 sentences: 302.0 pages: flesch: 47.0 cache: ./cache/cord-315085-rucfowvv.txt txt: ./txt/cord-315085-rucfowvv.txt summary: In this study we report postmortem findings and detection and sequencing of SARS-CoV-2 viral RNA from formalin-fixed paraffinembedded (FFPE) samples of multiple organs collected in 2 patients with antemortem detection of SARS-CoV-2. The patient''s medical history was otherwise notable for dementia, radiologic evidence of a left lung mass (managed with hospice care), coronary artery disease (status post coronary artery bypass grafting), atrial fibrillation (biventricular pacemaker implanted), congestive heart failure, peripheral artery disease (status post iliac stenting), diabetes mellitus, hypertension, dyslipidemia, chronic kidney disease, gout, smoking, cerebrovascular accidents, and urinary tract infections. On day 1 after admission, ❚Image 2❚ (Case 1) Postmortem microscopic examination of the lungs showed diffuse alveolar damage characterized by hyaline membrane formation (A, ×100) and scattered squamous metaplasia of distal airways (B, ×100) on a background of emphysematous changes. abstract: OBJECTIVES: To report methods and findings of 2 autopsies with molecular evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive individuals. METHODS: Postmortem examination was completed following Centers for Disease Control and Prevention public guidelines. Numerous formalin-fixed paraffin-embedded (FFPE) tissue types from each case were surveyed for SARS-CoV-2 RNA by quantitative reverse transcription polymerase chain reaction (qRT-PCR). SARS-CoV-2 viral genome was sequenced by next-generation sequencing (NGS) from FFPE lung tissue blocks. RESULTS: Postmortem examinations revealed diffuse alveolar damage, while no viral-associated hepatic, cardiac, or renal damage was observed. Viral RNA was detected in lungs, bronchi, lymph nodes, and spleen in both cases using qRT-PCR method. RNA sequencing using NGS in case 1 revealed mutations most consistent with Western European Clade A2a with ORF1a L3606F mutation. CONCLUSIONS: SARS-CoV-2 testing and viral sequencing can be performed from FFPE tissue. Detection and sequencing of SARS-CoV-2 in combination with morphological findings from postmortem tissue examination can aid in gaining a better understanding of the virus’s pathophysiologic effects on human health. url: https://doi.org/10.1093/ajcp/aqaa091 doi: 10.1093/ajcp/aqaa091 id: cord-342634-4ouhdjsr author: Semrad, Katharina title: Proteins with RNA Chaperone Activity: A World of Diverse Proteins with a Common Task—Impediment of RNA Misfolding date: 2010-12-26 words: 7141.0 sentences: 399.0 pages: flesch: 52.0 cache: ./cache/cord-342634-4ouhdjsr.txt txt: ./txt/cord-342634-4ouhdjsr.txt summary: In brief, the group of proteins with RNA chaperone activity includes proteins that, first, open up misfolded structures without requirement of ATP and that, second, are dispensable once the RNA has been folded. coli showed that 1/3 of the tested proteins possesses strong RNA chaperone activity in vitro in the trans-splicing assay [21] . E. coli contains nine members of the csp family and CspA, the major cold-shock protein and CspE were identified to interact non-specifically with RNA molecules and to possess nucleic acid melting activities [44] [45] [46] . Later, a detailed study on possible functions of Ro RNPs, which are Ro ribonucleoprotein complexes, composed of a small noncoding cytoplasmic RNA, termed Y RNA and its protein partners was conducted: besides the permanently associated proteins Ro60 and La, subpopulations of Ro-RNPs also contain hnRNP I and hnRNP K, both of which exhibited strong RNA chaperone activity in vitro in the transsplicing and the cis-splicing assay [22] . abstract: Proteins with RNA chaperone activity are ubiquitous proteins that play important roles in cellular mechanisms. They prevent RNA from misfolding by loosening misfolded structures without ATP consumption. RNA chaperone activity is studied in vitro and in vivo using oligonucleotide- or ribozyme-based assays. Due to their functional as well as structural diversity, a common chaperoning mechanism or universal motif has not yet been identified. A growing database of proteins with RNA chaperone activity has been established based on evaluation of chaperone activity via the described assays. Although the exact mechanism is not yet understood, it is more and more believed that disordered regions within proteins play an important role. This possible mechanism and which proteins were found to possess RNA chaperone activity are discussed here. url: https://www.ncbi.nlm.nih.gov/pubmed/21234377/ doi: 10.1155/2011/532908 id: cord-269496-tnw7sxlh author: Sen Gupta, Parth Sarthi title: Binding mechanism and structural insights into the identified protein target of COVID-19 and importin-α with in-vitro effective drug ivermectin date: 2020-10-28 words: 4910.0 sentences: 246.0 pages: flesch: 53.0 cache: ./cache/cord-269496-tnw7sxlh.txt txt: ./txt/cord-269496-tnw7sxlh.txt summary: Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of −187.3 kJ/mol, almost twice that of Helicase (−94.6 kJ/mol) and even lower than that of Importin-α (−156.7 kJ/mol). Together, being conserved and a necessary component for the replication of coronavirus, a multi-functional protein, Nsp13-helicase, is another vital SARS-COV-2 target (Jia et al., 2019) , which can be considered further for antiviral drug discovery provided a very small number of Nsp13 inhibitors reported to date . Molecular docking of Ivermectin with twelve SARS-COV-2''s targets along with Importin-a was carried out, followed by binding mechanism exploration and structural stability analysis using molecular dynamics (MD) simulation through the root-meansquare deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (R g ), and binding free energy of the complexes of Ivermectin with the best targets. abstract: While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by ∼5000 folds within 48 h, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets along with Importin-α studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting −10.4 kcal/mol and −9.6 kcal/mol, respectively, followed by Importin-α with −9.0 kcal/mol. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site and Importin-α, with MM/PBSA free energy of −187.3 kJ/mol, almost twice that of Helicase (−94.6 kJ/mol) and even lower than that of Importin-α (−156.7 kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration. url: https://doi.org/10.1080/07391102.2020.1839564 doi: 10.1080/07391102.2020.1839564 id: cord-342756-rgm9ffpk author: Senger, Mario Roberto title: COVID-19: molecular targets, drug repurposing and new avenues for drug discovery date: 2020-10-02 words: 16108.0 sentences: 1024.0 pages: flesch: 51.0 cache: ./cache/cord-342756-rgm9ffpk.txt txt: ./txt/cord-342756-rgm9ffpk.txt summary: Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. In the following topic, we will review SARS-CoV-2 structure and mechanism of infection in order to discuss molecular targets from the virus or its human host that are being considered for drug repurposing and perhaps future development of new drugs. (128) Its role as a functional receptor of SARS-CoV-2 S protein in host cells makes this protein a potential drug target to treat COVID-19. (138) TMPRSS2 has a major role in SARS-CoV-2 cell entry and replication, and thus represents an interesting therapeutic target since its inhibitors could potentially block virus infection in its initial stages. (199) A robust preclinical drug discovery pipeline comprising in vitro, and in vivo models of SARS-CoV-2 infection is particularly important to identify new antivirals for human COVID-19 treatment. abstract: Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious infection that may break the healthcare system of several countries. Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. Finally, we also discuss patent protection issues, cost effectiveness and scalability of synthetic routes for some of the most studied repurposing candidates since these are key aspects to meet global demand for COVID-19 treatment. url: https://www.ncbi.nlm.nih.gov/pubmed/33027420/ doi: 10.1590/0074-02760200254 id: cord-295217-z2erqkr9 author: Seow, Justine Jia Wen title: Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art date: 2020-06-02 words: 4353.0 sentences: 249.0 pages: flesch: 48.0 cache: ./cache/cord-295217-z2erqkr9.txt txt: ./txt/cord-295217-z2erqkr9.txt summary: Majority of scRNA-seq approaches provide the steady state kinetics of mRNA (messenger RNA) expression without deeper insights into transcriptional dynamics of cells. However, a recent method called scSLAMseq (single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing) profiles the transcriptional activity at the singlecell resolution which can help in differentiating old and new RNA for thousands of genes 14 A very recent method SMART-Seq3 provides the allele and isoform resolution in scRNA-seq approach 17 . This results in a data set that is roughly symmetric and often roughly normal Mutual Nearest Neighbours: a pair of cells from each batch is contained in each other''s set of nearest neighbours Batch correction: scRNA-seq datasets generated across different conditions or from technologies that contain batch specific systematic bias leading to batch-effect. From single-cell transcriptomic data, Cell-PhoneDB calculates significant receptor-ligand pairs from cluster information and differentially expressed genes. A benchmark of batch-effect correction methods for single-cell RNA sequencing data abstract: Tumors exhibit genetic and phenotypic diversity leading to intra-tumor heterogeneity (ITH). Further complex ecosystem (stromal and immune cells) of tumors contributes into the ITH. This ITH allows tumors to overcome various selection pressures such as anti-cancer therapies and metastasis at distant organs. Single-cell RNA-seq (scRNA-seq) has provided unprecedented insights into ITH and its implications in drug resistance and metastasis. As scRNA-seq technology grows and provides many new findings, new tools on different programming platforms are frequently generated. Here, we aim to provide a framework and guidelines for new entrants into the field of scRNA-seq. In this review, we discuss the current state-of-art of scRNA-seq analysis step-by-step including filtering, normalization and analysis. First, we discuss the brief history of experimental methods, followed by data processing and implications in precision oncology. url: https://doi.org/10.1007/s41745-020-00178-1 doi: 10.1007/s41745-020-00178-1 id: cord-262282-9xh51cd1 author: Serwer, Philip title: Optimizing Anti-Viral Vaccine Responses: Input from a Non-Specialist date: 2020-05-15 words: 4323.0 sentences: 260.0 pages: flesch: 57.0 cache: ./cache/cord-262282-9xh51cd1.txt txt: ./txt/cord-262282-9xh51cd1.txt summary: Without going into details concerning live vaccine production via eukaryotic viruses, I think it reasonable to assume that eukaryotic virus production is more difficult, more expensive and less rapid than the production of phages. However, current efforts to human-engineer improved antigens for anti-RNA virus vaccines have shown that neutralizing antibodies typically react with viral proteins that are in states that are context dependent and unstable [12, 13, 15, 20] . I take the liberty of responding here to the obvious objection that no membrane-covered, single-stranded RNA phage has ever been isolated [21] and that the pandemic viruses include influenza, Zika-type and coronaviruses, all in this category. A non-specialist observer reasonably concludes that DNA and RNA vaccines, when viewed in the context of our overall objective, are examples of type 2 strategy options. Given that eukaryotic viruses have doubling times much greater than those of phages (2-5 min for typical coliphages), meeting this objective implies that a live virus vaccine has to be already present in the environment. abstract: Recently, the research community has had a real-world look at reasons for improving vaccine responses to emerging RNA viruses. Here, a vaccine non-specialist suggests how this might be done. I propose two alternative options and compare the primary alternative option with current practice. The basis of comparison is feasibility in achieving what we need: a safe, mass-produced, emerging virus-targeted vaccine on 2–4 week notice. The primary option is the following. (1) Start with a platform based on live viruses that infect bacteria, but not humans (bacteriophages, or phages). (2) Isolate phages (to be called pathogen homologs) that resemble and provide antigenic context for membrane-covered, pathogenic RNA viruses; coronavirus-phage homologs will probably be found if the search is correctly done. (3) Upon isolating a viral pathogen, evolve its phage homolog to bind antibodies neutralizing for the viral pathogen. Vaccinate with the evolved phage homolog by generating a local, non-hazardous infection with the phage host and then curing the infection by propagating the phage in the artificially infecting bacterial host. I discuss how this alternative option has the potential to provide what is needed after appropriate platforms are built. url: https://www.ncbi.nlm.nih.gov/pubmed/32429032/ doi: 10.3390/antibiotics9050255 id: cord-312223-qgwzgazd author: Shafagati, Nazly title: The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus date: 2013-07-04 words: 8834.0 sentences: 495.0 pages: flesch: 57.0 cache: ./cache/cord-312223-qgwzgazd.txt txt: ./txt/cord-312223-qgwzgazd.txt summary: RESULTS: Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Our study demonstrates that NanoTrap particles are capable of capturing whole virus, and can be assayed with both qRT-PCR and plaque assays. A) Seven different types of NanoTrap particles were incubated with viral supernatants containing RVFV (1E+7 pfu/ml) for 30 minutes at room temperature and washed 4 times with water. In order to determine if the amplification observed in the qRT-PCR assay was due to the NanoTrap particle capturing intact viral particles or association of viral RNA (presumably due to lysed virus) with the particles, plaque assays were performed. abstract: BACKGROUND: Rift Valley Fever Virus (RVFV) is a zoonotic virus that is not only an emerging pathogen but is also considered a biodefense pathogen due to the threat it may cause to public health and national security. The current state of diagnosis has led to misdiagnosis early on in infection. Here we describe the use of a novel sample preparation technology, NanoTrap particles, to enhance the detection of RVFV. Previous studies demonstrated that NanoTrap particles lead to both 100 percent capture of protein analytes as well as an improvement of more than 100-fold in sensitivity compared to existing methods. Here we extend these findings by demonstrating the capture and enrichment of viruses. RESULTS: Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. Importantly, NT53 capture of RVFV resulted in greater than 100-fold enrichment from low viral titers when other diagnostics assays may produce false negatives. NT53 was also capable of capturing and enhancing RVFV detection from serum samples. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Furthermore, both NP-40-lysed virus and purified RVFV RNA were bound by NT53. Importantly, NT53 protected viral RNA from RNase A degradation, which was not observed with other commercially available beads. Incubation of RVFV samples with NT53 also resulted in increased viral stability as demonstrated through preservation of infectivity at elevated temperatures. Finally, NanoTrap particles were capable of capturing VEEV and HIV, demonstrating the broad applicability of NanoTrap particles for viral diagnostics. CONCLUSION: This study demonstrates NanoTrap particles are capable of capturing, enriching, and protecting RVFV virions. Furthermore, the use of NanoTrap particles can be extended to a variety of viruses, including VEEV and HIV. url: https://www.ncbi.nlm.nih.gov/pubmed/23861988/ doi: 10.1371/journal.pntd.0002296 id: cord-351837-vasuu70k author: Shannon, Ashleigh title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis date: 2020-09-17 words: 6507.0 sentences: 349.0 pages: flesch: 50.0 cache: ./cache/cord-351837-vasuu70k.txt txt: ./txt/cord-351837-vasuu70k.txt summary: title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. This enzyme readily incorporates T-705-ribose-5′-phosphate into viral RNA in vitro, and cell culture based infectious virus studies show an increase in mutations in the presence of Favipiravir. To determine the efficacy and MoA of T-705 against SARS-CoV we first characterised nsp12 primerdependent activity using traditional annealed primer-template (PT) and self-priming hairpin (HP) RNAs that may confer additional stability on the elongation complex ( Supplementary Fig. 1c) . These data reveal that the SARS-CoV nsp12 is the fastest viral RdRp known, with rates significantly faster than the 5-20 s −1 observed for picornaviral polymerases at room temperature [33] [34] [35] and 4-18 s −1 for hepatitis C and dengue virus polymerases at 30 and 37°C 36, 37 . abstract: The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. We demonstrate here that Favipiravir predominantly exerts an antiviral effect through lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19. url: https://www.ncbi.nlm.nih.gov/pubmed/32943628/ doi: 10.1038/s41467-020-18463-z id: cord-290472-w77cmljm author: Sharon, Donald title: Systems Biology Approaches to Disease Marker Discovery date: 2010-06-09 words: 8665.0 sentences: 393.0 pages: flesch: 39.0 cache: ./cache/cord-290472-w77cmljm.txt txt: ./txt/cord-290472-w77cmljm.txt summary: These markers, such as protein (including autoantibodies, which are antibodies specific to self-antigens [43] ), hormonal markers (such as lack of insulin in Type I diabetic patients [89] ), and genetic/genomic markers (such as BRCA1 mutation in breast cancer patients [52] ), enable clinicians to diagnose the disease while it is still at early stages, to ensure appropriate surgical intervention, efficient drug treat-ment and monitoring, and to predict an individual''s risk of developing specific diseases before they experience symptoms. Scientists, such as the group led by Gil Mor at Yale University, recruited proteomics-based approaches using antibody-based protein microarrays to identify new serum biomarkers, which, in combination with CA-125, may enhance the early detection of ovarian cancer [48, 66, 110] . To date, no studies that attempt to identify novel breast cancer markers have been performed using high-density protein microarrays. abstract: Our understanding of human disease and potential therapeutics is improving rapidly. In order to take advantage of these developments it is important to be able to identify disease markers. Many new high-throughput genomics and proteomics technologies are being implemented to identify candidate disease markers. These technologies include protein microarrays, next-generation DNA sequencing and mass spectrometry platforms. Such methods are particularly important for elucidating the repertoire of molecular markers in the genome, transcriptome, proteome and metabolome of patients with diseases such as cancer, autoimmune diseases, and viral infections, resulting from the disruption of many biological pathways. These new technologies have identified many potential disease markers. These markers are expected to be valuable to achieve the promise of truly personalized medicine. url: https://www.ncbi.nlm.nih.gov/pubmed/20534906/ doi: 10.3233/dma-2010-0707 id: cord-277687-u3q36o3e author: Shean, Ryan C. title: VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank date: 2019-01-23 words: 4071.0 sentences: 212.0 pages: flesch: 49.0 cache: ./cache/cord-277687-u3q36o3e.txt txt: ./txt/cord-277687-u3q36o3e.txt summary: title: VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank In order to accept submitted viral genomic data, NCBI GenBank requires 1) viral sequence complete with at least one protein annotation, 2) author/depositor metadata, and 3) viral sequence metadata, such as strain, collection date, collection location, and coverage. VAPiD handles batch submissions of multiple viruses of different types without prior knowledge of the viral species, correctly annotates RNA editing and ribosomal slippage, performs spellchecking on annotations, handles batch or individual submission of metadata, runs with a simple one-line command, and creates annotated viral sequence files for GenBank submission. This first example is the task that the authors originally wrote VAPiD for -annotating large numbers of genomes from different viral species, which mirrors the type of data that many clinical and public health laboratories may encounter. abstract: BACKGROUND: With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available. GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions. RESULTS: We present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1–4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems. CONCLUSIONS: We have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found at https://github.com/rcs333/VAPiD. url: https://www.ncbi.nlm.nih.gov/pubmed/30674273/ doi: 10.1186/s12859-019-2606-y id: cord-003070-6oca1mrm author: Shen, Wen-Jun title: RPiRLS: Quantitative Predictions of RNA Interacting with Any Protein of Known Sequence date: 2018-02-28 words: 5476.0 sentences: 339.0 pages: flesch: 56.0 cache: ./cache/cord-003070-6oca1mrm.txt txt: ./txt/cord-003070-6oca1mrm.txt summary: On the non-redundant benchmark test sets extracted from the PRIDB, the RPiRLS method outperformed RPI-Pred and IPMiner in terms of accuracy, specificity and sensitivity. The computational results showed that the RPiRLS classifier outperformed the RPiRLS-7G classifier in terms of various performance measurements, indicating that the diversity of amino acids at a sequence is important for the prediction of RPIs. The performance of predicting RPIs was evaluated by using 10-fold stratified cross-validation on the RPI2662 data set. For the RPI369 data set as shown in Table 4 , the performance of the RPiRLS method was 0.85, 0.92, 0.84 and 0.86 for predictive accuracy, AUC, specificity and sensitivity, respectively. The work presented here provided a computational method, called RPiRLS, to classify RNA-protein pairs as interacting or non-interacting by integrating a sequence-based derived kernel with regularized least squares. abstract: RNA-protein interactions (RPIs) have critical roles in numerous fundamental biological processes, such as post-transcriptional gene regulation, viral assembly, cellular defence and protein synthesis. As the number of available RNA-protein binding experimental data has increased rapidly due to high-throughput sequencing methods, it is now possible to measure and understand RNA-protein interactions by computational methods. In this study, we integrate a sequence-based derived kernel with regularized least squares to perform prediction. The derived kernel exploits the contextual information around an amino acid or a nucleic acid as well as the repetitive conserved motif information. We propose a novel machine learning method, called RPiRLS to predict the interaction between any RNA and protein of known sequences. For the RPiRLS classifier, each protein sequence comprises up to 20 diverse amino acids but for the RPiRLS-7G classifier, each protein sequence is represented by using 7-letter reduced alphabets based on their physiochemical properties. We evaluated both methods on a number of benchmark data sets and compared their performances with two newly developed and state-of-the-art methods, RPI-Pred and IPMiner. On the non-redundant benchmark test sets extracted from the PRIDB, the RPiRLS method outperformed RPI-Pred and IPMiner in terms of accuracy, specificity and sensitivity. Further, RPiRLS achieved an accuracy of 92% on the prediction of lncRNA-protein interactions. The proposed method can also be extended to construct RNA-protein interaction networks. The RPiRLS web server is freely available at http://bmc.med.stu.edu.cn/RPiRLS. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6017498/ doi: 10.3390/molecules23030540 id: cord-103015-3dxwbmd2 author: Shengjuler, Djoshkun title: The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain date: 2017-08-04 words: 7069.0 sentences: 411.0 pages: flesch: 63.0 cache: ./cache/cord-103015-3dxwbmd2.txt txt: ./txt/cord-103015-3dxwbmd2.txt summary: Molecular-docking simulations revealed a putative site of PIP binding to poliovirus (PV) 3C protein that was validated using NMR spectroscopy. 93 Validation of PIP-binding sites by NMR 94 In order to test the validity of our docking observations, we titrated 15 N-labeled 3C protein 95 with soluble dibutyl-PI4P to observe potential NMR chemical shift perturbations (CSPs), which 96 would indicate chemical environment changes in the presence of PI4P (Figure 2) . Out of the three 97 basic residues of the major cluster that were predicted to interact with the PI4P, R13 showed the 98 largest CSP (Figure 2A ). Titration of PI4P into a solution containing 3C caused CSPs that were consistent 249 with the major PI4P-binding site observed computationally (Figure 2A) . abstract: Some viruses use phosphatidylinositol phosphate (PIP) to mark membranes used for genome replication or virion assembly. PIP-binding motifs of cellular proteins do not exist in viral proteins. Molecular-docking simulations revealed a putative site of PIP binding to poliovirus (PV) 3C protein that was validated using NMR spectroscopy. The PIP-binding site was located on a highly dynamic α-helix that also functions in RNA binding. Broad PIP-binding activity was observed in solution using a fluorescence polarization assay or in the context of a lipid bilayer using an on-chip, fluorescence assay. All-atom molecular dynamics simulations of the 3C protein-membrane interface revealed PIP clustering and perhaps PIP-dependent conformations. PIP clustering was mediated by interaction with residues that interact with the RNA phosphodiester backbone. We conclude that 3C binding to membranes will be determined by PIP abundance. We suggest that the duality of function observed for 3C may extend to RNA-binding proteins of other viruses. Highlights A viral PIP-binding site identified, validated and characterized PIP-binding site overlaps the known RNA-binding site PIP-binding site clusters PIPs and perhaps regulates conformation and function Duality of PIP- and RNA-binding sites may extend to other viruses In Brief The absence of conventional PIP-binding domains in viral proteins suggests unique structural solutions to this problem. Shengjuler et al. show that a viral RNA-binding site can be repurposed for PIP binding. PIP clustering can be achieved. The nature of the PIP may regulate protein conformation. url: https://doi.org/10.1101/172742 doi: 10.1101/172742 id: cord-302085-xyru2q9o author: Shepard, Samuel S. title: Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler date: 2016-09-05 words: 10341.0 sentences: 540.0 pages: flesch: 50.0 cache: ./cache/cord-302085-xyru2q9o.txt txt: ./txt/cord-302085-xyru2q9o.txt summary: IRMA provides segment level read sorting based on LABEL, a sequence classification tool ideal for segmented genomes [11] ; iteratively gathers reads and iteratively edits the reference templates to account for high population diversity and mutational rates; and provides redesigned variant calling (heuristics as well as statistical tests) and phasing to allow for the analysis of diverse viral sub-populations. We solve these referenced-based assembly complications by using iterative refinement-moving the reference template closer to the reads-to obtain quality assemblies with increased sensitivity to distant and novel reads BLAT* or LABEL match sort into segments rough align chimeric low quality high quality templates removed module consensuses [1] de-multiplexed sample [1] [2] [3] [4] [5] READ GATHERING: do steps [3] to [5] optimize assembly [6] insertion, deletion, substitution merge reads+ [7] call variants [8] phase variants [9] Perl scripts, samtools, R Steps in (b) are also labeled under the steps of (a) where they correspond genetic variants. abstract: BACKGROUND: Deep sequencing makes it possible to observe low-frequency viral variants and sub-populations with greater accuracy and sensitivity than ever before. Existing platforms can be used to multiplex a large number of samples; however, analysis of the resulting data is complex and involves separating barcoded samples and various read manipulation processes ending in final assembly. Many assembly tools were designed with larger genomes and higher fidelity polymerases in mind and do not perform well with reads derived from highly variable viral genomes. Reference-based assemblers may leave gaps in viral assemblies while de novo assemblers may struggle to assemble unique genomes. RESULTS: The IRMA (iterative refinement meta-assembler) pipeline solves the problem of viral variation by the iterative optimization of read gathering and assembly. As with all reference-based assembly, reads are included in assembly when they match consensus template sets; however, IRMA provides for on-the-fly reference editing, correction, and optional elongation without the need for additional reference selection. This increases both read depth and breadth. IRMA also focuses on quality control, error correction, indel reporting, variant calling and variant phasing. In fact, IRMA’s ability to detect and phase minor variants is one of its most distinguishing features. We have built modules for influenza and ebolavirus. We demonstrate usage and provide calibration data from mixture experiments. Methods for variant calling, phasing, and error estimation/correction have been redesigned to meet the needs of viral genomic sequencing. CONCLUSION: IRMA provides a robust next-generation sequencing assembly solution that is adapted to the needs and characteristics of viral genomes. The software solves issues related to the genetic diversity of viruses while providing customized variant calling, phasing, and quality control. IRMA is freely available for non-commercial use on Linux and Mac OS X and has been parallelized for high-throughput computing. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3030-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1186/s12864-016-3030-6 doi: 10.1186/s12864-016-3030-6 id: cord-333429-bq7kfpby author: Shi, Ding title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study date: 2020-07-02 words: 3513.0 sentences: 251.0 pages: flesch: 57.0 cache: ./cache/cord-333429-bq7kfpby.txt txt: ./txt/cord-333429-bq7kfpby.txt summary: title: Clinical characteristics and factors associated with long-term viral excretion in patients with SARS-CoV-2 infection: a single center 28-day study Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. We identified that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV A c c e p t e d M a n u s c r i p t combination therapy and corticosteroid treatment were not independent factors. In conclusion, we found that male sex, immunoglobulin use, APACHE II score, and lymphopenia were independent risk factors associated with the duration of SARS-CoV-2 RNA shedding, whereas ARV combination therapy and corticosteroid treatment were not. abstract: BACKGROUND: Despite the ongoing spread of COVID-19, knowledge about factors affecting prolonged viral excretion is limited. METHODS: In this study, we retrospectively collected data from 99 hospitalized patients with COVID-19 between January 19 and February 17 in Zhejiang Province, China. We classified them into two groups based on whether the virus test results eventually became negative. Cox proportional hazards regression was used to evaluate factors associated with SARS-CoV-2 shedding. RESULTS: Among 99 patients, 61 patients had SARS-CoV-2 clearance (virus-negative group), but 38 patients had sustained positive results (virus-positive group). The median duration of SARS-CoV-2 excretion was 15 days (IQR 12-19) among the virus-negative patients. The shedding time was significantly increased if fecal SARS-CoV-2 RNA test results was positive. Male sex (HR, 0.58 [95% CI, 0.35-0.98]), immunoglobulin use (HR, 0.42 [95% CI, 0.24-0.76]), APACHE II score (HR, 0.89 [95% CI, 0.84-0.96]), and lymphocyte count (HR, 1.81 [95% CI, 1.05-3.1]) were independent factors associated with a prolonged duration of SARS-CoV-2 shedding. Antiviral therapy and corticosteroid treatment were not independent factors. CONCLUSIONS: SARS-CoV-2 RNA clearance time was associated with sex, disease severity and lymphocyte function. The current antiviral protocol and low-to-moderate dosage of corticosteroid had little effect on the duration of viral excretion. url: https://doi.org/10.1093/infdis/jiaa388 doi: 10.1093/infdis/jiaa388 id: cord-048204-6lvn10f4 author: Shi, Stephanie T. title: Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus date: 2000-09-01 words: 7656.0 sentences: 378.0 pages: flesch: 56.0 cache: ./cache/cord-048204-6lvn10f4.txt txt: ./txt/cord-048204-6lvn10f4.txt summary: In order to demonstrate the involvement of hnRNP A1 in MHV RNA replication and transcription, we established several DBT cell lines stably expressing either the wildtype (wt) hnRNP A1 or a C-terminus-truncated mutant lacking the M9 sequence and part of the glycine-rich domain. We showed that the mutant hnRNP A1, which was localized predominantly in the cytoplasm, exhibited dominant-negative effects on viral genomic RNA replication and subgenomic mRNA transcription. Cells infected with P0 viruses did not yield detectable amounts of DIssE, but contained the naturally occurring A59 DI RNA, whose replication was inhibited more strongly than the synthesis of MHV genomic and subgenomic RNAs in DBT-A1DC cells ( Figures 5B, lanes 8±10 and 6B, lanes 1± 3). In the present study, we established that MHV RNA transcription and replication were enhanced by overexpression of the wt hnRNP A1 protein, but inhibited by expression of a dominant-negative hnRNP A1 mutant in DBT cell lines. abstract: Heterogeneous nuclear ribonucleoprotein (hnRNP A1) is involved in pre-mRNA splicing in the nucleus and translational regulation in the cytoplasm. In the present study, we demonstrate that hnRNP A1 also participates in the transcription and replication of a cytoplasmic RNA virus, mouse hepatitis virus (MHV). Overexpression of hnRNP A1 accelerated the kinetics of viral RNA synthesis, whereas the expression in the cytoplasm of a dominant-negative hnRNP A1 mutant that lacks the nuclear transport domain significantly delayed it. The hnRNP A1 mutant caused a global inhibition of viral mRNA transcription and genomic replication, and also a preferential inhibition of the replication of defective-interfering RNAs. Similar to the wild-type hnRNP A1, the hnRNP A1 mutant complexed with an MHV polymerase gene product, the nucleocapsid protein and the viral RNA. However, in contrast to the wild-type hnRNP A1, the mutant protein failed to bind a 250 kDa cellular protein, suggesting that the recruitment of cellular proteins by hnRNP A1 is important for MHV RNA synthesis. Our findings establish the importance of cellular factors in viral RNA-dependent RNA synthesis. url: http://europepmc.org/articles/pmc302072?pdf=render doi: 10.1093/emboj/19.17.4701 id: cord-325966-0g7a9s5z author: Shih, Hsin-I. title: Fighting COVID-19: a quick review of diagnoses, therapies, and vaccines date: 2020-05-30 words: 7324.0 sentences: 365.0 pages: flesch: 39.0 cache: ./cache/cord-325966-0g7a9s5z.txt txt: ./txt/cord-325966-0g7a9s5z.txt summary: Some candidate drugs targeting different levels and stages of human responses against COVID-19 such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, interleukin 6 blocker, and convalescent plasma may improve the clinical outcomes of critical COVID-19 patients. However, these clinical, laboratory, and imaging findings are nonspecific and cannot differentiate COVID-19 from other viral respiratory infections; viral diagnostic methods specific for SARS-CoV-2 should be applied for disease confirmation. An open-label study published in 2004 suggested, by comparison with a control group that received only ribavirin, that the addition of lopinavir-ritonavir (400 mg and 100 mg, respectively) to ribavirin reduced the risk of adverse clinical outcomes (acute respiratory distress syndrome or death) and viral load among patients with SARS [29] . Some available candidate drugs targeting different levels of human responses to COVID-19, such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, IL-6 blocker and convalescent plasma, may improve the clinical outcomes of critical COVID-19 patients. abstract: The COVID-19 pandemic caused by a novel coronavirus, SARS-CoV-2, has infected more than 4.9 million individuals and resulted in over 300,000 deaths globally. The rapid spread of the virus and the precipitously increasing numbers of cases necessitate the urgent development of accurate diagnostic methods, effective treatments, and vaccines. Here, we review the progress of developing diagnostic methods, therapies, and vaccines for SARS-CoV-2 with a focus on current clinical trials and their challenges. For diagnosis, nucleic acid amplification tests remain the mainstay diagnostics for laboratory confirmation of SARS-CoV-2 infection, while serological antibody tests are used to aid contact tracing, epidemiological, and vaccine evaluation studies. Viral isolation is not recommended for routine diagnostic procedures due to safety concerns. Currently, no single effective drug or specific vaccine is available against SARS-CoV-2. Some candidate drugs targeting different levels and stages of human responses against COVID-19 such as cell membrane fusion, RNA-dependent RNA polymerase, viral protease inhibitor, interleukin 6 blocker, and convalescent plasma may improve the clinical outcomes of critical COVID-19 patients. Other supportive care measures for critical patients are still necessary. Advances in genetic sequencing and other technological developments have sped up the establishment of a variety of vaccine platforms. Accordingly, numerous vaccines are under development. Vaccine candidates against SARS-CoV-2 are mainly based upon the viral spike protein due to its vital role in viral infectivity, and most of these candidates have recently moved into clinical trials. Before the efficacy of such vaccines in humans is demonstrated, strong international coordination and collaboration among studies, pharmaceutical companies, regulators, and governments are needed to limit further damage due the emerging SARS-CoV-2 virus. url: https://doi.org/10.1016/j.bj.2020.05.021 doi: 10.1016/j.bj.2020.05.021 id: cord-018944-du42ho11 author: Shin, Jeong Hwan title: Nucleic Acid Extraction and Enrichment date: 2018-11-10 words: 6857.0 sentences: 355.0 pages: flesch: 41.0 cache: ./cache/cord-018944-du42ho11.txt txt: ./txt/cord-018944-du42ho11.txt summary: [6, 7] as follows: (1) extraction should be simple and rapid and should show high sensitivity and specificity; (2) it is preferred that there be no requirements for specialized equipment or special knowledge and skills; (3) the final nucleic acid should be pure and easy to modify for various amplification techniques; (4) the reagents and their product should be harmless; and (5) the process of preparation should resist contamination with other specimens. Although the phenolchloroform method is relatively easy compared with the CsCl/EtBr gradient and is very useful for the extraction of nucleic acids, it also is problematic for the clinical microbiology laboratory because phenol has important limitations due to its being toxic, caustic, and flammable [5, 15, 16] . In recent years, it has become possible to extract viral nucleic acid from clinical specimens having cellular components, and there have been trials of these commercially available kits to detect various clinically important viruses [30] [31] [32] . abstract: Nucleic acid extraction is the first step of any amplification experiment no matter what kind of amplification is used to detect a specific pathogen. Efficient nucleic acid extraction is essential to obtain good results using any molecular test. The optimal extraction method should fulfill the following conditions: speed, short working time, cost-effectiveness, high sensitivity and specificity, good reproducibility, and safety. The methods can be divided into solution or column based according to differences of their principles. The automated extraction instruments have many advantages, and these have proven to be very useful. Moreover, in recent years, fully automated instruments combining NA extraction and amplification have been commercially available. However, the method itself does not provide assurance, and the DNA recovery can be different among various kits or instruments that use the similar principles. Therefore, it is important to carefully evaluate the performance of any extraction method used in the clinical microbiology laboratory even though manufacturers may have reported good validation results with specific organisms. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123959/ doi: 10.1007/978-3-319-33900-9_13 id: cord-000715-zl1s82yi author: Shulman, Lester M. title: Evaluation of Four Different Systems for Extraction of RNA from Stool Suspensions Using MS-2 Coliphage as an Exogenous Control for RT-PCR Inhibition date: 2012-07-16 words: 4786.0 sentences: 248.0 pages: flesch: 50.0 cache: ./cache/cord-000715-zl1s82yi.txt txt: ./txt/cord-000715-zl1s82yi.txt summary: These samples were selected from among archived stool samples previously tested for enterovirus and MS2 after extraction by QIAamp Viral RNA Mini Kit. A sufficient number of samples with high, intermediate, and low levels of inhibitors were chosen for re-analysis to enable comparison between extraction procedures at each of these levels of inhibition. Analysis of variance ( Fig. 3 , part 2), indicated that there was no significant difference (paired t-test, P.0.05) between the inhibition of rRT-PCR of the MS2 external control and the added enterovirus (P.0.05) for protocols A, C, and D. Stool suspensions (N = 185) prepared for routine analysis of clinical stool samples sent to the Central Virology Laboratory (CVL) at Chaim Sheba Medical Center in Israel were used to evaluate the efficiency of four different RNA extraction systems in excluding inhibitors of rRT-PCR. abstract: Knowing when, and to what extent co-extracted inhibitors interfere with molecular RNA diagnostic assays is of utmost importance. The QIAamp Viral RNA Mini Kit (A); MagNA Pure LC2.0 Automatic extractor (B); KingFisher (C); and NucliSENS EasyMag (D) RNA extraction systems were evaluated for extraction efficiency and co-purification of inhibitors from stool suspensions. Real-Time Reverse Transcriptase Polymerase Chain Reaction (rRT-PCR) of MS-2 coliphage spiked into each system’s lysis buffer served as an external control for both. Cycle thresholds (Cts) of the MS2 were determined for RNA extracted from stool suspensions containing unknown (n = 93) or varying amounts of inhibitors (n = 92). Stool suspensions from the latter group were also used to determine whether MS-2 and enterovirus rRT-PCR inhibitions were correlated. Specifically 23 RNA extracts from stool suspensions were spiked with enterovirus RNA after extraction and 13 of these stool suspension were spiked with intact enterovirus before extraction. MS2 rRT-PCR inhibition varied for RNAs extracted by the different systems. Inhibition was noted in 12 (13.0%), 26 (28.3%), 7 (7.6%), and 7 (7.6%) of the first 93 RNA extracts, and 58 (63.0%), 55 (59.8%), 37 (40.2%) and 30 (32.6%) of the second 92 extracts for A, B, C, and D, respectively. Furthermore, enterovirus rRT-PCR inhibition correlated with MS2 rRT-PCR inhibition for added enterovirus RNA or virus particles. In conclusion, rRT-PCR for MS-2 RNA is a good predictor of inhibition of enterovirus RNA extracted from stool suspensions. EasyMag performed the best, however all four extraction methods were suitable provided that external controls identified problematic samples. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3397973/ doi: 10.1371/journal.pone.0039455 id: cord-278055-v2ed3tei author: Sia, Sin Fun title: Pathogenesis and transmission of SARS-CoV-2 in golden Syrian hamsters date: 2020-05-14 words: 5396.0 sentences: 292.0 pages: flesch: 56.0 cache: ./cache/cord-278055-v2ed3tei.txt txt: ./txt/cord-278055-v2ed3tei.txt summary: Previous study of SARS-CoV (Urbani strain) in 5-weeks-old golden Syrian hamsters showed robust viral replication with peak viral titers detected in the lungs on 2 dpi, followed by rapid viral clearance by 7 dpi, but without weight loss or evidence of disease in the inoculated animals 20 . Our results indicate that the golden Syrian hamster is a suitable experimental animal model for SARS-CoV-2, as there is apparent weight loss in the inoculated and naturally-infected hamsters and evidence of efficient viral replication in the nasal mucosa and lower respiratory epithelial cells. c, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one inoculated donor on 1 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. e, Transmission of SARS-CoV-2 to naïve hamsters (N=3) that were each co-housed with one donor on 6 dpi; infectious viral load and viral RNA copy numbers detected in the nasal washes of contact hamsters were shown. abstract: SARS-CoV-2, a novel coronavirus with high nucleotide identity to SARS-CoV and SARS-related coronaviruses detected in horseshoe bats, has spread across the world and impacted global healthcare systems and economy1,2. A suitable small animal model is needed to support vaccine and therapy development. We report the pathogenesis and transmissibility of the SARS-CoV-2 in golden Syrian hamsters. Immunohistochemistry demonstrated viral antigens in nasal mucosa, bronchial epithelial cells, and in areas of lung consolidation on days 2 and 5 post-inoculation (dpi), followed by rapid viral clearance and pneumocyte hyperplasia on 7 dpi. Viral antigen was also found in the duodenum epithelial cells with viral RNA detected in feces. Notably, SARS-CoV-2 transmitted efficiently from inoculated hamsters to naïve hamsters by direct contact and via aerosols. Transmission via fomites in soiled cages was less efficient. Although viral RNA was continuously detected in the nasal washes of inoculated hamsters for 14 days, the communicable period was short and correlated with the detection of infectious virus but not viral RNA. Inoculated and naturally-infected hamsters showed apparent weight loss, and all animals recovered with the detection of neutralizing antibodies. Our results suggest that SARS-CoV-2 infection in golden Syrian hamsters resemble features found in humans with mild infections. url: https://www.ncbi.nlm.nih.gov/pubmed/32408338/ doi: 10.1038/s41586-020-2342-5 id: cord-010374-z9ygudv6 author: Siddell, S.G. title: Coronaviridae1 date: 2008-07-24 words: 1541.0 sentences: 111.0 pages: flesch: 51.0 cache: ./cache/cord-010374-z9ygudv6.txt txt: ./txt/cord-010374-z9ygudv6.txt summary: The main characteristics of the member viruses are: (i) Morphological: Enveloped pleomorphic particles typically 100 nm in diameter (range 60-220 nm), bearing about 20 nm long club-shaped surface projections, (ii) Structural: A single-stranded infectious molecule of genomic RNA of about (5-7) × 10(6) molecular weight. (iv) Antigenic: 3 major antigens, each corresponding to one class of virion protein, (v) Biological: Predominantly restricted to infection of natural vertebrate hosts by horizontal transmission via the fecal/oral route. Recently, there have been reports of virus-specific RNA poly merases in coronavirus-infected cells, but the components of the enzyme have not been iden tified. UV inactivation studies in dicate that coronavirus mRNAs are not pro duced by the processing of a larger RNA, although extensive sequence homologies have been detected at the 5'' ends of ail murine hepatitis virus-specific subgenomic RNAs. For murine hepatitis virus, the mRNA function of each of the subgenomic viral RNAs has been demonstrated in vitro, and the mRNAs encod ing each of the virion proteins, or its precur sors, have been identified ( fig. abstract: The family Coronavirtdae comprises a monogeneric group of 11 viruses which infect vertebrates. The main characteristics of the member viruses are: (i) Morphological: Enveloped pleomorphic particles typically 100 nm in diameter (range 60-220 nm), bearing about 20 nm long club-shaped surface projections, (ii) Structural: A single-stranded infectious molecule of genomic RNA of about (5-7) × 10(6) molecular weight. A phosphorylated nucleocapsid protein [mol.wt. (50-60) × 10(3)] complexed with the genome as a helical ribonucleoprotein; a surface (peplomer) protein, associated with one or two glycosylated polypeptides [mol.wt. (90-180) × 10(3)]; a transmembrane (matrix) protein, associated with one polypeptide which may be glycosylated to different degrees [mol.wt. (20-35) × 10(3)]. (iii) Replicative: Production in infected cells of multiple 3′ coterminal sub genomic mRNAs extending for different lengths in the 5′ direction. Virions bud intracytoplasmically. (iv) Antigenic: 3 major antigens, each corresponding to one class of virion protein, (v) Biological: Predominantly restricted to infection of natural vertebrate hosts by horizontal transmission via the fecal/oral route. Responsible mainly for respiratory and gastrointestinal disorders. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7182641/ doi: 10.1159/000149390 id: cord-005377-36io7zsm author: Sidoti, Francesca title: Alternative Molecular Tests for Virological Diagnosis date: 2012-04-09 words: 5994.0 sentences: 292.0 pages: flesch: 35.0 cache: ./cache/cord-005377-36io7zsm.txt txt: ./txt/cord-005377-36io7zsm.txt summary: The main isothermal methods reviewed here include loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), and helicase-dependent amplification (HDA). Development and evaluation of a novel loop mediated isothermal amplification (LAMP) method for rapid detection of SARS Corona virus Rapid detection of norovirus from fecal specimens by real-time reverse transcription-loop-mediated isothermal amplification assay Rapid detection and quantification of Japanese encephalitis virus by real-time reverse transcription loop-mediated isothermal amplification. Rapid and real-time detection of chikungunya virus by reverse transcription loop mediated isothermal amplification assay Development and evaluation of reverse transcription Loop mediated isothermal amplification assay for rapid and real-time detection of Japanese encephalitis virus Development of a quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes Development and evaluation of a real-time nucleic acid sequence based amplification assay for rapid detection of influenza A abstract: Several nucleic acid amplification techniques (NAATs), particularly PCR and real-time PCR, are currently used in the routine clinical laboratories. Such approaches have allowed rapid diagnosis with a high degree of sensitivity and specificity. However, conventional PCR methods have several intrinsic disadvantages such as the requirement for temperature cycling apparatus, and sophisticated and costly analytical equipments. Therefore, amplification at a constant temperature is an attractive alternative method to avoid these requirements. A new generation of isothermal amplification techniques are gaining a wide popularity as diagnostic tools due to their simple operation, rapid reaction and easy detection. The main isothermal methods reviewed here include loop-mediated isothermal amplification, nucleic acid sequence-based amplification, and helicase-dependent amplification. In this review, design criteria, potential of amplification, and application of these alternative molecular tests will be discussed and compared to conventional NAATs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091206/ doi: 10.1007/s12033-012-9533-8 id: cord-005392-0pgcfk6b author: Sidoti, Francesca title: Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes date: 2011-07-05 words: 3621.0 sentences: 167.0 pages: flesch: 41.0 cache: ./cache/cord-005392-0pgcfk6b.txt txt: ./txt/cord-005392-0pgcfk6b.txt summary: title: Development of a Quantitative Real-Time Nucleic Acid Sequence-Based Amplification Assay with an Internal Control Using Molecular Beacon Probes for Selective and Sensitive Detection of Human Rhinovirus Serotypes In this study, we developed the first quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes. Aim of this study was to develop the first quantitative real-time nucleic acid sequence-based amplification assay internally controlled using molecular beacon for selective and sensitive detection of HRV serotypes. To estimate the dynamic range of the real-time NASBA assay (range of concentrations over which the method performs in a linear manner with an acceptable level of trueness and precision), we used HRV standard dilutions from 10 8 copies/ll to 1 copy/ll. Evaluation of a real-time nucleic acid sequence-based amplification assay using molecular beacons for detection of human immunodeficiency virus type 1 abstract: Evidence demonstrating that human rhinovirus (HRV) disease is not exclusively limited to the upper airways and may cause lower respiratory complications, together with the frequency of HRV infections and the increasing number of immunocompromised patients underline the need for rapid and accurate diagnosis of HRV infections. In this study, we developed the first quantitative real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective and sensitive detection of human rhinovirus serotypes. We described a simple method to accurately quantify RNA target by computing the time to positivity (TTP) values for HRV RNA. Quantification capacity was assessed by plotting these TTP values against the starting number of target molecules. By using this simple method, we have significantly increased the diagnostic accuracy, precision, and trueness of real-time NASBA assay. Specificity of the method was verified in both in silico and experimental studies. Moreover, for assessment of clinical reactivity of the assay, NASBA has been validated on bronchoalveolar lavage (BAL) specimens. Our quantitative NASBA assay was found to be very specific, accurate, and precise with high repeatability and reproducibility. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091405/ doi: 10.1007/s12033-011-9432-4 id: cord-326257-rcv8sh22 author: Simmonds, P. title: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories date: 2020-05-01 words: 3499.0 sentences: 172.0 pages: flesch: 47.0 cache: ./cache/cord-326257-rcv8sh22.txt txt: ./txt/cord-326257-rcv8sh22.txt summary: C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5''U/A and 3''U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. The possibility that the initial diversity within a viral population was largely host-induced would have major implications for 70 evolutionary reconstruction of SARS-CoV-2 variants in the current pandemic, as well as in our understanding both of host antiviral pathways against coronaviruses and the longer term shaping effects on their genome composition. To formally analyse 105 the excess of C->U transitions we calculated an index of asymmetry (frequency[C->U] / f[U->C]) x (fU/fC) and compared this with degrees of sequence divergence and dN/dS ratio in SARS-CoV-2 and other coronavirus datasets (Fig. 2B, 2C ). abstract: The pandemic of SARS coronavirus 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus substitution rate of 3×10−4 substitutions/site/year. Almost half of sequence changes were C->U transitions with an 8-fold base frequency normalised directional asymmetry between C->U and U->C substitutions. Elevated ratios were observed in other recently emerged coronaviruses (SARS-CoV and MERS-CoV) and to a decreasing degree in other human coronaviruses (HCoV-NL63, -OC43, -229E and -HKU1) proportionate to their increasing divergence. C->U transitions underpinned almost half of the amino acid differences between SARS-CoV-2 variants, and occurred preferentially in both 5’U/A and 3’U/A flanking sequence contexts comparable to favoured motifs of human APOBEC3 proteins. Marked base asymmetries observed in non-pandemic human coronaviruses (U>>A>G>>C) and low G+C contents may represent long term effects of prolonged C->U hypermutation in their hosts. Importance The evidence that much of sequence change in SARS-CoV-2 and other coronaviruses may be driven by a host APOBEC-like editing process has profound implications for understanding their short and long term evolution. Repeated cycles of mutation and reversion in favoured mutational hotspots and the widespread occurrence of amino acid changes with no adaptive value for the virus represents a quite different paradigm of virus sequence change from neutral and Darwinian evolutionary frameworks that are typically used in molecular epidemiology investigations. url: https://doi.org/10.1101/2020.05.01.072330 doi: 10.1101/2020.05.01.072330 id: cord-010273-0c56x9f5 author: Simmonds, Peter title: Virology of hepatitis C virus date: 2001-10-10 words: 7897.0 sentences: 337.0 pages: flesch: 41.0 cache: ./cache/cord-010273-0c56x9f5.txt txt: ./txt/cord-010273-0c56x9f5.txt summary: 1,2 The identification of HCV led to the development of diagnostic assays for infection, based either on detection of antibody to recombinant polypeptides expressed from cloned HCV sequences or direct detection of virus ribonucleic acid (RNA) sequences by polymerase chain reaction (PCR) using primers complimentary to the HCV genome. 6 ''13 Remarkably, a series of plant viruses that are structurally distinct from each of the mammalian virus groups, and with different genome organizations, have RNA-dependent RNA polymerase amino acid sequences that are perhaps more similar to those of HCV than are the flaviviruses. In contrast to the highly restricted sequence diversity of the 5''NCR and adjacent core region, the two putative envelope genes are highly divergent between different variants of HCV (Table III) 111-114 and show a three-to-four-times higher rate of sequence change with time in persistently infected patients, ll5 Because these proteins are likely to lie on the outside of the virus, they would be the principal targets of the humoral immune response to HCV elicited on infection. abstract: Hepatitis C virus (HCV) has been identified as the main causative agent of post-transfusion non-A, non-B hepatitis. Through recently developed diagnostic assays, routine serologic screening of blood donors has prevented most cases of post-transfusion hepatitis. The purpose of this paper is to comprehensively review current information regarding the virology of HCV. Recent findings on the genome organization, its relationship to other viruses, the replication of HCV ribonucleic acid, HCV translation, and HCV polyprotein expression and processing are discussed. Also reviewed are virus assembly and release, the variability of HCV and its classification into genotypes, the geographic distribution of HCV genotypes, and the biologic differences between HCV genotypes. The assays used in HCV genotyping are discussed in terms of reliability and consistency of results, and the molecular epidemiology of HCV infection is reviewed. These approaches to HCV epidemiology will prove valuable in documenting the spread of HCV in different risk groups, evaluating alternative (nonparenteral) routes of transmission, and in understanding more about the origins and evolution of HCV. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173289/ doi: 10.1016/s0149-2918(96)80193-7 id: cord-281285-5g1rw202 author: Simonis, Alexander title: A comparative analysis of remdesivir and other repurposed antivirals against SARS‐CoV‐2 date: 2020-11-03 words: 9501.0 sentences: 504.0 pages: flesch: 46.0 cache: ./cache/cord-281285-5g1rw202.txt txt: ./txt/cord-281285-5g1rw202.txt summary: Based on its MOA, repurposed drugs with anti-SARS-CoV-2 activity can be divided into substances that prevent viral entry into host cells (1-2) and inhibit viral proteases (3) and inhibitors of viral replicase (4). The disappointing clinical results might be related to sub-therapeutic levels for inhibition of SARS-COV-2 because application of 400/100 mg of lopinavir/ritonavir twice daily was shown to yield median serum concentrations of 7.2 mg/l (11.5 µM) in patients with HIV (van der Lugt et al, 2009), which is significantly lower than the observed EC 50 in the in vitro studies. In this comparative review, we focus on repurposed drugs with antiviral effects against SARS-CoV-2 in cell-based assays as those substances offer great opportunities for a treatment early in the course of COVID-19 by inhibition of viral replication and might be even suitable for preventive strategies as shown for neuraminidase inhibitors in case of influenza (Jefferson et al, 2014) . abstract: The ongoing SARS‐CoV‐2 pandemic stresses the need for effective antiviral drugs that can quickly be applied in order to reduce morbidity, mortality, and ideally viral transmission. By repurposing of broadly active antiviral drugs and compounds that are known to inhibit viral replication of related viruses, several advances could be made in the development of treatment strategies against COVID‐19. The nucleoside analog remdesivir, which is known for its potent in vitro activity against Ebolavirus and other RNA viruses, was recently shown to reduce the time to recovery in patients with severe COVID‐19. It is to date the only approved antiviral for treating COVID‐19. Here, we provide a mechanism and evidence‐based comparative review of remdesivir and other repurposed drugs with proven in vitro activity against SARS‐CoV‐2. url: https://doi.org/10.15252/emmm.202013105 doi: 10.15252/emmm.202013105 id: cord-349249-jwvz1ux2 author: Singh, Gagandeep title: A Minimally Replicative Vaccine Protects Vaccinated Piglets Against Challenge With the Porcine Epidemic Diarrhea Virus date: 2019-10-22 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Porcine epidemic diarrhea virus (PEDV), is an economically important enteric coronavirus, with over a 90% mortality rate in neonatal piglets. The virus emerged in the US in 2013, resulting in severe production losses. Effective vaccine development against PEDV is a challenge. Inactivated vaccines are of questionable efficacy. Attenuated vaccines, while more effective, require a relatively long lead development time, are associated with safety concerns and are also unable to prevent new field outbreaks. To combine the safety and efficacy advantages of inactivated and attenuated PEDV vaccines, respectively, in this study, we tested the hypothesis that subjecting PEDV virions to heat treatment at 44°C for 10 min to reversibly unfold structural proteins, followed by exposure to RNAse to fragment the genome, would result in a vaccine preparation with intact viral structure/antigenicity but highly diminished replicative abilities. We expected the vaccine to be both safe and effective in a piglet challenge model. Following the heat and RNAse treatment, PEDV virions had an intact electron microscopic ultrastructure and were amplified only in the 3rd passage in Vero cells, indicating that diminished replication was achieved in vitro. Strong PEDV spike-protein specific and virus neutralizing antibody responses were elicited in vaccinated piglets. Upon challenge, all vaccinated pigs were protected against fecal viral shedding and intestinal pathology, while the unvaccinated controls were not. The vaccine virus was not detected in the fecal matter of vaccinated pigs prior to challenge; nor did they develop intestinal lesions. Thus, the described approach has significant promise in improving current approaches for PEDV immunization. url: https://doi.org/10.3389/fvets.2019.00347 doi: 10.3389/fvets.2019.00347 id: cord-021481-tvs1pnib author: Singh, Gatikrushna title: Cellular RNA Helicases Support Early and Late Events in Retroviral Replication date: 2018-08-17 words: 6039.0 sentences: 359.0 pages: flesch: 43.0 cache: ./cache/cord-021481-tvs1pnib.txt txt: ./txt/cord-021481-tvs1pnib.txt summary: Introns FIGURE 7.1 Critical events in HIV-1 replication are supported by RNA helicases Early steps in HIV-1 replication involve reverse transcription in the cytosol of capsid-associated viral RNA (n = 2) to double-stranded cDNA that transits the nuclear pore and integrates into the host chromosome (blue lines) to form a provirus (red line surrounded by black dotted line) with the involvement of at least two RHs (DHX9, DDX19A). The study of CTE/TAP activity significantly expanded knowledge of nucleocytoplasmic transport of cell mRNAs and regulation by many virus RNAs. Ten years ago and in context RSV, a genetically simple avian retrovirus, DDX19B/yeast DBP5 was determined to facilitate nuclear export of genome-length unspliced RNA (LeBlanc et al., 2007) . Influenza A virus polymerase recruits the RNA helicase DDX19 to promote the nuclear export of viral mRNAs RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs abstract: Retroviruses commandeer cell RNA helicases (RHs). Cell RHs are necessary for early and late events in retrovirus replication. The provirus is adopted by the cell-endogenous nuclear and cytoplasmic gene expression types of machinery. Whereas retroviruses engender the supportive activity of cell RHs, other RNA viruses provoke theantiviral role of this superfamily of conserved proteins. In this chapter, we contrast retrovirus reliance on host RNA helicases to support their replication cycle, with the virus-encoded helicaseactivity utilized by RNA viruses in cytoplasmic factories. Ironically, RHs are agonists to retroviruses and antagonists to other RNA viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149973/ doi: 10.1016/b978-0-12-811185-7.00007-8 id: cord-336554-n8n5ii5k author: Singh, Thakur Uttam title: Drug repurposing approach to fight COVID-19 date: 2020-09-05 words: 13032.0 sentences: 690.0 pages: flesch: 44.0 cache: ./cache/cord-336554-n8n5ii5k.txt txt: ./txt/cord-336554-n8n5ii5k.txt summary: Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. Outbreaks of novel emerging infections such as coronavirus disease 2019 (COVID19) have unique challenges in front of the health professionals to select appropriate therapeutics/pharmacological treatments in the clinical setup with very little time available for the new drug discovery [3] . Currently, with the lack of effective agents against SARS-CoV2 as well as public-health emergency, WHO has identified some therapies which doctors and researchers believe are the most promising, such as a combination of two HIV drugs (lopinavir and ritonavir), anti-malarial drugs (chloroquine and hydroxychloroquine), and an experimental antiviral compound remdesivir. Ribavirin at a dose rate of 500 mg 2-3 times/day in combination with other drugs such as lopinavir/ritonavir or interferon (IFN)-α through intravenous route for not more than 10 days made the SARS-CoV2 infected patients more resistant to respiratory distress syndrome as well as death [41] . abstract: Currently, there are no treatment options available for the deadly contagious disease, coronavirus disease 2019 (COVID-19). Drug repurposing is a process of identifying new uses for approved or investigational drugs and it is considered as a very effective strategy for drug discovery as it involves less time and cost to find a therapeutic agent in comparison to the de novo drug discovery process. The present review will focus on the repurposing efficacy of the currently used drugs against COVID-19 and their mechanisms of action, pharmacokinetics, dosing, safety, and their future perspective. Relevant articles with experimental studies conducted in-silico, in-vitro, in-vivo, clinical trials in humans, case reports, and news archives were selected for the review. Number of drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, darunavir, arbidol, chloroquine, hydroxychloroquine, tocilizumab and interferons have shown inhibitory effects against the SARS-CoV2 in-vitro as well as in clinical conditions. These drugs either act through virus-related targets such as RNA genome, polypeptide packing and uptake pathways or target host-related pathways involving angiotensin-converting enzyme-2 (ACE2) receptors and inflammatory pathways. Using the basic knowledge of viral pathogenesis and pharmacodynamics of drugs as well as using computational tools, many drugs are currently in pipeline to be repurposed. In the current scenario, repositioning of the drugs could be considered the new avenue for the treatment of COVID-19. url: https://doi.org/10.1007/s43440-020-00155-6 doi: 10.1007/s43440-020-00155-6 id: cord-280427-smqc23vr author: Singla, Rubal title: Human animal interface of SARS-CoV-2 (COVID-19) transmission: a critical appraisal of scientific evidence date: 2020-09-14 words: 7194.0 sentences: 381.0 pages: flesch: 58.0 cache: ./cache/cord-280427-smqc23vr.txt txt: ./txt/cord-280427-smqc23vr.txt summary: The various evidence from the past clearly suggest that the evolution of the virus in both reservoir and intermediate animal hosts needs to be explored to better evaluate the emergence of SARS-CoV-2 in humans. The qPCR and virus titration test conducted on the various isolated organs of the ferrets on day 4 post inoculation detected infectious virus in the nasal turbinate, soft palate and tonsils of ferrets indicating the possible replication of the virus in the upper respiratory tract of the ferrets while no infection was found in other organs such as trachea, lung, heart, spleen, kidneys, pancreas, small intestine, brain and liver of the ferrets (Kim et al. This study results stipulate ferret to have high susceptibility for the SARS-CoV-2 and this infectious virus sheds by multiple routes of body discharge specimens such as urine and faeces of the infected ferrets which serve as a potential source of viral transmission to close contact. abstract: Coronaviruses are a large family of viruses that are known to infect both humans and animals. However, the evidence of inter-transmission of coronavirus between humans and companion animals is still a debatable issue. There is substantial evidence that the virus outbreak is fueled by zoonotic transmission because this new virus belongs to the same family of viruses as SARS-CoV associated with civet cats, and MERS-CoV associated with dromedary camels. While the whole world is investigating the possibility about the transmission of this virus, the transmission among humans is established, but the interface between humans and animals is not much evident. Not only are the lives of human beings at risk, but there is an equal potential threat to the animal world. With multiple reports claiming about much possibility of transmission of COVID-19 from humans to animals, there has been a significant increase in the number of pets being abandoned by their owners. Additionally, the risk of reverse transmission of COVID-19 virus from companion pets like cats and dogs at home is yet another area of concern. The present article highlights different evidence of human-animal interface and necessitates the precautionary measures required to combat with the consequences of this interface. The Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) have suggested various ways to promote awareness and corroborate practices for helping people as well as animals to stay secure and healthy. url: https://www.ncbi.nlm.nih.gov/pubmed/32926266/ doi: 10.1007/s11259-020-09781-0 id: cord-314316-hsspggp8 author: Sirinarumitr, Theerapol title: Rapid in situ hybridization technique for the detection of ribonucleic acids in tissues using radiolabelled and fluorescein-labelled riboprobes date: 1997-08-31 words: 3838.0 sentences: 205.0 pages: flesch: 53.0 cache: ./cache/cord-314316-hsspggp8.txt txt: ./txt/cord-314316-hsspggp8.txt summary: Small intestinal sections from pigs experimentally and naturally infected with TGEV were hybridized for various times at 52°C and 70°C with a radiolabelled or a fluorescein-labelled RNA probe in a standard hybridization or a REH buffer. Small intestinal sections from pigs experimentally and naturally infected with TGEV were hybridized for various times at 52°C and 70°C with a radiolabelled or a fluorescein-labelled RNA probe in a standard hybridization or a REH buffer. With the fluorescein-labelled probe, viral RNA was detected in virus-infected cells of the intestines after 30 min of hybridization by using the REH buffer. With the fluorescein-labelled probe, viral RNA was detected in virus-infected cells of the intestines after 30 min of hybridization by using the REH buffer. Signal intensity was greater with the REH buffer than with the standard hybridization buffer when compared at each hybridization time and hybridization temperature using both radiolabelled and fluorescein-labelled probes. abstract: Abstract In situhybridization (ISH) is a useful diagnostic and research tool, but is also time consuming. This study was conducted to determine if a rate enhancement hybridization (REH) buffer, developed for membrane hybridization, could be used to decrease hybridization time for ISH. Tissue from swine with an enteric disease produced by a swine coronavirus, transmissible gastroenteritis virus (TGEV), was used as a model to standardize hybridization conditions for a rapid ISH technique. Small intestinal sections from pigs experimentally and naturally infected with TGEV were hybridized for various times at 52°C and 70°C with a radiolabelled or a fluorescein-labelled RNA probe in a standard hybridization or a REH buffer. Viral RNA was detected in intestines from as early as 30 min of hybridization by using both buffers with the radiolabelled probe; however, the signal was stronger with the REH buffer. With the fluorescein-labelled probe, viral RNA was detected in virus-infected cells of the intestines after 30 min of hybridization by using the REH buffer. Signal intensity was greater with the REH buffer than with the standard hybridization buffer when compared at each hybridization time and hybridization temperature using both radiolabelled and fluorescein-labelled probes. With the REH buffer, hybridization signal intensity was greater at 70°C than at 52°C for both probes. The best results were obtained when small intestinal sections were hybridized at 70°C for 2 h using a radiolabelled or a fluorescein-labelled probe diluted in the REH buffer. The fluorescein-labelled RNA probe with REH buffer resulted in a minimal non-specific signal when compared with the radiolabelled probe. These studies demonstrated that the REH buffer can be used to decrease the time of ISH for the detection of viral RNA. This rapid ISH technique should have broad applications in the utilization of probe technology in diagnostics and research for the detection of target ribonucleic acidsin situ url: https://api.elsevier.com/content/article/pii/S0890850897901146 doi: 10.1006/mcpr.1997.0114 id: cord-260225-bc1hr0fr author: Sirpilla, Olivia title: SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes date: 2020-07-20 words: 8918.0 sentences: 582.0 pages: flesch: 44.0 cache: ./cache/cord-260225-bc1hr0fr.txt txt: ./txt/cord-260225-bc1hr0fr.txt summary: Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. Additional SARS-CoV-2 proteins with mentions include nsp12 (RNA-directed RNA polymerase, 20/71), nucleocapsid (N, 17/71), membrane (M, 5/48), envelope (E, 4/31), nsp5 (3CLPro/Mpro, 7/26), nsp8 (3/19), nsp16 (2′-O-methyltransferase, 3/14), ORF8 (1/10), nsp10 (3/9), nsp14 (guanine-N7 methyltransferase, 1/8), nsp3 (papain-like protease, 16/6), and nsp15 (uridylate-specific endoribonuclease, 16/4). abstract: [Image: see text] SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics. url: https://doi.org/10.1021/acs.jproteome.0c00421 doi: 10.1021/acs.jproteome.0c00421 id: cord-262609-cssgzvus author: Sivakumaran, K title: RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis date: 1999-12-03 words: 10580.0 sentences: 550.0 pages: flesch: 55.0 cache: ./cache/cord-262609-cssgzvus.txt txt: ./txt/cord-262609-cssgzvus.txt summary: title: RNA sequence and secondary structural determinants in a minimal viral promoter that directs replicase recognition and initiation of genomic plus-strand RNA synthesis In contrast, we find that position-specific changes in the RNA sequence will affect replicase recognition, modulate the polymerization process, and contribute to the differential accumulation of viral RNAs. These functional results are in agreement with the phylogenetic analysis of BMV and related viral sequences and suggest that a similar mechanism of RNA synthesis takes place for members of the alphavirus superfamily. Results herein demonstrate that the endscript directing genomic plus-strand synthesis also interacts with the viral replicase via a mechanism that does not depend on a speci®c preformed RNA structure. An interesting conclusion from our analysis of the BMV genomic minus-strand RNA endscript is that template sequence may regulate the amount of RNA synthesis in a manner independent of replicase-promoter interaction. abstract: Viral RNA replication provides a useful system to study the structure and function of RNAs and the mechanism of RNA synthesis from RNA templates. Previously we demonstrated that a 27 nt RNA from brome mosaic virus (BMV) can direct correct initiation of genomic plus-strand RNA synthesis by the BMV replicase. In this study, using biochemical, nuclear magnetic resonance, and thermodynamic analyses, we determined that the secondary structure of this 27 nt RNA can be significantly altered and retain the ability to direct RNA synthesis. In contrast, we find that position-specific changes in the RNA sequence will affect replicase recognition, modulate the polymerization process, and contribute to the differential accumulation of viral RNAs. These functional results are in agreement with the phylogenetic analysis of BMV and related viral sequences and suggest that a similar mechanism of RNA synthesis takes place for members of the alphavirus superfamily. url: https://api.elsevier.com/content/article/pii/S0022283699932977 doi: 10.1006/jmbi.1999.3297 id: cord-103163-0rreoh4o author: Smith, Sydni Caet title: Reovirus RNA recombination is sequence directed and generates internally deleted defective genome segments during passage date: 2020-10-22 words: 8965.0 sentences: 456.0 pages: flesch: 46.0 cache: ./cache/cord-103163-0rreoh4o.txt txt: ./txt/cord-103163-0rreoh4o.txt summary: We determined the titers and RNA segment profiles of reovirus (rsT1L and rsT3D I ) and rotavirus (rsSA11) laboratory strains that had been rescued by reverse genetics then serially passaged ten times, each in triplicate lineages, in cultured cells. The two reoviruses accumulated non-canonical RNAs that retain 5′ and 3′ termini and feature one or more large internal deletions, while the rotavirus rarely accumulated such DVGs. Analyses of next-generation RNA-sequencing data sets from purified rsT1L reovirus RNA revealed many junctions, with hot spots for recombination in specific viral gene segments. Taken together, lin1 RNA profiles suggest non-canonical RNA species that differ in length but have identical termini to the parental segments accumulate variably during reovirus and rotavirus serial passage in cultured cells. abstract: For viruses with segmented genomes, genetic diversity is generated by genetic drift, reassortment, and recombination. Recombination produces RNA populations distinct from full-length gene segments and can influence viral population dynamics, persistence, and host immune responses. Viruses in the Reoviridae family, including rotavirus and mammalian orthoreovirus (reovirus), have been reported to package segments containing rearrangements or internal deletions. Rotaviruses with RNA segments containing rearrangements have been isolated from immunocompromised and immunocompetent children and in vitro following serial passage at high multiplicity. Reoviruses that package small, defective RNA segments have established chronic infections in cells and in mice. However, the mechanism and extent of Reoviridae RNA recombination are undefined. Towards filling this gap in knowledge, we determined the titers and RNA segment profiles for reovirus and rotavirus following serial passage in cultured cells. The viruses exhibited occasional titer reductions characteristic of interference. Reovirus strains frequently accumulated segments that retained 5′ and 3′ terminal sequences and featured large internal deletions, while similar segments were rarely detected in rotavirus populations. Using next-generation RNA-sequencing to analyze RNA molecules packaged in purified reovirus particles, we identified distinct recombination sites within individual viral gene segments. Recombination junction sites were frequently associated with short regions of identical sequence. Taken together, these findings suggest that reovirus accumulates defective gene segments featuring internal deletions during passage and undergoes sequence-directed recombination at distinct sites. IMPORTANCE Viruses in the Reoviridae family include important pathogens of humans and other animals and have segmented RNA genomes. Recombination in RNA virus populations can facilitate novel host exploration and increased disease severity. The extent, patterns, and mechanisms of Reoviridae recombination and the functions and effects of recombined RNA products are poorly understood. Here, we provide evidence that mammalian orthoreovirus regularly synthesizes RNA recombination products that retain terminal sequences but contain internal deletions, while rotavirus rarely synthesizes such products. Recombination occurs more frequently at specific sites in the mammalian orthoreovirus genome, and short regions of identical sequence are often detected at junction sites. These findings suggest that mammalian orthoreovirus recombination events are directed in part by RNA sequences. An improved understanding of recombined viral RNA synthesis may enhance our capacity to engineer improved vaccines and virotherapies in the future. url: https://doi.org/10.1101/2020.10.19.346031 doi: 10.1101/2020.10.19.346031 id: cord-259603-bh198xgl author: Snijder, E.J. title: The Nonstructural Proteins Directing Coronavirus RNA Synthesis and Processing date: 2016-09-14 words: 24187.0 sentences: 1090.0 pages: flesch: 50.0 cache: ./cache/cord-259603-bh198xgl.txt txt: ./txt/cord-259603-bh198xgl.txt summary: Reverse-genetics studies targeting specific residues in SARS-CoV nsp7 confirmed the protein''s importance for virus replication (Subissi et al., 2014b) , although the impact of single point mutations was smaller than anticipated on the basis of the biochemical characterization of the RNA-binding properties of nsp7-containing protein complexes in vitro (see later). The large number of viral subunits in these complexes (Subissi et al., 2014a) , the likely requirement for host factors (van Hemert et al., 2008) , and the concept of RNA synthesis occurring in a dedicated microenvironment in the infected cell (Knoops et al., 2008; V''Kovski et al., 2015) complicate the straightforward characterization of the CoV RdRp. To reconstitute the enzyme''s activities in vitro, purified recombinant nsp12 is a key reagent but, for many years, such studies were hampered by poor nsp12 expression in Escherichia coli. abstract: Coronaviruses are animal and human pathogens that can cause lethal zoonotic infections like SARS and MERS. They have polycistronic plus-stranded RNA genomes and belong to the order Nidovirales, a diverse group of viruses for which common ancestry was inferred from the common principles underlying their genome organization and expression, and from the conservation of an array of core replicase domains, including key RNA-synthesizing enzymes. Coronavirus genomes (~ 26–32 kilobases) are the largest RNA genomes known to date and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. The primary functions that direct coronavirus RNA synthesis and processing reside in nonstructural protein (nsp) 7 to nsp16, which are cleavage products of two large replicase polyproteins translated from the coronavirus genome. Significant progress has now been made regarding their structural and functional characterization, stimulated by technical advances like improved methods for bioinformatics and structural biology, in vitro enzyme characterization, and site-directed mutagenesis of coronavirus genomes. Coronavirus replicase functions include more or less universal activities of plus-stranded RNA viruses, like an RNA polymerase (nsp12) and helicase (nsp13), but also a number of rare or even unique domains involved in mRNA capping (nsp14, nsp16) and fidelity control (nsp14). Several smaller subunits (nsp7–nsp10) act as crucial cofactors of these enzymes and contribute to the emerging “nsp interactome.” Understanding the structure, function, and interactions of the RNA-synthesizing machinery of coronaviruses will be key to rationalizing their evolutionary success and the development of improved control strategies. url: https://api.elsevier.com/content/article/pii/S0065352716300471 doi: 10.1016/bs.aivir.2016.08.008 id: cord-103739-mmkrwj8t author: Snijder, Eric J. title: A unifying structural and functional model of the coronavirus replication organelle: tracking down RNA synthesis date: 2020-03-24 words: 3808.0 sentences: 223.0 pages: flesch: 48.0 cache: ./cache/cord-103739-mmkrwj8t.txt txt: ./txt/cord-103739-mmkrwj8t.txt summary: Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). In infected cells, the CoV RNA-23 synthesizing machinery associates with modified endoplasmic reticulum membranes that are 24 transformed into the viral replication organelle (RO). 106 double-membrane spherules (DMSs) 107 We first set out to analyse the ultrastructure of MERS-CoV-infected Huh7 cells under sample 108 preparation conditions favourable for autoradiography (see Materials and Methods) (Fig 1, S1 109 Video). Association of polioviral proteins of the P2 89 genomic region with the viral replication complex and virus-induced membrane synthesis as 90 visualized by electron microscopic immunocytochemistry and autoradiography abstract: Zoonotic coronavirus (CoV) infections, like those responsible for the current SARS-CoV-2 epidemic, cause grave international public health concern. In infected cells, the CoV RNA-synthesizing machinery associates with modified endoplasmic reticulum membranes that are transformed into the viral replication organelle (RO). While double-membrane vesicles (DMVs) appear to be a pan-coronavirus RO element, studies to date describe an assortment of additional coronavirus-induced membrane structures. Despite much speculation, it remains unclear which RO element(s) accommodate viral RNA synthesis. Here we provide detailed 2D and 3D analyses of CoV ROs and show that diverse CoVs essentially induce the same membrane modifications, including the small open double-membrane spherules (DMSs) previously thought to be restricted to gamma- and delta-CoV infections and proposed as sites of replication. Metabolic labelling of newly-synthesized viral RNA followed by quantitative EM autoradiography revealed abundant viral RNA synthesis associated with DMVs in cells infected with the beta-CoVs MERS-CoV and SARS-CoV, and the gamma-CoV infectious bronchitis virus. RNA synthesis could not be linked to DMSs or any other cellular or virus-induced structure. Our results provide a unifying model of the CoV RO and clearly establish DMVs as the central hub for viral RNA synthesis and a potential drug target in coronavirus infection. url: https://doi.org/10.1101/2020.03.24.005298 doi: 10.1101/2020.03.24.005298 id: cord-296977-yzhsdz9c author: Soares, R. R. G. title: Point-of-care detection of SARS-CoV-2 in nasopharyngeal swab samples using an integrated smartphone-based centrifugal microfluidic platform date: 2020-11-06 words: 6533.0 sentences: 391.0 pages: flesch: 55.0 cache: ./cache/cord-296977-yzhsdz9c.txt txt: ./txt/cord-296977-yzhsdz9c.txt summary: ; https://doi.org/10.1101/2020.11.04.20225888 doi: medRxiv preprint imaging camera and SYBR Green I derived fluorescence transduction by naked eye or smartphone camera 27 ; (3) Microfluidic cartridge combining immune-capture, lysis and LAMP to detect viable bacteria using a reader platform comprising two light sources for fluorometric and/or turbidimetric analysis resorting to a smartphone camera 30 ; (4) a hermetic container providing power-free chemical-based heating for LAMP amplification followed by detection using a smartphone flashlight and camera for fluorometric detection 32 ; (5) Centrifugal platform combining silica-based DNA extraction and integrated LFA strips to multiplex the detection of multiple LAMP products using anti-DIG antibodies and colorimetric detection 32 ; (6) Centrifugal platform with automated bead-beating lysis followed by direct RT-LAMP by continuous measurement of fluorescence with UVC illumination and a standard camera 22 ; and (7) Centrifugal platform incorporating non-contact heating of the disc and colorimetric detection of LAMP products using a white LED for illumination and filtered photodiodes for signal acquisition 24 . abstract: With its origin estimated around December 2019 in Wuhan, China, the ongoing 2020 SARS-CoV-2 pandemic is a major global health challenge, resulting in more than 45 million infections and 1.2 million deaths. The demand for scalable, rapid and sensitive viral diagnostics is thus particularly pressing at present to help contain the rapid spread of infection and prevent overwhelming the capacity of health systems. While high-income countries have managed to rapidly expand diagnostic capacities, such is not the case in resource-limited settings of low- to medium-income countries. Aiming at developing cost-effective viral load detection systems for point-of-care COVID-19 diagnostics in resource-limited and resource-rich settings alike, we report the development of an integrated modular centrifugal microfluidic platform to perform loop-mediated isothermal amplification (LAMP) of viral RNA directly from heat-inactivated nasopharyngeal swab samples. The discs were pre-packed with dried n-benzyl-n-methylethanolamine modified agarose beads used as a versatile post-nucleic acid amplification signal enhancement strategy, allowing fluorescence detection via a smartphone camera and simple optics. The platform provided sample-to-answer analysis within 1 hour from sample collection and a detection limit between 100 and 1000 RNA copies in 10 L reaction volume. Furthermore, direct detection of non-extracted SARS-CoV-2 RNA in nasopharyngeal swab samples from patients with Ct values below 26 (n=25 plus 6 PCR negative samples) was achieved with ~94% sensitivity and 100% specificity, thus being fit-for-purpose to diagnose patients with a high risk of viral transmission. These results show significant promise towards bringing routine point-of-care COVID-19 diagnostics closer to resource-limited settings. url: http://medrxiv.org/cgi/content/short/2020.11.04.20225888v1?rss=1 doi: 10.1101/2020.11.04.20225888 id: cord-002608-zn7tm1ww author: Sokoloski, Kevin J. title: Identification of Interactions between Sindbis Virus Capsid Protein and Cytoplasmic vRNA as Novel Virulence Determinants date: 2017-06-29 words: 11224.0 sentences: 549.0 pages: flesch: 41.0 cache: ./cache/cord-002608-zn7tm1ww.txt txt: ./txt/cord-002608-zn7tm1ww.txt summary: A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. The data presented in this report indicates that the SINV capsid protein binds to specific viral RNA sequences in the cytoplasm of infected cells, but its interaction with genomic RNA in mature extracellular viral particles is largely non-specific in terms of nucleotide sequence. This report details our efforts to identify and characterize the sites of interaction between the viral capsid protein and the genomic RNA using the model alphavirus Sindbis virus (SINV). C) The infectivity of the individual SINV C:R interaction site mutants and parental wild type virus as reported as the ratio of total particles per infectious unit as determined using BHK-21 cells. abstract: Alphaviruses are arthropod-borne viruses that represent a significant threat to public health at a global level. While the formation of alphaviral nucleocapsid cores, consisting of cargo nucleic acid and the viral capsid protein, is an essential molecular process of infection, the precise interactions between the two partners are ill-defined. A CLIP-seq approach was used to screen for candidate sites of interaction between the viral Capsid protein and genomic RNA of Sindbis virus (SINV), a model alphavirus. The data presented in this report indicates that the SINV capsid protein binds to specific viral RNA sequences in the cytoplasm of infected cells, but its interaction with genomic RNA in mature extracellular viral particles is largely non-specific in terms of nucleotide sequence. Mutational analyses of the cytoplasmic viral RNA-capsid interaction sites revealed a functional role for capsid binding early in infection. Interaction site mutants exhibited decreased viral growth kinetics; however, this defect was not a function of decreased particle production. Rather mutation of the cytoplasmic capsid-RNA interaction sites negatively affected the functional capacity of the incoming viral genomic RNAs leading to decreased infectivity. Furthermore, cytoplasmic capsid interaction site mutants are attenuated in a murine model of neurotropic alphavirus infection. Collectively, the findings of this study indicate that the identified cytoplasmic interactions of the viral capsid protein and genomic RNA, while not essential for particle formation, are necessary for genomic RNA function early during infection. This previously unappreciated role of capsid protein during the alphaviral replication cycle also constitutes a novel virulence determinant. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507600/ doi: 10.1371/journal.ppat.1006473 id: cord-022348-w7z97wir author: Sola, Monica title: Drift and Conservatism in RNA Virus Evolution: Are They Adapting or Merely Changing? date: 2007-09-02 words: 10892.0 sentences: 671.0 pages: flesch: 56.0 cache: ./cache/cord-022348-w7z97wir.txt txt: ./txt/cord-022348-w7z97wir.txt summary: An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. Under the rubric replication, a virus could vary to increase its fitness, exploit different target cells or evade adaptive immune responses. For a given virus, different protein sequence sets were compared to a given reference such as RT in the case of HIV/SIV. Although these data were derived from completely sequenced primate immunodeficiency viral genomes, analyses on larger data sets, such as p17 Gag/p24 Gag or gp120/gp41, yielded relative values that differed from those given in Table 6 .1 by at most 14%. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships (Table 6 .1). In the clear cases where genetic variation is exploited by RNA viruses, it is used to overcome barriers to transmission set up by the host population, e.g. herd immunity. abstract: This chapter argues that the vast majority of genetic changes or mutations fixed by RNA viruses are essentially neutral or nearly neutral in character. In molecular evolution one of the remarkable observations has been the uniformity of the molecular clock. An analysis of proteins derived from complete potyvirus genomes, positive-stranded RNA viruses, yielded highly significant linear relationships. These analyses indicate that viral protein diversification is essentially a smooth process, the major parameter being the nature of the protein more than the ecological niche it finds itself in. Synonymous changes are invariably more frequent than nonsynonymous changes. Positive selection exploits a small proportion of genetic variants, while functional sequence space is sufficiently dense, allowing viable solutions to be found. Although evolution has connotations of change, what has always counted is natural selection or adaptation. It is the only force for the genesis of a novel replicon. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155598/ doi: 10.1016/b978-012220360-2/50007-6 id: cord-323845-s78t5qxj author: Soliman, H. title: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) date: 2006-05-31 words: 3908.0 sentences: 217.0 pages: flesch: 54.0 cache: ./cache/cord-323845-s78t5qxj.txt txt: ./txt/cord-323845-s78t5qxj.txt summary: title: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) A one step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of viral hemorrhagic septicaemia virus (VHS). Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viral hemorrhagic septicaemia virus (VHS) The aim of the present study was to develop a onestep, single-tube, accelerated RT-LAMP reaction for rapid detection of different serotypes of VHS virus. The specificity of the VHS-LAMP primers and conditions to VHS virus was confirmed by its aptitude to amplify only RNA from VHS virus serotypes, with no amplification of IHNVor non-infected fish (Fig. 5) . Detection of viral hemorrhagic septicaemia virus (VHS) in rainbow trout (Oncorhynchus mykiss) by reverse transcription followed by polymerase chain reaction. A loop mediated isothermal amplification (LAMP) method for detection of infectious hematopoietic necrosis virus (IHNV) in rainbow trout (Oncorhynchus mykiss) abstract: A one step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of viral hemorrhagic septicaemia virus (VHS). A set of six primers were designed, based on the G-protein sequence of the VHS virus serotypes (He, F1, 23.75, Klapmolle and Rindsholm). The assay was optimised to amplify VHS RNA by incubation at 63 °C for only 1 h, and required only a simple water bath or heating block to provide a constant temperature of 63 °C. RT-LAMP amplification products were detected by visual inspection using SYBR Green I stain and had a ladder-like appearance when electrophoresed on an agarose gel. The detection limit of the RT-LAMP assay was found to be similar to the commonly used RT-PCR method: both methods detected VHS RNA at a dilution of 10(6). The assay was evaluated using clinical samples and the results indicated the suitability and simplicity of the test as a rapid, field diagnostic tool for VHS virus. url: https://api.elsevier.com/content/article/pii/S0378113505004463 doi: 10.1016/j.vetmic.2005.11.063 id: cord-355499-5vj3oasa author: Song, Xiangjun title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 date: 2015-06-07 words: 4223.0 sentences: 275.0 pages: flesch: 53.0 cache: ./cache/cord-355499-5vj3oasa.txt txt: ./txt/cord-355499-5vj3oasa.txt summary: title: Transmissible Gastroenteritis Virus (TGEV) Infection Alters the Expression of Cellular MicroRNA Species That Affect Transcription of TGEV Gene 7 In this study, we performed microRNA microarray assay and predicted targets of altered miRNAs. The results showed TGEV infection caused the change of miRNAs profile. In conclusion, differentially expressed miR-4331 that is caused by TGEV infection can suppress transcription of TGEV gene 7 via targeting cellular CDCA7. Overall, we observed that TGEV infection caused the change of miRNA profile and miR-4331 suppressed transcription of TGEV gene 7 via directly targeting CDCA7. The major findings in this study are that TGEV infection leads to the change of cellular miRNAs expression profile, and altered miRNAs regulate transcription of TGEV gene 7 through targeting cellular CDCA7. In conclusion, the results of the present study provide evidence that TGEV infection resulted in altered profiles of miRNAs in PK-15 cells and the differentially expressed miR-4331 was involved in regulation of TGEV transcription by targeting cellular CDCA7. abstract: Transmissible gastroenteritis virus (TGEV) is a member of Coronaviridae family. TGEV infection has emerged as a major cause of severe gastroenteritis and leads to alterations of many cellular processes. Meanwhile, the pathogenic mechanism of TGEV is still unclear. microRNAs (miRNAs) are a novel class of small non-coding RNAs which are involved in the regulation of numerous biological processes such as viral infection and cell apoptosis. Accumulating data show that miRNAs are involved in the process of coronavirus infection such as replication of severe acute respiratory syndrome coronavirus (SARS-CoV). However, the link between miRNAs and TGEV infection is unknown. In this study, we performed microRNA microarray assay and predicted targets of altered miRNAs. The results showed TGEV infection caused the change of miRNAs profile. Then we selected miR-4331 for further analysis and subsequently identified cell division cycle-associated protein 7 (CDCA7) as the target of miR-4331. Moreover, miR-4331 showed the ability to inhibit transcription of TGEV gene 7 (a non-structure gene) via directly targeting CDCA7. In conclusion, differentially expressed miR-4331 that is caused by TGEV infection can suppress transcription of TGEV gene 7 via targeting cellular CDCA7. Our key finding is that TGEV selectively manipulates the expression of some cellular miRNAs to regulate its subgenomic transcription. url: https://www.ncbi.nlm.nih.gov/pubmed/26157346/ doi: 10.7150/ijbs.11585 id: cord-281124-4nhy35xn author: Soowannayan, Chumporn title: RNA-Binding Domain in the Nucleocapsid Protein of Gill-Associated Nidovirus of Penaeid Shrimp date: 2011-08-03 words: 5596.0 sentences: 259.0 pages: flesch: 53.0 cache: ./cache/cord-281124-4nhy35xn.txt txt: ./txt/cord-281124-4nhy35xn.txt summary: To examine this domain in more detail, the 18 aa peptide (M(11)PVRRPLPPQPPRNARLI(29)) encompassing this sequence was synthesized and found to bind nucleic acids similarly to the full-length N protein in EMSAs. The data indicate a fundamental role for the GAV N protein proline/arginine-rich domain in nucleating genomic ssRNA to form nucleocapsids. In a preliminary attempt to identify an RNA packaging signal in the GAV genome, EMSAs were performed using ssRNAs synthesized to various genome regions including (i) an ORF1b gene 39-region spanning the relative position to the genome packaging signal identified in MHV [28] , (ii) a 39-terminal genome region corresponding in position to the region in the infectious bronchitis virus (IBV) genome reported to contain an RNA binding domain [29] and (iii) the 59-genomic RNA terminus which, in coronaviruses, has also been reported to interact specifically with N protein [30] . abstract: Gill-associated virus (GAV) infects Penaeus monodon shrimp and is the type species okavirus in the Roniviridae, the only invertebrate nidoviruses known currently. Electrophoretic mobility shift assays (EMSAs) using His(6)-tagged full-length and truncated proteins were employed to examine the nucleic acid binding properties of the GAV nucleocapsid (N) protein in vitro. The EMSAs showed full-length N protein to bind to all synthetic single-stranded (ss)RNAs tested independent of their sequence. The ssRNAs included (+) and (−) sense regions of the GAV genome as well as a (+) sense region of the M RNA segment of Mourilyan virus, a crustacean bunya-like virus. GAV N protein also bound to double-stranded (ds)RNAs prepared to GAV ORF1b gene regions and to bacteriophage M13 genomic ssDNA. EMSAs using the five N protein constructs with variable-length N-terminal and/or C-terminal truncations localized the RNA binding domain to a 50 amino acid (aa) N-terminal sequence spanning Met(11) to Arg(60). Similarly to other RNA binding proteins, the first 16 aa portion of this sequence was proline/arginine rich. To examine this domain in more detail, the 18 aa peptide (M(11)PVRRPLPPQPPRNARLI(29)) encompassing this sequence was synthesized and found to bind nucleic acids similarly to the full-length N protein in EMSAs. The data indicate a fundamental role for the GAV N protein proline/arginine-rich domain in nucleating genomic ssRNA to form nucleocapsids. Moreover, as the synthetic peptide formed higher-order complexes in the presence of RNA, the domain might also play some role in protein/protein interactions stabilizing the helical structure of GAV nucleocapsids. url: https://www.ncbi.nlm.nih.gov/pubmed/21857914/ doi: 10.1371/journal.pone.0022156 id: cord-000822-iuglkdcp author: Sperschneider, Jana title: Predicting pseudoknotted structures across two RNA sequences date: 2012-12-01 words: 5494.0 sentences: 386.0 pages: flesch: 61.0 cache: ./cache/cord-000822-iuglkdcp.txt txt: ./txt/cord-000822-iuglkdcp.txt summary: One strong point of the DotKnot method for single sequence pseudoknot prediction (Sperschneider and Datta, 2010; Sperschneider et al., 2011) is that the set of possible H-type pseudoknot candidates (and secondary structure elements) is explicitly computed and thus readily available for further investigation. (3) Use significant pairs to calculate the set of conserved structure elements and pseudoknots for the two sequences that maximizes a combined free energy and similarity score. The key point of the DotKnot-PW approach is how to score the similarity of stems, secondary structure elements and H-type pseudoknot candidates derived from sequences Seq x and Seq y . The optimal structure element alignment, which preserves the interval ordering includes structure elements p 1 , p 4 , p 7 in the first sequence and p 1 , p 4 , p 6 in the second sequence pairwise prediction with highest combined free energy and similarity score is taken, DotKnot-PW has an improved average MCC of 0.81. abstract: Motivation: Laboratory RNA structure determination is demanding and costly and thus, computational structure prediction is an important task. Single sequence methods for RNA secondary structure prediction are limited by the accuracy of the underlying folding model, if a structure is supported by a family of evolutionarily related sequences, one can be more confident that the prediction is accurate. RNA pseudoknots are functional elements, which have highly conserved structures. However, few comparative structure prediction methods can handle pseudoknots due to the computational complexity. Results: A comparative pseudoknot prediction method called DotKnot-PW is introduced based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on a hand-curated test set of RNA structures with experimental support. Availability: DotKnot-PW and the RNA structure test set are available at the web site http://dotknot.csse.uwa.edu.au/pw. Contact: janaspe@csse.uwa.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516145/ doi: 10.1093/bioinformatics/bts575 id: cord-006331-s2qf98lj author: Spiridonova, V. A. title: Molecular recognition elements: DNA/RNA-aptamers to proteins date: 2010-05-23 words: 7144.0 sentences: 412.0 pages: flesch: 57.0 cache: ./cache/cord-006331-s2qf98lj.txt txt: ./txt/cord-006331-s2qf98lj.txt summary: After 16 rounds of selection from the 2'' amino modified RNA library the isolated aptamers formed a complex with FVIIa characterized by the K d value of 11.3 ± 1.3 nM. performed RNA selection to FIXa; after eight rounds of selection they found an aptamer, which bound to FIXa with the K d value of 0.65 ± 0.2 nM and exhibited 5000 fold higher affinity to FIXa compared with FVIIa, FXa, FXIa and activated protein C [20] . These aptamers formed a complex with ΔNS3 with the K d value of 10 nM, caused 90% inhibition of protease activity of the ΔNS3 peptide and full sized NS3 bound to a maltose binding protein (MBP NS3). Four teen rounds of selection yielded the RNA aptamer, exhibiting high affinity binding to p50 and inhibition of NF kB binding to DNA by preventing protein dimerization [91] . abstract: The review summarizes data on DNA/RNA aptamers, a novel class of molecular recognition elements. Special attention is paid to the aptamers to proteins involved into pathogenesis of wide spread human diseases. These include aptamers to serine proteases, cytokines, influenza viral proteins, immune deficiency virus protein and nucleic acid binding proteins. High affinity and specific binding of aptamers to particular protein targets make them attractive as direct protein inhibitors. They can inhibit pathogenic proteins and data presented here demonstrate that the idea that nucleic acid aptamers can regulate (inhibit) activity of protein targets has been transformed from the stage of basic developments into the stage of realization of practical tasks. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101625/ doi: 10.1134/s1990750810020046 id: cord-329493-ueqlhgn0 author: Stadler, Konrad title: SARS — beginning to understand a new virus date: 2003 words: 5146.0 sentences: 248.0 pages: flesch: 51.0 cache: ./cache/cord-329493-ueqlhgn0.txt txt: ./txt/cord-329493-ueqlhgn0.txt summary: A new infectious disease, known as severe acute respiratory syndrome (SARS), appeared in the Guangdong province of southern China in 2002. When Thiel and colleagues 20 isolated one genomic and eight subgenomic RNAs from the FRA strain and sequenced their 5′ ends, they identified a conserved sequence (5′ACGAAC3′) that was located in coronaviruses: S, spike protein; E, envelope protein; M, membrane glycoprotein; and N, nucleocapsid protein. Alternatively, these antigens could be delivered by DNA immunization by Figure 6 | The S1 domain of SARS-CoV spike is structurally related to group 2 coronaviruses. Schematic representation of cysteine positions in the S1 domains of group 1, 2 and 3 coronaviruses, compared with the SARS-CoV spike protein. The complete genome sequence of a SARS-CoV isolate (FRA) and experimental data on its key RNA elements and protein functions are described. Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection abstract: The 114-day epidemic of the severe acute respiratory syndrome (SARS) swept 29 countries, affected a reported 8,098 people, left 774 patients dead and almost paralysed the Asian economy. Aggressive quarantine measures, possibly aided by rising summer temperatures, successfully terminated the first eruption of SARS and provided at least a temporal break, which allows us to consolidate what we have learned so far and plan for the future. Here, we review the genomics of the SARS coronavirus (SARS-CoV), its phylogeny, antigenic structure, immune response and potential therapeutic interventions should the SARS epidemic flare up again. url: https://www.ncbi.nlm.nih.gov/pubmed/15035025/ doi: 10.1038/nrmicro775 id: cord-355357-b6aklh44 author: Stapleford, Kenneth A. title: Viral Polymerase-Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion date: 2015-08-26 words: 7650.0 sentences: 342.0 pages: flesch: 43.0 cache: ./cache/cord-355357-b6aklh44.txt txt: ./txt/cord-355357-b6aklh44.txt summary: IMPORTANCE Previous studies using the RNA mutagen ribavirin to select for drug-resistant variants have highlighted the essential role of the viral RNA-dependent RNA polymerase in regulating replication fidelity. Similar to other studies, we previously utilized the RNA mutagens ribavirin and 5-fluorouracil to study drug-resistant mutations in alphaviruses (CHIKV and SINV) and identified residue 483 of the RdRp nsP4 as a key determinant of polymerase fidelity (10, 11) . Furthermore, given that both the CHIKV high-fidelity polymerase variant nsP4 (C483Y) and the novel nsP2 (G641D) variants were isolated in the same antiviral treatment, we addressed their additive roles in resistance to the RNA mutagens ribavirin and 5-fluorouracil (Fig. 1B) . By treating cells during viral infection with each compound, we found that the high-fidelity nsP2 variant and double mutant were more resistant to both nucleotide-depleting compounds ( Fig. 7B and C) , similar to what we observed with ribavirin treatment. abstract: To date, the majority of work on RNA virus replication fidelity has focused on the viral RNA polymerase, while the potential role of other viral replicase proteins in this process is poorly understood. Previous studies used resistance to broad-spectrum RNA mutagens, such as ribavirin, to identify polymerases with increased fidelity that avoid misincorporation of such base analogues. We identified a novel variant in the alphavirus viral helicase/protease, nonstructural protein 2 (nsP2) that operates in concert with the viral polymerase nsP4 to further alter replication complex fidelity, a functional linkage that was conserved among the alphavirus genus. Purified chikungunya virus nsP2 presented delayed helicase activity of the high-fidelity enzyme, and yet purified replication complexes manifested stronger RNA polymerization kinetics. Because mutagenic nucleoside analogs such as ribavirin also affect intracellular nucleotide pools, we addressed the link between nucleotide depletion and replication fidelity by using purine and pyrimidine biosynthesis inhibitors. High-fidelity viruses were more resistant to these conditions, and viral growth could be rescued by the addition of exogenous nucleosides, suggesting that mutagenesis by base analogues requires nucleotide pool depletion. This study describes a novel function for nsP2, highlighting the role of other components of the replication complex in regulating viral replication fidelity, and suggests that viruses can alter their replication complex fidelity to overcome intracellular nucleotide-depleting conditions. IMPORTANCE Previous studies using the RNA mutagen ribavirin to select for drug-resistant variants have highlighted the essential role of the viral RNA-dependent RNA polymerase in regulating replication fidelity. However, the role of other viral replicase components in replication fidelity has not been studied in detail. We identified here an RNA mutagen-resistant variant of the nsP2 helicase/protease that conferred increased fidelity and yet could not operate in the same manner as high-fidelity polymerases. We show that the alphavirus helicase is a key component of the fidelity-regulating machinery. Our data show that the RNA mutagenic activity of compounds such as ribavirin is coupled to and potentiated by nucleotide depletion and that RNA viruses can fine-tune their replication fidelity when faced with an intracellular environment depleted of nucleotides. url: https://www.ncbi.nlm.nih.gov/pubmed/26311883/ doi: 10.1128/jvi.01553-15 id: cord-001655-uqw74ra0 author: Stenglein, Mark D. title: Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus Infections date: 2015-05-20 words: 8100.0 sentences: 479.0 pages: flesch: 48.0 cache: ./cache/cord-001655-uqw74ra0.txt txt: ./txt/cord-001655-uqw74ra0.txt summary: The sets of viral genotypes ranged from that which would be expected for a straightforward co-infection by 2 virus strains in snake #45, to more complex combinations such as that in snake #33, which contained the sequences of 1 S and 10 distinct L segments. We applied homogenates from samples to cultures of boa constrictor-derived JK cells and monitored levels of virus RNA by qRT-PCR using genotype-discriminating primers. Thus, sequences of multiple viral genotypes Recombinant genome segments with unusual organizations. Virus populations replicate as stable ensembles in culture: (A) Liver homogenate from snake #38 was applied to cultures of JK cells and replication was monitored by measuring supernatant viral RNA levels using qRT-PCR and genotype-specific primers. Although we detected many instances of snake tissues containing multiple viral genotypes, our results do not prove that individual cells in these animals were multiply infected. abstract: Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438980/ doi: 10.1371/journal.ppat.1004900 id: cord-027865-p1epjn51 author: Sterchi, Diane L. title: Molecular pathology date: 2020-06-22 words: 13228.0 sentences: 841.0 pages: flesch: 54.0 cache: ./cache/cord-027865-p1epjn51.txt txt: ./txt/cord-027865-p1epjn51.txt summary: ISH is a method of localizing and detecting specific mRNA sequences in preserved tissue sections or cell preparations by hybridizing the complementary strand of a nucleotide probe to the sequence of interest. (See Data Sheet Kappa and Lambda Probe ISH Kit, Novacastra.) (Fig. 21.3.) Chromogenic in situ hybridization (CISH) is a method ''that enables the detection of gene expression in the nucleus using a conventional histochemical reaction'' (White 2005) ; it is used for the detection of abnormal genes and to identify a gene therapy treatment direction. However, FISH still has an advantage over chromogenic methods for labeling specific nucleic acid sequences in cells and tissues. This may be done by using the normal detection procedure for the ISH method on dots of labeled nucleic acid sequence and a labeled control applied at matching descending concentrations on a positively charged nylon membrane. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315333/ doi: 10.1016/b978-0-7020-4226-3.00021-4 id: cord-256325-q70rky3r author: Stewart, Cameron R. title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease date: 2017-07-04 words: 8310.0 sentences: 409.0 pages: flesch: 43.0 cache: ./cache/cord-256325-q70rky3r.txt txt: ./txt/cord-256325-q70rky3r.txt summary: title: A Functional Genomics Approach to Henipavirus Research: The Role of Nuclear Proteins, MicroRNAs and Immune Regulators in Infection and Disease Here we largely focus on findings from two recent RNAi screens to identify protein-coding genes and host-encoded microRNAs impacting the henipavirus infection cycle in human cells. X-ray data have suggested that the methylation of rRNA requires the formation of this complex with involvement of four fibrillarin molecules interacting with different regions of the target rRNAs. The yeast equivalent of fibrillarin, NOP1, has been more extensively studied than the human counterpart but fibrillarin is a well-conserved protein in most organisms, reinforcing the notion that all post-transcriptional processes involving fibrillarin such as chemical modification (methylation) of rRNA, pre-rRNA cleavage and ribosome assembly are essential for proper cellular functioning (Rodriguez-Corona et al. Deffrasnes and colleagues showed that siRNA-mediated knockdown of fibrillarin expression dramatically reduced HeV protein production and viral genome replication but did not impact viral fusion, and that fibrillarin catalytic activity was essential to henipavirus infection. abstract: Hendra and Nipah viruses (family Paramyxoviridae, genus Henipavirus) are zoonotic RNA viruses that cause lethal disease in humans and are designated as Biosafety Level 4 (BSL4) agents. Moreover, henipaviruses belong to the same group of viruses that cause disease more commonly in humans such as measles, mumps and respiratory syncytial virus. Due to the relatively recent emergence of the henipaviruses and the practical constraints of performing functional genomics studies at high levels of containment, our understanding of the henipavirus infection cycle is incomplete. In this chapter we describe recent loss-of-function (i.e. RNAi) functional genomics screens that shed light on the henipavirus–host interface at a genome-wide level. Further to this, we cross-reference RNAi results with studies probing host proteins targeted by henipavirus proteins, such as nuclear proteins and immune modulators. These functional genomics studies join a growing body of evidence demonstrating that nuclear and nucleolar host proteins play a crucial role in henipavirus infection. Furthermore these studies will underpin future efforts to define the role of nucleolar host–virus interactions in infection and disease. url: https://doi.org/10.1007/82_2017_28 doi: 10.1007/82_2017_28 id: cord-342676-ykog278j author: Stewart, H. title: Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging date: 2016-03-14 words: 6858.0 sentences: 338.0 pages: flesch: 46.0 cache: ./cache/cord-342676-ykog278j.txt txt: ./txt/cord-342676-ykog278j.txt summary: To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We wished to investigate the possibility that similar specific secondary structures are present within HCV RNAs destined for packaging, and whether their interactions with Core cooperatively drive the RNA encapsidation and nucleocapsid assembly processes. A mutant genome unable to form such structures displays impaired viral infectivity whilst RNA replication is unaffected, indicating these motifs may interact specifically with Core. Role of RNA structures in genome terminal sequences of the hepatitis C virus for replication and assembly abstract: The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core-RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We postulated that interactions of these motifs, as well as sub-motifs which were present in HCV genomes at statistically significant levels, with the Core protein may drive virion assembly. We mutated 8 of these predicted motifs within the HCV infectious molecular clone JFH-1, thereby producing a range of mutant viruses predicted to possess altered RNA secondary structures. RNA replication and viral titre were unaltered in viruses possessing only one mutated structure. However, infectivity titres were decreased in viruses possessing a higher number of mutated regions. This work thus identified multiple novel RNA motifs which appear to contribute to genome packaging. We suggest that these structures act as cooperative packaging signals to drive specific RNA encapsidation during HCV assembly. url: https://www.ncbi.nlm.nih.gov/pubmed/26972799/ doi: 10.1038/srep22952 id: cord-297880-jlnv90vn author: Stewart, Hazel title: Transcriptional and Translational Landscape of Equine Torovirus date: 2018-08-16 words: 10291.0 sentences: 491.0 pages: flesch: 49.0 cache: ./cache/cord-297880-jlnv90vn.txt txt: ./txt/cord-297880-jlnv90vn.txt summary: Using the prototype species equine torovirus (EToV), we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyze the relative expression levels of the known torovirus proteins and transcripts, chimeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle), and changes in host transcription and translation as a result of EToV infection. The genomes of members of the order Nidovirales are positive-sense, polycistronic RNAs. One of the hallmarks of this virus order is the utilization of an unusual transcription mechanism to express the genes encoding structural and accessory proteins, which reside downstream of the large replicase open reading frames (ORFs) 1a and 1b (Fig. 1) . RNA sequencing (RNA-seq) confirmed previous reports that EToV utilizes a unique combination of both discontinuous and nondiscontinuous RNA synthesis to generate its repertoire of sgRNAs. Strikingly, we also identified a small proportion of chimeric transcripts spanning from the leader to the body TRS of the N protein gene, indicating that discontinuous and nondiscontinuous mechanisms compete in this location. abstract: The genus Torovirus (subfamily Torovirinae, family Coronaviridae, order Nidovirales) encompasses a range of species that infect domestic ungulates, including cattle, sheep, goats, pigs, and horses, causing an acute self-limiting gastroenteritis. Using the prototype species equine torovirus (EToV), we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyze the relative expression levels of the known torovirus proteins and transcripts, chimeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle), and changes in host transcription and translation as a result of EToV infection. RNA sequencing confirmed that EToV utilizes a unique combination of discontinuous and nondiscontinuous RNA synthesis to produce its subgenomic RNAs (sgRNAs); indeed, we identified transcripts arising from both mechanisms that would result in sgRNAs encoding the nucleocapsid. Our ribosome profiling analysis revealed that ribosomes efficiently translate two novel CUG-initiated open reading frames (ORFs), located within the so-called 5′ untranslated region. We have termed the resulting proteins U1 and U2. Comparative genomic analysis confirmed that these ORFs are conserved across all available torovirus sequences, and the inferred amino acid sequences are subject to purifying selection, indicating that U1 and U2 are functionally relevant. This study provides the first high-resolution analysis of transcription and translation in this neglected group of livestock pathogens. IMPORTANCE Toroviruses infect cattle, goats, pigs, and horses worldwide and can cause gastrointestinal disease. There is no treatment or vaccine, and their ability to spill over into humans has not been assessed. These viruses are related to important human pathogens, including severe acute respiratory syndrome (SARS) coronavirus, and they share some common features; however, the mechanism that they use to produce sgRNA molecules differs. Here, we performed deep sequencing to determine how equine torovirus produces sgRNAs. In doing so, we also identified two previously unknown open reading frames “hidden” within the genome. Together these results highlight the similarities and differences between this domestic animal virus and related pathogens of humans and livestock. url: https://www.ncbi.nlm.nih.gov/pubmed/29950409/ doi: 10.1128/jvi.00589-18 id: cord-018724-ss8x2g3b author: Stobbe, Anthony title: Plant Virus Diversity and Evolution date: 2016-06-22 words: 7456.0 sentences: 360.0 pages: flesch: 47.0 cache: ./cache/cord-018724-ss8x2g3b.txt txt: ./txt/cord-018724-ss8x2g3b.txt summary: The variation we see within a single plant host has profound effects on the how the virus responds to selective pressures associated with new hosts, and factors such as the bottleneck events associated with cell-to-cell movement or vectoring. However, several forms of virus variation, such as the high mutation rates of RNA and some DNA viruses, recombination, and reassortment lead to resistance breaking (Duffy and Holmes 2008; McDonald and Linde 2002; Harrison 2002) . For example, genetic diversity (heterosis) induced tolerance to Turnip mosaic virus in wild cress (Lepidium sp.) hybrids, while plants that were selfed were more susceptable to disease, suggesting that small populations with low genetic diversity could lead to increased disease symptoms, and infection rates (Houliston et al. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus abstract: Historically, the majority of plant virology focused on agricultural systems. Recent efforts have expanded our knowledge of the true diversity of plant viruses by studying those viruses that infect wild, undomesticated plants. Those efforts have provided answers to basic ecological questions regarding viruses in the wild, and insights into evolutionary questions, regarding the origins of viruses. While much work has been done, we have merely scratched the surface of the diversity that is estimated to exist. In this chapter we discuss the state of our knowledge of virus diversity, both in agricultural systems as well as in native wild systems, the border between these two systems and how viruses adapt and move across this border into an artificial, domesticated environment. We look at how this diversity has affected our outlook on viruses as a whole, shifting our past view of viruses as purely antagonistic entities of destruction to one where viruses are in a mutually beneficial relationship with their hosts. Additionally, we discuss the current work that plant virology has put forth regarding the evolutionary mechanisms, the life histories, and the deep evolution of viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7123681/ doi: 10.1007/978-3-319-32919-2_8 id: cord-012420-llh22iq2 author: Stott, Robert J. title: Distinct Molecular Mechanisms of Host Immune Response Modulation by Arenavirus NP and Z Proteins date: 2020-07-21 words: 12015.0 sentences: 579.0 pages: flesch: 41.0 cache: ./cache/cord-012420-llh22iq2.txt txt: ./txt/cord-012420-llh22iq2.txt summary: Interestingly, non-pathogenic OW Mopeia virus (MOPV), a close genetic relative to LASV, induces a strong initial IFN and cytokine response in infected moDCs and macrophages leading to a sustained T cell activation and immune response [67, 68] . Similar to NP, interaction of arenavirus Z proteins with RIG-I prevents further binding to MAVS and therefore inhibits the production of IFN-β and reduces antiviral host immune responses. Although the inhibition of RIG-I signalling by highly pathogenic arenaviruses in vitro suggests that there should be limited IFN1 response, it is notable that in vivo infection with some of these viruses (LCMV, JUNV) induces high levels of IFN1, ISGs and cytokines suggesting that this strategy is not completely effective or is widely varied in cell type and differs from host to host [134, 135, 186] . abstract: Endemic to West Africa and South America, mammalian arenaviruses can cross the species barrier from their natural rodent hosts to humans, resulting in illnesses ranging from mild flu-like syndromes to severe and fatal haemorrhagic zoonoses. The increased frequency of outbreaks and associated high fatality rates of the most prevalent arenavirus, Lassa, in West African countries, highlights the significant risk to public health and to the socio-economic development of affected countries. The devastating impact of these viruses is further exacerbated by the lack of approved vaccines and effective treatments. Differential immune responses to arenavirus infections that can lead to either clearance or rapid, widespread and uncontrolled viral dissemination are modulated by the arenavirus multifunctional proteins, NP and Z. These two proteins control the antiviral response to infection by targeting multiple cellular pathways; and thus, represent attractive targets for antiviral development to counteract infection. The interplay between the host immune responses and viral replication is a key determinant of virus pathogenicity and disease outcome. In this review, we examine the current understanding of host immune defenses against arenavirus infections and summarise the host protein interactions of NP and Z and the mechanisms that govern immune evasion strategies. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7412275/ doi: 10.3390/v12070784 id: cord-332356-au7s3dmp author: Strandin, Tomas title: The cytoplasmic tail of hantavirus Gn glycoprotein interacts with RNA date: 2011-09-15 words: 6554.0 sentences: 329.0 pages: flesch: 53.0 cache: ./cache/cord-332356-au7s3dmp.txt txt: ./txt/cord-332356-au7s3dmp.txt summary: The results indicate that the binding ability of Gn-CT towards nucleic acids is rather unspecific since in addition to genomic RNA, also unrelated RNA as well as single-stranded DNA was able to interact with Gn-CTs of PUUV and TULV. Purified, lysed and micrococcal nuclease (MNase)-treated virus preparation and in vitro transcribed and radiolabeled genomic PUUV S segment were allowed to form RNA-protein complexes prior to UV cross-linking. The capability of structural proteins to bind RNA was analyzed by incubating purified, lysed and micrococcal nuclease (MNase)-treated virus preparations with radioactive PUUV S segment RNA in the case of PUUV ( The samples were immunoprecipitated with MAbs or PAbs specific to N, Gn or Gc and retained radioactivity on protein G beads after washing was measured by scintillation counting. The mapping indicated that the same peptides that were previously shown to interact with RNP and N protein (Hepojoki et al., 2010b) were capable of binding also nucleic acids (Fig. 5A ). abstract: We recently characterized the interaction between the intraviral domains of envelope glycoproteins (Gn and Gc) and ribonucleoprotein (RNP) of Puumala and Tula hantaviruses (genus Hantavirus, family Bunyaviridae). Herein we report a direct interaction between spike-forming glycoprotein and nucleic acid. We show that the envelope glycoprotein Gn of hantaviruses binds genomic RNA through its cytoplasmic tail (CT). The nucleic acid binding of Gn-CT is unspecific, as demonstrated by interactions with unrelated RNA and with single-stranded DNA. Peptide scan and protein deletions of Gn-CT mapped the nucleic acid binding to regions that overlap with the previously characterized N protein binding sites and demonstrated the carboxyl-terminal part of Gn-CT to be the most potent nucleic acid-binding site. We conclude that recognition of the RNP complex by the Gn-CT could be mediated by interactions with both genomic RNA and the N protein. This would provide the required selectivity for the genome packaging of hantaviruses. url: https://www.ncbi.nlm.nih.gov/pubmed/21807393/ doi: 10.1016/j.virol.2011.06.030 id: cord-293375-qcy56ui7 author: Strauss, Ellen G. title: Identification of the active site residues in the nsP2 proteinase of sindbis virus date: 1992-12-31 words: 5192.0 sentences: 265.0 pages: flesch: 56.0 cache: ./cache/cord-293375-qcy56ui7.txt txt: ./txt/cord-293375-qcy56ui7.txt summary: coma-, nepo-, and potyviruses; coronaviruses; and flaviviruses (and their proposed relatives pestiviruses and hepatitis C virus.) Originally these domains were predicted to have proteolytic activity based on the presence of certain conserved amino acid residues and on the basis of protein-modeling studies (Bazan and Fletterick, 1989; Boege et a/., 1981; Gorbalenya et al., 1989; Hahn eta/., 1985) . Furthermore, we present data to show that none of the asparagine residues in the proteinase domain of Sindbis nsP2 that are conserved among alphaviruses are absolutely required for proteolytic activity, but that Trp-559, adjacent to His-558, is essential for function. We also examined the effect of changing Cys-525, one of the two remaining conserved cysteine residues in the C-terminal half of nsP2, to serine or arginine, as well as changing Ser-535, which is found in a domain of limited similarity to the active site serine of serine proteinases, to threonine. abstract: Abstract The nonstructural polyproteins of Sindbis virus are processed by a virus-encoded proteinase which is located in the C-terminal domain of nsP2. Here we have performed a mutagenic analysis to identify the active site residues of this proteinase. Substitution of other amino acids for either Cys-481 or His-558 completely abolished proteolytic processing of Sindbis virus polyproteins in vitro. Substitutions within this domain for a second cysteine conserved among alphaviruses, for four other conserved histidines, or for a conserved serine did not affect the activity of the enzyme. These results suggest that nsP2 is a papain-like proteinase whose catalytic dyad is composed of Cys-481 and His-558. Since an asparagine residue has been implicated in the active site of papain, we changed the four conserved asparagine residues in the C-terminal half of nsP2 and found that all could be substituted without total loss of activity. Among papain-like proteinases, the residue following the catalytic histidine is alanine or glycine in the plant and animal enzymes, and the presence of Trp-559 in alphaviruses is unusual. A mutant enzyme containing Ala-559 was completely inactive, implying that Trp-559 is essential for a functional proteinase. All of these mutations were introduced into a full-length clone of Sindbis virus from which infectious RNA could be transcribed in vitro, and the effects of these changes on viability were tested. In all cases it was found that mutations which abolished proteolytic activity were lethal, whether or not these mutations were in the catalytic residues, indicating that proteolysis of the nonstructural polyprotein is essential for Sindbis replication. url: https://www.sciencedirect.com/science/article/pii/004268229290268T doi: 10.1016/0042-6822(92)90268-t id: cord-338307-vfutmwxq author: Sturman, Lawrence S. title: The Molecular Biology of Coronaviruses date: 1983-12-31 words: 21959.0 sentences: 1287.0 pages: flesch: 52.0 cache: ./cache/cord-338307-vfutmwxq.txt txt: ./txt/cord-338307-vfutmwxq.txt summary: The pattern of three major structural proteins and their organization in the virion as shown for MHV-A59 in Fig. 3 is generally applicable to most other species of coronaviruses (reviewed in detail by Siddell et al., 1982) . (1981b) , using a cDNA probe prepared against the mRNA of MHV-A59 which coded for the nucleocapsid protein, obtained evidence of 7 0 4 0 % homology by analysis of hybridization kinetics of viral RNA from cells infected with MHV-1, -3, -S, and -JHM. t 1980) demonstrated that different size classes of poly(A)containing intracellular MHV-JHM RNAs fractionated on sucroseformamide gradients directed the synthesis of different structural proteins in cell-free translation systems. The studies showed that, like avian coronaviruses, for the murine coronavirus MHV-A59, the oligonucleotides of each of the subgenomic RNAs were included within the next larger species, starting from the 3'' end of the genome. abstract: Publisher Summary Coronaviruses have recently emerged as an important group of animal and human pathogens that share a distinctive replicative cycle. Some of the unique characteristics in the replication of coronaviruses include generation of a 3' coterminal-nested set of five or six subgenomic mRNAs, each of which appears to direct the synthesis of one protein. Two virus-specific RNA polymerase activities have been identified. Many of the distinctive features of coronavirus infection and coronavirus-induced diseases may result from the properties of the two coronavirus glycoproteins. The intracellular budding site, which may be important in the establishment and maintenance of persistent infections, appears to be due to the restricted intracytoplasmic migration of the E1 glycoprotein, which acts as a matrix-like transmembrane glycoprotein. E1 also exhibits distinctive behavior by self-aggregating on heating at 100°C in sodium dodecyl sulfate (SDS) and by its interaction with RNA in the viral nucleocapsid. The E1 of mouse hepatitis virus (MHV) is an O-linked glycoprotein, unlike most other viral glycoproteins. Thus, the coronavirus system may be a useful model for the study of synthesis, glycosylation, and transport of O-linked cellular glycoproteins. url: https://www.ncbi.nlm.nih.gov/pubmed/6362367/ doi: 10.1016/s0065-3527(08)60721-6 id: cord-272378-umvi0veu author: Subramanian, Subbaya title: Special Issue: MicroRNA Regulation in Health and Disease date: 2019-06-15 words: 2126.0 sentences: 120.0 pages: flesch: 47.0 cache: ./cache/cord-272378-umvi0veu.txt txt: ./txt/cord-272378-umvi0veu.txt summary: MicroRNAs are single-stranded non-coding RNAs that are typically 18-25 nucleotides (nts) in length and are best known for their role in the post-transcriptional regulation of gene expression. However, it is possible that the frequency of MREs in the entire transcriptome of a given cell contributes to the dynamic gene regulatory process by acting as a sponge for mature miRNAs, thus regulating their functional availability. Thus, gene expression regulation is a complex process involving the dynamic interactions between miRNA-mRNA-lncRNA-circRNA. This Special Issue of Genes, entitled "MicroRNA Regulation in Health and Disease" consists of a series of articles spanning the clinical realm from colorectal cancer to pulmonary fibrosis. Somatostatin (SST) analogues were used to control the proliferation and symptoms of neuroendocrine tumors (NETs) in an article by Døssing et al., entitled "Somatostatin Analogue Treatment Primarily Induce miRNA Expression Changes and Up-Regulates Growth Inhibitory miR-7 and miR-148a in Neuroendocrine Cells" [15] . abstract: Our understanding of non-coding RNA has significantly changed based on recent advances in genomics and molecular biology, and their role is recognized to include far more than a link between the sequence of DNA and synthesized proteins [...]. url: https://doi.org/10.3390/genes10060457 doi: 10.3390/genes10060457 id: cord-000063-tex6bgab author: Sui, Hong-Yan title: Small Interfering RNA Targeting M2 Gene Induces Effective and Long Term Inhibition of Influenza A Virus Replication date: 2009-05-22 words: 3501.0 sentences: 189.0 pages: flesch: 50.0 cache: ./cache/cord-000063-tex6bgab.txt txt: ./txt/cord-000063-tex6bgab.txt summary: Using this vector that also expresses enhanced green fluorescence protein (EGFP) as surrogate marker, stable shRNA-expressing cell lines were successfully established and the inhibition efficiencies of rationally designed siRNAs targeting to conserved regions of influenza A virus genome were assessed. It was further demonstrated that no siRNA-resistant viral mutation appeared in siM2 targeting sequence even after the virus was cultured in the shRNA expressing stable cell line for 40 passages. A recent report by Zhou et al [30] also showed that several siRNAs targeting NP and M genes exhibited effective inhibition against influenza A virus replication in cultured MDCK cells and in animal models. Taken together, all the findings about effective RNAi target, lentiviral vector delivery and the establishment of stable shRNA expressing cell lines in our study provide rational information for the development of siRNAs as prophylaxis and therapy for influenza virus infection in humans. abstract: RNA interference (RNAi) provides a powerful new means to inhibit viral infection specifically. However, the selection of siRNA-resistant viruses is a major concern in the use of RNAi as antiviral therapeutics. In this study, we conducted a lentiviral vector with a H1-short hairpin RNA (shRNA) expression cassette to deliver small interfering RNAs (siRNAs) into mammalian cells. Using this vector that also expresses enhanced green fluorescence protein (EGFP) as surrogate marker, stable shRNA-expressing cell lines were successfully established and the inhibition efficiencies of rationally designed siRNAs targeting to conserved regions of influenza A virus genome were assessed. The results showed that a siRNA targeting influenza M2 gene (siM2) potently inhibited viral replication. The siM2 was not only effective for H1N1 virus but also for highly pathogenic avian influenza virus H5N1. In addition to its M2 inhibition, the siM2 also inhibited NP mRNA accumulation and protein expression. A long term inhibition effect of the siM2 was demonstrated and the emergence of siRNA-resistant mutants in influenza quasispecies was not observed. Taken together, our study suggested that M2 gene might be an optimal RNAi target for antiviral therapy. These findings provide useful information for the development of RNAi-based prophylaxis and therapy for human influenza virus infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682565/ doi: 10.1371/journal.pone.0005671 id: cord-000640-t0y0b0gb author: Sumibcay, Laarni title: Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Côte d''Ivoire date: 2012-01-26 words: 2219.0 sentences: 109.0 pages: flesch: 44.0 cache: ./cache/cord-000640-t0y0b0gb.txt txt: ./txt/cord-000640-t0y0b0gb.txt summary: Following numerous failed attempts, hantavirus RNA was detected in ethanol-fixed liver tissue from two banana pipistrelles (Neoromicia nanus), captured near Mouyassué village in Côte d''Ivoire, West Africa, in June 2011. Phylogenetic analysis of partial L-segment sequences using maximum-likelihood and Bayesian methods revealed that the newfound hantavirus, designated Mouyassué virus (MOUV), was highly divergent and basal to all other rodentand soricomorph-borne hantaviruses, except for Nova virus in the European common mole (Talpa europaea). After innumerable failed attempts, hantavirus RNA was detected by RT-PCR in ethanol-fixed liver tissues from two of 12 banana pipistrelles (Neoromicia nanus Peters 1852), captured during June 2011 near Mouyassué village (5°22''07"N, 3°05''37"W) in Aboisso District, 130 km from Abidjan, in the extreme southeastern region of Côte d''Ivoire in West Africa ( Figure 1 ). The newfound hantavirus, designated Mouyassué virus (MOUV), exhibited low nucleotide and amino acid sequence similarity of less than 69% to all representative soricomorph-and rodent-associated hantaviruses, except for the 76.3% sequence similarity with Nova virus (NVAV), previously reported in the European common mole (Talpa europaea) [12] . abstract: Recently identified hantaviruses harbored by shrews and moles (order Soricomorpha) suggest that other mammals having shared ancestry may serve as reservoirs. To investigate this possibility, archival tissues from 213 insectivorous bats (order Chiroptera) were analyzed for hantavirus RNA by RT-PCR. Following numerous failed attempts, hantavirus RNA was detected in ethanol-fixed liver tissue from two banana pipistrelles (Neoromicia nanus), captured near Mouyassué village in Côte d'Ivoire, West Africa, in June 2011. Phylogenetic analysis of partial L-segment sequences using maximum-likelihood and Bayesian methods revealed that the newfound hantavirus, designated Mouyassué virus (MOUV), was highly divergent and basal to all other rodent- and soricomorph-borne hantaviruses, except for Nova virus in the European common mole (Talpa europaea). Full genome sequencing of MOUV and further surveys of other bat species for hantaviruses, now underway, will provide critical insights into the evolution and diversification of hantaviruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331809/ doi: 10.1186/1743-422x-9-34 id: cord-007236-8hiymqyb author: Sun, Ji-Min title: Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway date: 2011-11-09 words: 4983.0 sentences: 276.0 pages: flesch: 47.0 cache: ./cache/cord-007236-8hiymqyb.txt txt: ./txt/cord-007236-8hiymqyb.txt summary: title: Inhibition of hepatitis C virus replication by Monascus pigment derivatives that interfere with viral RNA polymerase activity and the mevalonate biosynthesis pathway We demonstrated that a group of Monascus orange pigment (MOP) derivatives effectively inhibited NS5B RdRp activity and interfered with the mevalonate synthesis pathway, thereby suppressing HCV replication in cells harbouring an HCV genotype 1b subgenomic replicon and in cells infected with genotype 2a HCV. As shown in Figure 2 (a), among the selected group of MOP AADs that inhibited NS5B RdRp activity in vitro, Lys, Phe, Val, Leu and Ile derivatives also inhibited HCV replication in Huh7 cells, which harbour a HCV subgenomic replicon RNA. Together, these results suggest that in addition to a direct inhibition of NS5B RdRp activity, these MOP AAD compounds also inhibit HCV replication by interfering with the cholesterol biosynthetic pathway downstream of the HMG-CoA reductase step. abstract: OBJECTIVES: Hepatitis C virus (HCV) infection causes chronic liver disease and is a major public health problem worldwide. The aim of this study was to evaluate the potential of Monascus pigment derivatives, which were derived from a microbial secondary metabolite synthesized from polyketides by Monascus spp., as HCV antiviral agents. METHODS: We performed an in vitro RNA-dependent RNA polymerase (RdRp) assay to screen for HCV RdRp inhibitors. The anti-HCV activity of RdRp inhibitors in HCV-replicating cells was evaluated by quantification of the RNA viral genome. Molecular docking analysis was performed to predict the binding sites of the selected RdRp inhibitors. RESULTS: We have identified a Monascus pigment and its derivatives as inhibitors of the HCV NS5B RdRp. A group of Monascus orange pigment (MOP) amino acid derivatives, in which the reactive oxygen moiety was changed to amino acids, significantly inhibited HCV replication. Further, combination of the MOP derivatives (Phe, Val or Leu conjugates) with interferon (IFN)-α inhibited HCV replication more than IFN-α treatment alone. Lastly, molecular docking studies indicate the inhibitors may bind to a thumb subdomain allosteric site of NS5B. The antiviral activity of the MOP derivatives was related to a modulation of the mevalonate pathway, since the mevalonate-induced increase in HCV replication was suppressed by the MOP compounds. CONCLUSIONS: Our results identify amino acid derivatives of MOP as potential anti-HCV agents and suggest that their combination with IFN-α might offer an alternative strategy for the control of HCV replication. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109977/ doi: 10.1093/jac/dkr432 id: cord-330045-4gj9d181 author: Sun, Jiufeng title: Prolonged Persistence of SARS-CoV-2 RNA in Body Fluids date: 2020-08-17 words: 1541.0 sentences: 93.0 pages: flesch: 57.0 cache: ./cache/cord-330045-4gj9d181.txt txt: ./txt/cord-330045-4gj9d181.txt summary: We recruited hospitalized patients with COVID-19 from 2 designated provincial emergency hospitals for e merging infectious diseases in Guangdong, China, and tested specimens by real-time reverse transcription PCR (rRT-PCR) to estimate the duration of the detection of SARS-CoV-2 RNA in various body fluids, using an accelerated failure time (AFT)-based modeling study. We used parametric Weibull regression models (AFT) to estimate the time until the loss of SARS-CoV-2 RNA detection in each body fluid and reported findings in medians and 95th percentiles using R software version 3.6.1 with flexsurv, survival, and survminer packages (9) . We used Weibull models to estimate the median and the 95th percentile for the time until the loss of SARS-CoV-2 RNA detection in swab, sputum, and fecal samples (Table; Figures 1, 2) . In this study, we estimated the time for COVID-19 case-patients to clear SARS-CoV-2 RNA in the acute phase of infection through an AFT-based modeling study. abstract: We prospectively assessed 49 coronavirus disease cases in Guangdong, China, to estimate the frequency and duration of detectable severe acute respiratory syndrome coronavirus 2 RNA in human body fluids. The prolonged persistence of virus RNA in various body fluids may guide the clinical diagnosis and prevention of onward virus transmission. url: https://doi.org/10.3201/eid2608.201097 doi: 10.3201/eid2608.201097 id: cord-336093-ic6q6ke8 author: Sun, Ying title: Yeast-based assays for the high-throughput screening of inhibitors of coronavirus RNA cap guanine-N7-methyltransferase date: 2014-02-11 words: 6321.0 sentences: 361.0 pages: flesch: 57.0 cache: ./cache/cord-336093-ic6q6ke8.txt txt: ./txt/cord-336093-ic6q6ke8.txt summary: Abbreviations: SARS, severe acute respiratory syndrome; SARS-CoV, SARS coronavirus; nsp, nonstructural protein; N7-MTase, guanine-N7-methyltransferase; 2 0 -O-MTase, 2 0 -O-methyltransferase; AdoMet, S-adenosyl-L-methionine; AdoHcy, S-adenosyl-L-homocysteine; ATA, aurintricarboxylic acid; IC 50 , inhibitory concentration at 50% activity. A single transformed colony of the YBS40 strain containing plasmids expressing human N7-MTase (MT-Human), SARS-CoV N7-MTase (MT-SARS), N7-MTases of other coronaviruses (MT-MHV, MT-TGEV, and MT-IBV), and the pMceK294A vector as control (representing the yeast N7-MTase [MT-Yeast]), were inoculated separately into 5 ml of a basic medium (Min SD Base) lacking tryptophan and incubated at 30°C for 21-24 h until reaching a similar final cell density in the stationary phase (0.5-1.0 Â 10 8 cells/ml) (Chrebet et al., 2005) . Although AdoHcy, ATA and sinefungin, were previously reported to be inhibitors of coronavirus RNA MTases in vitro , only sinefungin significantly suppressed the growth of the MT-yeast, MT-human, and MT-SARS yeast cells (Fig. 3 ). abstract: The 5′-cap structure is a distinct feature of eukaryotic mRNAs and is important for RNA stability and protein translation by providing a molecular signature for the distinction of self or non-self mRNA. Eukaryotic viruses generally modify the 5′-end of their RNAs to mimic the cellular mRNA structure, thereby facilitating viral replication in host cells. However, the molecular organization and biochemical mechanisms of the viral capping apparatus typically differ from its cellular counterpart, which makes viral capping enzymes attractive targets for drug discovery. Our previous work showed that SARS coronavirus (SARS-CoV) non-structural protein 14 represents a structurally novel and unique guanine-N7-methyltransferase (N7-MTase) that is able to functionally complement yeast cellular N7-MTase. In the present study, we developed a yeast-based system for identifying and screening inhibitors against coronavirus N7-MTase using both 96-well and 384-well microtiter plates. The MTase inhibitors previously identified by in vitro biochemical assays were tested, and some, such as sinefungin, effectively suppressed N7-MTase in the yeast system. However, other compounds, such as ATA and AdoHcy, did not exert an inhibitory effect within a cellular context. These results validated the yeast assay system for inhibitor screening yet also demonstrated the difference between cell-based and in vitro biochemical assays. The yeast system was applied to the screening of 3000 natural product extracts, and three were observed to more potently inhibit the activity of coronavirus than human N7-MTase. url: https://api.elsevier.com/content/article/pii/S0166354214000369 doi: 10.1016/j.antiviral.2014.02.002 id: cord-335864-392xmrq0 author: Sun, Yu-Meng title: Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application date: 2020-08-10 words: 13942.0 sentences: 786.0 pages: flesch: 45.0 cache: ./cache/cord-335864-392xmrq0.txt txt: ./txt/cord-335864-392xmrq0.txt summary: With recent developments in sequencing methods and information analysis, an increasing number of novel ncRNAs have been identified, including long noncoding RNAs (lncRNAs) [5, 6] , circular RNAs (circRNAs) [7, 8] , and novel small ncRNAs [9] [10] [11] . Most circRNAs derived from mRNA back-splicing lose translational capacity because of the lack of effective ORFs or ribosome entry approaches, while a few circRNAs from coding or Sno-lncRNAs maintain their stability by their classical stem-loop structures of snoRNAs. c Alternative splicing within circRNAs. d A number of novel small ncRNAs derived from rRNAs (rRFs), tRNAs (tsRNAs), and snoRNAs (sdRNAs) have also been found to be enriched in RNA-induced silencing complexes (RISCs) and function in a miRNA-like pathway This approach can provide in-depth analysis of transcripts from target regions of genome. abstract: Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of innovative technologies, an increasing number of novel ncRNAs have been uncovered; information about their prominent tissue-specific expression patterns, various interaction networks, and subcellular locations will undoubtedly enhance our understanding of their potential functions. Here, we summarized the principles and innovative methods for identifications of novel ncRNAs that have potential functional roles in cancer biology. Moreover, this review also provides alternative ncRNA databases based on high-throughput sequencing or experimental validation, and it briefly describes the current strategy for the clinical translation of cancer-associated ncRNAs to be used in diagnosis. url: https://doi.org/10.1186/s13045-020-00945-8 doi: 10.1186/s13045-020-00945-8 id: cord-316134-lkd2mj27 author: Sungsuwan, Suttipun title: Nucleocapsid proteins from other swine enteric coronaviruses differentially modulate PEDV replication date: 2020-01-15 words: 9236.0 sentences: 495.0 pages: flesch: 52.0 cache: ./cache/cord-316134-lkd2mj27.txt txt: ./txt/cord-316134-lkd2mj27.txt summary: Investigation of possible molecular interactions between components of PEDV, PDCoV and TGEV and their influence on replication of each virus would provide a crucial insight into comprehensive understanding of these CoVs. Of all viral proteins, we have chosen to start with the N protein, as it is among the most abundant and ubiquitous structural proteins in infected cells. For viral infection in the transient CoV N expression experiment, VeroE6 cells were transfected with 1 or 2 μg of pCAGGS-PEDV N-Myc, pCAGGS-PDCoV N-HA, pCAGGS-TGEV N-FLAG, or the empty pCAGGS vector and were incubated for 24 h to allow for protein expression. To investigate how this protein-protein interaction might affect PEDV replication, we transiently transfected VeroE6 cells with varying amounts of the pCAGGS plasmid expressing N proteins from either PDCoV or TGEV for 24 h before infection with PEDV-mCherry (MOI = 0.0001) and followed the course of viral replication for each condition. abstract: Porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV) and porcine deltacoronavirus (PDCoV) share tropism for swine intestinal epithelial cells. Whether mixing of viral components during co-infection alters pathogenic outcomes or viral replication is not known. In this study, we investigated how different coronavirus nucleocapsid (CoV N) proteins interact and affect PEDV replication. We found that PDCoV N and TGEV N can competitively interact with PEDV N. However, the presence of PDCoV or TGEV N led to very different outcomes on PEDV replication. While PDCoV N significantly suppresses PEDV replication, overexpression of TGEV N, like that of PEDV N, increases production of PEDV RNA and virions. Despite partial interchangeability in nucleocapsid oligomerization and viral RNA synthesis, endogenous PEDV N cannot be replaced in the production of infectious PEDV particles. Results from this study give insights into functional compatibilities and evolutionary relationship between CoV viral proteins during viral co-infection and co-evolution. url: https://www.sciencedirect.com/science/article/pii/S0042682219303150 doi: 10.1016/j.virol.2019.11.007 id: cord-023865-6rafp3x3 author: Surjit, Milan title: The Nucleocapsid Protein of the SARS Coronavirus: Structure, Function and Therapeutic Potential date: 2009-07-22 words: 9210.0 sentences: 448.0 pages: flesch: 45.0 cache: ./cache/cord-023865-6rafp3x3.txt txt: ./txt/cord-023865-6rafp3x3.txt summary: Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. Interestingly, biochemically mediated inhibition of GSK3 activity in SARS-CoV infected cells also leads to around 80% reduction in viral titer and subsequent induction of a virus-induced cytopathic effect. Further, S-phase specific gene products like cyclin E and CDK2 were found to be downregulated in SARS-CoV infected cell lysate, which suggested that the observed phenomenon may be relevant in vivo. Based on this observation, Palese''s laboratory has studied the IFN inhibitory property of different SARS-CoV proteins, which revealed that ORF3, ORF6 as well as the N-protein have the ability to independently inhibit IFN production through different mechanisms. Intracellular localization of the severe acute respiratory syndrome coronavirus nucleocapsid protein: absence of nucleolar accumulation during infection and after expression as a recombinant protein in vero cells abstract: As in other coronaviruses, the nucleocapsid protein is one of the core components of the SARS coronavirus (CoV). It oligomerizes to form a closed capsule, inside which the genomic RNA is securely stored thus providing the SARS-CoV genome with its first line of defense from the harsh conditions of the host environment and aiding in replication and propagation of the virus. In addition to this function, several reports have suggested that the SARS-CoV nucleocapsid protein modulates various host cellular processes, so as to make the internal milieu of the host more conducive for survival of the virus. This article will analyze and discuss the available literature regarding these different properties of the nucleocapsid protein. Towards the end of the article, we will also discuss some recent reports regarding the possible clinically relevant use of the nucleocapsid protein, as a candidate diagnostic tool and vaccine against SARS-CoV infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176212/ doi: 10.1007/978-3-642-03683-5_9 id: cord-102892-nt1zoktv author: Sweeney, Blake A. title: R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types date: 2020-09-11 words: 3366.0 sentences: 188.0 pages: flesch: 54.0 cache: ./cache/cord-102892-nt1zoktv.txt txt: ./txt/cord-102892-nt1zoktv.txt summary: Consensus tRNA primary 213 sequence with 2D structure for each isotype of each taxonomic domain was generated based 214 on the tRNA alignments used for building the isotype-specific covariance models in tRNAscan-215 SE 2.0 16 . 270 R2DT templates model the conserved core of most structured RNAs We classified each nucleotide in the resulting diagrams according to whether it matched a 282 template and found that 90.6% of nucleotides were displayed using the nucleotide locations 283 encoded in the templates, while 6.0% of nucleotides represented insertions compared to the 284 templates, and 3.4% of nucleotides matched the templates but required automatic repositioning 285 by the Traveler software (Table 2) . In addition, R2DT will benefit from the ongoing development Isotype-specific consensus tRNA sequences and 2D structures were generated using R-scape 52 389 from the alignments that were used to train and build the corresponding covariance models in 390 tRNAscan-SE 16 . abstract: Non-coding RNAs (ncRNA) are essential for all life, and the functions of many ncRNAs depend on their secondary (2D) and tertiary (3D) structure. Despite proliferation of 2D visualisation software, there is a lack of methods for automatically generating 2D representations in consistent, reproducible, and recognisable layouts, making them difficult to construct, compare and analyse. Here we present R2DT, a comprehensive method for visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,632 templates representing the majority of known structured RNAs, from small RNAs to the large subunit ribosomal RNA. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world’s largest RNA 2D structure dataset. The software is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt. url: https://doi.org/10.1101/2020.09.10.290924 doi: 10.1101/2020.09.10.290924 id: cord-337998-08tknscm author: Sztuba-Solinska, Joanna title: A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8 date: 2016-11-16 words: 8269.0 sentences: 434.0 pages: flesch: 51.0 cache: ./cache/cord-337998-08tknscm.txt txt: ./txt/cord-337998-08tknscm.txt summary: Selective 2′-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3′ stem-loop (nucleotides 1868–1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. 3E-5E-GFP minigenome RNA secondary structure and host protein interactions were examined using selective 2 -hydroxyl acylation analyzed by primer extension (SHAPE) (38, 39) , antisense-interfered SHAPE (aiSHAPE) (40) , electrophoretic mobility shift assays (EMSA), siRNA, and mutational analysis, using both the 3E-5E-GFP minigenome system and EBOV reverse genetics. The secondary structure of the EBOV 3E-5E-GFP minigenome RNA predicted by RNAstructure software version 5.7 (48) and chemical probing data from SHAPE were used to generate 10 three-dimensional (3D) models for the trailer-to-leader panhandle interaction in the wt-EBOV genome and variants, A30U and A26U/A30U, using open-source RNAComposer, version 1.0 (http://rnacomposer.cs.put.poznan.pl/). abstract: Ebola virus (EBOV) is a single-stranded negative-sense RNA virus belonging to the Filoviridae family. The leader and trailer non-coding regions of the EBOV genome likely regulate its transcription, replication, and progeny genome packaging. We investigated the cis-acting RNA signals involved in RNA–RNA and RNA–protein interactions that regulate replication of eGFP-encoding EBOV minigenomic RNA and identified heat shock cognate protein family A (HSC70) member 8 (HSPA8) as an EBOV trailer-interacting host protein. Mutational analysis of the trailer HSPA8 binding motif revealed that this interaction is essential for EBOV minigenome replication. Selective 2′-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3′ stem-loop (nucleotides 1868–1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. Results of minigenome assays and an EBOV reverse genetic system rescue support a role for both the panhandle domain and HSPA8 motif 1 in virus replication. url: https://www.ncbi.nlm.nih.gov/pubmed/27651462/ doi: 10.1093/nar/gkw825 id: cord-294260-g410mavp author: Sztuba-Solińska, Joanna title: Subgenomic messenger RNAs: Mastering regulation of (+)-strand RNA virus life cycle date: 2011-04-10 words: 9531.0 sentences: 506.0 pages: flesch: 54.0 cache: ./cache/cord-294260-g410mavp.txt txt: ./txt/cord-294260-g410mavp.txt summary: Arrow, RNA3 start site at nt 2721 (Lindenbach et al., 2002) ; (D) Schematic of the RCNMV genome showing the relative positions of the in trans interacting RNA elements: the loop portion of a stem-loop in RNA2 (termed trans-activator or TA) and a complementary sequence in RNA1 (termed TA binding site or TABS) located just upstream from the initiation site for SG mRNA transcription (Guenther et al., 2004) ; (E) Representation of CLSV genome and the proposed AS2 and RS2 interaction during regulation of SG RNA2 synthesis (Xu and White, 2008) ; (F) Overview of the BYDV genome and the in cisinteraction between genomic 5′-UTR stem-loop (BCL) and the genomic 3′-BTE, and the in trans interaction between the genomic 3′ BTE and the 5′ UTR of SG RNA1 . abstract: Many (+)-strand RNA viruses use subgenomic (SG) RNAs as messengers for protein expression, or to regulate their viral life cycle. Three different mechanisms have been described for the synthesis of SG RNAs. The first mechanism involves internal initiation on a (−)-strand RNA template and requires an internal SGP promoter. The second mechanism makes a prematurely terminated (−)-strand RNA which is used as template to make the SG RNA. The third mechanism uses discontinuous RNA synthesis while making the (−)-strand RNA templates. Most SG RNAs are translated into structural proteins or proteins related to pathogenesis: however other SG RNAs regulate the transition between translation and replication, function as riboregulators of replication or translation, or support RNA–RNA recombination. In this review we discuss these functions of SG RNAs and how they influence viral replication, translation and recombination. url: https://doi.org/10.1016/j.virol.2011.02.007 doi: 10.1016/j.virol.2011.02.007 id: cord-274463-0nvw2egm author: Sánchez-Navarro, Jesús A. title: Plant tissue distribution and chemical inactivation of six carnation viruses date: 2006-12-11 words: 2940.0 sentences: 203.0 pages: flesch: 55.0 cache: ./cache/cord-274463-0nvw2egm.txt txt: ./txt/cord-274463-0nvw2egm.txt summary: Viral RNA or DNA accumulation on root, stem, leaf, sepal, petal, stamen, pistil and ovary tissues of infected carnation or Saponaria vaccaria plants was analysed by non-isotopic molecular hybridisation. A negative hybridisation signal was also observed in root tissue of CVMV infected carnation plants (Fig. 1B) whereas the viral RNA accumulation was determined to be 625 ng g À1 of infected pistil tissue (dilution 5 À3 ) followed by petal, stamen and pistil with 125 ng (dilution 5 À2 ) and sepal with 25 ng (5 À1 ) ( Table 1 ). The viral distribution results showed two patterns for the six carnation viruses: high titres of CarMV, CRSV, CIRV, and CLV accumulated with small differences among the plant tissue analysed whereas there were low amounts of CERV and CVMV irregularly distributed over the infected plant. abstract: Carnation mottle virus (CarMV), Carnation etched ring virus (CERV), Carnation vein mottle virus (CVMV), Carnation ringspot virus (CRSV), Carnation Italian ringspot virus (CIRV) and Carnation latent virus (CLV) are the most important viruses affecting carnation crops. All except CERV are RNA viruses. Viral RNA or DNA accumulation on root, stem, leaf, sepal, petal, stamen, pistil and ovary tissues of infected carnation or Saponaria vaccaria plants was analysed by non-isotopic molecular hybridisation. High-titres of CarMV, CRSV, CIRV, and CLV accumulated in all plant tissues whereas CERV and CVMV were irregularly distributed over the plant. High-titres of all viruses accumulated in leaf, petal, stamen, pistil, and ovary tissues, so leaves or petals are a good tissue for routine diagnosis. Six chemicals were evaluated for inactivation of all carnation viruses in infected extracts. Commercial bleach at 7% (v/v) or NaOH at 0.5% (w/v) was found to inactivate all viruses after 60 s treatment in a systemic S. vaccaria bioassay. url: https://api.elsevier.com/content/article/pii/S0261219406003061 doi: 10.1016/j.cropro.2006.09.016 id: cord-003505-qr6ukfti author: Tabraue-Chávez, Mavys title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species date: 2019-03-06 words: 5655.0 sentences: 331.0 pages: flesch: 50.0 cache: ./cache/cord-003505-qr6ukfti.txt txt: ./txt/cord-003505-qr6ukfti.txt summary: In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. Once the abasic PNA probes hybridize with target sequences, the SMART-C-Biotin dynamic incorporation takes place, enabling the unequivocal identification of the parasite present in the amplicon sample, because of the unique colorimetric pattern that each Trypanosomatid amplicon generates. DNA amplicon products were denatured and then together with the dynamic chemistry reaction reagents added directly into the internal column of the Spin-Tube that supports the nylon membrane for the color-development assay (Fig. 4) . 20 ng of human gDNA were used as PCR template for its amplification with the set of primers described in our study and neither colorimetric signals nor bands were detected using the Spin-Tube and capillary electrophoresis analysis respectively (Fig. 5 , column 2: 2A and 2B), hence probing the specificity when human gDNA is present. abstract: Leishmaniasis and Chagas disease are endemic in many countries, and re-emerging in the developed countries. A rapid and accurate diagnosis is important for early treatment for reducing the duration of infection as well as for preventing further potential health complications. In this work, we have developed a novel colorimetric molecular assay that integrates nucleic acid analysis by dynamic chemistry (ChemNAT) with reverse dot-blot hybridization in an array format for a rapid and easy discrimination of Leishmania major and Trypanosoma cruzi. The assay consists of a singleplex PCR step that amplifies a highly homologous DNA sequence which encodes for the RNA component of the large ribosome subunit. The amplicons of the two different parasites differ between them by single nucleotide variations, known as “Single Nucleotide Fingerprint” (SNF) markers. The SNF markers can be easily identified by naked eye using a novel micro Spin-Tube device "Spin-Tube", as each of them creates a specific spot pattern. Moreover, the direct use of ribosomal RNA without requiring the PCR pre-amplification step is also feasible, further increasing the simplicity of the assay. The molecular assay delivers sensitivity capable of identifying up to 8.7 copies per µL with single mismatch specificity. The Spin-Tube thus represents an innovative solution providing benefits in terms of time, cost, and simplicity, all of which are crucial for the diagnosis of infectious disease in developing countries. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6403333/ doi: 10.1038/s41598-019-39946-0 id: cord-007009-4wbvdg1r author: Takahashi, Toru title: The First Identification and Retrospective Study of Severe Fever With Thrombocytopenia Syndrome in Japan date: 2014-03-15 words: 4686.0 sentences: 236.0 pages: flesch: 47.0 cache: ./cache/cord-007009-4wbvdg1r.txt txt: ./txt/cord-007009-4wbvdg1r.txt summary: Severe fever with thrombocytopenia syndrome (SFTS), an infectious disease with a high case-fatality rate, is caused by SFTS virus (SFTSV), a novel bunyavirus reported to be endemic to central and northeastern parts of China [1, 2] . Vero cells were inoculated with RT-PCR-positive patient sera for virus isolation, cultured for 4-7 days, and examined for SFTSV antigen detection by indirect immunofluorescence assay (IFA) with a polyclonal antibody raised against SFTSV recombinant NP (rNP; rabbit anti-SFTSV rNP serum), which was produced as follows. Physicians were asked to volunteer information if they had treated patients who satisfied the following case definition: (1) fever of >38°C; (2) gastrointestinal tract symptoms, such as nausea, vomiting, abdominal pain, diarrhea, and melena; (3) thrombocytopenia, with <100 × 10 9 platelets/L; (4) leukopenia, with <4 × 10 9 white blood cells/L; (5) elevated levels of aspartate aminotransferase, alanine aminotransferase, and lactate dehydrogenase; (6) absence of other causes; and (7) death or admission to an intensive care unit because of the severity symptoms. Detection of severe fever with thrombocytopenia syndrome virus (SFTSV) RNA in the right cervical lymph node by the in situ hybridization ATtailing method. abstract: Background. Severe fever with thrombocytopenia syndrome (SFTS) is caused by SFTS virus (SFTSV), a novel bunyavirus reported to be endemic in central and northeastern China. This article describes the first identified patient with SFTS and a retrospective study on SFTS in Japan. Methods. Virologic and pathologic examinations were performed on the patient's samples. Laboratory diagnosis of SFTS was made by isolation/genome amplification and/or the detection of anti-SFTSV immunoglobulin G antibody in sera. Physicians were alerted to the initial diagnosis and asked whether they had previously treated patients with symptoms similar to those of SFTS. Results. A female patient who died in 2012 received a diagnosis of SFTS. Ten additional patients with SFTS were then retrospectively identified. All patients were aged ≥50 years and lived in western Japan. Six cases were fatal. The ratio of males to females was 8:3. SFTSV was isolated from 8 patients. Phylogenetic analyses indicated that all of the Japanese SFTSV isolates formed a genotype independent to those from China. Most patients showed symptoms due to hemorrhage, possibly because of disseminated intravascular coagulation and/or hemophagocytosis. Conclusions. SFTS has been endemic to Japan, and SFTSV has been circulating naturally within the country. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107388/ doi: 10.1093/infdis/jit603 id: cord-325280-4whzcmqv author: Takizawa, Naoki title: Current landscape and future prospects of antiviral drugs derived from microbial products date: 2017-10-11 words: 6601.0 sentences: 365.0 pages: flesch: 34.0 cache: ./cache/cord-325280-4whzcmqv.txt txt: ./txt/cord-325280-4whzcmqv.txt summary: In this review, we summarize antiviral microbial products discovered by Institute of Microbial Chemistry (IMC) and discuss antiviral compounds against influenza virus and HBV, because these two viruses threaten global human health now and antiviral drug against these two viruses have been developed. THE CONTRIBUTIONS OF IMC TO ANTIVIRAL RESEARCH Nucleos(t)ide analogs are a major class of approved antiviral drugs that exert therapeutic effects through incorporation into viral DNA and RNA to inhibit virus replication. Viral polymerase complex is a promising target for the development of anti-influenza drugs, because transcription and replication are critical steps for virus propagation. Potential applications of microbial products in anti-HBV drug development Approved nucleos(t)ide analogs competitively inhibit DNA elongation of viral polymerase after the conversion to triphosphate form by cellular enzymes. abstract: Viral infections are a major global health threat. Over the last 50 years, significant efforts have been devoted to the development of antiviral drugs and great success has been achieved for some viruses. However, other virus infections, such as epidemic influenza, still spread globally and new threats continue to arise from emerging and re-emerging viruses and drug-resistant viruses. In this review, the contributions of microbial products isolated in Institute of Microbial Chemistry for antiviral research are summarized. In addition, the current state of development of antiviral drugs that target influenza virus and hepatitis B virus, and the future prospects for antivirals from natural products are described and discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/29018267/ doi: 10.1038/ja.2017.115 id: cord-254100-u6x5zd4i author: Taliansky, M.E. title: Involvement of the Plant Nucleolus in Virus and Viroid Infections: Parallels with Animal Pathosystems date: 2010-10-15 words: 13988.0 sentences: 662.0 pages: flesch: 40.0 cache: ./cache/cord-254100-u6x5zd4i.txt txt: ./txt/cord-254100-u6x5zd4i.txt summary: An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. As their name suggests, MPs are involved in virus spread in infected plants, and the potential role of fibrillarin in this process will be discussed in Section IV.B. The multifunctional PVA (potato virus A)-encoded viral genomelinked protein (VPg) is also able to interact with fibrillarin (Rajamäki and Bonfiglioli et al. abstract: The nucleolus is a dynamic subnuclear body with roles in ribosome subunit biogenesis, mediation of cell-stress responses, and regulation of cell growth. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. This chapter will highlight studies showing how plant viruses recruit nucleolar functions to facilitate virus translation and replication, virus movement and assembly of virus-specific ribonucleoprotein (RNP) particles, and to counteract plant host defense responses. Plant viruses also provide a valuable tool to gain new insights into novel nucleolar functions and processes. Investigating the interactions between plant viruses and the nucleolus will facilitate the design of novel strategies to control plant virus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/20951872/ doi: 10.1016/b978-0-12-385034-8.00005-3 id: cord-322062-nnefbeo6 author: Tam, Albert W. title: Hepatitis E virus (HEV): Molecular cloning and sequencing of the full-length viral genome date: 1991-11-30 words: 5738.0 sentences: 296.0 pages: flesch: 49.0 cache: ./cache/cord-322062-nnefbeo6.txt txt: ./txt/cord-322062-nnefbeo6.txt summary: We now report on the molecular cloning and sequencing of the complete HEV (Burma; B) viral genome together with the deduced amino acid sequences of viral-encoded proteins General perspectives on the genetic organization of the virus, as deduced from sequence and open reading frame analyses, indicate that HEV bears some similarity to the caliciviridae but may represent a new class of nonenveloped RNA virus. Bife was chosen as the RNA source for cDNA synthesis because it contained relatively large numbers of virus particles when HEV cDNA clones were identified from libraries made from randomly primed cyno bile (solid square), or from cyno liver after priming by oligo-dT (solid circle), random sequence hexamers (open circle) and HEV-sequence specific oligonucleotides (open square). The presence of HEV-specific subgenomic RNAs localized to the 3'' one-third of the genome suggests that these may be the transcripts from which these 3'' end ORFs are expressed and is indicative of a unique expression strategy among nonenveloped positive-sense RNA viruses infecting humans. abstract: Abstract We have recently described the cloning of a portion of the hepatitis E virus (HEV) and confirmed its etiologic association with enterically transmitted (waterborne, epidemic) non-A, non-B hepatitis. The virus consists of a single-stranded, positive-sense RNA genome of approximately 7.5 kb, with a polyadenylated 3' end. We now report on the cloning and nucleotide sequencing of an overlapping, contiguous set of cDNA clones representing the entire genome of the HEV Burma strain [HEV(B)]. The largest open reading frame extends approximately 5 kb from the Fend and contains the RNA-directed RNA polymerase and nucleoside triphosphate binding motifs. The second major open reading frame (ORF2) begins 37 by downstream of the first and extends approximately 2 kb to the termination codon present 65 by from the 3' terminal stretch of poly(A) residues. ORF2 contains a consensus signal peptide sequence at its amino terminus and a capsid-like region with a high content of basic amino acids similar to that seen with other virus capsid proteins. A third open reading frame partially overlaps the first and second and encompasses only 369 bp. In addition to the 7.5-kb full-length genomic transcript, two subgenomic polyadenylated messages of approximately 3.7 and 2.0 kb were detected in infected liver using a probe from the 3' third of the genome. The genomic organization of the virus is consistent with the Fend encoding nonstructural and the 3' end encoding the viral structural gene(s). The expression strategy of the virus involves the use of three different open reading frames and at least three different transcripts. HEV was previously determined to be a nonenveloped particle with a diameter of 27–34 nm. These findings on the genetic organization and expression strategy of HEV suggest that it is the prototype human pathogen for a new class of RNA virus or perhaps a separate genus within the Caliciviridae family url: https://www.ncbi.nlm.nih.gov/pubmed/1926770/ doi: 10.1016/0042-6822(91)90760-9 id: cord-294718-n3gx862b author: Tam, Patrick C K title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) date: 2020-05-30 words: 1606.0 sentences: 135.0 pages: flesch: 61.0 cache: ./cache/cord-294718-n3gx862b.txt txt: ./txt/cord-294718-n3gx862b.txt summary: title: Detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in human breast milk of a mildly symptomatic patient with coronavirus disease 2019 (COVID-19) Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. The first sampling of human milk occurred five days following maternal symptom onset with no episodes of breastfeeding in those five days prior to collection of the sample. An additional six samples of human milk were collected with one further sample demonstrating detectable SARS-COV-2 RNA (Figure 1 ). These samples continued to have detectable RNA sixty-six days following infant symptom onset (Figure 1 ). To our knowledge, this is the first case of detectable SARS-CoV-2 RNA from human milk in a patient with COVID-19. abstract: SARS-CoV-2 is a novel coronavirus and causative pathogen to the pandemic illness COVID-19. Although RNA has been detected in various clinical samples, no reports to date have documented SARS-CoV-2 in human milk. This case report describes an actively breastfeeding patient with COVID-19 infection with detectable viral RNA in human milk. url: https://doi.org/10.1093/cid/ciaa673 doi: 10.1093/cid/ciaa673 id: cord-353810-mf753ae9 author: Tan, Cedric Chih Shen title: A novel method for the capture-based purification of whole viral native RNA genomes date: 2019-04-08 words: 5929.0 sentences: 352.0 pages: flesch: 54.0 cache: ./cache/cord-353810-mf753ae9.txt txt: ./txt/cord-353810-mf753ae9.txt summary: This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes. Based on the mapping rates to human and DENV1 reference genomes for pre and post-capture groups, shown in Table 2 , purification factor was calculated to be 272-fold. The minimum coverage required for variant calling was, as described above, benchmarked to that of Illumina reads so that the effectiveness of our capture-based purification method could be more accurately evaluated based on the higher error read rates of direct RNA sequencing technology. Indeed, after comparison of the postcapture and concentrated post-capture sequencing runs (Table 2) , the 2.5-fold increase in the percentage of reads mapping to DENV1 suggests that scaling our method greatly improved the signal-to-noise ratio of this particular downstream RNA assay. abstract: Current technologies for targeted characterization and manipulation of viral RNA primarily involve amplification or ultracentrifugation with isopycnic gradients of viral particles to decrease host RNA background. The former strategy is non-compatible for characterizing properties innate to RNA strands such as secondary structure, RNA–RNA interactions, and also for nanopore direct RNA sequencing involving the sequencing of native RNA strands. The latter strategy, ultracentrifugation, causes loss in genomic information due to its inability to retrieve unassembled viral RNA. To address this, we developed a novel application of current nucleic acid hybridization technologies for direct characterization of RNA. In particular, we modified a current enrichment protocol to capture whole viral native RNA genomes for downstream RNA assays to circumvent the abovementioned problems. This technique involves hybridization of biotinylated baits at 500 nucleotides (nt) intervals, stringent washes and release of free native RNA strands using DNase I treatment, with a turnaround time of about 6 h 15 min. RT-qPCR was used as the primary proof of concept that capture-based purification indeed removes host background. Subsequently, capture-based purification was applied to direct RNA sequencing as proof of concept that capture-based purification can be coupled with downstream RNA assays. We report that this protocol was able to successfully purify viral RNA by 561- to 791-fold. We also report that application of this protocol to direct RNA sequencing yielded a reduction in human host RNA background by 1580-fold, a 99.91% recovery of viral genome with at least 15× coverage, and a mean coverage across the genome of 120×. This report is, to the best of our knowledge, the first description of a capture-based purification method for assays that involve direct manipulation or characterisation of native RNA. This report also describes a successful application of capture-based purification as a direct RNA sequencing strategy that addresses certain limitations of current strategies in sequencing RNA viral genomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13568-019-0772-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30963294/ doi: 10.1186/s13568-019-0772-y id: cord-003676-kr4o8hoc author: Tan, Chee Wah title: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans date: 2019-05-28 words: 3944.0 sentences: 217.0 pages: flesch: 55.0 cache: ./cache/cord-003676-kr4o8hoc.txt txt: ./txt/cord-003676-kr4o8hoc.txt summary: title: Serological evidence and experimental infection of cynomolgus macaques with pteropine orthoreovirus reveal monkeys as potential hosts for transmission to humans In this study, we screened 517 cynomolgus macaques caught in Singapore for evidence of exposure to PRV3M (also known as Melaka virus), which was first isolated from human patients in Melaka, Malaysia. We provide evidence that PRV exposure in the macaque population in Singapore occurs at a relatively high prevalence and this study suggests that cynomolgus macaques may be an intermediate or reservoir host for PRVs. Pteropine orthoreoviruses (PRVs) are a group of emerging bat-borne viruses, belonging to the genus Orthoreovirus within the family Reoviridae. Given the cross-species transmission of PRVs and frequent human-monkey interaction in Singapore and surrounding regions, we initiated this study to determine the seroprevalence of PRV3M in wild cynomolgus macaques and to examine the susceptibility of cynomolgus macaques to experimental infection with PRV3M and their potential role in acting as hosts facilitating cross-species transmission. abstract: Pteropine orthoreoviruses (PRV) are emerging bat-borne viruses with proven zoonotic transmission. We recently demonstrated human exposure to PRV in Singapore, which together with previous reports from Malaysia and Vietnam suggest that human infection of PRV may occur periodically in the region. This raises the question whether bats are the only sources of human infection. In this study, we screened 517 cynomolgus macaques caught in Singapore for evidence of exposure to PRV3M (also known as Melaka virus), which was first isolated from human patients in Melaka, Malaysia. We found that 67 serum samples were PRV3M positive by ELISA and 34 were also positive by virus neutralization assay. To investigate whether monkeys could act as hosts for PRV transmission, we experimentally infected cynomolgus macaques with PRV3M and housed these animals with uninfected monkeys. Although no clinical signs of infection were observed in infected animals, viral RNA was detected in nasal and rectal swabs and all infected macaques seroconverted. Additionally, one of the uninfected animals seroconverted, implying active shedding and transmission of PRV3M. We provide evidence that PRV exposure in the macaque population in Singapore occurs at a relatively high prevalence and this study suggests that cynomolgus macaques may be an intermediate or reservoir host for PRVs. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542153/ doi: 10.1080/22221751.2019.1621668 id: cord-268718-tt07cwrf author: Tan, Heng Wee title: Angiotensin‐converting enzyme 2: The old door for new severe acute respiratory syndrome coronavirus 2 infection date: 2020-06-30 words: 6346.0 sentences: 400.0 pages: flesch: 52.0 cache: ./cache/cord-268718-tt07cwrf.txt txt: ./txt/cord-268718-tt07cwrf.txt summary: 54 Virus infectivity study has indicated that the SARS-CoV-2 is able to utilize ACE2 of human, Chinese horseshoe bats, civet, and pig but was not able to use mouse ACE2. The roles of ACE2 expression in SARS-CoV-2 pathogenesis and human COVID-19 susceptibility are largely unknown. B, ACE2 expression in lung cancer patients with different smoking histories analyzed using similar methods as described previously 106 other symptoms in addition to respiratory symptoms, suggesting that SARS-CoV-2 could perhaps infect other organs (Figure 3 ). 118 In addition to sputum, SARS-CoV-2 RNA has been detected in the stools of a COVID-19 patient, 119 F I G U R E 3 Tissue distribution of angiotensin-converting enzyme 2 (ACE2) expression and potential COVID-19 susceptibility. Expression of elevated levels of proinflammatory cytokines in SARS-CoV-infected ACE2 + cells in SARS patients: relation to the acute lung injury and pathogenesis of SARS abstract: Coronavirus (CoV) disease 2019 (COVID‐19) is an ongoing pandemic caused by severe acute respiratory syndrome CoV 2 (SARS‐CoV‐2). The highly contagious SARS‐CoV‐2 belongs to the genus Betacoronavirus, and it is phylogenetically closely related to SARS‐CoV, a human CoV that caused an outbreak back in 2002 to 2003. Both SARS‐CoV‐2 and SARS‐CoV enter human cells via the interactions between viral crown‐like spike protein and human angiotensin‐converting enzyme 2 (ACE2) receptor. Here, we aim to review the involvement of ACE2 in human CoV infections by discussing the roles of ACE2 in CoV evolution, cross‐species transmissibility, and COVID‐19 susceptibility. We also provide our perspectives on COVID‐19 treatment and prevention. url: https://www.ncbi.nlm.nih.gov/pubmed/32602627/ doi: 10.1002/rmv.2122 id: cord-003898-y6zpvw84 author: Tan, Kai Sen title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications date: 2019-08-27 words: 7671.0 sentences: 386.0 pages: flesch: 44.0 cache: ./cache/cord-003898-y6zpvw84.txt txt: ./txt/cord-003898-y6zpvw84.txt summary: title: RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications The aim of this study was to utilize RNA sequencing (RNAseq) technology to not only reveal the hNEC responses (from multiple individuals) against influenza infection, but also to identify those genes with high magnitude changes to serve as potential reference markers of the innate responses of influenza infection. After deriving the transcriptomes by RNAseq, we then further investigated whether the changes in expression of genes resulted in alterations in secretory cytokines and chemokines early in the infection of hNECs. Initially, we detected significant reductions in multiple cytokines at 8 hpi, with the exception of IL-15 which was increased ( Figure S2 ). In conclusion, RNAseq technology allowed us to accurately quantify the magnitude of gene expression changes, as well as the relevant enriched pathways during H3N2 influenza virus infection of hNECs, which can serve as a baseline for future clinical studies. abstract: The human nasal epithelium is the primary site of exposure to influenza virus, the initiator of host responses to influenza and the resultant pathologies. Influenza virus may cause serious respiratory infection resulting in major complications, as well as severe impairment of the airways. Here, we elucidated the global transcriptomic changes during H3N2 infection of human nasal epithelial cells from multiple individuals. Using RNA sequencing, we characterized the differentially-expressed genes and pathways associated with changes occurring at the nasal epithelium following infection. We used in vitro differentiated human nasal epithelial cell culture model derived from seven different donors who had no concurrent history of viral infections. Statistical analysis highlighted strong transcriptomic signatures significantly associated with 24 and 48 h after infection, but not at the earlier 8-h time point. In particular, we found that the influenza infection induced in the nasal epithelium early and altered responses in interferon gamma signaling, B-cell signaling, apoptosis, necrosis, smooth muscle proliferation, and metabolic alterations. These molecular events initiated at the infected nasal epithelium may potentially adversely impact the airway, and thus the genes we identified could serve as potential diagnostic biomarkers or therapeutic targets for influenza infection and associated disease management. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770044/ doi: 10.3390/cells8090986 id: cord-012552-porty653 author: Tan, Kun title: The role of the NMD factor UPF3B in olfactory sensory neurons date: 2020-08-10 words: 11512.0 sentences: 600.0 pages: flesch: 52.0 cache: ./cache/cord-012552-porty653.txt txt: ./txt/cord-012552-porty653.txt summary: Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. We identified UPF3B-regulated genes in mOSNs by performing RNA-seq analysis on FACSpurified mOSNs (YFP+ cells) from R26-eYFP; Omp-Cre mice (Figure 1-figure supplement 1B) . Among the antimicrobial genes expressed and upregulated in Upf3b-null OSN precursors and OSNs was Camp (also known as ''Cramp''), which encodes a member of the cathelicidin family of antimicrobial peptides that has an important role in the defense against microbial infections, and functions in cell chemotaxis, immune mediator induction, and inflammatory response regulation (Zhang and Gallo, 2016) . abstract: The UPF3B-dependent branch of the nonsense-mediated RNA decay (NMD) pathway is critical for human cognition. Here, we examined the role of UPF3B in the olfactory system. Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. UPF3B also regulates the expression of a large cadre of antimicrobial genes in OSNs, and promotes the selection of specific olfactory receptor (Olfr) genes for expression in mature OSNs (mOSNs). RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. Together, our data provides a valuable resource for the olfactory field and insights into the roles of NMD in vivo. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7452722/ doi: 10.7554/elife.57525 id: cord-297092-oq14cwka author: Tan, Shaoyuan title: Characterization of Emerging Swine Viral Diseases through Oxford Nanopore Sequencing Using Senecavirus A as a Model date: 2020-10-07 words: 6982.0 sentences: 332.0 pages: flesch: 53.0 cache: ./cache/cord-297092-oq14cwka.txt txt: ./txt/cord-297092-oq14cwka.txt summary: This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases. For the sequencing of cell culture samples, raw pass reads were mapped to the SVA reference genome (GenBank: MN164664) using Minimap2 [34] , then analyzed using Qualimap [35] , generating raw error rates and coverage information which was then visualized using GraphPad prism software (GraphPad Software, San Diego, CA, USA). After determining the consensus generation strategies for both sequencing methods, optimization was performed in terms of total input sequencing yield and the pre-treatment of raw reads using the cell culture virus in which the whole genome sequence was already known. In order to evaluate and compare the general performance of DRS and PCS for viral whole genome recovery, two whole genome sequencing runs using a cell culture-grown virus with a known reference sequence were carried out for each method (Table 1 ). abstract: Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the growing concern about SVA, there is a lack of preventive and diagnostic strategies, which is also a problem for all emerging infectious diseases. Using SVA as a model, we demonstrated that Oxford Nanopore MinION sequencing could be used as a robust tool for the investigation and surveillance of emerging viral diseases. Our results identified that MinION sequencing allowed for rapid, unbiased pathogen detection at the species and strain level for clinical cases. SVA whole genome sequences were generated using both direct RNA sequencing and PCR-cDNA sequencing methods, with an optimized consensus accuracy of 94% and 99%, respectively. The advantages of direct RNA sequencing lie in its shorter turnaround time, higher analytical sensitivity and its quantitative relationship between input RNA and output sequencing reads, while PCR-cDNA sequencing excelled at creating highly accurate sequences. This study developed whole genome sequencing methods to facilitate the control of SVA and provide a reference for the timely detection and prevention of other emerging infectious diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/33036361/ doi: 10.3390/v12101136 id: cord-269150-d1sgnxc0 author: Tan, Yong Wah title: Binding of the 5′-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription date: 2012-02-22 words: 6977.0 sentences: 346.0 pages: flesch: 53.0 cache: ./cache/cord-269150-d1sgnxc0.txt txt: ./txt/cord-269150-d1sgnxc0.txt summary: In a screen based on a yeast three-hybrid system using the 5′-untranslated region (5′-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. In this study, we describe the interaction of a cellular protein, MADP1 (zinc finger CCHC-type and RNA binding motif 1) with the 5 0 -UTR of IBV and SARS-CoV, using yeast-based three hybrid screen (34) and RNA-binding assays. Using indirect immunofluorescence, we confirmed that MADP1, despite being reported as a nuclear protein (35) , was detected in the cytoplasm of virus-infected cells and partially co-localized with the RTCs. Upon silencing of MADP1 using siRNA, viral RNA synthesis on general has been affected, resulting in a lower replication efficiency and infectivity. abstract: Coronaviruses RNA synthesis occurs in the cytoplasm and is regulated by host cell proteins. In a screen based on a yeast three-hybrid system using the 5′-untranslated region (5′-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. This interaction was subsequently confirmed in coronavirus infectious bronchitis virus (IBV). The specificity of the interaction between MADP1 and the 5′-UTR of IBV was investigated and confirmed by using an RNA pull-down assay. The RNA-binding domain was mapped to the N-terminal region of MADP1 and the protein binding sequence to stem–loop I of IBV 5′-UTR. MADP1 was found to be translocated to the cytoplasm and partially co-localized with the viral replicase/transcriptase complexes (RTCs) in IBV-infected cells, deviating from its usual nuclear localization in a normal cell using indirect immunofluorescence. Using small interfering RNA (siRNA) against MADP1, defective viral RNA synthesis was observed in the knockdown cells, therefore indicating the importance of the protein in coronaviral RNA synthesis. url: https://doi.org/10.1093/nar/gks165 doi: 10.1093/nar/gks165 id: cord-255252-md0avnqg author: Tang, Julian W. title: Quantitative temporal‐spatial distribution of severe acute respiratory syndrome‐associated coronavirus (SARS‐CoV) in post‐mortem tissues date: 2007-07-02 words: 5317.0 sentences: 326.0 pages: flesch: 70.0 cache: ./cache/cord-255252-md0avnqg.txt txt: ./txt/cord-255252-md0avnqg.txt summary: SARS‐CoV viral load and SARS‐CoV/GAPDH RNA ratio for each organ type were related to four time durations: onset of illness to death, death to post‐mortem tissue sampling, and total durations of treatment with ribavirin and hydrocortisone. Post-mortem tissues were collected with great care from the major organs including heart, kidney, liver, spleen, lung, small bowel, psoas (skeletal) muscle, and bone marrow. Figures 1-6 show the results, using semi-log plots, for each organ: heart, kidney, liver, spleen, lung, and small bowel, respectively, for SARS-CoV, GAPDH and the SARS-CoV/GAPDH RNA ratio. In the organspecific viral load results, the overall picture made up from the data points from the seven different patients with different durations of SARS illness, generally, the SARS-CoV/GAPDH RNA ratio never reached above one in heart, kidney, liver, and spleen tissue for all x-axis parameters analyzed. abstract: Few post‐mortem studies have been performed on patients who have died from severe acute respiratory syndrome (SARS). No studies have examined how the SARS‐associated coronavirus (SARS‐CoV) loads in different organs with respect to time, post‐mortem. The aim of this study was to determine the quantitative temporal‐spatial distribution of SARS‐CoV in the post‐mortem tissue samples of seven patients. Quantitation of a house‐keeping gene, glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) was undertaken to standardize the amount of tissue tested. SARS‐CoV viral load and SARS‐CoV/GAPDH RNA ratio for each organ type were related to four time durations: onset of illness to death, death to post‐mortem tissue sampling, and total durations of treatment with ribavirin and hydrocortisone. The SARS‐CoV/GAPDH RNA ratio remained relatively stable in most organ tissue types for all these time durations. The ratio reached the highest value of equal to or greater than one for lung and small bowel, whereas those for heart, liver, spleen, and kidney were always less than one. It is concluded that SARS‐CoV viral loads in these organs remain relatively stable, post‐mortem. This quantitative assessment further supports SARS‐CoV has a specific tropism for the human respiratory and gastrointestinal tracts, which may be related to the density of SARS‐CoV receptors. J. Med. Virol. 79:1245–1253, 2007. © Wiley‐Liss, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/17607787/ doi: 10.1002/jmv.20873 id: cord-013784-zhgjmt2j author: Tang, Min title: Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions date: 2020-06-04 words: 13704.0 sentences: 794.0 pages: flesch: 45.0 cache: ./cache/cord-013784-zhgjmt2j.txt txt: ./txt/cord-013784-zhgjmt2j.txt summary: To move beyond serum-free sphere culture-based models, we utilized a DLP-based rapid 3D bioprinting system to generate 3D tri-culture or tetra-culture glioblastoma tissue models, with a background "normal brain" made up of NPCs and astrocytes and a tumor mass generated by GSCs, with or without macrophage, using brain-specific extracellular matrix (ECM) materials (Fig. 1a ). 35 While patient-derived glioblastoma cells grown under serum-free conditions enrich for stem-like tumor cells (GSCs) that form spheres and more closely replicate transcriptional profiles and invasive potential than standard culture conditions, we previously demonstrated that spheres display differential transcriptional profiles and cellular dependencies in an RNA interference screen compared to in vivo xenografts. [49] [50] [51] g Therapeutic efficacy prediction of drugs in all cancer cells in the CTRP dataset based on differentially expressed genes between the 3D tetra-culture model and GSCs grown in sphere culture as defined by RNA-seq. abstract: Brain tumors are dynamic complex ecosystems with multiple cell types. To model the brain tumor microenvironment in a reproducible and scalable system, we developed a rapid three-dimensional (3D) bioprinting method to construct clinically relevant biomimetic tissue models. In recurrent glioblastoma, macrophages/microglia prominently contribute to the tumor mass. To parse the function of macrophages in 3D, we compared the growth of glioblastoma stem cells (GSCs) alone or with astrocytes and neural precursor cells in a hyaluronic acid-rich hydrogel, with or without macrophage. Bioprinted constructs integrating macrophage recapitulate patient-derived transcriptional profiles predictive of patient survival, maintenance of stemness, invasion, and drug resistance. Whole-genome CRISPR screening with bioprinted complex systems identified unique molecular dependencies in GSCs, relative to sphere culture. Multicellular bioprinted models serve as a scalable and physiologic platform to interrogate drug sensitivity, cellular crosstalk, invasion, context-specific functional dependencies, as well as immunologic interactions in a species-matched neural environment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608409/ doi: 10.1038/s41422-020-0338-1 id: cord-352768-16vgnq14 author: Tang, Qingquan title: Application of siRNA Against SARS in the Rhesus Macaque Model date: 2008 words: 4389.0 sentences: 274.0 pages: flesch: 48.0 cache: ./cache/cord-352768-16vgnq14.txt txt: ./txt/cord-352768-16vgnq14.txt summary: Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen''s genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. A pair of siRNAs showing prominent prophylactic and therapeutic activities in the cell culture study (29), referred to as siSC2 and siSC5, were further evaluated in vivo, first in mice using a reporter gene assay and subsequently using a clinically acceptable intranasal administration in the recently established rhesus macaque SARS model (23-26). abstract: Containment of the SARS coronavirus (SCV) outbreak was accompanied by the rapid characterization of this new pathogen's genome sequence in 2003, encouraging the development of anti-SCV therapeutics using short interfering RNA (siRNA) inhibitors. A pair of siRNA duplexes identified as potent SCV inhibitors in vitro was evaluated for in vivo efficacy and safety in a rhesus macaque SARS model using intranasal administration with clinical viable delivery carrier in three dosing regimens. Observations of SCV-induced SARS-like symptoms, measurements of SCV RNA presence in the respiratory tract, microscopic inspections of lung histopathology, and immunohistochemistry sections from 21 tested macaques consistently demonstrated siRNA-mediated anti-SCV activity. The prophylactic and therapeutic efficacies resulted in relief of animals from SCV infection-induced fever, diminished SCV in upper airway and lung alveoli, and milder acute diffuse alveoli damage (DAD). The dosages of siRNA used, 10 to 40 mg/kg, did not show any sign of siRNA-induced toxicity. These results support that a clinical investigation of this anti-SARS siRNA therapeutic agent is warranted. The study also illustrates the capability of siRNA to enable a massive reduction in development time for novel targeted therapeutic agents. We detail a representative example of large-mammal siRNA use. url: https://doi.org/10.1007/978-1-59745-191-8_11 doi: 10.1007/978-1-59745-191-8_11 id: cord-283998-whwksoxt author: Tannock, Gregory A. title: The RNA of human coronavirus OC-43 date: 1977-12-31 words: 3978.0 sentences: 213.0 pages: flesch: 57.0 cache: ./cache/cord-283998-whwksoxt.txt txt: ./txt/cord-283998-whwksoxt.txt summary: Abstract A homogeneous RNA complex with a sedimentation coefficient of 70 S and an apparent molecular weight of approximately 6.1 × 106 was released from purified 32P-labeled, mouse-brain-derived OC-43 virus after treatment with 1% sodium dodecyl sulfate (SDS) for 15 min at 23°. This suggests that (a) extensive nicking of a large RNA molecule has occurred during viral growth, due to ribonucleases which are inactivated during phenol extractions; (b) heterogeneity for OC-43 RNA is not due to internal ribonuclease activity and fragments are held together by noncovalent linkages much weaker than those present in the 70 S retroviral RNA complex, or by small proteins; or, most probably, (c) a combination of extensive nicking and weak noncovalent linkages results in the heterogeneous denaturation products. The RNA of avian infectious bronchitis virus (IBV) was first described by Tannock (1973) , who obtained from purified virions a highly heterogeneous array of RNA fragments using a phenol-sodium dodecyl sulfate (SDS) extraction procedure. abstract: Abstract A homogeneous RNA complex with a sedimentation coefficient of 70 S and an apparent molecular weight of approximately 6.1 × 106 was released from purified 32P-labeled, mouse-brain-derived OC-43 virus after treatment with 1% sodium dodecyl sulfate (SDS) for 15 min at 23°. The complex was highly susceptible to heat, releasing 4 S RNA fragments at 37° and breaking down to fragments of 4–70 S at 60°; it was also degraded by centrifugation through dimethyl sulfoxide gradients. Unlike tobacco mosaic virus or Rous sarcoma virus RNA, OC-43 RNA prepared by extraction with phenol-SDS or phenol-chloroform degraded into a range of fragments with coefficients of 15–55 S; 4 S RNA was also present as a minor component. This suggests that (a) extensive nicking of a large RNA molecule has occurred during viral growth, due to ribonucleases which are inactivated during phenol extractions; (b) heterogeneity for OC-43 RNA is not due to internal ribonuclease activity and fragments are held together by noncovalent linkages much weaker than those present in the 70 S retroviral RNA complex, or by small proteins; or, most probably, (c) a combination of extensive nicking and weak noncovalent linkages results in the heterogeneous denaturation products. url: https://api.elsevier.com/content/article/pii/004268227790126X doi: 10.1016/0042-6822(77)90126-x id: cord-001109-xs7df6a7 author: Tapia, Karla title: Defective Viral Genomes Arising In Vivo Provide Critical Danger Signals for the Triggering of Lung Antiviral Immunity date: 2013-10-31 words: 7169.0 sentences: 360.0 pages: flesch: 50.0 cache: ./cache/cord-001109-xs7df6a7.txt txt: ./txt/cord-001109-xs7df6a7.txt summary: We demonstrate that these defective viral genomes (DVGs) are generated naturally during respiratory infections in vivo even in mice lacking the type I IFN receptor, and their appearance coincides with the production of cytokines during infections with Sendai virus (SeV) or influenza virus. To further investigate the cellular mechanisms responsible for the efficient activation of the antiviral response by SeV DVGs, we evaluated the phosphorylation of transcription factors that are critical for the expression of type I IFNs in cells infected with equivalent amounts of infectious particles of a SeV strain Cantell stock containing high levels of copy-back DVGs (SeV Cantell HD) or with SeV Cantell depleted of DVGs (SeV Cantell LD). Based on the potent ability of SeV stocks containing a high content of copy-back DVGs to induce the host response to infection in vitro [23, 24, 25, 28] (Fig. 1 ) and on our prior reports of strong host responses to DVGs regardless of the presence of functional virus-encoded antagonists [23, 24] , we hypothesized that DVGs that arise in situ during viral infections provide essential stimuli to initiate an antiviral immune response. abstract: The innate immune response to viruses is initiated when specialized cellular sensors recognize viral danger signals. Here we show that truncated forms of viral genomes that accumulate in infected cells potently trigger the sustained activation of the transcription factors IRF3 and NF-κB and the production type I IFNs through a mechanism independent of IFN signaling. We demonstrate that these defective viral genomes (DVGs) are generated naturally during respiratory infections in vivo even in mice lacking the type I IFN receptor, and their appearance coincides with the production of cytokines during infections with Sendai virus (SeV) or influenza virus. Remarkably, the hallmark antiviral cytokine IFNβ is only expressed in lung epithelial cells containing DVGs, while cells within the lung that contain standard viral genomes alone do not express this cytokine. Together, our data indicate that DVGs generated during viral replication are a primary source of danger signals for the initiation of the host immune response to infection. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814336/ doi: 10.1371/journal.ppat.1003703 id: cord-027975-77544sed author: Tars, Kaspars title: ssRNA Phages: Life Cycle, Structure and Applications date: 2020-06-30 words: 11655.0 sentences: 582.0 pages: flesch: 55.0 cache: ./cache/cord-027975-77544sed.txt txt: ./txt/cord-027975-77544sed.txt summary: Several of the studied ssRNA characteristics, such as coat protein–RNA interactions and the ability to readily form virus-like particles in recombinant expression systems, have fueled many practical applications such as RNA labeling and tracking systems and vaccine development. Bacteriophages belonging to the family Leviviridae are among the simplest known viruses, exhibiting positive-sense single-stranded RNA (ssRNA) genomes of just 3.5-4.5 kilobases, typically encoding only 4 proteins. Due to their simplicity, ssRNA phages have been used as models to study various processes in molecular biology and virology, including translation repression, RNA-protein interactions and virus evolution. For quite some time, the only available structural information about protein-RNA interactions in ssRNA phage particles came from the studies of CP dimers in complex with a 19 nucleotide-long stem-loop fragment known as TR (translation repression) from the genome region located around the replicase start codon in bacteriophage MS2 ). abstract: ssRNA phages belonging to the family Leviviridae are among the tiniest viruses, infecting various Gram-negative bacteria by adsorption to their pilus structures. Due to their simplicity, they have been intensively studied as models for understanding various problems in molecular biology and virology. Several of the studied ssRNA characteristics, such as coat protein–RNA interactions and the ability to readily form virus-like particles in recombinant expression systems, have fueled many practical applications such as RNA labeling and tracking systems and vaccine development. In this chapter, we review the life cycle, structure and applications of these small yet fascinating viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7322243/ doi: 10.1007/978-3-030-45885-0_13 id: cord-103823-3rchp9yy author: Taufer, Michela title: RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology date: 2008-11-30 words: 10168.0 sentences: 462.0 pages: flesch: 50.0 cache: ./cache/cord-103823-3rchp9yy.txt txt: ./txt/cord-103823-3rchp9yy.txt summary: Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. Of course, the scientist who uses such an approach of sampling and rebuilding from segments to predict longer secondary structures has to benefit from the computing capabilities of such a framework without being required to cut and paste results from one code output to another, redirecting or reformatting output files (e.g., from FASTA to EMBL format) before forwarding them to the next step in the analysis, or dealing with distributed computer systems. RNAVLab addresses the challenges above by combining sampling of nucleotide sequences, predictions based on different codes and supported by grid computing technology, and analysis of large sets of secondary structures with different scientific scopes. abstract: Abstract As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family Nodaviridae. url: https://api.elsevier.com/content/article/pii/S0167819108000902 doi: 10.1016/j.parco.2008.08.002 id: cord-018164-h5k1zsyg author: Taylor, Milton W. title: What Is a Virus? date: 2014-07-22 words: 4769.0 sentences: 260.0 pages: flesch: 60.0 cache: ./cache/cord-018164-h5k1zsyg.txt txt: ./txt/cord-018164-h5k1zsyg.txt summary: Studies of viral replication indicate that most viruses self-assemble as a result of interactions between the viral proteins to form a viral capsid that interacts with the nucleic acid to form the whole. The viral proteins are produced in one part of the cell, the replicated nucleic acid in another, and somehow they find each other, interact, and form virus particles that are expelled from the cell. Indirect contact spread includes cases where mucus from a runny nose may get onto the hands, or virus may be left on a surface such as a doorknob, telephone, or countertops, and is picked up by a second individual, who then touches his eyes or nose, resulting in infection. Vector transmission is a very common means of transmission; the best studied cases include yellow fever, dengue virus, and West Nile fever-viruses all transmitted by mosquitoes. As many as 400 million people are infected annually by dengue virus, which is caused by any one of four related viruses transmitted by mosquitoes. abstract: Viruses are built from short sequences of nucleic acid, either DNA or RNA wrapped in a protein shell. Until the invention of the electron microscope, it was impossible to visualize a virus. The first viruses to be visualized were bacteriophage, which appeared to have a head and tail-like structure. Only the nucleic acid entered the bacterial cell through the tail. Animal viruses were described as spherical or rod-shaped; they were bound to receptors and were taken up by the cell. After the crystallization of the tobacco mosaic virus, there was much discussion as to whether viruses were “living” organisms; the controversy continues to this day. Although viruses were defined in part on the basis of size and filterability, viruses much larger than the traditional viruses have recently been isolated. Studies of viral replication indicate that most viruses self-assemble as a result of interactions between the viral proteins to form a viral capsid that interacts with the nucleic acid to form the whole. The viral replication cycle and synthesis is presented in this chapter. Viral classification into a Linnaean scheme has been proposed, but newer methods using nucleic acid homologies are changing classification. Viruses are spread in the human population by various means, including airborne particles, fecal-oral contact, clothing, insects, and contact with other animals (zoonosis). url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7122971/ doi: 10.1007/978-3-319-07758-1_2 id: cord-278482-j5zlismf author: Taylor, Raymond title: BCX4430 – A broad-spectrum antiviral adenosine nucleoside analog under development for the treatment of Ebola virus disease date: 2016-06-30 words: 2543.0 sentences: 131.0 pages: flesch: 47.0 cache: ./cache/cord-278482-j5zlismf.txt txt: ./txt/cord-278482-j5zlismf.txt summary: Summary The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. In a study in cynomolgus macaques infected with MARV [5] , 0/6 controls survived compared to 17/18 animals treated with a 15 mg/kg BD dose of The maximum viral load, as measured by quantitation of viral RNA copies in the peripheral blood, was reduced by ∼600-fold (geometric mean 0.008 × 10 9 compared to 4.79 × 10 9 copies/mL, p < 0.0005). The slope of the relationship of the dose of BCX4430 to both antiviral effect and survival in nonclinical models of lethal viral infections is steep. abstract: Summary The adenosine nucleoside analog BCX4430 is a direct-acting antiviral drug under investigation for the treatment of serious and life-threatening infections from highly pathogenic viruses, such as the Ebola virus. Cellular kinases phosphorylate BCX4430 to a triphosphate that mimics ATP; viral RNA polymerases incorporate the drug's monophosphate nucleotide into the growing RNA chain, causing premature chain termination. BCX4430 is active in vitro against many RNA viral pathogens, including the filoviruses and emerging infectious agents such as MERS-CoV and SARS-CoV. In vivo, BCX4430 is active after intramuscular, intraperitoneal, and oral administration in a variety of experimental infections. In nonclinical studies involving lethal infections with Ebola virus, Marburg virus, Rift Valley fever virus, and Yellow Fever virus, BCX4430 has demonstrated pronounced efficacy. In experiments conducted in several models, both a reduction in the viral load and an improvement in survival were found to be related to the dose of BCX4430. A Phase 1 clinical trial of intramuscular administration of BCX4430 in healthy subjects is currently ongoing. url: https://api.elsevier.com/content/article/pii/S1876034116300193 doi: 10.1016/j.jiph.2016.04.002 id: cord-350533-fp1ctpax author: Tchesnokov, Egor P. title: Independent inhibition of the polymerase and deubiquitinase activities of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein date: 2020-06-04 words: 6033.0 sentences: 346.0 pages: flesch: 50.0 cache: ./cache/cord-350533-fp1ctpax.txt txt: ./txt/cord-350533-fp1ctpax.txt summary: Moreover, we identified 2''-deoxy-2''-amino-CTP as a novel inhibitor of CCHFV RdRp. We further show that CC.4 inhibits the CCHFV-associated DUB activity of the full-length L protein and the isolated DUB domain to a similar extent. Inhibition of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein ribavirin-TP or favipiravir-TP are also used as substrates opposite template C (Fig 3, middle) . Inhibition of the Crimean-Congo Hemorrhagic Fever Virus full-length L-protein CCHFV L full-length protein and the isolated OTU domain cleave ubiquitin-AMC in a time dependent manner with similar velocities illustrated by the slopes of the initial linear portion of product formation (Fig 8B) . The identification of small molecule compounds that inhibit viral RNA synthesis relies on the availability of recombinant L protein, which is a multifunctional protein with a high molecular weight of~450 kDa. Here we report the expression of full-length CCHFV L protein that possess active RdRp and DUB domains. abstract: BACKGROUND: The Crimean-Congo hemorrhagic fever virus (CCHFV) is a segmented negative-sense RNA virus that can cause severe human disease. The World Health Organization (WHO) has listed CCHFVas a priority pathogen with an urgent need for enhanced research activities to develop effective countermeasures. Here we adopted a biochemical approach that targets the viral RNA-dependent RNA polymerase (RdRp). The CCHFV RdRp activity is part of a multifunctional L protein that is unusually large with a molecular weight of ~450 kDa. The CCHFV L-protein also contains an ovarian tumor (OTU) domain that exhibits deubiquitinating (DUB) activity, which was shown to interfere with innate immune responses and viral replication. We report on the expression, characterization and inhibition of the CCHFV full-length L-protein and studied both RNA synthesis and DUB activity. METHODOLOGY/PRINCIPLE FINDINGS: Recombinant full-length CCHFV L protein was expressed in insect cells and purified to near homogeneity using affinity chromatography. RdRp activity was monitored with model primer/templates during elongation in the presence of divalent metal ions. We observed a 14-mer full length RNA product as well as the expected shorter products when omitting certain nucleotides from the reaction mixture. The D2517N mutation of the putative active site rendered the enzyme inactive. Inhibition of RNA synthesis was studies with the broad-spectrum antivirals ribavirin and favipiravir that mimic nucleotide substrates. The triphosphate form of these compounds act like ATP or GTP; however, incorporation of ATP or GTP is markedly favored over the inhibitors. We also studied the effects of bona fide nucleotide analogues 2’-deoxy-2’-fluoro-CTP (FdC) and 2’-deoxy-2’-amino-CTP and demonstrate increased inhibitory effects due to higher rates of incorporation. We further show that the CCHFV L full-length protein and the isolated OTU domain cleave Lys48- and Lys63-linked polyubiqutin chains. Moreover, the ubiquitin analogue CC.4 inhibits the CCHFV-associated DUB activity of the full-length L protein and the isolated DUB domain to a similar extent. Inhibition of DUB activity does not affect elongation of RNA synthesis, and inhibition of RNA synthesis does not affect DUB activity. Both domains are functionally independent under these conditions. CONCLUSIONS/SIGNIFICANCE: The requirements for high biosafety measures hamper drug discovery and development efforts with infectious CCHFV. The availability of full-length CCHFV L-protein provides an important tool in this regard. High-throughput screening (HTS) campaigns are now feasible. The same enzyme preparations can be employed to identify novel polymerase and DUB inhibitors. url: https://www.ncbi.nlm.nih.gov/pubmed/32497085/ doi: 10.1371/journal.pntd.0008283 id: cord-102412-cnlvyey4 author: Tekman, Mehmet title: A single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework date: 2020-08-28 words: 6419.0 sentences: 300.0 pages: flesch: 53.0 cache: ./cache/cord-102412-cnlvyey4.txt txt: ./txt/cord-102412-cnlvyey4.txt summary: Results Here we outline several Galaxy workflows and learning resources for scRNA-seq, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The analysis of scRNA-seq within Galaxy was a two-pronged e ort concentrated on bringing high quality single-cell tools into Galaxy, and providing the necessary work ows and training to accompany them. The training pictographically guides users through the concepts of extracting cell barcodes from the protocol, explains the signi cance of UMIs in the process of read deduplication with illustrative examples, and instructs the user in the process of performing further quality controls on their data during the post-mapping process via RNA STAR and other tools that are native to Galaxy. A Galaxy-based training resource for single-cell RNA-sequencing quality control and analyses abstract: Background The vast ecosystem of single-cell RNA-seq tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically-driven methods needed to process and understand these ever-growing datasets. Results Here we outline several Galaxy workflows and learning resources for scRNA-seq, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows and trainings that not only enable users to perform one-click 10x preprocessing, but also empowers them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a wide range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal and clustering. The teaching resources cover an assortment of different concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal. Conclusions The reproducible and training-oriented Galaxy framework provides a sustainable HPC environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy Community provide a means for users to learn, publish and teach scRNA-seq analysis. Key Points Single-cell RNA-seq has stabilised towards 10x Genomics datasets. Galaxy provides rich and reproducible scRNA-seq workflows with a wide range of robust tools. The Galaxy Training Network provides tutorials for the processing of both 10x and non-10x datasets. url: https://doi.org/10.1101/2020.06.06.137570 doi: 10.1101/2020.06.06.137570 id: cord-266960-kyx6xhvj author: Temple, Mark D. title: Real-time audio and visual display of the Coronavirus genome date: 2020-10-02 words: 6780.0 sentences: 360.0 pages: flesch: 56.0 cache: ./cache/cord-266960-kyx6xhvj.txt txt: ./txt/cord-266960-kyx6xhvj.txt summary: The sonification of codons derived from all three reading frames of the viral RNA sequence in combination with sonified metadata provide the framework for this display. CONCLUSION: The auditory display in combination with real-time animation of the process of translation and transcription provide a unique insight into the large body of evidence describing the metabolism of the RNA genome. Audio generated from each of these sequence motifs and metadata were combined to create a complex auditory display to represent either transcription or translation. High resolution analysis of gene expression in Coronavirus genomes has detected ribosome protected fragments which map to non-canonical ORF''s, these may be novel protein-coding ORFs and short regulatory uORFs. The tool highlights the occurrence of one such uORF of 30 nucleotides (including the stop codon) in the 5′ untranslated region downstream of TRS1 [35] that is not documented in the GenBank metadata. In the Additional file 4: supplementary example ''Sonification Sub-genomic RNA'' the auditory display represents the process of transcription. abstract: BACKGROUND: This paper describes a web based tool that uses a combination of sonification and an animated display to inquire into the SARS-CoV-2 genome. The audio data is generated in real time from a variety of RNA motifs that are known to be important in the functioning of RNA. Additionally, metadata relating to RNA translation and transcription has been used to shape the auditory and visual displays. Together these tools provide a unique approach to further understand the metabolism of the viral RNA genome. This audio provides a further means to represent the function of the RNA in addition to traditional written and visual approaches. RESULTS: Sonification of the SARS-CoV-2 genomic RNA sequence results in a complex auditory stream composed of up to 12 individual audio tracks. Each auditory motive is derived from the actual RNA sequence or from metadata. This approach has been used to represent transcription or translation of the viral RNA genome. The display highlights the real-time interaction of functional RNA elements. The sonification of codons derived from all three reading frames of the viral RNA sequence in combination with sonified metadata provide the framework for this display. Functional RNA motifs such as transcription regulatory sequences and stem loop regions have also been sonified. Using the tool, audio can be generated in real-time from either genomic or sub-genomic representations of the RNA. Given the large size of the viral genome, a collection of interactive buttons has been provided to navigate to regions of interest, such as cleavage regions in the polyprotein, untranslated regions or each gene. These tools are available through an internet browser and the user can interact with the data display in real time. CONCLUSION: The auditory display in combination with real-time animation of the process of translation and transcription provide a unique insight into the large body of evidence describing the metabolism of the RNA genome. Furthermore, the tool has been used as an algorithmic based audio generator. These audio tracks can be listened to by the general community without reference to the visual display to encourage further inquiry into the science. url: https://doi.org/10.1186/s12859-020-03760-7 doi: 10.1186/s12859-020-03760-7 id: cord-265095-lf5j4ic7 author: Ten Dam, Edwin B. title: RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs date: 1990 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Ribosomal frameshifting on retroviral RNAs has been proposed to be mediated by slippage of two adjacent tRNAs into the — 1 direction at a specific heptanucleotide sequence. Here we report a computer-aided analysis of the structure around the established or putative frameshift sites in a number of retroviral, coronaviral, toroviral, and luteoviral RNAs and two dsRNA yeast viruses. In almost all cases a stable hairpin was predicted four to nine nucleotides downstream of the shifty heptanucleotide. More than half of the resulting hairpin loops give rise to potential pseudoknotting with sequences downstream of this hairpin. Especially in the case of the shifty heptanucleotides U UUA AAC and G GGA AAC, stable downstream pseudoknots are present. Indications were also found for the presence of pseudoknots downstream of amber stop condons at readthrough sites in some retroviral RNAs. url: https://www.ncbi.nlm.nih.gov/pubmed/2402881/ doi: 10.1007/bf00678404 id: cord-345413-bsd32j8r author: Terada, Yutaka title: Establishment of a Virulent Full-Length cDNA Clone for Type I Feline Coronavirus Strain C3663 date: 2019-08-02 words: 7979.0 sentences: 438.0 pages: flesch: 56.0 cache: ./cache/cord-345413-bsd32j8r.txt txt: ./txt/cord-345413-bsd32j8r.txt summary: To determine viral RNA replication in A72 cells, A72, MDCK, DH82, and Fcwf-4 cells were infected with rC3663-Nluc virus at an MOI of 0.01, followed by real-time RT-PCR analysis of RNA extracted at 24, 48, and 72 hpi. Next, we determined the levels of production of infectious virus particles from rC3663-Nluc-infected A72 cells by collecting the culture supernatants at 24, 48, and 72 hpi and measuring viral titers by plaque assays with Fcwf-4 cells (Fig. 3E ). Thus, to determine expression levels of sg N mRNA (sg mRNA6), total RNAs extracted from rC3663 virus-infected or mock-infected Fcwf-4 and A72 cells at 48 and 72 hpi were subjected to Northern blot analysis with a specific type I FCoV 3= untranslated region (3=UTR) probe (Fig. 5A) . We further examined the expression levels of viral sg mRNAs in cells infected with the parental C3663 strain or type I FCoV strain Yayoi using Northern blot analysis with specific RNA probes against the 3=-UTR. abstract: Feline infectious peritonitis (FIP) is one of the most important infectious diseases in cats and is caused by feline coronavirus (FCoV). Tissue culture-adapted type I FCoV shows reduced FIP induction in experimental infections, which complicates the understanding of FIP pathogenesis caused by type I FCoV. We previously found that the type I FCoV strain C3663 efficiently induces FIP in specific-pathogen-free cats through the naturally infectious route. In this study, we employed a bacterial artificial chromosome-based reverse genetics system to gain more insights into FIP caused by the C3633 strain. We successfully generated recombinant virus (rC3663) from Fcwf-4 cells transfected with infectious cDNA that showed growth kinetics similar to those shown by the parental virus. Next, we constructed a reporter C3663 virus carrying the nanoluciferase (Nluc) gene to measure viral replication with high sensitivity. The inhibitory effects of different compounds against rC3663-Nluc could be measured within 24 h postinfection. Furthermore, we found that A72 cells derived from canine fibroblasts permitted FCoV replication without apparent cytopathic effects. Thus, our reporter virus is useful for uncovering the infectivity of type I FCoV in different cell lines, including canine-derived cells. Surprisingly, we uncovered aberrant viral RNA transcription of rC3663 in A72 cells. Overall, we succeeded in obtaining infectious cDNA clones derived from type I FCoV that retained its virulence. Our recombinant FCoVs are powerful tools for increasing our understanding of the viral life cycle and pathogenesis of FIP-inducing type I FCoV. IMPORTANCE Feline coronavirus (FCoV) is one of the most significant coronaviruses, because this virus induces feline infectious peritonitis (FIP), which is a lethal disease in cats. Tissue culture-adapted type I FCoV often loses pathogenicity, which complicates research on type I FCoV-induced feline infectious peritonitis (FIP). Since we previously found that type I FCoV strain C3663 efficiently induces FIP in specific-pathogen-free cats, we established a reverse genetics system for the C3663 strain to obtain recombinant viruses in the present study. By using a reporter C3663 virus, we were able to examine the inhibitory effect of 68 compounds on C3663 replication in Fcwf-4 cells and infectivity in a canine-derived cell line. Interestingly, one canine cell line, A72, permitted FCoV replication but with low efficiency and aberrant viral gene expression. url: https://jvi.asm.org/content/jvi/93/21/e01208-19.full.pdf doi: 10.1128/jvi.01208-19 id: cord-339288-y8woqsii author: Tews, Birke Andrea title: Self-Replicating RNA date: 2016-06-11 words: 7567.0 sentences: 338.0 pages: flesch: 44.0 cache: ./cache/cord-339288-y8woqsii.txt txt: ./txt/cord-339288-y8woqsii.txt summary: Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. Three years later, the performance of poliovirus cDNA clones could be significantly ameliorated through the introduction of SV40 transcription and replication signals and transfection of the resulting construct into cells expressing the SV40 large T antigen [14] , thus ensuring replication of the DNA-plasmid in eukaryotic cells leading to a higher yield of viral RNA and recovered virus (Fig. 2, left part) . The resulting virus CP7_E2alf was only able to infect pigs and thus displayed the Fig. 3 Generation of a chimeric viral genome from two parental RNAs. On the level of a cDNA construct, one protein-coding sequence is replaced by the corresponding gene of the other virus (principle used for the pestivirus vaccine CP7_E2alf [58] ). abstract: Self-replicating RNA derived from the genomes of positive strand RNA viruses represents a powerful tool for both molecular studies on virus biology and approaches to novel safe and effective vaccines. The following chapter summarizes the principles how such RNAs can be established and used for design of vaccines. Due to the large variety of strategies needed to circumvent specific pitfalls in the design of such constructs the technical details of the experiments are not described here but can be found in the cited literature. url: https://www.ncbi.nlm.nih.gov/pubmed/27987141/ doi: 10.1007/978-1-4939-6481-9_2 id: cord-320501-xqgqq55q author: Theobald, Nigel title: Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine date: 2020-06-24 words: 1203.0 sentences: 58.0 pages: flesch: 47.0 cache: ./cache/cord-320501-xqgqq55q.txt txt: ./txt/cord-320501-xqgqq55q.txt summary: title: Emerging vaccine delivery systems for COVID-19: Functionalised silica nanoparticles offer a potentially safe and effective alternative delivery system for DNA/RNA vaccines and may be useful in the hunt for a COVID-19 vaccine Liposomal encapsulation of drugs with bioavailability issues was a proven approach in small molecule pharma, and it was apparent to biopharma R&D scientists that LNPs could meet the basic requirements of an RNA/DNA delivery system too, namely to protect nucleic acid from in vivo digestion as it travels to the target. As scientists looked to alternative carriers that could be adapted to encapsulate and protect nucleic acids, mesoporous silica nanoparticles (MSNs)silica-based nanostructured materials with excellent biocompatibility and chemical stability This surface simply and effectively traps and protects nucleic acids (such as mRNA/pDNA) from nuclease enzymes as it travels to the cells. Once inside the cell, the DNA/RNA is released and will result in synthesis of the foreign/target protein which will activate the immune system, leading to both a cellular and humoral immune response. abstract: nan url: https://doi.org/10.1016/j.drudis.2020.06.020 doi: 10.1016/j.drudis.2020.06.020 id: cord-344421-rmnck42f author: Theuns, Sebastiaan title: Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus date: 2018-06-29 words: 8648.0 sentences: 453.0 pages: flesch: 50.0 cache: ./cache/cord-344421-rmnck42f.txt txt: ./txt/cord-344421-rmnck42f.txt summary: Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (10(6.42)–10(7.01) copies/swab) and diarrheic signs was not observed during a follow-up study. Third-generation sequencing using MinION (Oxford Nanopore Technologies, ONT) might be a useful and affordable diagnostic tool for swine veterinary medicine as it allows rapid sample preparation and real-time sequence analysis. The shedding of porcine kobuvirus, RVA and rotavirus C (RVC) was quantitatively investigated in 5 suckling pigs of the same farm from which the diarrheic feces originated. The third-generation sequencing device MinION (ONT), holds promise as a diagnostic platform, as it allows real-time sequencing and analyses of all DNA/RNA in a sample, theoretically without needing pre-amplification of viral nucleic acids. In the present study, a novel RT-qPCR assay, targeting the conserved 3D gene encoding the RNA-dependent-RNA-polymerase, was developed and used to assess, for the first time, longitudinal quantitative shedding kinetics of porcine kobuvirus in pigs under field conditions. abstract: Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet’s microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (10(6.42)–10(7.01) copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded. url: https://doi.org/10.1038/s41598-018-28180-9 doi: 10.1038/s41598-018-28180-9 id: cord-004509-jkzqmkz6 author: Thirion, Laurence title: Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solution for Standardization of Real-Time PCR and RT-qPCR Diagnostics in Virology date: 2020-01-30 words: 4393.0 sentences: 194.0 pages: flesch: 47.0 cache: ./cache/cord-004509-jkzqmkz6.txt txt: ./txt/cord-004509-jkzqmkz6.txt summary: In conclusion, Lyoph-P&P holds several advantages over extemporaneously preparer liquid formulation that merit to be considered when a novel real-time molecular assay is implemented in a laboratory in charge of routine diagnostic activity. Selected assays target two emerging viruses that are listed on the blueprint of the WHO as to be considered for preparedness and response actions [5] : chikungunya virus (CHIKV), a single-stranded positive-sense RNA alphavirus, and Rift Valley fever phlebovirus (RVFV), a tri-segmented, single-stranded negative-sense RNA phlebovirus. Detection of CHIKV RNA using Lyoph-P&P provides results in clinical samples that are at least equal and often better than those obtained with the extemporaneously prepared liquid formulation used as reference. Indeed, at laboratory level, it is likely that one or two different formats (number of tests per vial) will be either prepared or ordered; as a consequence, the time during which rehydrated material can be stored without affecting the expected performances of the assay is a key factor. abstract: Real-time molecular techniques have become the reference methods for direct diagnosis of pathogens. The reduction of steps is a key factor in order to decrease the risk of human errors resulting in invalid series and delayed results. We describe here a process of preparation of oligonucleotide primers and hydrolysis probe in a single tube at predefined optimized concentrations that are stabilized via lyophilization (Lyoph-P&P). Lyoph-P&P was compared versus the classic protocol using extemporaneously prepared liquid reagents using (i) sensitivity study, (ii) long-term stability at 4 °C, and (iii) long-term stability at 37 °C mimicking transportation without cold chain. Two previously published molecular assays were selected for this study. They target two emerging viruses that are listed on the blueprint of the WHO as to be considered for preparedness and response actions: chikungunya virus (CHIKV) and Rift Valley fever phlebovirus (RVFV). Results of our study demonstrate that (i) Lyoph-P&P is stable for at least 4 days at 37 °C supporting shipping without the need of cold chain, (ii) Lyoph-P&P rehydrated solution is stable at +4 °C for at least two weeks, (iii) sensitivity observed with Lyoph-P&P is at least equal to, often better than, that observed with liquid formulation, (iv) validation of results observed with low-copy specimens is rendered easier by higher fluorescence level. In conclusion, Lyoph-P&P holds several advantages over extemporaneously preparer liquid formulation that merit to be considered when a novel real-time molecular assay is implemented in a laboratory in charge of routine diagnostic activity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077261/ doi: 10.3390/v12020159 id: cord-000532-e18licyc author: Tholstrup, Jesper title: mRNA pseudoknot structures can act as ribosomal roadblocks date: 2011-09-08 words: 5809.0 sentences: 270.0 pages: flesch: 57.0 cache: ./cache/cord-000532-e18licyc.txt txt: ./txt/cord-000532-e18licyc.txt summary: The results shown in Figure 2 revealed that a 1D SDS-PAGE assay could not firmly identify polypeptides originating from a À1 frameshifted ribosome stalled in the pseudoknot from the non-frameshifted product in a ''Downstream Stop'' construct. In order to quantify the amount of À1 frameshifted ribosomes stalled inside the pseudoknot, we performed a 2D SDS-PAGE separation of the radioactively labelled proteins originating from the ''Upstream Stop'' construct (Supplementary Figures S4 and S5) , which is the type of construct most commonly used throughout literature. In the ''Upstream Stop'' construct the non-frameshifting ribosomes will translate gene10 and terminate at a UAA stop codon in the spacer sequence and produce a 28 kDa polypeptide. In the following subsections ''Identification of transcripts from the T7gene10-PK-lacZ gene fusions'', ''Messenger RNA stability'' and ''Coupling between translation and transcription is required for full-length transcripts'', we will show that the observed proteins did indeed originate from stalled ribosomes and that they were not caused by other effects. abstract: Several viruses utilize programmed ribosomal frameshifting mediated by mRNA pseudoknots in combination with a slippery sequence to produce a well defined stochiometric ratio of the upstream encoded to the downstream-encoded protein. A correlation between the mechanical strength of mRNA pseudoknots and frameshifting efficiency has previously been found; however, the physical mechanism behind frameshifting still remains to be fully understood. In this study, we utilized synthetic sequences predicted to form mRNA pseudoknot-like structures. Surprisingly, the structures predicted to be strongest lead only to limited frameshifting. Two-dimensional gel electrophoresis of pulse labelled proteins revealed that a significant fraction of the ribosomes were frameshifted but unable to pass the pseudoknot-like structures. Hence, pseudoknots can act as ribosomal roadblocks, prohibiting a significant fraction of the frameshifted ribosomes from reaching the downstream stop codon. The stronger the pseudoknot the larger the frameshifting efficiency and the larger its roadblocking effect. The maximal amount of full-length frameshifted product is produced from a structure where those two effects are balanced. Taking ribosomal roadblocking into account is a prerequisite for formulating correct frameshifting hypotheses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245918/ doi: 10.1093/nar/gkr686 id: cord-008613-tysyq6o4 author: Thomas, Sheila M. title: Two mRNAs that differ by two nontemplated nucleotides encode the amino coterminal proteins P and V of the paramyxovirus SV5 date: 1988-09-09 words: 8410.0 sentences: 433.0 pages: flesch: 60.0 cache: ./cache/cord-008613-tysyq6o4.txt txt: ./txt/cord-008613-tysyq6o4.txt summary: Simian virus 5 (SV5), a prototype paramyxovirus, has a single-stranded, negative sense genomic RNA (vRNA) approximately 15,000 nucleotides in chain length that is transcribed in infected cells by the virion-associated RNA transcriptase to yield virus-specific mRNAs. The SV5 "P" gene has been shown to encode both the P protein (Mr = 44,000), and protein V (Mr = 24,000) by the arrest of translation in vitro of both P and V using a cDNA clone derived from SV5-specific mRNAs (Paterson et al., 1984) . Antigenic Region Mapping of the P and V Monoclonal Antibodies on the P and V Gene Using T7 RNA Polymerase Runoff Transcripts, In Vitro Translation, and Immunoprecipitation The full-length P203-1 DNA insert cloned using Xbal linkers (XX) and a Hindlll to Xbal fragment (HX) containing the 3'' two-thirds of the P203-1 DNA were placed under the control of the T7 promoter in the plasmid pGEM-2. abstract: The “P≓ gene of the paramyxovirus SV5 encodes two known proteins, P (M(r) ≈ 44,000) and V (M(r) ≈ 24,000). The complete nucleotide sequence of the “P≓ gene has been obtained and is found to contain two open reading frames, neither of which is large enough to encode the P protein. We have shown that the P and V proteins are translated from two mRNAs that differ by the presence of two nontemplated G residues in the P mRNA. These two additional nucleotides convert the two open reading frames to one of 392 amino acids. The P and V proteins are amino coterminal and have 164 amino acids in common. The unique C terminus of V consists of a cysteine-rich region that resembles a cysteine-rich metal binding domain. An open reading frame that contains this cysteine-rich region exists in all other paramyxovirus “P≓ gene sequences examined, which suggests that it may have important biological significance. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133244/ doi: 10.1016/s0092-8674(88)91285-8 id: cord-319729-6lzjhn8j author: Tian, Bin title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway date: 2018-01-19 words: 7804.0 sentences: 409.0 pages: flesch: 50.0 cache: ./cache/cord-319729-6lzjhn8j.txt txt: ./txt/cord-319729-6lzjhn8j.txt summary: title: Lab-Attenuated Rabies Virus Causes Abortive Infection and Induces Cytokine Expression in Astrocytes by Activating Mitochondrial Antiviral-Signaling Protein Signaling Pathway Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. To assess innate immune responses in astrocytes, cells were infected with DRV or B2c at an MOI of 0.1 and the expression of several proteins involved in the MAVS signaling pathway, namely, RIG-I, p-IRF7, STAT1 and IFIT1 (ISG56), was measured by Western blot. abstract: Rabies is an ancient disease but remains endemic in most parts of the world and causes approximately 59,000 deaths annually. The mechanism through which the causative agent, rabies virus (RABV), evades the host immune response and infects the host central nervous system (CNS) has not been completely elucidated thus far. Our previous studies have shown that lab-attenuated, but not wild-type (wt), RABV activates the innate immune response in the mouse and dog models. In this present study, we demonstrate that lab-attenuated RABV causes abortive infection in astrocytes, the most abundant glial cells in the CNS. Furthermore, we found that lab-attenuated RABV produces more double-stranded RNA (dsRNA) than wt RABV, which is recognized by retinoic acid-inducible gene I (RIG-I) or melanoma differentiation-associated protein 5 (MDA5). Activation of mitochondrial antiviral-signaling protein (MAVS), the common adaptor molecule for RIG-I and MDA5, results in the production of type I interferon (IFN) and the expression of hundreds of IFN-stimulated genes, which suppress RABV replication and spread in astrocytes. Notably, lab-attenuated RABV replicates in a manner identical to that of wt RABV in MAVS−/− astrocytes. It was also found that lab-attenuated, but not wt, RABV induces the expression of inflammatory cytokines via the MAVS- p38/NF-κB signaling pathway. These inflammatory cytokines increase the blood–brain barrier permeability and thus enable immune cells and antibodies infiltrate the CNS parenchyma, resulting in RABV control and elimination. In contrast, wt RABV restricts dsRNA production and thus evades innate recognition by RIG-I/MDA5 in astrocytes, which could be one of the mechanisms by which wt RABV evades the host immune response in resident CNS cells. Our findings suggest that astrocytes play a critical role in limiting the replication of lab-attenuated RABV in the CNS. url: https://doi.org/10.3389/fimmu.2017.02011 doi: 10.3389/fimmu.2017.02011 id: cord-271434-30nh2gc7 author: Tian, Fei title: A fully automated centrifugal microfluidic system for sample-to-answer viral nucleic acid testing date: 2020-07-27 words: 4323.0 sentences: 209.0 pages: flesch: 49.0 cache: ./cache/cord-271434-30nh2gc7.txt txt: ./txt/cord-271434-30nh2gc7.txt summary: In this work, we develop an automated centrifugal microfluidic system (Figure 1 ) consisting of a microfluidic disc and a customized instrument for rapid sample-to-answer detection of SARS-CoV-2 armored RNA particles with high sensitivity and specificity. Virus lysis buffer, RT-LAMP reagents, and mineral oil were sequentially injected into the microfluidic disc for on-chip release of viral nucleic acids, amplification of target RNA, and sealing of reaction unit. To demonstrate the automated detection of viral nucleic acids by the centrifugal microfluidic system, we loaded different concentrations of SARS-CoV-2 armored RNA particles with N gene (0.5, 1, 10, 10 2 , 10 3 copies/μL) into five reaction units of the microfluidic disc, and used the instrument to carry out on-chip release of viral nuclei acids, RT-LAMP, and realtime fluorescence signal detection. abstract: The outbreak of virus-induced infectious diseases poses a global public-health challenge. Nucleic acid amplification testing (NAAT) enables early detection of pandemic viruses and plays a vital role in preventing onward transmission. However, the requirement of skilled operators, expensive instrumentation, and biosafety laboratories has hindered the use of NAAT for screening and diagnosis of suspected patients. Here we report development of a fully automated centrifugal microfluidic system with sample-in-answer-out capability for sensitive, specific, and rapid viral nucleic acid testing. The release of nucleic acids and the subsequent reverse transcription loop-mediated isothermal amplification (RT-LAMP) were integrated into the reaction units of a microfluidic disc. The whole processing steps such as injection of reagents, fluid actuation by rotation, heating and temperature control, and detection of fluorescence signals were carried out automatically by a customized instrument. We validate the centrifugal microfluidic system using oropharyngeal swab samples spiked with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) armored RNA particles. The estimated limit of detection for armored RNA particles is 2 copies per reaction, the throughput is 21 reactions per disc, and the assay sample-to-answer time is approximately 70 min. This enclosed and automated microfluidic system efficiently avoids viral contamination of aerosol, and can be readily adapted for virus detection outside the diagnostic laboratory. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at 10.1007/s11426-020-9800-6 and is accessible for authorized users. url: https://doi.org/10.1007/s11426-020-9800-6 doi: 10.1007/s11426-020-9800-6 id: cord-351365-dc9t3vh3 author: Todt, Daniel title: Mutagenic Effects of Ribavirin on Hepatitis E Virus—Viral Extinction versus Selection of Fitness-Enhancing Mutations date: 2016-10-13 words: 6318.0 sentences: 320.0 pages: flesch: 40.0 cache: ./cache/cord-351365-dc9t3vh3.txt txt: ./txt/cord-351365-dc9t3vh3.txt summary: Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis. Figure 1 provides an overview of a selection of RNA viruses against which RBV was shown to be active: hepatitis C virus (HCV, Flaviviridae), dengue virus (DENV, Flaviviridae), respiratory syncytial virus (RSV, Paramyxoviridae), influenza A and B virus (Orthomyxoviridae), chikungunya virus (CHIKV, Togaviridae), poliovirus (Picornaviridae), Hantaan virus (Bunyaviridae), and Lassa virus (Arenaviridae) [28, 29] ( Figure 1 ). Furthermore, mechanisms on the virus itself were described by inhibition of the capping efficiency, the viral polymerase, and a mutagenic effect on newly synthesized RNA genomes. A Mutation in the hepatitis E virus RNA polymerase promotes its replication and associates with ribavirin treatment failure in organ transplant recipients abstract: Hepatitis E virus (HEV), an important agent of viral hepatitis worldwide, can cause severe courses of infection in pregnant women and immunosuppressed patients. To date, HEV infections can only be treated with ribavirin (RBV). Major drawbacks of this therapy are that RBV is not approved for administration to pregnant women and that the virus can acquire mutations, which render the intra-host population less sensitive or even resistant to RBV. One of the proposed modes of action of RBV is a direct mutagenic effect on viral genomes, inducing mismatches and subsequent nucleotide substitutions. These transition events can drive the already error-prone viral replication beyond an error threshold, causing viral population extinction. In contrast, the expanded heterogeneous viral population can facilitate selection of mutant viruses with enhanced replication fitness. Emergence of these mutant viruses can lead to therapeutic failure. Consequently, the onset of RBV treatment in chronically HEV-infected individuals can result in two divergent outcomes: viral extinction versus selection of fitness-enhanced viruses. Following an overview of RNA viruses treated with RBV in clinics and a summary of the different antiviral modes of action of this drug, we focus on the mutagenic effect of RBV on HEV intrahost populations, and how HEV is able to overcome lethal mutagenesis. url: https://www.ncbi.nlm.nih.gov/pubmed/27754363/ doi: 10.3390/v8100283 id: cord-000295-ft5wl70x author: Tomankova, Tereza title: Involvement of microRNAs in physiological and pathological processes in the lung date: 2010-11-23 words: 4778.0 sentences: 318.0 pages: flesch: 46.0 cache: ./cache/cord-000295-ft5wl70x.txt txt: ./txt/cord-000295-ft5wl70x.txt summary: These short, single-stranded RNA molecules originate from larger precursor molecules that fold to produce hairpin structures, which are subsequently processed by ribonucleases Drosha/Pasha and Dicer to form mature miRNAs. MiRNAs play role in the posttranscriptional regulation of about one third of human genes, mainly via degradation of target mRNAs. Whereas the target mRNAs are often involved in the regulation of diverse physiological processes ranging from developmental timing to apoptosis, miRNAs have a strong potential to regulate fundamental biological processes also in the lung compartment. Small non-coding RNAs (miRNAs) play pivotal role in the posttranscriptional regulation of numerous human genes, mainly via degradation of target mRNAs. There is evidence that the lung has a very specific miRNA expression profile undergoing changes during the lung development. abstract: To date, at least 900 different microRNA (miRNA) genes have been discovered in the human genome. These short, single-stranded RNA molecules originate from larger precursor molecules that fold to produce hairpin structures, which are subsequently processed by ribonucleases Drosha/Pasha and Dicer to form mature miRNAs. MiRNAs play role in the posttranscriptional regulation of about one third of human genes, mainly via degradation of target mRNAs. Whereas the target mRNAs are often involved in the regulation of diverse physiological processes ranging from developmental timing to apoptosis, miRNAs have a strong potential to regulate fundamental biological processes also in the lung compartment. However, the knowledge of the role of miRNAs in physiological and pathological conditions in the lung is still limited. This review, therefore, summarizes current knowledge of the mechanism, function of miRNAs and their contribution to lung development and homeostasis. Besides the involvement of miRNAs in pulmonary physiological conditions, there is evidence that abnormal miRNA expression may lead to pathological processes and development of various pulmonary diseases. Next, the review describes current state-of-art on the miRNA expression profiles in smoking-related diseases including lung cancerogenesis, in immune system mediated pulmonary diseases and fibrotic processes in the lung. From the current research it is evident that miRNAs may play role in the posttranscriptional regulation of key genes in human pulmonary diseases. Further studies are, therefore, necessary to explore miRNA expression profiles and their association with target mRNAs in human pulmonary diseases. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001429/ doi: 10.1186/1465-9921-11-159 id: cord-004507-ezuyjcxs author: Tomazatos, Alexandru title: Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix) date: 2020-02-21 words: 6326.0 sentences: 348.0 pages: flesch: 49.0 cache: ./cache/cord-004507-ezuyjcxs.txt txt: ./txt/cord-004507-ezuyjcxs.txt summary: The study provided complete genome sequences for nine Letea virus strains and new information about orbivirus diversity, host range, ecology and evolution. The phylogenetic clustering of Orbivirus members results in clades indicating their putative or potential arthropod vectors: Culicoidesor sand fly-borne (C/SBOV), mosquito-borne (MBOV) and tick-borne orbiviruses (TBOV) [9] . Evolutionary relationship of LEAV with representative members of the Orbivirus genus were analyzed by inferring phylogenetic trees with amino acid and nucleotide ORF sequences of conserved genes encoding the polymerase (VP1), the subcore shell protein T2 (VP2/VP3) and the major core surface protein T13 (VP7) [5, 6] . Inclusion and demarcation of species within the Orbivirus genus considers several criteria, such as sequence identity of segments encoding the polymerase (VP1) and major subcore shell protein T2, gene reassortment between close strains, high levels of serological cross-reactivity against conserved antigens like the T13 protein, conservation of UTR terminal nucleotides, range of hosts and vectors or the clinical signs associated with orbivirus infection [1] . abstract: The discovery and characterization of novel arthropod-borne viruses provide valuable information on their genetic diversity, ecology, evolution and potential to threaten animal or public health. Arbovirus surveillance is not conducted regularly in Romania, being particularly very scarce in the remote and diverse areas like the Danube Delta. Here we describe the detection and genetic characterization of a novel orbivirus (Reoviridae: Orbivirus) designated as Letea virus, which was found in grass snakes (Natrix natrix) during a metagenomic and metatranscriptomic survey conducted between 2014 and 2017. This virus is the first orbivirus discovered in reptiles. Phylogenetic analyses placed Letea virus as a highly divergent species in the Culicoides-/sand fly-borne orbivirus clade. Gene reassortment and intragenic recombination were detected in the majority of the nine Letea virus strains obtained, implying that these mechanisms play important roles in the evolution and diversification of the virus. However, the screening of arthropods, including Culicoides biting midges collected within the same surveillance program, tested negative for Letea virus infection and could not confirm the arthropod vector of the virus. The study provided complete genome sequences for nine Letea virus strains and new information about orbivirus diversity, host range, ecology and evolution. The phylogenetic associations warrant further screening of arthropods, as well as sustained surveillance efforts for elucidation of Letea virus natural cycle and possible implications for animal and human health. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077223/ doi: 10.3390/v12020243 id: cord-306934-29ljbl7g author: Tonelli, Michele title: Antiviral and cytotoxic activities of aminoarylazo compounds and aryltriazene derivatives date: 2009-07-01 words: 8526.0 sentences: 442.0 pages: flesch: 58.0 cache: ./cache/cord-306934-29ljbl7g.txt txt: ./txt/cord-306934-29ljbl7g.txt summary: Finally, molecular modeling investigations indicated that compounds of structure A–C, active against BVDV, could work targeting the viral RNA-dependent RNA-polymerase (RdRp), having been observed a good agreement between the trends of the estimated IC50 and the experimental EC50 values. First of all, the binding site identified by our procedure is very close to the putative binding site proposed for two allosteric inhibitors of BVDV RdRp, VP32947 and BPIP, 23 Table 5 Cytotoxicity against MT-4, MDBK, BHK and Vero-76 cell lines and YFV, Reo-1, CVB-2, RSV, HSV-1 and Sb-1 inhibitory activity of triazene derivatives of structure F and G Tables 3 and 4. In view of these considerations, molecular modeling investigations were performed to study wether the active compounds of structures A-C could target the BVDV RNA-dependent RNA-polymerase (RdRp), which shares some structural similarity with HCV RdRp. Indeed a good agreement was observed between the trend exhibited by the IC 50 (calculated from the estimated free energies of binding) and the corresponding biological activities determined for these compounds in BVDV infected MDBK cell line. abstract: Abstract Twelve aminoarylazocompounds (A–C) and 46 aryltriazene 7 derivatives (D–G) have been synthesized and evaluated in cell-based assays for cytotoxicity and antiviral activity against a panel of 10 RNA and DNA viruses. Eight aminoazocompounds and 27 aryltriazene derivatives exhibited antiviral activity, sometimes of high level, against one or more viruses. A marked activity against BVDV and YFV was prevailing among the former compounds, while the latter type of compounds affected mainly CVB-2 and RSV. None of the active compounds inhibited the multiplication of HIV-1, VSV and VV. Arranged in order of decreasing potency and selectivity versus the host cell lines, the best compounds are the following; BVDV: 1 > 7 > 8 > 4; YFV: 7 > 5; CVB-2: 25 > 56 > 18; RSV: 14 > 20 > 55 > 38 > 18 > 19; HSV-1: 2. For these compounds the EC50 ranged from 1.6μM (1) to 12μM (18), and the S. I. from 19.4 (1) to 4.2 (2). Thus the aminoarylazo and aryltriazene substructures appear as interesting molecular component for developing antiviral agents against ss RNA viruses, particularly against RSV and BVDV, which are important human and veterinary pathogens. Finally, molecular modeling investigations indicated that compounds of structure A–C, active against BVDV, could work targeting the viral RNA-dependent RNA-polymerase (RdRp), having been observed a good agreement between the trends of the estimated IC50 and the experimental EC50 values. url: https://www.ncbi.nlm.nih.gov/pubmed/19482481/ doi: 10.1016/j.bmc.2009.05.020 id: cord-274536-fv7mltj7 author: Tong, Yongqing title: Necessity for detection of SARS-CoV-2 RNA in multiple types of specimens for the discharge of the patients with COVID-19 date: 2020-11-02 words: 3120.0 sentences: 188.0 pages: flesch: 59.0 cache: ./cache/cord-274536-fv7mltj7.txt txt: ./txt/cord-274536-fv7mltj7.txt summary: RESULTS: Of the enrolled 1008 severe patients, the nasopharyngeal swab specimens showed the highest positive rate of SARS-CoV-2 RNA (71.06%), followed by alveolar lavage fluid (66.67%), oropharyngeal swab (30.77%), sputum (28.53%), urine (16.30%), blood (12.5%), stool (12.21%), anal swab (11.22%) and corneal secretion (2.99%), and SARS-CoV-2 RNA couldn''t be detected in other types of specimen in this study. Firstly, we analyzed the possible sites of infection in hospitalized patients with COVID-19 by detecting viral RNA with 12 different types of specimens, including nasopharyngeal swab, oropharyngeal swab, sputum, bronchoalveolar lavage fluid (BALF), stool, anal swab, urine, peritoneal dialysis fluid (PDF), blood, sweat, cerebrospinal fluid (CSF) and corneal secretion. The 20 discharged cases of COVID-19, the criteria [12] for which was the SARS-CoV-2 virus RNA detection negative in two consecutive respiratory specimens (at least 1 day of time interval of sampling) for patients who have reached the standards of isolation period (14 days) after clinical cured, during the isolation period were selected to detect SARS-CoV-2 RNA with multiple specimens including nasopharyngeal swab, oropharyngeal swab, sputum, stool, anal swab, urine and blood. abstract: BACKGROUND: The SARS-CoV-2 RNA was detected positive again after discharged from hospital in some COVID-19 patients, with or without clinical symptoms such as fever or dry cough. METHODS: 1008 severe COVID-19 patients, with SARS-CoV-2 RNA positive detected with the mixed specimen of nasopharyngeal swab and oropharyngeal swab by real-time fluorescence quantitative PCR (RT-qPCR), were selected to monitor SARS-CoV-2 RNA with the 12 types of specimens by RT-qPCR during hospitalization. All of 20 discharged cases with COVID-19 were selected to detect SARS-CoV-2 RNA in isolation period with 7 types of specimens by RT-qPCR before releasing the isolation period. RESULTS: Of the enrolled 1008 severe patients, the nasopharyngeal swab specimens showed the highest positive rate of SARS-CoV-2 RNA (71.06%), followed by alveolar lavage fluid (66.67%), oropharyngeal swab (30.77%), sputum (28.53%), urine (16.30%), blood (12.5%), stool (12.21%), anal swab (11.22%) and corneal secretion (2.99%), and SARS-CoV-2 RNA couldn’t be detected in other types of specimen in this study. Of the 20 discharged cases during the isolation period, the positive rate of SARS-CoV-2 RNA was 30% (6/20): 2 cases were positive in sputum at the eighth and ninth day after discharge, respectively, 1 case was positive in nasopharynx swab at the sixth day after discharge, 1 case was positive in anal swab at the eighth day after discharge, and 1 case was positive in 3 specimens (nasopharynx swab, oropharynx swab and sputum) simultaneously at the fourth day after discharge, and no positive SARS-CoV-2 RNA was detected in other specimens including stool, urine and blood at the discharged patients. CONCLUSIONS: SARS-CoV-2 RNA should be detected in multiple specimens, such as nasopharynx swab, oropharynx swab, sputum, and if necessary, stool and anal swab specimens should be performed simultaneously at discharge when the patients were considered for clinical cure and before releasing the isolation period. url: https://doi.org/10.1186/s12967-020-02580-w doi: 10.1186/s12967-020-02580-w id: cord-325479-2r4oomdp author: Torii, Shotaro title: Applicability of polyethylene glycol precipitation followed by acid guanidinium thiocyanate-phenol-chloroform extraction for the detection of SARS-CoV-2 RNA from municipal wastewater date: 2020-10-17 words: 5881.0 sentences: 363.0 pages: flesch: 58.0 cache: ./cache/cord-325479-2r4oomdp.txt txt: ./txt/cord-325479-2r4oomdp.txt summary: This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate–phenol–chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. This study aims (1) to compare the combination of primary concentration (UF, EMV, and PEG) and RNA extraction (QIAamp Viral RNA Mini Kit and TRIzol) for the whole process recovery of nonenveloped and enveloped virus surrogates and (2) to test the applicability of the method providing the highest φ6 recovery to detect SARS-CoV-2 abstract: The primary concentration and molecular process are critical to implement wastewater-based epidemiology for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the previously developed methods were optimized for nonenveloped viruses. Few studies evaluated if the methods are applicable to the efficient recovery of enveloped viruses from various types of raw sewage. This study aims (1) to compare the whole process recovery of Pseudomonas phage φ6, a surrogate for enveloped viruses, among combinations of primary concentration [ultrafiltration (UF), electronegative membrane vortex (EMV), and polyethylene glycol precipitation (PEG)] and RNA extraction methods (spin column-based method using QIAamp Viral RNA Mini Kit and acid guanidinium thiocyanate–phenol–chloroform extraction using TRIzol reagent) for three types of raw sewage and (2) to test the applicability of the method providing the highest φ6 recovery to the detection of SARS-CoV-2 RNA. Among the tested combinations, PEG+TRIzol provided the highest φ6 recovery ratio of 29.8% to 49.8% (geometric mean). UF+QIAamp Viral RNA Mini Kit provided the second highest φ6 recovery of 6.4% to 35.8%. The comparable φ6 recovery was observed for UF+TRIzol (13.8 – 30.0 %). PEG+QIAamp Viral RNA Mini Kit provided only 1.4% to 3.0% of φ6 recovery, while coliphage MS2, a surrogate for nonenveloped viruses, was recovered comparably with PEG+TRIzol. This indicated that the nonenveloped surrogate (MS2) did not necessarily validate the efficient recovery for enveloped viruses. EMV+QIAamp Viral RNA Mini Kit provided significantly different φ6 recovery (1.6 – 21 %) among the types of raw sewage. Then, the applicability of modified PEG+TRIzol was examined for the raw sewage collected in Tokyo, Japan. Of the 12 grab samples, 4 were positive for SARS-CoV-2 CDC N1 and N3 assay. Consequently, PEG+TRIzol provided the highest φ6 recovery and allowed for the detection of SARS-CoV-2 RNA from raw sewage. url: https://www.ncbi.nlm.nih.gov/pubmed/33131851/ doi: 10.1016/j.scitotenv.2020.143067 id: cord-289535-srrfr1es author: Tregoning, J. S. title: Vaccines for COVID‐19 date: 2020-10-18 words: 14329.0 sentences: 793.0 pages: flesch: 44.0 cache: ./cache/cord-289535-srrfr1es.txt txt: ./txt/cord-289535-srrfr1es.txt summary: One concern with vaccine development for SARS-CoV-2 is that the immune response can cause disease, often in the act of clearing the infection. Preclinical animal studies have demonstrated that DNA vaccines encoding the M, N, 3a or S proteins of the SARS-CoV-1 virus could elicit immune responses [180] [181] [182] . The S protein is the target of the only SARS-CoV-1 DNA vaccine to progress to Phase I clinical trial, delivered by bio-injector, and it was safe and induced neutralizing antibody responses [183] . T cell responses are required for protection from clinical disease and for virus clearance in severe acute respiratory syndrome coronavirus-infected mice Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals A SARS DNA vaccine induces neutralizing antibody and cellular immune responses in healthy adults in a Phase I clinical trial abstract: Since the emergence of COVID‐19, caused by the SARS‐CoV‐2 virus at the end of 2019, there has been an explosion of vaccine development. By 24 September 2020, a staggering number of vaccines (more than 200) had started preclinical development, of which 43 had entered clinical trials, including some approaches that have not previously been licensed for human vaccines. Vaccines have been widely considered as part of the exit strategy to enable the return to previous patterns of working, schooling and socializing. Importantly, to effectively control the COVID‐19 pandemic, production needs to be scaled‐up from a small number of preclinical doses to enough filled vials to immunize the world’s population, which requires close engagement with manufacturers and regulators. It will require a global effort to control the virus, necessitating equitable access for all countries to effective vaccines. This review explores the immune responses required to protect against SARS‐CoV‐2 and the potential for vaccine‐induced immunopathology. We describe the profile of the different platforms and the advantages and disadvantages of each approach. The review also addresses the critical steps between promising preclinical leads and manufacturing at scale. The issues faced during this pandemic and the platforms being developed to address it will be invaluable for future outbreak control. Nine months after the outbreak began we are at a point where preclinical and early clinical data are being generated for the vaccines; an overview of this important area will help our understanding of the next phases. url: https://www.ncbi.nlm.nih.gov/pubmed/32935331/ doi: 10.1111/cei.13517 id: cord-283895-1p5uog38 author: Trottier, J. title: Post-lockdown detection of SARS-CoV-2 RNA in the wastewater of Montpellier, France date: 2020-07-09 words: 1925.0 sentences: 125.0 pages: flesch: 61.0 cache: ./cache/cord-283895-1p5uog38.txt txt: ./txt/cord-283895-1p5uog38.txt summary: Indeed, several reports indicate that SARS-CoV-2 RNA was readily detected in wastewater, and it is proposed that such approach could anticipate the occurrence of novel COVID-19 outbreaks in low prevalence regions , La Rosa et al., 2020 , Medema et al., 2020 , Orive et al., 2020 , Randazzo et al., 2020 . First, we showed that the Ebola standard (Ebo Std) primer/probe set was not detecting RNA from SARS-CoV-2-infected Vero E6 cells (Table 1) . . https://doi.org/10.1101/2020.07.08.20148882 doi: medRxiv preprint Next, we measured the SARS-CoV-2 RNA levels using N1 and N3 primer/probe sets in wastewater collected upstream of the main WWTP of the Montpellier metropolitan area on May 7 th , 18 th , 26 th , June 4 th , 15 th and 25 th (Figure 2A ). This intriguing result is reminiscent of a recent Spanish study, in which the authors could detect SARS-CoV-2 RNA in wastewater weeks before the first COVID-19 cases were reported (Randazzo et al., 2020) . abstract: The evolution of the COVID-19 pandemic can be monitored through the detection of SARS-CoV-2 RNA in sewage. Here, we measured the amount of SARS-CoV-2 RNA at the inflow point of the main waste water treatment plant (WWTP) of Montpellier, France. We collected samples 4 days before the end of lockdown and up to 45 days post-lockdown. We detected increased amounts of SARS-CoV-2 RNA at the WWTP, which was not correlated with the number of newly diagnosed patients. Future epidemiologic investigations may explain such asynchronous finding. url: https://doi.org/10.1101/2020.07.08.20148882 doi: 10.1101/2020.07.08.20148882 id: cord-265173-70wyecwj author: Trujillo-Uscanga, Adrian title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication date: 2020-08-27 words: 5671.0 sentences: 282.0 pages: flesch: 53.0 cache: ./cache/cord-265173-70wyecwj.txt txt: ./txt/cord-265173-70wyecwj.txt summary: title: Host cell p53 associates with the feline calicivirus major viral capsid protein VP1, the protease-polymerase NS6/7, and the double-stranded RNA playing a role in virus replication Viruses modulate p53 functions in different manners: single-stranded RNA viruses such as the human coronavirus NL63 (HCoV-NL63) induces its degradation of p53 (Yuan et al., 2015) to ensure viral growth in infected cells (Ma-Lauer et al., 2016) , Zika (ZIKV) and West Nile (WNV) activate p53 to facilitate their replication (El Ghouzzi et al., 2016) (Teng et al., 2017) (Yang et al., 2008) while Adenovirus Even though p53 is implicated in the induction of apoptosis and in many viral infections, its role during calicivirus infection has not been studied. Here we found that p53 interacts with FCV dsRNA, the protease-polymerase NS6/7, and VP1 in the RC; moreover, knockdown of p53 resulted in a significant reduction of the NS viral protein synthesis and virus production, indicating its role for efficient viral replication. abstract: p53 is implicated in several cellular pathways such as induction of cell-cycle arrest, differentiation, senescence, and apoptosis. p53 is activated by a broad range of stress signals, including viral infections. While some viruses activate p53, others induce its inactivation, and occasionally p53 is differentially modulated during the replicative cycle. During calicivirus infections, apoptosis is required for virus exit and spread into the host; yet, the role of p53 during infection is unknown. By confocal microscopy, we found that p53 associates with FCV VP1, the protease-polymerase NS6/7, and the dsRNA. This interaction was further confirmed by proximity ligation assays, suggesting that p53 participates in the FCV replication. Knocked-down of p53 expression in CrFK cells before infection, resulted in a strong reduction of the non-structural protein levels and a decrease of the viral progeny production. These results indicate that p53 is associated with the viral replication complex and is required for an efficient FCV replication. url: https://api.elsevier.com/content/article/pii/S0042682220301616 doi: 10.1016/j.virol.2020.08.008 id: cord-343470-w215pzdc author: Tsai, Kevin title: Epigenetic and epitranscriptomic regulation of viral replication date: 2020-06-12 words: 9761.0 sentences: 452.0 pages: flesch: 41.0 cache: ./cache/cord-343470-w215pzdc.txt txt: ./txt/cord-343470-w215pzdc.txt summary: Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. First, the viral protein VP16, which is packaged into the tegument layer of incoming virions, recruits host proteins, including host-cell factor 1 (HCF-1) and octamer-binding factor (Oct-1), in order to form a complex that recruits the histone demethylases lysine-specific demethylase 1 (LSD1) and Jumonji domain 2 (JMJD2) family members as a means to remove repressive H3K9 marks from viral immediate early promoters 42 Upon entry into the cell nucleus, the DNA of many viruses initiates the replication process adjacent to subnuclear structures called pro-myelocytic leukaemia nuclear bodies (PML-NBs). abstract: Eukaryotic gene expression is regulated not only by genomic enhancers and promoters, but also by covalent modifications added to both chromatin and RNAs. Whereas cellular gene expression may be either enhanced or inhibited by specific epigenetic modifications deposited on histones (in particular, histone H3), these epigenetic modifications can also repress viral gene expression, potentially functioning as a potent antiviral innate immune response in DNA virus-infected cells. However, viruses have evolved countermeasures that prevent the epigenetic silencing of their genes during lytic replication, and they can also take advantage of epigenetic silencing to establish latent infections. By contrast, the various covalent modifications added to RNAs, termed epitranscriptomic modifications, can positively regulate mRNA translation and/or stability, and both DNA and RNA viruses have evolved to utilize epitranscriptomic modifications as a means to maximize viral gene expression. As a consequence, both chromatin and RNA modifications could serve as novel targets for the development of antivirals. In this Review, we discuss how host epigenetic and epitranscriptomic processes regulate viral gene expression at the levels of chromatin and RNA function, respectively, and explore how viruses modify, avoid or utilize these processes in order to regulate viral gene expression. url: https://www.ncbi.nlm.nih.gov/pubmed/32533130/ doi: 10.1038/s41579-020-0382-3 id: cord-351559-az4pgi9k author: Turjya, Rafeed Rahman title: Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection date: 2020-06-29 words: 2438.0 sentences: 173.0 pages: flesch: 48.0 cache: ./cache/cord-351559-az4pgi9k.txt txt: ./txt/cord-351559-az4pgi9k.txt summary: Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. abstract: Background Since December 2019, the world is experiencing an unprecedented crisis due to a novel coronavirus, SARS-CoV-2. Owing to poor understanding of pathogenicity, the virus is eluding treatment and complicating recovery. Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells. Results Our analyses uncover 21 differentially expressed lncRNAs whose functions are broadly involved in cell survival and regulation of gene expression. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. These genes are involved in cellular signaling, metabolism, immune response and RNA homeostasis. Since lncRNAs have been known to sponge microRNAs and protect expression of upregulated genes, we also identified 9 microRNAs that are induced in viral infections; however, some lncRNAs are able to block their usual suppressive effect on overexpressed genes and consequently contribute to host defense and cell survival. Conclusions Our investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option. url: https://doi.org/10.1101/2020.06.29.177204 doi: 10.1101/2020.06.29.177204 id: cord-001090-qg2r691d author: Twin, Jimmy title: The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis date: 2013-09-27 words: 3944.0 sentences: 201.0 pages: flesch: 44.0 cache: ./cache/cord-001090-qg2r691d.txt txt: ./txt/cord-001090-qg2r691d.txt summary: BACKGROUND: The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex. An amplicon-based metagenomic library was generated from the extracted DNA using the universal bacterial PCR primers 27F and 338R that target the V1-V2 hypervariable regions of the 16S rRNA gene as previously described [15] . Comparison of cDNA to DNA from Nugent 10 patient All of the predominant bacteria with .1% total abundance identified in the cDNA library were also detected using the 16S rRNA gene amplicon-based approach on extracted DNA. abstract: BACKGROUND: The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. METHODOLOGY/PRINCIPAL FINDINGS: The sample from the BV patient underwent total RNA extraction, followed by physical subtraction of human rRNA and whole transcriptome amplification. The metatranscriptome was sequenced using Roche 454 titanium chemistry. The bioinformatics pipeline MG-RAST and desktop DNA analysis platforms were utilised to analyse results. Bacteria of the genus Prevotella (predominately P. amnii) constituted 36% of the 16S rRNA reads, followed by Megasphaera (19%), Leptotrichia/Sneathia (8%) and Fusobacterium (8%). Comparison of the abundances of several bacteria to quantitative PCR (qPCR) screening of extracted DNA revealed comparable relative abundances. This suggests a correlation between what was present and transcriptionally active in this sample: however distinct differences were seen when compared to the microbiome determined by 16S rRNA gene amplicon sequencing. To assess the presence of P. amnii in a larger pool of samples, 90 sexually active women were screened using qPCR. This bacterium was found to be strongly associated with BV (P<0.001, OR 23.3 (95%CI:2.9–190.7)) among the 90 women. CONCLUSIONS/SIGNIFICANCE: This study highlighted the potential of metatranscriptomics as a tool for characterising metabolically active microbiota and identifying targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3785445/ doi: 10.1371/journal.pone.0076892 id: cord-303153-z7bdiuvx author: Ulasli, Mustafa title: Qualitative and quantitative ultrastructural analysis of the membrane rearrangements induced by coronavirus date: 2010-01-20 words: 8709.0 sentences: 521.0 pages: flesch: 59.0 cache: ./cache/cord-303153-z7bdiuvx.txt txt: ./txt/cord-303153-z7bdiuvx.txt summary: This approach has allowed us to establish that MHV induces the formation of six membranous rearrangements in the following order: DMVs, CMs, virions, LVCVs, TBs and CMSs. Importantly, we were able to show that most membrane rearrangements (LVCVs, TBs, CMSs and possibly CMs) observed in addition to the key structures in the infection (DMVs and virions) actually appear to be the consequence of a massive synthesis of viral proteins. In order to be able to correlate our EM and IEM analyses with the progression of a CoV infection inside the host cells, we first measured important known parameters that reflect the CoV life cycle: viral RNA replication/transcription, viral protein synthesis and secretion of progeny virus. In the centre of the DMV clusters, we frequently observed a small network of membranes with a diameter varying from 200 to 600 nm, which have recently been described in SARS-CoV-infected cells and called CMs [ Fig. 2A and B, arrowheads; (Knoops et al., 2008) . abstract: Coronaviruses (CoV) are enveloped positive‐strand RNA viruses that induce different membrane rearrangements in infected cells in order to efficiently replicate and assemble. The origin, the protein composition and the function of these structures are not well established. To shed further light on these structures, we have performed a time‐course experiment in which the mouse hepatitis virus (MHV)‐induced membrane rearrangements were examined qualitatively and quantitatively by (immuno)‐electron microscopy. With our approach we were able to confirm the appearance of 6, previously reported, membranous structures during the course of a complete infection cycle. These structures include the well‐characterized double‐membrane vesicles (DMVs), convoluted membranes (CMs) and virions but also the more enigmatic large virion‐containing vacuoles (LVCVs), tubular bodies (TBs) and cubic membrane structures (CMSs). We have characterized the LVCVs, TBs and CMSs, and found that the CoV‐induced structures appear in a strict order. By combining these data with quantitative analyses on viral RNA, protein synthesis and virion release, this study generates an integrated molecular and ultrastructural overview of CoV infection. In particular, it provides insights in the role of each CoV‐induced structure and reveals that LVCVs are ERGIC/Golgi compartments that expand to accommodate an increasing production of viral particles. url: https://doi.org/10.1111/j.1462-5822.2010.01437.x doi: 10.1111/j.1462-5822.2010.01437.x id: cord-019076-4qu9j953 author: Ulferts, Rachel title: Expression and Functions of SARS Coronavirus Replicative Proteins date: 2009-07-22 words: 10036.0 sentences: 516.0 pages: flesch: 52.0 cache: ./cache/cord-019076-4qu9j953.txt txt: ./txt/cord-019076-4qu9j953.txt summary: In this chapter, we review our current understanding of the expression and functions of key replicative enzymes, such as RNA polymerases, helicase, ribonucleases, ribose-2′-O-methyltransferase and other replicase gene-encoded proteins involved in genome expression, virus–host interactions and other processes. The RTC includes the key replicative proteins of the virus, such as RNA-dependent RNA polymerase (RdRp) and helicase activities, as well as enzymes that are thought to be involved in the processing and modification of viral and/or cellular RNAs, such as primase, endoribonuclease, exoribonuclease and ribose-2 0 -O-methyltransferase activities (for recent reviews, see Masters 2006; Ziebuhr 2005 Ziebuhr , 2008 . SARS-CoV pp1a and pp1ab are co-and post-translationally processed by two proteases, a papain-like protease (PL pro ) and the main protease (M pro , nsp5), resulting in 16 mature products called nonstructural proteins (nsps) 1-16 The 5 0 -terminal ORF(s) expressed from specific RNAs is/are shown as boxes. abstract: The discovery of a previously unknown coronavirus as the causative agent of the SARS epidemic in 2002/2003 stimulated a large number of studies into the molecular biology of SARS coronavirus (SARS-CoV) and related viruses. This research has provided significant new insight into the functions and activities of the coronavirus replicase–transcriptase complex, a multiprotein complex that directs coordinated processes of both continuous and discontinuous RNA synthesis to replicate and transcribe the large coronavirus genome, a single-stranded, positive-sense RNA of ~30 kb. In this chapter, we review our current understanding of the expression and functions of key replicative enzymes, such as RNA polymerases, helicase, ribonucleases, ribose-2′-O-methyltransferase and other replicase gene-encoded proteins involved in genome expression, virus–host interactions and other processes. Collectively, these recent studies reveal fascinating details of an enzymatic machinery that, in the RNA virus world, is unparalleled in terms of the number and nature of virally encoded activities involved in virus replication and host interactions. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124140/ doi: 10.1007/978-3-642-03683-5_6 id: cord-313541-fpqwzf9k author: Ulloa, S. title: A simple method for SARS-CoV-2 detection by rRT-PCR without the use of a commercial RNA extraction kit date: 2020-08-22 words: 1776.0 sentences: 104.0 pages: flesch: 55.0 cache: ./cache/cord-313541-fpqwzf9k.txt txt: ./txt/cord-313541-fpqwzf9k.txt summary: The growing demand for commercial kits used for automated extraction of SARS-CoV-2 RNA, a key step before rRT-PCR diagnosis, could cause a shortage of stocks that hinders the rapid processing of samples. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction and inactivating samples at 95 °C for 5 minutes, was showed from specimens placed in UTM and molecular water, but not from samples in Hanks medium and saline buffer (Merindol et al., 2020) . Thus, the four different media used in this study (UTM, PBS 1x solution, Hanks medium and DNA/RNA Shield TM ) did not affect analytical results, because all precipitated samples were able to be detected by rRT-PCR using the whole viral panel (Orf1ab, N and S genes) and the internal control gene. Here, a simple protocol to detect SARS-CoV-2 from NPSs using rRT-PCR after a heat inactivation and a precipitation/concentration step is proposed. abstract: The World Health Organization (WHO) has declared a pandemic caused by a new coronavirus named SARS-CoV-2. The growing demand for commercial kits used for automated extraction of SARS-CoV-2 RNA, a key step before rRT-PCR diagnosis, could cause a shortage of stocks that hinders the rapid processing of samples. Although the recommendation is to use automated methods for nucleic acid extraction, alternatives are necessary to replace commercial kits. However, these alternatives should be as reliable as automated methods. This work describes a simple method to detect SARS-CoV-2 from specimens collected in different preservation media. Samples were previously inactivated by heating and precipitating with a PEG/NaCl solution before rRT-PCR assays for Orf1ab, N and S genes. The new method was compared with an automated protocol of nucleic acid extraction. Both procedures showed similar analytical results. Consequently, this simple and inexpensive method is a suitable procedure for laboratory diagnosis of SARS-CoV-2 infection. url: https://doi.org/10.1016/j.jviromet.2020.113960 doi: 10.1016/j.jviromet.2020.113960 id: cord-001985-iwfidoer author: Urayama, Syun-ichi title: FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance date: 2016-02-13 words: 5007.0 sentences: 281.0 pages: flesch: 50.0 cache: ./cache/cord-001985-iwfidoer.txt txt: ./txt/cord-001985-iwfidoer.txt summary: This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. We herein established a novel strategy to obtain full-length RNA virus sequences with extremely high efficiency by applying a short dsRNA full-length cloning method (8) for physically fragmented dsRNAs. The improved method, named FLDS (fragmented and loop primer ligated dsRNA sequencing), was applied to a diatom colony in a tide pool and revealed previously unidentified RNA viruses. These results indicated that FLDS effectively enriched dsRNA reads, thereby allowing the retrieval of complete genome sequences including terminal regions without the requirement for the additional rapid amplification of cDNA ends (RACE). A phylogenetic analysis of RdRp in DCASSRV-2 suggested that the RNA virus was classified into the genus Mitovirus, which has a non-segmented ssRNA genome, infects the mitochondria of fungi, and lacks viral particles (Fig. S4E) . abstract: Knowledge of the distribution and diversity of RNA viruses is still limited in spite of their possible environmental and epidemiological impacts because RNA virus-specific metagenomic methods have not yet been developed. We herein constructed an effective metagenomic method for RNA viruses by targeting long double-stranded (ds)RNA in cellular organisms, which is a hallmark of infection, or the replication of dsRNA and single-stranded (ss)RNA viruses, except for retroviruses. This novel dsRNA targeting metagenomic method is characterized by an extremely high recovery rate of viral RNA sequences, the retrieval of terminal sequences, and uniform read coverage, which has not previously been reported in other metagenomic methods targeting RNA viruses. This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. Our approach will be a powerful tool for cataloging RNA viruses associated with organisms of interest. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4791113/ doi: 10.1264/jsme2.me15171 id: cord-323756-atnrw9ew author: Vabret, Nicolas title: Sensing Microbial RNA in the Cytosol date: 2013-12-25 words: 6409.0 sentences: 355.0 pages: flesch: 45.0 cache: ./cache/cord-323756-atnrw9ew.txt txt: ./txt/cord-323756-atnrw9ew.txt summary: When Janeway formulated the theory of pattern recognition in 1989, he proposed that host cells could sense microbial infection owing to receptors able to recognize invariant molecular structures defined as pathogen-associated molecular patterns (PAMPs). They share a similar organization with three distinct domains: (i) a C-terminal repressor domain (RD) embedded within the C-terminal domain (CTD); (ii) a central ATPase containing DExD/H-box helicase domain able to bind RNA; and (iii) a N-terminal tandem CARD domain that mediates downstream signaling, and which is present in RIG-I and MDA5 but absent in LGP2. DDX60 has also been shown to enhance the IFN-I response to RNA and DNA stimulation through formation of complexes with Frontiers in Immunology | Molecular Innate Immunity RIG-I, MDA5, and LGP2 but not with MAVS. Structural basis for the activation of innate immune pattern-recognition receptor RIG-I by viral RNA Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses abstract: The innate immune system faces the difficult task of keeping a fine balance between sensitive detection of microbial presence and avoidance of autoimmunity. To this aim, key mechanisms of innate responses rely on isolation of pathogens in specialized subcellular compartments, or sensing of specific microbial patterns absent from the host. Efficient detection of foreign RNA in the cytosol requires an additional layer of complexity from the immune system. In this particular case, innate sensors should be able to distinguish self and non-self molecules that share several similar properties. In this review, we discuss this interplay between cytosolic pattern recognition receptors and the microbial RNA they detect. We describe how microbial RNAs gain access to the cytosol, which receptors they activate and counter-strategies developed by microorganisms to avoid this response. url: https://www.ncbi.nlm.nih.gov/pubmed/24400006/ doi: 10.3389/fimmu.2013.00468 id: cord-286416-8eu6wp9b author: Valiente-Echeverría, Fernando title: Viral modulation of stress granules date: 2012-06-14 words: 5570.0 sentences: 290.0 pages: flesch: 49.0 cache: ./cache/cord-286416-8eu6wp9b.txt txt: ./txt/cord-286416-8eu6wp9b.txt summary: If deadenylation (e.g., CCR4/Not1), destabilization (e.g., TTP/XRN1) and decapping (e.g., DCP1/DCP2) complex; and even RISC (Ago) complex are recruited to mRNA, these will be targeted to PBs. Conversely, if TIA-1/TIAR or proteins such as G3BP/USP10 are recruited to the stalled initiation complexes, these will be directed to SGs. Different pathways in SG assembly are described (in red): (i) phosphorylation of eIF2␣ induced by the exposure to different stress inducers (e.g., arsenite and thapsigargin) (Fig. 1) ; (ii) Hippuristanol and Pateamine A, drugs that inhibit the helicase activity of eIF4A altering ATP binding or ATPase activity; and (iii) the overexpression of SG markers, such as G3BP or TIA-1. West Nile virus infections suppress early viral RNA synthesis and avoid inducing the cell stress granule response Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly abstract: Following viral infection, the host responds by mounting a robust anti-viral response with the aim of creating an unfavorable environment for viral replication. As a countermeasure, viruses have elaborated mechanisms to subvert the host response in order to maintain viral protein synthesis and production. In the last decade, several reports have shown that viruses modulate the assembly of stress granules (SGs), which are translationally silent ribonucleoproteins (RNPs) and sites of RNA triage. This review discusses recent advances in our understanding of the interactions between viruses and the host response and how virus-induced modulations in SG abundance play fundamental roles in dictating the success of viral replication. url: https://www.sciencedirect.com/science/article/pii/S0168170212002018 doi: 10.1016/j.virusres.2012.06.004 id: cord-255576-738khdwv author: Van Duyne, Rachel title: Localization and Sub-Cellular Shuttling of HTLV-1 Tax with the miRNA Machinery date: 2012-07-10 words: 9845.0 sentences: 517.0 pages: flesch: 56.0 cache: ./cache/cord-255576-738khdwv.txt txt: ./txt/cord-255576-738khdwv.txt summary: We have previously shown that Tax interacts directly with the cellular Rb (Retinoblastoma) protein and targets Rb for degradation via the proteasome pathway, resulting in a decrease in Rb protein expression in HTLV-1 infected cells and a dysregulation of the cell cycle [47] . Collectively, these data indicate that the Drosha in Tax-containing and HTLV-1 infected cells is mostly functionally inactive and the functional suppression of Drosha is dependent on its interaction with a small region of the N-terminus of Tax. We have shown above that Drosha is downregulated, degraded, and mostly inactive in HTLV-1 infected cells, however, it was not clear what effect this dysregulation of Drosha would have on viral replication. Collectively, these data indicate that proteins, such as IKK-b, among others, may directly be regulated by the Tax/Drosha interaction in HTLV infected cells. abstract: The innate ability of the human cell to silence endogenous retroviruses through RNA sequences encoding microRNAs, suggests that the cellular RNAi machinery is a major means by which the host mounts a defense response against present day retroviruses. Indeed, cellular miRNAs target and hybridize to specific sequences of both HTLV-1 and HIV-1 viral transcripts. However, much like the variety of host immune responses to retroviral infection, the virus itself contains mechanisms that assist in the evasion of viral inhibition through control of the cellular RNAi pathway. Retroviruses can hijack both the enzymatic and catalytic components of the RNAi pathway, in some cases to produce novel viral miRNAs that can either assist in active viral infection or promote a latent state. Here, we show that HTLV-1 Tax contributes to the dysregulation of the RNAi pathway by altering the expression of key components of this pathway. A survey of uninfected and HTLV-1 infected cells revealed that Drosha protein is present at lower levels in all HTLV-1 infected cell lines and in infected primary cells, while other components such as DGCR8 were not dramatically altered. We show colocalization of Tax and Drosha in the nucleus in vitro as well as coimmunoprecipitation in the presence of proteasome inhibitors, indicating that Tax interacts with Drosha and may target it to specific areas of the cell, namely, the proteasome. In the presence of Tax we observed a prevention of primary miRNA cleavage by Drosha. Finally, the changes in cellular miRNA expression in HTLV-1 infected cells can be mimicked by the add back of Drosha or the addition of antagomiRs against the cellular miRNAs which are downregulated by the virus. url: https://www.ncbi.nlm.nih.gov/pubmed/22808228/ doi: 10.1371/journal.pone.0040662 id: cord-243806-26n22jbx author: Vandelli, Andrea title: Structural analysis of SARS-CoV-2 and prediction of the human interactome date: 2020-03-30 words: 5252.0 sentences: 317.0 pages: flesch: 52.0 cache: ./cache/cord-243806-26n22jbx.txt txt: ./txt/cord-243806-26n22jbx.txt summary: Here, we performed sequence and structural alignments among 62 SARS-CoV-2 strains and identified the conservation of specific elements in the spike S region, which provides clues on the evolution of domains involved in the binding to ACE2 and sialic acid. As highly structured regions of RNA molecules have strong propensity to form stable contacts with proteins 14 and promote assembly of specific complexes 15, 16 , SARS-CoV-2 domains enriched in double-stranded content are expected to establish interactions within host cells that are important to replicate the virus 17 . Analysis of functional annotations carried out with GeneMania 46 revealed that proteins interacting with the 5'' of SARS-CoV-2 RNA are associated with regulatory pathways involving NOTCH2, MYC and MAX that have been previously connected to viral infection processes ( Fig. 4E) 47, 48 . abstract: Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of>2500 coronaviruses and computed>100000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We found that the 3 and 5 prime ends are the most structured elements in the viral genome and the 5 prime end has the strongest propensity to associate with human proteins. The domain encompassing nucleotides 23000-24000 is highly conserved both at the sequence and structural level, while the region upstream varies significantly. These two sequences code for a domain of the viral protein Spike S that interacts with the human receptor angiotensin-converting enzyme 2 (ACE2) and has the potential to bind sialic acids. Our predictions indicate that the first 1000 nucleotides in the 5 prime end can interact with proteins involved in viral RNA processing such as double-stranded RNA specific editases and ATP-dependent RNA-helicases, in addition to other high-confidence candidate partners. These interactions, previously reported to be also implicated in HIV, reveal important information on host-virus interactions. The list of transcriptional and post-transcriptional elements recruited by SARS-CoV-2 genome provides clues on the biological pathways associated with gene expression changes in human cells. url: https://arxiv.org/pdf/2003.13655v4.pdf doi: nan id: cord-339209-oe8onyr9 author: Vasilakis, Nikos title: Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range date: 2014-05-20 words: 5817.0 sentences: 272.0 pages: flesch: 46.0 cache: ./cache/cord-339209-oe8onyr9.txt txt: ./txt/cord-339209-oe8onyr9.txt summary: The organization of each genome was similar to that described previously for the mesoniviruses (NDiV, CavV, HanaV, NseV and MenoV), featuring a long 5''-untranslated region (5''-UTR) of 359 to 370 nt, six major long open reading frames (ORFs), and a long terminal region of 1780 to 1804 nt preceding the poly[A] tail ( Figure 2 ). To determine the phylogenetic relationships of the newly identified insect viruses, maximum likelihood (ML) phylogenetic trees were constructed based on the amino acid alignments of ORF2a (unprocessed S protein) and a concatenated region of the highly conserved domains within ORF1ab (3CL pro , RdRp and ZnHel1). A Clustal X alignment of the mesonivirus ORF3a proteins and individual structural analyses using SignalP and TMHMM and NetNGlyc (www.expasy.org) indicated that each is a class I transmembrane glycoprotein with a predicted N-termimal signal peptide, an ectodomain containing a conserved set of 6 cysteine residues and a single conserved N-glycosylation site, a transmembrane domain and a C-terminal cytoplasmic domain ( Figure 4A, 4D) . abstract: BACKGROUND: The family Mesoniviridae (order Nidovirales) comprises of a group of positive-sense, single-stranded RNA ([+]ssRNA) viruses isolated from mosquitoes. FINDINGS: Thirteen novel insect-specific virus isolates were obtained from mosquitoes collected in Indonesia, Thailand and the USA. By electron microscopy, the virions appeared as spherical particles with a diameter of ~50 nm. Their 20,129 nt to 20,777 nt genomes consist of positive-sense, single-stranded RNA with a poly-A tail. Four isolates from Houston, Texas, and one isolate from Java, Indonesia, were identified as variants of the species Alphamesonivirus-1 which also includes Nam Dinh virus (NDiV) from Vietnam and Cavally virus (CavV) from Côte d’Ivoire. The eight other isolates were identified as variants of three new mesoniviruses, based on genome organization and pairwise evolutionary distances: Karang Sari virus (KSaV) from Java, Bontag Baru virus (BBaV) from Java and Kalimantan, and Kamphaeng Phet virus (KPhV) from Thailand. In comparison with NDiV, the three new mesoniviruses each contained a long insertion (180 – 588 nt) of unknown function in the 5’ region of ORF1a, which accounted for much of the difference in genome size. The insertions contained various short imperfect repeats and may have arisen by recombination or sequence duplication. CONCLUSIONS: In summary, based on their genome organizations and phylogenetic relationships, thirteen new viruses were identified as members of the family Mesoniviridae, order Nidovirales. Species demarcation criteria employed previously for mesoniviruses would place five of these isolates in the same species as NDiV and CavV (Alphamesonivirus-1) and the other eight isolates would represent three new mesonivirus species (Alphamesonivirus-5, Alphamesonivirus-6 and Alphamesonivirus-7). The observed spatiotemporal distribution over widespread geographic regions and broad species host range in mosquitoes suggests that mesoniviruses may be common in mosquito populations worldwide. url: https://doi.org/10.1186/1743-422x-11-97 doi: 10.1186/1743-422x-11-97 id: cord-015933-x5cq4k4x author: Verbrugh, H.A. title: 1 Micro-organismen, de mens en het ontstaan van infectieziekten: algemene principes date: 2011 words: 19354.0 sentences: 1625.0 pages: flesch: 54.0 cache: ./cache/cord-015933-x5cq4k4x.txt txt: ./txt/cord-015933-x5cq4k4x.txt summary: Virussen vormen een geheel aparte groep biologische agentia die ziekte bij de mens kunnen veroorzaken; hun meest karakteristieke eigenschap is dat zij voor hun vermeerdering afhankelijk zijn van levende gastheercellen. Dit duidt er dus tevens op dat een micro-organisme over een complex geheel van genetische eigenschappen moet beschikken, wil het pathogene betekenis voor de mens krijgen; dergelijke eigenschappen worden ook wel virulentiefactoren genoemd. Een aantal virussen staat bekend als tumorvirus omdat zij een permanente maligne transformatie in hun gastheercel kunnen teweegbrengen; het virus beïnvloedt dan de transcriptie van specifieke cellulaire oncogenen of andere gastheergenen, genen die betrokken zijn bij de regulatie van celdeling of spontane celdood (apoptose). Hoewel sommige micro-organismen (stafylokokken) zich direct aan dergelijke kunststoffen kunnen hechten, is het in de praktijk zo dat het oppervlak ervan snel door neerslag met bovengenoemde matrixeiwitten als fibronectine wordt bedekt, een proces dat ook wel conditionering van het biomateriaal wordt genoemd. abstract: Infectieziekten zijn te beschouwen als een aparte groep ziekten van de mens. Steeds gaat het om ziekten die het gevolg zijn van een interactie tussen de mens en een ander biologisch agens: een micro-organisme. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120058/ doi: 10.1007/978-90-313-7944-6_1 id: cord-329687-vhi4tbnc author: Verdugo, C. title: A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing. date: 2020-06-03 words: 3497.0 sentences: 207.0 pages: flesch: 61.0 cache: ./cache/cord-329687-vhi4tbnc.txt txt: ./txt/cord-329687-vhi4tbnc.txt summary: title: A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing. However, the most efficient system for massive surveillance, the pre-RNA extraction pooling approach, was obtained with the probe-based assay in test up to 10 samples adding 13.5 uL of RNA template. In this study, we compared a dye-based and probe-based real-time RT-qPCR assay for the economic and rapid detection and quantification of SARS-CoV-2 in human samples by individual and pooling testing. Our results showed that using the dye-based assay describe here, the SARS-CoV-2 can be detected up to 50 viral copies (a dilution of 10 copies/µL) of the RNA template, showing a similar analytical sensitivity obtained with the probe-based standard technique ( Table 2) showed no significant differences in CT values between pooled and individual samples, suggesting that sensitivity was not affected by pooling specimens, regardless of the viral load (Wacharapluesadee et al, 2020). abstract: Effective interventions are mandatory to control the transmission and spread of SARS-CoV-2, a highly contagious virus causing devastating effects worldwide. Cost-effective approaches are pivotal tools required to increase the detection rates and escalate further in massive surveillance programs, especially in countries with limited resources that most of the efforts have focused on symptomatic cases only. Here, we compared the performance of the RT-qPCR using an intercalating dye with the probe-based assay. Then, we tested and compared these two RT-qPCR chemistries in different pooling systems: after RNA extraction (post-RNA extraction) and before RNA extraction (pre-RNA extraction) optimizing by pool size and template volume. We evaluated these approaches in 610 clinical samples. Our results show that the dye-based technique has a high analytical sensitivity similar to the probe-based detection assay used worldwide. Further, this assay may also be applicable in testing by pool systems post-RNA extraction up to 20 samples. However, the most efficient system for massive surveillance, the pre-RNA extraction pooling approach, was obtained with the probe-based assay in test up to 10 samples adding 13.5 uL of RNA template. The low cost and the potential use in pre-RNA extraction pool systems, place of this assays as a valuable resource for scalable sampling to larger populations. Implementing a pool system for population sampling results in an important savings of laboratory resources and time, which are two key factors during an epidemic outbreak. Using the pooling approaches evaluated here, we are confident that it can be used as a valid alternative assay for the detection of SARS-CoV-2 in human samples. url: https://doi.org/10.1101/2020.05.30.20117721 doi: 10.1101/2020.05.30.20117721 id: cord-285505-8norumv6 author: Vere Hodge, R. Anthony title: Meeting report: 27th International conference on antiviral research, in Raleigh, NC, USA date: 2014-09-16 words: 10276.0 sentences: 566.0 pages: flesch: 58.0 cache: ./cache/cord-285505-8norumv6.txt txt: ./txt/cord-285505-8norumv6.txt summary: The focus of John''s presentation was on the research conducted in his own and his collaborators'' laboratories that ultimately led to the invention of three compounds which were discovered to have antiviral activity against human cytomegalovirus (HCMV) and which later entered clinical trials: BDCRB pyranoside (GW275175X) (Phase I), maribavir (Phases I, II and III) and cyclopropavir (Phase I). In monotherapy studies after oral dosing with TDF (300 mg) and TAF (25 mg), the plasma TFV AUC is reduced from 1920 to 268 ng.h/ml respectively whereas the reduction in HIV load from baseline is improved, from log 10 0.97 to log 10 1.46 copies/ml, respectively, reflecting the more efficient delivery of TAF to target cells and tissues. David Margolis, University of North Carolina, NC, USA In HIV-infected patients, there is a long-lasting reservoir of HIV in the form of integrated viral DNA in resting CD4+ memory cells of the host immune system. abstract: The 27th International Conference on Antiviral Research (ICAR) was held in Raleigh, North Carolina, USA from May 12 to 16, 2014. This article summarizes the principal invited lectures. John Drach (Elion Award) described the early days of antiviral drugs and their novel modes of action. Piet Herdewijn (Holý Award) used evolutionary pressure to select DNA polymerases that accept nucleoside analogs. Replacing thymine by 5-chlorouracil led to the generation of a new form of Escherichia coli. Adrian Ray (Prusoff Award) demonstrated how prodrugs can markedly improve both the efficacy and safety of potential drugs. The keynote addresses, by David Margolis and Myron Cohen, tackled two emerging areas of HIV research, to find an HIV “cure” and to prevent HIV transmission, respectively. These topics were discussed further in other presentations – a cure seems to be a distant prospect but there are exciting developments for reducing HIV transmission. TDF-containing vaginal rings and GSK-744, as a long-lasting injection, offer great hope. There were three mini-symposia. Although therapy with TDF/FTC gives excellent control of HBV replication, there are only a few patients who achieve a functional cure. Myrcludex, an entry inhibitor, is active against both HBV and HDV. The recent progress with HBV replication in cell cultures has transformed the search for new antiviral compounds. The HBV capsid protein has been recognized as key player in HBV DNA synthesis. Unexpectedly, compounds which enhance capsid formation, markedly reduce HBV DNA synthesis. The development of BCX4430, which is active against Marburg and Ebola viruses, is of great current interest. url: https://api.elsevier.com/content/article/pii/S0166354214002460 doi: 10.1016/j.antiviral.2014.08.009 id: cord-289926-y1rjgbui author: Veretnik, S. title: RNA binding domain of HDV antigen is homologous to the HMG box of SRY date: 2014-05-18 words: 6679.0 sentences: 309.0 pages: flesch: 53.0 cache: ./cache/cord-289926-y1rjgbui.txt txt: ./txt/cord-289926-y1rjgbui.txt summary: Using sequence analysis methods we have discovered significant sequence similarity between this central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene [40] , whose product binds to DNA and is essential for sex determination. The sequence similarity between the central domain of HDAg and the HMG (High Mobility Group) box of the SRY gene suggests that SRY may be a cellular cognate of HDAg. Another candidate for the ''captured'' cellular RNA was recently proposed: a 202 residue cellular protein referred to as DIPA (delta interacting protein A) was identified by co-immunoprecipitation with HDAg and by its in vivo ability to inhibit viral replication [5] . Statistically significant sequence similarities are limited to the functionally essential regions of both genes: in the SRY gene the similarity is confined to the HMG (High Mobility Group) box, a DNA binding motif found in the HMG protein superfamily [24, 31] , in HDAg the similarity is limited to RNA-binding domain. abstract: The delta antigen of hepatitis delta virus exhibits sequence specific binding to its own RNA and is essential for viral replication. Using statistical methods we have detected significant similarity between the RNA-binding domain of the hepatitis delta antigen and the HMG box of SRY. Our analysis suggests that the RNA-binding domain of HDV antigen evolved from the DNA-binding domain of the HMG box. SRY, or a related protein, is a probable cellular cognate of HDV. url: https://www.ncbi.nlm.nih.gov/pubmed/10446649/ doi: 10.1007/s007050050575 id: cord-277566-j3ehiwn9 author: Verheije, Monique H. title: Mouse Hepatitis Coronavirus RNA Replication Depends on GBF1-Mediated ARF1 Activation date: 2008-06-13 words: 8918.0 sentences: 449.0 pages: flesch: 49.0 cache: ./cache/cord-277566-j3ehiwn9.txt txt: ./txt/cord-277566-j3ehiwn9.txt summary: Here, we study the involvement of the secretory pathway in mouse hepatitis coronavirus (MHV) replication by using the drug brefeldin A (BFA), which is known to interfere with ER-Golgi membrane traffic by inhibiting the activation of ADP-ribosylation factor (ARF) small GTPases. Therefore, LR7 cells infected with MHV-A59 were treated with BFA for 30 minutes starting 5.5 h p.i. They were subsequently fixed and processed for immunofluorescence using antibodies both against nsp8, which served as a protein marker for the MHV replication sites [50, 51] , and against the viral structural protein M, known to reside in the Golgi [52] . In complete agreement with the luciferase expression data shown above, this result demonstrates that BFA inhibits, but does not completely block, the formation of RCs. To study the effects of BFA on the DMVs at an ultrastructural level, MHV-infected LR7 cells were fixed at 6 h p.i. and embedded in Epon resin in order to be analyzed by electron microscopy. abstract: Coronaviruses induce in infected cells the formation of double membrane vesicles, which are the sites of RNA replication. Not much is known about the formation of these vesicles, although recent observations indicate an important role for the endoplasmic reticulum in the formation of the mouse hepatitis coronavirus (MHV) replication complexes (RCs). We now show that MHV replication is sensitive to brefeldin A (BFA). Consistently, expression of a dominant-negative mutant of ARF1, known to mimic the action of the drug, inhibited MHV infection profoundly. Immunofluorescence analysis and quantitative electron microscopy demonstrated that BFA did not block the formation of RCs per se, but rather reduced their number. MHV RNA replication was not sensitive to BFA in MDCK cells, which are known to express the BFA-resistant guanine nucleotide exchange factor GBF1. Accordingly, individual knockdown of the Golgi-resident targets of BFA by transfection of small interfering RNAs (siRNAs) showed that GBF1, but not BIG1 or BIG2, was critically involved in MHV RNA replication. ARF1, the cellular effector of GBF1, also appeared to be involved in MHV replication, as siRNAs targeting this small GTPase inhibited MHV infection significantly. Collectively, our results demonstrate that GBF1-mediated ARF1 activation is required for efficient MHV RNA replication and reveal that the early secretory pathway and MHV replication complex formation are closely connected. url: https://doi.org/10.1371/journal.ppat.1000088 doi: 10.1371/journal.ppat.1000088 id: cord-007621-rapinodd author: Vidovic, Maria title: Induction and regulation of class II major histocompatibility complex mRNA expression in astrocytes by interferon-γ and tumor necrosis factor-α date: 2002-11-13 words: 6680.0 sentences: 365.0 pages: flesch: 57.0 cache: ./cache/cord-007621-rapinodd.txt txt: ./txt/cord-007621-rapinodd.txt summary: Previous data from this laboratory had shown that the cytokine tumor necrosis factor-α (TNF-α) enhances IFN-γ-mediated class II antigen expression on astrocytes. To determine the steady-state level of mRNA for class II, Northern blot analysis was performed using a eDNA probe for murine class Ii genes (E-a), with total RNA isolated from cultured astrocytes. The duration of protein synthesis required to allow expression of the class II MHC gene in astrocytes was examined in cells that were pretreated with IFN-y or IFN-7/TNF-a for different lengths of time prior to the addition of CHX. In this study we have shown that primary neonatal rat astrocytes, upon stimulation with IFN-~,, express mRNA transcripts for class II MHC genes, and that TNF-a enhances the expression of IFN-~,-induced class II mRNA. The expression of class II mRNA was completely inhibited when CHX was included with IFN-~, and IFN-''t/TNF-~ treatment, indicating that newly synthesized protein is required for astrocyte class II MHC gene expression. abstract: Astrocytes can function as antigen-presenting cells (APC) upon expression of class II major histocompatibility complex (MHC) antigens, which are induced by interferon-γ (IFN-γ). Previous data from this laboratory had shown that the cytokine tumor necrosis factor-α (TNF-α) enhances IFN-γ-mediated class II antigen expression on astrocytes. We have now investigated the effect of IFN-γ and TNF-α on class II MHC mRNA expression in astrocytes using Northern blot analysis. Astrocytes do not constitutively express mRNA for class II MHC. Kinetic analysis of class II MHC mRNA expression in IFN-γ-treated cells demonstrated an 8 h time lag, which was followed by an increase over the next 16 h. Optimal expression of class II mRNA was detected after a 24 h incubation with IFN-γ. This level of expression was further enhanced by the simultaneous addition of IFN-γ and TNF-α to the astrocytes, while TNF-α alone had no effect on class II mRNA expression. TNF-α does not act by increasing the stability of IFN-γ-induced class II mRNA, indicating its action is not at that specific level of post-transcriptional control. Furthermore, astrocyte class II mRNA expression was inhibited when cycloheximide (CHX) was added together with IFN-γ or IFN-γ/TNF-α, and when CHX was added up to 4 h after treatment with IFN-γ or IFN-γ/TNF-α. These results indicate that astrocyte class II mRNA expression is mediated by newly synthesized proteins induced by IFN-γ and/or IFN-γ/TNF-α. The expression of class II antigens on astrocytes, and cytokine modulation of their expression, may be important in the initiation and perpetuation of intracerebral immune responses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7119667/ doi: 10.1016/0165-5728(90)90103-t id: cord-016095-jop2rx61 author: Vignais, Pierre V. title: Challenges for Experimentation on Living Beings at the Dawn of the 21(st) Century date: 2010-06-08 words: 42843.0 sentences: 1503.0 pages: flesch: 43.0 cache: ./cache/cord-016095-jop2rx61.txt txt: ./txt/cord-016095-jop2rx61.txt summary: Instead of setting out to discover unknown mechanisms by analyzing effects that are dependent on specific causes, with some uncertainty as to the possible success of the enterprise being undertaken, which is the foundation stone of the Bernardian paradigm of the experimental method, many current research projects give themselves achievable and programmable objectives that depend upon the means available to them: sequencing of genomes with a view to comparing them, recognition of sequence similarities in proteins coded for by genes belonging to different species, with the aim of putting together phylogenetic trees, synthesis of interesting proteins in transgenic animals and plants, analysis of the three-dimensional structure of proteins, in order to find sites that are likely to fix medicinal substances, and synthesis of molecular species able to recognize pathogenic targets. abstract: “We can talk endlessly about moral progress, about social progress, about poetic progress, about progress made in happiness; nevertheless, there is a type of progress that defies any discussion, and that is scientific progress, as soon as we judge it within the hierarchy of knowledge, from a specifically intellectual point of view.” url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7120277/ doi: 10.1007/978-90-481-3767-1_5 id: cord-318495-1w74wf02 author: Vignuzzi, Marco title: Defective viral genomes are key drivers of the virus–host interaction date: 2019-06-03 words: 8876.0 sentences: 429.0 pages: flesch: 33.0 cache: ./cache/cord-318495-1w74wf02.txt txt: ./txt/cord-318495-1w74wf02.txt summary: The demonstration of hotspots for the generation of copyback DVGs from respiratory syncytial virus (RSV) and the identification of specific nucleotides that determine where copy-back DVGs rejoin further demonstrate that the generation of copy-back DVGs is not completely random, but instead that specific sequences encoded in the viral genome direct or facilitate their formation 50 in some infections, DVG generation is not a completely stochastic process and, instead, virus-encoded sequences favour the production and/or amplification of predominant DVGs. It remains to be determined whether conservation is a property of certain DVG types and which specific sequences and/or RNA structures lead to DVG generation in these conditions. Persistent infection with infectious pancreatic necrosis virus mediated by defective-interfering (DI) virus particles in a cell line showing strong interference but little DI replication I Interferon-inducing defective-interfering particles as mediators of cell sparing: possible role in persistent infection by vesicular stomatitis virus abstract: Viruses survive often harsh host environments, yet we know little about the strategies they utilize to adapt and subsist given their limited genomic resources. We are beginning to appreciate the surprising versatility of viral genomes and how replication-competent and -defective virus variants can provide means for adaptation, immune escape and virus perpetuation. This Review summarizes current knowledge of the types of defective viral genomes generated during the replication of RNA viruses and the functions that they carry out. We highlight the universality and diversity of defective viral genomes during infections and discuss their predicted role in maintaining a fit virus population, their impact on human and animal health, and their potential to be harnessed as antiviral tools. url: https://doi.org/10.1038/s41564-019-0465-y doi: 10.1038/s41564-019-0465-y id: cord-343604-v986m9jd author: Vijayakumar, Balaji Gowrivel title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 date: 2020-08-06 words: 1258.0 sentences: 90.0 pages: flesch: 47.0 cache: ./cache/cord-343604-v986m9jd.txt txt: ./txt/cord-343604-v986m9jd.txt summary: title: In silico pharmacokinetic and molecular docking studies of natural flavonoids and synthetic indole chalcones against essential proteins of SARS-CoV-2 Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential. Coronavirus main 403 proteinase (3CLpro) structure: basis for design of anti-SARS drugs Structural basis for inhibition 675 of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is distinctly infective and there is an ongoing effort to find a cure for this pandemic. Flavonoids exist in many diets as well as in traditional medicine, and their modern subset, indole-chalcones, are effective in fighting various diseases. Hence, these flavonoids and structurally similar indole chalcones derivatives were studied in silico for their pharmacokinetic properties including absorption, distribution, metabolism, excretion, toxicity (ADMET) and anti-SARS-CoV-2 properties against their proteins, namely, RNA dependent RNA polymerase (rdrp), main protease (M(pro)) and Spike (S) protein via homology modelling and docking. Interactions were studied with respect to biology and function of SARS-CoV-2 proteins for activity. Functional/structural roles of amino acid residues of SARS-CoV-2 proteins and, the effect of flavonoid and indole chalcone interactions which may cause disease suppression are discussed. The results reveal that 30 compounds are capable of M(pro) deactivation as well as potentially lowering the efficiency of M(pro) function. Cyanidin may inhibit RNA polymerase function and, Quercetin is found to block interaction sites on the viral spike. These results suggest flavonoids and their modern pharmaceutical cousins, indole chalcones are capable of fighting SARS-CoV-2. The in vitro anti-SARS-CoV-2 activity of these 30 compounds needs to be studied further for complete understanding and confirmation of their inhibitory potential. url: https://api.elsevier.com/content/article/pii/S0014299920305409 doi: 10.1016/j.ejphar.2020.173448 id: cord-002179-v8lpw4r7 author: Viktorovskaya, Olga V. title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements date: 2016-08-24 words: 8021.0 sentences: 418.0 pages: flesch: 49.0 cache: ./cache/cord-002179-v8lpw4r7.txt txt: ./txt/cord-002179-v8lpw4r7.txt summary: title: Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements Previously, we have described a high-throughput mass spectrometry method termed TUX-MS (thiouracil cross-linking mass spectrometry) to identify host factors that interact with viral RNA during a live infection in cell culture [15] . Development of a quantitative thiouridine cross-linking mass spectrometry (qTUX-MS) method for identification of proteins associated with the DENV RNA TUX-MS can be used to identify host factors by incorporating 4-thiouridine (4sU), a zero-distance cross-linker, into the viral RNA (vRNA) to enable cross-linking of proteins bound to vRNA during a live infection in cell culture [15] . Since some of hnRNPs are known to modulate cellular gene expression in response to dengue infection [60, 61] , we can not rule out that some of the observed effects on virus titers derive from their roles in regulating host mRNAs. Among the numerous qTUX-MS identified factors of interest, our study is the first to demonstrate the involvement of HMCES (or C3orf37) in viral infection. abstract: BACKGROUND: There are currently no vaccines or antivirals available for dengue virus infection, which can cause dengue hemorrhagic fever and death. A better understanding of the host pathogen interaction is required to develop effective therapies to treat DENV. In particular, very little is known about how cellular RNA binding proteins interact with viral RNAs. RNAs within cells are not naked; rather they are coated with proteins that affect localization, stability, translation and (for viruses) replication. METHODOLOGY/PRINCIPAL FINDINGS: Seventy-nine novel RNA binding proteins for dengue virus (DENV) were identified by cross-linking proteins to dengue viral RNA during a live infection in human cells. These cellular proteins were specific and distinct from those previously identified for poliovirus, suggesting a specialized role for these factors in DENV amplification. Knockdown of these proteins demonstrated their function as viral host factors, with evidence for some factors acting early, while others late in infection. Their requirement by DENV for efficient amplification is likely specific, since protein knockdown did not impair the cell fitness for viral amplification of an unrelated virus. The protein abundances of these host factors were not significantly altered during DENV infection, suggesting their interaction with DENV RNA was due to specific recruitment mechanisms. However, at the global proteome level, DENV altered the abundances of proteins in particular classes, including transporter proteins, which were down regulated, and proteins in the ubiquitin proteasome pathway, which were up regulated. CONCLUSIONS/SIGNIFICANCE: The method for identification of host factors described here is robust and broadly applicable to all RNA viruses, providing an avenue to determine the conserved or distinct mechanisms through which diverse viruses manage the viral RNA within cells. This study significantly increases the number of cellular factors known to interact with DENV and reveals how DENV modulates and usurps cellular proteins for efficient amplification. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4996428/ doi: 10.1371/journal.pntd.0004921 id: cord-264884-ydkigome author: Villarreal, Luis P. title: The Widespread Evolutionary Significance of Viruses date: 2008-07-05 words: 23138.0 sentences: 1203.0 pages: flesch: 47.0 cache: ./cache/cord-264884-ydkigome.txt txt: ./txt/cord-264884-ydkigome.txt summary: For example, common structural motifs from phage to eukaryotic DNA viruses (T4 and herpesvirus) suggest very ancient links in virus evolution that span all domains of life (see below). On an evolutionary time-scale, the majority of viral lineages tend to exist as species-specifi c persistent (aka temperate, latent, and chronic) infections in which individual hosts will be colonized by mostly silent (asymptomatic) viruses for the duration of their life . It has distinct genetic, fi tness, and evolutionary characteristics that require intimate, host (tissue)-specifi c viral strategies and precise gene functions to attain stable maintenance in the presence of immunity and to allow biologically controlled reactivation. Thus, the phycodnaviruses appear to represent a basal but diverse viral lineage that has both acute and persistent lifestyle and have some clear relationships to most large eukaryotic DNA viruses and many phage. abstract: In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution. This chapter reviews the developments that have brought us to this new appreciation for the general significance of virus evolution to all life. We now know that viruses numerically dominate all habitats of life, especially the oceans. Theoretical developments in the 1970s regarding quasispecies, error rates, and error thresholds have yielded many practical insights into virus–host dynamics. The human diseases of HIV-1 and hepatitis C virus cannot be understood without this evolutionary framework. Yet recent developments with poliovirus demonstrate that viral fitness can be the result of a consortia, not one fittest type, a basic Darwinian concept in evolutionary biology. Darwinian principles do apply to viruses, such as with Fisher population genetics, but other features, such as reticulated and quasispecies-based evolution distinguish virus evolution from classical studies. The available phylogenetic tools have greatly aided our analysis of virus evolution, but these methods struggle to characterize the role of virus populations. Missing from many of these considerations has been the major role played by persisting viruses in stable virus evolution and disease emergence. In many cases, extreme stability is seen with persisting RNA viruses. Indeed, examples are known in which it is the persistently infected host that has better survival. We have also recently come to appreciate the vast diversity of phage (DNA viruses) of prokaryotes as a system that evolves by genetic exchanges across vast populations (Chapter 10). This has been proposed to be the “big bang” of biological evolution. In the large DNA viruses of aquatic microbes we see surprisingly large, complex and diverse viruses. With both prokaryotic and eukaryotic DNA viruses, recombination is the main engine of virus evolution, and virus host co-evolution is common, although not uniform. Viral emergence appears to be an unending phenomenon and we can currently witness a selective sweep by retroviruses that infect and become endogenized in koala bears. url: https://api.elsevier.com/content/article/pii/B9780123741530000217 doi: 10.1016/b978-0-12-374153-0.00021-7 id: cord-281281-knelqmzx author: Villas-Boas, Gustavo R. title: The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents date: 2020-09-07 words: 15780.0 sentences: 708.0 pages: flesch: 42.0 cache: ./cache/cord-281281-knelqmzx.txt txt: ./txt/cord-281281-knelqmzx.txt summary: The use of bioinformatics and other computational tools in addition to molecular modeling has helped researchers from different areas in the search for strategies for diagnosing viral infection, in the development of vaccines for its prevention, as well as in the discovery of new anti-SARS-CoV-2 agents. In the context of COVID-19, this characteristic was important for a better understanding of the origin of SARS-CoV-2 from the comparative analysis of genomic data of the new virus with others from the same family, suggesting its origin from natural selection, with modifications in its spike protein, more specifically in the host receptor binding domain, which may have enhanced its interaction and recognition by the human cell [83, 91] . The contributions of bioinformatics and molecular modeling in elucidating essential targets for the planning and development of new drugs, and the analysis of already known compounds, support the search for safer and more effective treatments against SARS-CoV-2 infection. abstract: On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, there is no doubt that the coronavirus has overloaded health systems globally. Practical actions against the recent emergence and rapid expansion of the SARS-CoV-2 require the development and use of tools for discovering new molecular anti-SARS-CoV-2 targets. Thus, this review presents bioinformatics and molecular modeling strategies that aim to assist in the discovery of potential anti-SARS-CoV-2 agents. Besides, we reviewed the relationship between SARS-CoV-2 and innate immunity, since understanding the structures involved in this infection can contribute to the development of new therapeutic targets. Bioinformatics is a technology that assists researchers in coping with diseases by investigating genetic sequencing and seeking structural models of potential molecular targets present in SARS-CoV2. The details provided in this review provide future points of consideration in the field of virology and medical sciences that will contribute to clarifying potential therapeutic targets for anti-SARS-CoV-2 and for understanding the molecular mechanisms responsible for the pathogenesis and virulence of SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32906733/ doi: 10.3390/molecules25184086 id: cord-277318-cwuls6xs author: Visscher, Koen title: −1 Programmed Ribosomal Frameshifting as a Force-Dependent Process date: 2016-02-02 words: 8568.0 sentences: 455.0 pages: flesch: 48.0 cache: ./cache/cord-277318-cwuls6xs.txt txt: ./txt/cord-277318-cwuls6xs.txt summary: 13 A recent single-molecule experiment indicates that ribosome helicase action during the translational elongation cycle may be twofold: it destabilizes the helical junction at the mRNA entry site favoring an open conformation, and it appears to pull mRNA strands apart during the translocation step when relatively large structural rearrangements occur on the ribosome. 26 We will review methods and experiments that apply force to the single molecules to determine the mechanical properties of codon-anticodon interaction at the slippery site, the stability of downstream mRNA structure motifs that give rise to −1 PRF, and elastic properties of the ssRNA elasticity bridging those elements. 104, 105 Single-molecule assays that probe the codon-anticodon dynamics at the slippery sequence and investigate the force dependence of the translation elongational cycle (discussed later in the chapter; see Fig. 8 ) should be fit to answer these questions and allow unfolding of −1 PRF mRNA structure motifs held at the ribosome''s entry site. abstract: −1 Programmed ribosomal frameshifting is a translational recoding event in which ribosomes slip backward along messenger RNA presumably due to increased tension disrupting the codon–anticodon interaction at the ribosome's coding site. Single-molecule physical methods and recent experiments characterizing the physical properties of mRNA's slippery sequence as well as the mechanical stability of downstream mRNA structure motifs that give rise to frameshifting are discussed. Progress in technology, experimental assays, and data analysis methods hold promise for accurate physical modeling and quantitative understanding of −1 programmed ribosomal frameshifting. url: https://doi.org/10.1016/bs.pmbts.2015.11.003 doi: 10.1016/bs.pmbts.2015.11.003 id: cord-304306-rxjahqwh author: Vlachakis, Dimitrios title: Molecular mechanisms of the novel coronavirus SARS-CoV-2 and potential anti-COVID19 pharmacological targets since the outbreak of the pandemic date: 2020-10-08 words: 8517.0 sentences: 459.0 pages: flesch: 48.0 cache: ./cache/cord-304306-rxjahqwh.txt txt: ./txt/cord-304306-rxjahqwh.txt summary: The currently available antiviral option for hospitalized patients is remdesivir, which may inhibit the replication process by targeting the RdRp. Previously proposed treatments for hospitalized patients included hydroxychloroquine, which thought to disrupt virus endocytosis, and lopinavir/ritonavir, which thought to inhibit SARs-CoV-2 main protease (Astuti and Ysrafil, 2020; Magro, 2020) . Silibilin is predicted to have a dual activity against SARS-CoV-2 infection; silibilin can potentially reduce viral replication activity by targeting NSP12 as a remdesivir-like inhibitor, and modulate inflammatory responses by direct inhibition of STAT3 (BoschBarrera et al., 2020) . A recombinant form of the human ACE2 protein was synthesized as a therapeutic treatment for COVID-19, functioning as a decoy for SARS-CoV-2 and essentially preventing the virus from binding to the cell surface ACE2 (Schuster et al., 2010) . Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An overview of viral structure and host response abstract: The novel coronavirus SARS-CoV-2 has emerged as a severe threat against public health and global economies. COVID-19, the disease caused by this virus, is highly contagious and has led to an ongoing pandemic. SARS-CoV-2 affects, mainly, the respiratory system, with most severe cases primarily showcasing acute respiratory distress syndrome. Currently, no targeted therapy exists, and since the number of infections and death toll keeps rising, it has become a necessity to study possible therapeutic targets. Antiviral drugs can target various stages of the viral infection, and in the case of SARS-CoV-2, both structural and non-structural proteins have been proposed as potential drug targets. This review focuses on the most researched SARS-CoV-2 proteins, their structure, function, and possible therapeutic approaches. url: https://doi.org/10.1016/j.fct.2020.111805 doi: 10.1016/j.fct.2020.111805 id: cord-354114-frdsct44 author: Vogel, Liesbeth title: Pathogenic characteristics of persistent feline enteric coronavirus infection in cats date: 2010-07-23 words: 5339.0 sentences: 266.0 pages: flesch: 53.0 cache: ./cache/cord-354114-frdsct44.txt txt: ./txt/cord-354114-frdsct44.txt summary: FECV is associated with asymptomatic persistent enteric infections, while FIPV causes feline infectious peritonitis (FIP), a usually fatal systemic disease in domestic cats and some wild Felidae. Faecal virus, i.e. genomic RNA, was detected during persistent FECV infection only in the large intestine, downstream of the appendix, and could occasionally be observed also in the blood. The cats were monitored for clinical signs, body weight, faecal virus shedding and serum antibody titres for 70 days post inoculation. In all animals, the amount of virus in the faeces subsequently increased within two days to peak levels of 10 6 -10 8 genomes/lL faeces, after which shedding remained high for an extended period until day 16 and day 23 post inoculation in FECV UCD and FECV RM infected cats, respectively. In order to determine in which part(s) of the gut virus was present during viral persistence, we screened the contents of the entire intestines of two FECV UCD infected cats. abstract: Feline coronaviruses (FCoV) comprise two biotypes: feline enteric coronaviruses (FECV) and feline infectious peritonitis viruses (FIPV). FECV is associated with asymptomatic persistent enteric infections, while FIPV causes feline infectious peritonitis (FIP), a usually fatal systemic disease in domestic cats and some wild Felidae. FIPV arises from FECV by mutation. FCoV also occur in two serotypes, I and II, of which the serotype I viruses are by far the most prevalent in the field. Yet, most of our knowledge about FCoV infections relates to serotype II viruses, particularly about the FIPV, mainly because type I viruses grow poorly in cell culture. Hence, the aim of the present work was the detailed study of the epidemiologically most relevant viruses, the avirulent serotype I viruses. Kittens were inoculated oronasally with different doses of two independent FECV field strains, UCD and RM. Persistent infection could be reproducibly established. The patterns of clinical symptoms, faecal virus shedding and seroconversion were monitored for up to 10 weeks revealing subtle but reproducible differences between the two viruses. Faecal virus, i.e. genomic RNA, was detected during persistent FECV infection only in the large intestine, downstream of the appendix, and could occasionally be observed also in the blood. The implications of our results, particularly our insights into the persistently infected state, are discussed. url: https://www.ncbi.nlm.nih.gov/pubmed/20663472/ doi: 10.1051/vetres/2010043 id: cord-297776-k38jssr0 author: Volk, Aaron title: Coronavirus Endoribonuclease and Deubiquitinating Interferon Antagonists Differentially Modulate the Host Response during Replication in Macrophages date: 2020-05-18 words: 5843.0 sentences: 293.0 pages: flesch: 42.0 cache: ./cache/cord-297776-k38jssr0.txt txt: ./txt/cord-297776-k38jssr0.txt summary: gene expression, we report significant transcriptional upregulation of multiple genes associated with activation of ER sensors IRE1, ATF6, and PERK, such as Edem1, Hspa5 (encoding BiP protein), and Ddit3 (encoding CHOP), in response to virus replication, with the most robust response detected in cells infected with the wild-type or DUBmut virus infection (Fig. 5B, C, and D) . Overall, these differential gene expression analyses in macrophages reveal similar host responses to the wild-type and DUBmut viruses that include activation of UPR pathways and proinflammatory genes, whereas a distinct transcriptional profile during infection with the EndoUmut virus is predominately defined by a focused, robust antiviral response. The results presented here, and from studies of the MERS-CoV dORF3-5 mutant virus (26) Upon infection of a BMDM with EndoUmut, host double-stranded RNA (dsRNA) sensors (including MDA5, PKR, and OAS) are activated, resulting in robust transcription of type I IFN genes and rapid induction of apoptosis, the latter of which precludes the development of a potent inflammatory response. abstract: Coronaviruses (CoVs) encode multiple interferon (IFN) antagonists that modulate the host response to virus replication. Here, we evaluated the host transcriptional response to infection with murine coronaviruses encoding independent mutations in one of two different viral antagonists, the deubiquitinase (DUB) within nonstructural protein 3 or the endoribonuclease (EndoU) within nonstructural protein 15. We used transcriptomics approaches to compare the scope and kinetics of the host response to the wild-type (WT), DUBmut, and EndoUmut viruses in infected macrophages. We found that the EndoUmut virus activates a focused response that predominantly involves type I interferons and interferon-related genes, whereas the WT and DUBmut viruses more broadly stimulate upregulation of over 2,800 genes, including networks associated with activating the unfolded protein response (UPR) and the proinflammatory response associated with viral pathogenesis. This study highlights the role of viral interferon antagonists in shaping the kinetics and magnitude of the host response during virus infection and demonstrates that inactivating a dominant viral antagonist, the coronavirus endoribonuclease, dramatically alters the host response in macrophages. IMPORTANCE Macrophages are an important cell type during coronavirus infections because they “notice” the infection and respond by inducing type I interferons, which limits virus replication. In turn, coronaviruses encode proteins that mitigate the cell’s ability to signal an interferon response. Here, we evaluated the host macrophage response to two independent mutant coronaviruses, one with reduced deubiquitinating activity (DUBmut) and the other containing an inactivated endoribonuclease (EndoUmut). We observed a rapid, robust, and focused response to the EndoUmut virus, which was characterized by enhanced expression of interferon and interferon-related genes. In contrast, wild-type virus and the DUBmut virus elicited a more limited interferon response and ultimately activated over 2,800 genes, including players in the unfolded protein response and proinflammatory pathways associated with progression of significant disease. This study reveals that EndoU activity substantially contributes to the ability of coronaviruses to evade the host innate response and to replicate in macrophages. url: https://www.ncbi.nlm.nih.gov/pubmed/32188729/ doi: 10.1128/jvi.00178-20 id: cord-276198-psjua913 author: V’kovski, Philip title: New insights on the role of paired membrane structures in coronavirus replication date: 2015-04-16 words: 6083.0 sentences: 303.0 pages: flesch: 44.0 cache: ./cache/cord-276198-psjua913.txt txt: ./txt/cord-276198-psjua913.txt summary: Many nidovirus and all coronavirus TM1 proteins contain one or more ubiquitin-like domains which may help to anchor the viral RNA to the membranes where replication takes place (Hurst et al., 2013) . The maze-like paired-membrane structures that resulted from coexpression of SARS-CoV TM1 and TM2 have not ever been reported in coronavirus-infected cells, suggesting that this should be interpreted as a conditional, or perhaps partial phenotype, that is not observed when the full viral replicase polyprotein is expressed. Since DMVs are reminiscent of the double-membranes of autophagosomes, several lines of controversial evidence hypothesized a diversion of Atg (autophagyrelated) proteins and autophagosome function during coronavirus replication, as it is the case for other +RNA viruses (Prentice et al., 2004; Snijder et al., 2006; Zhao et al., 2007; Maier and Britton, 2012; Richards and Jackson, 2013) . Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex abstract: The replication of coronaviruses, as in other positive-strand RNA viruses, is closely tied to the formation of membrane-bound replicative organelles inside infected cells. The proteins responsible for rearranging cellular membranes to form the organelles are conserved not just among the Coronaviridae family members, but across the order Nidovirales. Taken together, these observations suggest that the coronavirus replicative organelle plays an important role in viral replication, perhaps facilitating the production or protection of viral RNA. However, the exact nature of this role, and the specific contexts under which it is important have not been fully elucidated. Here, we collect and interpret the recent experimental evidence about the role and importance of membrane-bound organelles in coronavirus replication. url: https://api.elsevier.com/content/article/pii/S0168170214005358 doi: 10.1016/j.virusres.2014.12.021 id: cord-345817-rrf3dbnb author: WOOD, Lisa G. title: Persistence of rhinovirus RNA and IP‐10 gene expression after acute asthma date: 2011-01-27 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Background and objective: Viral nucleic acid may be detected for up to 6 months after an acute asthma deterioration, but the pattern and consequences of viral persistence after acute asthma are incompletely understood. This study investigates the frequency of viral persistence after acute asthma, assesses viral infectivity and determines the host inflammatory responses to viral persistence. Methods: Adults and children presenting to hospital with acute asthma and a confirmed respiratory virus infection were studied acutely and at recovery 4–6 weeks later by clinical evaluation and induced sputum for viral and inflammatory mediator detection. Results: Viral RNA was detected during both acute asthma and recovery visits in 17 subjects (viral persistence), whereas in 22 subjects viral RNA had cleared by recovery (viral clearance). The following viruses were detected at recovery: human rhinovirus: 16; respiratory syncytial virus: 2; influenza: 2. In subjects with viral persistence, eight isolates were different to the virus detected at Visit 1. Forty‐four per cent of the human rhinovirus isolates were infective at recovery. Asthma and infection severity were similar in the viral clearance and viral persistence groups. Viral persistence was associated with elevated IL‐10 mRNA and inducible protein‐10 gene expression. Conclusions: Respiratory viral detection after acute asthma is common, and most often persistence is with non‐infective human rhinovirus. There is a host inflammatory response with an altered cytokine environment, and the viral RNA can be source of persistent infection. These effects may have longer‐term consequences in asthma. url: https://www.ncbi.nlm.nih.gov/pubmed/21054674/ doi: 10.1111/j.1440-1843.2010.01897.x id: cord-347532-n51qv9pp author: Wacharapluesadee, Supaporn title: Group C Betacoronavirus in Bat Guano Fertilizer, Thailand date: 2013-08-17 words: 1191.0 sentences: 71.0 pages: flesch: 54.0 cache: ./cache/cord-347532-n51qv9pp.txt txt: ./txt/cord-347532-n51qv9pp.txt summary: To the Editor: Bats play a critical role in the transmission and origin of zoonotic diseases, primarily viral zoonoses associated with high casefatality rates, including those caused by Nipah virus (NiV) and severe acute respiratory syndrome (SARS)-like coronavirus (CoV) infections (1) . To assess pathogens in bat guano, we examined bat guano from a cave in the Khao Chong Phran Non-hunting Area (KCP-NHA) in Ratchaburi Province, Thailand, where bat guano was sold as agricultural fertilizer, for the presence of NiV, CoV, and H. The detection of CoVs in bat guano from the KCP-NHA cave in Ratchaburi was consistent with the previous finding of alphacoronavirus from Hipposideros armiger bats from the same province in 2007, but those researchers tested fresh bat feces (9) . Duplex nested RT-PCR for detection of Nipah virus RNA from urine specimens of bats abstract: nan url: https://doi.org/10.3201/eid1908.130119 doi: 10.3201/eid1908.130119 id: cord-272576-ez731lif author: Wada, Yoshiko title: Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count date: 2016-11-03 words: 5641.0 sentences: 273.0 pages: flesch: 50.0 cache: ./cache/cord-272576-ez731lif.txt txt: ./txt/cord-272576-ez731lif.txt summary: To face the world-wide threats caused by zoonotic RNA viruses, which suddenly cause serious outbreaks by invasion from nonhuman hosts and mutate rapidly, we must understand the molecular evolutionary changes in their genome sequences extensively by innovating various technologies, including those used in big data analyses, e.g., large-scale word count. The present time-series analysis on influenza A genomes showed that the 20-mers exhibiting the most evident directional changes observed in common for three different subtypes corresponded to several influenza A siRNAs, which were experimentally validated. The present study focused on time-series changes, but not on data variations caused largely by random mutations and sequencing uncertainty, and therefore, average characteristics of strains isolated in a similar period were analyzed, summing up the sequences isolated in one month and calculating an averaged mononucleotide composition for each month (Fig. 1b) . abstract: Ebolavirus, MERS coronavirus and influenza virus are zoonotic RNA viruses, which mutate very rapidly. Viral growth depends on many host factors, but human cells may not provide the ideal growth conditions for viruses invading from nonhuman hosts. The present time-series analyses of short and long oligonucleotide compositions in these genomes showed directional changes in their composition after invasion from a nonhuman host, which are thought to recur after future invasions. In the recent West Africa Ebola outbreak, directional time-series changes in a wide range of oligonucleotides were observed in common for three geographic areas, and the directional changes were observed also for the recent MERS coronavirus epidemics starting in the Middle East. In addition, common directional changes in human influenza A viruses were observed for three subtypes, whose epidemics started independently. Long oligonucleotides that showed an evident directional change observed in common for the three subtypes corresponded to some of influenza A siRNAs, whose activities have been experimentally proven. Predicting directional and reoccurring changes in oligonucleotide composition should become important for designing diagnostic RT-PCR primers and therapeutic oligonucleotides with long effectiveness. url: https://www.ncbi.nlm.nih.gov/pubmed/27808119/ doi: 10.1038/srep36197 id: cord-352991-duqkpkll author: Waghmare, Alpana title: Respiratory Syncytial Virus Lower Respiratory Disease in Hematopoietic Cell Transplant Recipients: Viral RNA Detection in Blood, Antiviral Treatment, and Clinical Outcomes date: 2013-09-24 words: 5112.0 sentences: 245.0 pages: flesch: 43.0 cache: ./cache/cord-352991-duqkpkll.txt txt: ./txt/cord-352991-duqkpkll.txt summary: Although RSV RNA has been detected in serum from patients with RSV lower respiratory disease (LRD) after HCT, the association with clinical outcomes has not been well established in multivariable models. Univariate analysis at day 90 following RSV LRD revealed several factors that were statistically significantly associated with overall mortality and pulmonary death including transplant year, cell source, conditioning regimen, WBC count, monocyte count, platelet count, oxygen requirement at diagnosis, steroid use at diagnosis, palivizumab treatment, and ribavirin treatment following LRD (Supplementary Table 1 ). Hazard ratios and 95% confidence intervals from multivariable models evaluating respiratory syncytial virus (RSV) RNA detection in blood as a risk factor for overall mortality and pulmonary death by day 90 following RSV lower respiratory disease (LRD; n = 92), including P values. abstract: Background. Respiratory syncytial virus (RSV) pneumonia after hematopoietic cell transplant (HCT) is associated with severe morbidity. Although RSV RNA has been detected in serum from patients with RSV lower respiratory disease (LRD) after HCT, the association with clinical outcomes has not been well established in multivariable models. Additionally, the role of antiviral treatment in HCT recipients has not been previously analyzed in multivariable models. Methods. We retrospectively identified HCT recipients with virologically confirmed RSV LRD and tested stored plasma/serum samples by quantitative reverse transcription polymerase chain reaction for RSV RNA. Risk factors for RSV RNA detection and the impact of RSV RNA in serum and antiviral therapy on outcomes were analyzed using multivariable Cox models. Results. RSV RNA was detected in plasma or serum from 28 of 92 (30%) patients at a median of 24.5 days following HCT and 2 days following LRD. In multivariable models, neutropenia, monocytopenia, thrombocytopenia, and mechanical ventilation increased the risk of plasma/serum RSV RNA detection; lymphopenia and steroid use did not. RSV RNA detection increased the risk of overall mortality in multivariable models (adjusted hazard ratio [aHR], 2.09 [P = .02]), whereas treatment with aerosolized ribavirin decreased the risk of overall mortality and pulmonary death (aHR, 0.33 [P = .001] and aHR 0.31 [P = .003], respectively). Conclusions. RSV RNA detection in plasma or serum may be a marker for lung injury and poor outcomes in HCT recipients with RSV LRD. Treatment with aerosolized ribavirin appeared to be protective against overall and pulmonary mortality. url: https://academic.oup.com/cid/article-pdf/57/12/1731/17350990/cit639.pdf doi: 10.1093/cid/cit639 id: cord-012484-c9ajmbw2 author: Wahlund, Martina title: The Feasibility of Host Transcriptome Profiling as a Diagnostic Tool for Microbial Etiology in Childhood Cancer Patients with Febrile Neutropenia date: 2020-07-26 words: 5085.0 sentences: 241.0 pages: flesch: 45.0 cache: ./cache/cord-012484-c9ajmbw2.txt txt: ./txt/cord-012484-c9ajmbw2.txt summary: The blood transcriptome of the children (n = 63) was investigated at time of FN diagnosed as viral, bacterial, co-infection or unknown etiology, respectively, and compared to control samples derived from 12 of the patients following the FN episode. In the present study of children during cancer treatment, the blood transcriptome was not suitable for determining the etiology of FN because of too few circulating immune cells for reliable gene expression analysis. To determine whether it is possible to detect pathogen-specific immune responses on the basis of gene expression in immunosuppressed children, we compared the blood transcriptomes of samples with viral infection, bacterial infection, co-infection, or unknown etiology with those of the control samples. To determine whether it is possible to detect pathogen-specific immune responses on the basis of gene expression in immunosuppressed children, we compared the blood transcriptomes of samples with viral infection, bacterial infection, co-infection, or unknown etiology with those of the control samples. abstract: Infection is a common and serious complication of cancer treatment in children that often presents as febrile neutropenia (FN). Gene-expression profiling techniques can reveal transcriptional signatures that discriminate between viral, bacterial and asymptomatic infections in otherwise healthy children. Here, we examined whether gene-expression profiling was feasible in children with FN who were undergoing cancer treatment. The blood transcriptome of the children (n = 63) was investigated at time of FN diagnosed as viral, bacterial, co-infection or unknown etiology, respectively, and compared to control samples derived from 12 of the patients following the FN episode. RNA sequencing was successful in 43 (68%) of the FN episodes. Only two genes were significantly differentially expressed in the bacterial versus the control group. Significantly up-regulated genes in patients with the other three etiologies versus the control group were enriched with cellular processes related to proliferation and cellular stress response, with no clear enrichment with innate responses to pathogens. Among the significantly down-regulated genes, a few clustered into pathways connected to responses to infection. In the present study of children during cancer treatment, the blood transcriptome was not suitable for determining the etiology of FN because of too few circulating immune cells for reliable gene expression analysis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7432212/ doi: 10.3390/ijms21155305 id: cord-001541-5d64esp4 author: Walker, Peter J. title: Evolution of Genome Size and Complexity in the Rhabdoviridae date: 2015-02-13 words: 9157.0 sentences: 398.0 pages: flesch: 45.0 cache: ./cache/cord-001541-5d64esp4.txt txt: ./txt/cord-001541-5d64esp4.txt summary: We demonstrate that remarkable changes in genome size and complexity have occurred in rhabdoviruses in a clade-specific manner, primarily by extension and insertion of additional transcriptional units in the structural protein gene junctions, followed by occasional losses. All rhabdovirus genomes contained the five canonical structural protein genes (N, P, M, G and L); however, there was remarkable diversity in the number and location of other long ORFs. Across the data set, we identified 179 additional ORFs 180 nt in length of which 142 shared no detectable protein sequence similarity with any other protein in our data set or with those in public databases (S2 Table) . Interestingly, although substantial variation in the length of gene junctions was observed in several genera (including ephemeroviruses and lyssaviruses), most variation in genome size occurred as the result of the presence of new, non-canonical ORFs in the regions between the structural protein genes (Table 1) . abstract: RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4334499/ doi: 10.1371/journal.ppat.1004664 id: cord-347710-ff64y6ef author: Wan, Qianya title: Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development date: 2020-07-13 words: 36567.0 sentences: 2487.0 pages: flesch: 46.0 cache: ./cache/cord-347710-ff64y6ef.txt txt: ./txt/cord-347710-ff64y6ef.txt summary: hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. 6, 13 It is well known that Hsp90 not only interacts and contributes to RNA polymerase assembly and nuclear import of some (−) ssRNA viruses (e.g., PB2 of influenza virus), but plays crucial roles in the folding process of viral capsid proteins and virion assemblies as well. 17, 18 As a critical component of cellular protein surveillance, the ATP-dependent molecular chaperone protects cells from damage caused by stress and takes part in a number of folding processes, including folding of newly synthesized polypeptides, recognition and refolding of misfolded or aggregated proteins, solubilization or degradation of proteins, transporting proteins, assembly or disassembly of oligomeric protein complexes, and the regulation of certain natively folded proteins. abstract: Stress proteins (SPs) including heat-shock proteins (HSPs), RNA chaperones, and ER associated stress proteins are molecular chaperones essential for cellular homeostasis. The major functions of HSPs include chaperoning misfolded or unfolded polypeptides, protecting cells from toxic stress, and presenting immune and inflammatory cytokines. Regarded as a double-edged sword, HSPs also cooperate with numerous viruses and cancer cells to promote their survival. RNA chaperones are a group of heterogeneous nuclear ribonucleoproteins (hnRNPs), which are essential factors for manipulating both the functions and metabolisms of pre-mRNAs/hnRNAs transcribed by RNA polymerase II. hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. Dysregulation of stress proteins is associated with many human diseases including human cancer, cardiovascular diseases, neurodegenerative diseases (e.g., Parkinson’s diseases, Alzheimer disease), stroke and infectious diseases. In this review, we summarized the biologic function of stress proteins, and current progress on their mechanisms related to virus reproduction and diseases caused by virus infections. As SPs also attract a great interest as potential antiviral targets (e.g., COVID-19), we also discuss the present progress and challenges in this area of HSP-based drug development, as well as with compounds already under clinical evaluation. url: https://www.ncbi.nlm.nih.gov/pubmed/32661235/ doi: 10.1038/s41392-020-00233-4 id: cord-351115-dy81dtnk author: Wang, Chen title: Identification of evolutionarily stable sites across the SARS-CoV-2 proteome date: 2020-10-20 words: 6133.0 sentences: 310.0 pages: flesch: 50.0 cache: ./cache/cord-351115-dy81dtnk.txt txt: ./txt/cord-351115-dy81dtnk.txt summary: This study addresses both by utilizing evolutionary information from SARS-CoV-2 sequence and structural data to search for actionable functional sites for each protein in the SARS-CoV-2 genome. Here we systematically suggest potential drug target sites for most SARS-CoV-2 proteins based on evolutionary information. This relative ranking re ects the variation entropy of each sequence position within and across the branches of an associated phylogenetic tree, revealing evolutionary pressure points that correspond to functional and structural determinants, and the protein sites at which they often cluster (30) . As in our approach to discover ET drug sites, we combined ET residue ranking information with sequencing data from SARS-CoV-2 isolates to arrive at linear peptides along the proteome that are evolutionarily important and also show little variation in the current outbreak ( Figure S6 , Dataset S5). The data include, for example, multiple sequence alignments, precalculated ET ranks, and predicted epitopes (both linear and structural) for all SARS-CoV-2 proteins. abstract: Since the first recognized case of COVID-19, more than 30 million people have been infected worldwide. Despite global efforts in drug and vaccine development to fight the disease, there is currently no vaccine or drug cure for COVID-19, though some drugs reduce severity and hasten recovery. Here we interrogate the evolutionary history of the entire SARS-CoV-2 proteome to identify functional sites that can inform the search for treatments. Combining this information with the mutations observed in the current COVID-19 outbreak, we systematically and comprehensively define evolutionarily stable sites that are useful drug targets. Several experimentally-validated effective drugs interact with these proposed target sites. In addition, the same evolutionary information can prioritize cross reactive antigens that are useful in directing multi-epitope vaccine strategies to illicit broadly neutralizing immune responses to the betacoronavirus family. Although the results are focused on SARS-CoV-2, these approaches are based upon evolutionary principles and are agnostic to organism or infective agent. url: https://doi.org/10.21203/rs.3.rs-95030/v1 doi: 10.21203/rs.3.rs-95030/v1 id: cord-352465-n746e8qt author: Wang, Fei title: Targeting stress granules: A novel therapeutic strategy for human diseases date: 2020-08-16 words: 9128.0 sentences: 555.0 pages: flesch: 40.0 cache: ./cache/cord-352465-n746e8qt.txt txt: ./txt/cord-352465-n746e8qt.txt summary: Chronic stress might even induce formation of cytotoxic pathological SGs. SGs participate in various biological functions including response to apoptosis, inflammation, immune modulation, and signalling pathways; moreover, SGs are involved in pathogenesis of neurodegenerative diseases, viral infection, aging, cancers and many other diseases. One of the most studied mRNP granules is SGs. SGs are a type of dynamic granular substance formed of mRNA of stagnant translation and RBPs in the cytoplasm of eukaryotic cells, the formation of which is stimulated by various stresses including oxidative stress, heat shock, hypoxia, or viral infection (Fig. 1) . For example, eIF2α phosphorylation-dependent SGs (Type I) induced by sodium arsenite (SA) and bortezomib [40] may protect cells in the stress response, inhibit apoptosis and promote cell survival by the sequestration of signalling molecules, such as RACK1 [41] , ROCK1 [42] and Raptor [43] . abstract: Abstract Stress granules (SGs) are assemblies of mRNA and proteins that form from mRNAs stalled in translation initiation in response to stress. Chronic stress might even induce formation of cytotoxic pathological SGs. SGs participate in various biological functions including response to apoptosis, inflammation, immune modulation, and signalling pathways; moreover, SGs are involved in pathogenesis of neurodegenerative diseases, viral infection, aging, cancers and many other diseases. Emerging evidence has shown that small molecules can affect SG dynamics, including assembly, disassembly, maintenance and clearance. Thus, targeting SGs is a potential therapeutic strategy for the treatment of human diseases and the promotion of health. The established methods for detecting SGs provided ready tools for large-scale screening of agents that alter the dynamics of SGs. Here, we describe the effects of small molecules on SG assembly, disassembly, and their roles in the disease. Moreover, we provide perspective for the possible application of small molecules targeting SGs in the treatment of human diseases. url: https://api.elsevier.com/content/article/pii/S1043661820314511 doi: 10.1016/j.phrs.2020.105143 id: cord-342653-bpyc2gbl author: Wang, Hai-Tao title: Substrate recognition by TRIM and TRIM-like proteins in innate immunity date: 2020-10-20 words: 8560.0 sentences: 478.0 pages: flesch: 49.0 cache: ./cache/cord-342653-bpyc2gbl.txt txt: ./txt/cord-342653-bpyc2gbl.txt summary: While E3 ligases are often thought to negatively regulate the stability of the target molecule by Ub-mediated proteasomal targeting, many TRIMs have been shown to enhance innate immune signaling pathways [15] , through both proteasome-dependent and -independent mechanisms. The study of RIG-I and RIPLET interaction provides a detailed example of how TRIM-like proteins utilize bivalency and CC for regulating substrate selectivity, higher-order oligomerization and innate immune function. Given that an increasing number of receptors and signaling molecules in the innate immune system are shown to multimerize upon activation [77] , it is tempting to speculate that TRIM/TRIM-like proteins may utilize multimer-specific substrate recognition as a common mechanism for regulating their immune functions. The avidity-driven substrate recognition mechanism of TRIM/TRIM-like proteins would thus ensure more precise control of innate immune signaling and restriction functions. abstract: TRIM (Tripartite motif) and TRIM-like proteins have emerged as an important class of E3 ligases in innate immunity. Their functions range from activation or regulation of innate immune signaling pathway to direct detection and restriction of pathogens. Despite the importance, molecular mechanisms for many TRIM/TRIM-like proteins remain poorly characterized, in part due to challenges of identifying their substrates. In this review, we discuss several TRIM/TRIM-like proteins in RNA sensing pathways and viral restriction functions. We focus on those containing PRY-SPRY, the domain most frequently used for substrate recognition, and discuss emerging mechanisms that are commonly utilized by several TRIM/TRIM-like proteins to tightly control their interaction with the substrates. url: https://www.ncbi.nlm.nih.gov/pubmed/33092958/ doi: 10.1016/j.semcdb.2020.09.013 id: cord-339976-tg2jkss7 author: Wang, Haibin title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome date: 2004-07-01 words: 2579.0 sentences: 120.0 pages: flesch: 50.0 cache: ./cache/cord-339976-tg2jkss7.txt txt: ./txt/cord-339976-tg2jkss7.txt summary: title: Detection and Monitoring of SARS Coronavirus in the Plasma and Peripheral Blood Lymphocytes of Patients with Severe Acute Respiratory Syndrome Reliable and sensitive determination of the SARS CoV load would aid in the early identification of infected individuals, provide guidance for treatment (especially the use of steroid hormones and antiviral agents), and aid in monitoring of a patient''s clinical course and outcome. The method could detect the CoV load during the SARS course, as demonstrated in Fig. 1B , representative data from the 44 patients tested. High frequency of point mutations clustered within the adenosine triphosphatebinding region of BCR/ABL in patients with chronic myeloid leukemia or Ph-positive acute lymphoblastic leukemia who develop imatinib (STI571) resistance Serial analysis of the plasma concentration of SARS coronavirus RNA in pediatric patients with severe acute respiratory syndrome Quantitative analysis and prognostic implication of SARS coronavirus RNA in the plasma and serum of patients with severe acute respiratory syndrome abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/15229153/ doi: 10.1373/clinchem.2004.031237 id: cord-259916-gr6v098c author: Wang, Hongliang title: Mechanisms of Cellular Membrane Reorganization to Support Hepatitis C Virus Replication date: 2016-05-20 words: 6186.0 sentences: 252.0 pages: flesch: 33.0 cache: ./cache/cord-259916-gr6v098c.txt txt: ./txt/cord-259916-gr6v098c.txt summary: Like all positive-sense RNA viruses, hepatitis C virus (HCV) induces host membrane alterations for its replication termed the membranous web (MW). This review will summarize the recent studies that have led to our current knowledge of the role of viral and host factors in the biogenesis of the MWs and discuss how HCV uses this specialized membrane structure for its replication. A later study of cells containing a subgenomic HCV replicon reported that the membrane alterations induced by HCV replication consisted in part of double-membrane vesicles (DMVs; Figure 1 ) with a diameter around 200 nm that were also positive on immunoelectron microscopy with antibodies against NS5A and double-stranded RNA (dsRNA) [15] . [10] first showed that expression of viral nonstructural proteins resulted in membrane alterations that morphologically resemble those observed in replicon cells, demonstrating that viral RNA replication is not required for membranous web formation. Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex abstract: Like all positive-sense RNA viruses, hepatitis C virus (HCV) induces host membrane alterations for its replication termed the membranous web (MW). Assembling replication factors at a membranous structure might facilitate the processes necessary for genome replication and packaging and shield viral components from host innate immune defenses. The biogenesis of the HCV MW is a complex process involving a concerted effort of HCV nonstructural proteins with a growing list of host factors. Although a comprehensive understanding of MW formation is still missing, a number of important viral and host determinants have been identified. This review will summarize the recent studies that have led to our current knowledge of the role of viral and host factors in the biogenesis of the MWs and discuss how HCV uses this specialized membrane structure for its replication. url: https://doi.org/10.3390/v8050142 doi: 10.3390/v8050142 id: cord-302409-40ktyt5q author: Wang, Jie title: SARS-CoV-2 RNA detection of hospital isolation wards hygiene monitoring during the Coronavirus Disease 2019 outbreak in a Chinese hospital date: 2020-04-18 words: 2771.0 sentences: 166.0 pages: flesch: 51.0 cache: ./cache/cord-302409-40ktyt5q.txt txt: ./txt/cord-302409-40ktyt5q.txt summary: OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. Detection of SARS-CoV-2 RNA among health-care settings, sewage, and staffs'' PPE In routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. With routine cleaning and disinfection, none of SARS-CoV-2 RNA was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. In conclusion, the SARS-CoV-2 RNA monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. abstract: OBJECTIVES: The aim of this paper was to monitor the presence of SARS-Cov-2 among hospital environment surfaces, sewage, and personal protective equipment (PPE) of staffs in isolation wards in the First Affiliated Hospital of Zhejiang University, China. METHODS: Surfaces of objects were routinely wiped with 1000 mg/L chlorine containing disinfectant. Air and sewage disinfection was proceeded routinely and strictly. Hospital environmental surfaces and PPE of staffs in isolation wards were sampled using swabs. The sewage from various inlet and outlets were sampled. The respiratory and stool specimens of patients were collected. The respiratory specimens of staffs in the isolation wards were also sampled once a week. Quantitative real-time reverse transcription PCR (qRT-PCR) methods were used to confirm the existence of SARS-Cov-2 RNA. Viral culture was done for the samples positive for SARS-Cov-2 RNA. RESULTS: During the study period, 33 laboratory-confirmed patients were hospitalized in isolation wards in the hospital. None of SARS-Cov-2 RNA was detected among the 36 objects surface samples and 9 staffs PPE samples in isolation wards. Though the 3 sewage samples from the inlet of preprocessing disinfection pool were positive for SARS-CoV-2 RNA and the sample from the outlet of preprocessing disinfection pool was weakly positive, the sewage sample from the outlet of the last disinfection pool was negative. All of the 5 sewage samples from various points were negative by viral culture of SARS-Cov-2. None of the respiratory specimens of staffs in the isolation wards were positive. CONCLUSIONS: Though SARS-Cov-2 RNA of the sewage samples were positive from inlets of the sewage disinfection pool and negative from the outlet of the last sewage disinfection pool, no viable virus was detected by culture. The monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated COVID-19 infection risk of the staffs in isolation wards. url: https://www.ncbi.nlm.nih.gov/pubmed/32311449/ doi: 10.1016/j.ijid.2020.04.024 id: cord-292112-dejrksum author: Wang, Jinglu title: Genome-Wide Analysis Reveals Changes in Long Noncoding RNAs in the Differentiation of Canine BMSCs into Insulin-Producing Cells date: 2020-08-03 words: 4709.0 sentences: 267.0 pages: flesch: 52.0 cache: ./cache/cord-292112-dejrksum.txt txt: ./txt/cord-292112-dejrksum.txt summary: This study provides a lncRNA catalog for future research concerning the mechanism of the transdifferentiation of cBMSCs into IPCs. Long noncoding RNAs (LncRNAs) are the rest of the protein-coding transcripts >200 nt in length that lack coding potential [1] . The expression levels were verified by qRT-PCR, and the trends were consistent with the RNA-Seq data; however, the expression level of the lncRNAs was much lower than that of the protein-coding transcripts (Figure 8 ). The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. The top 20 signaling pathways enriched by the colocalized genes of differentially expressed lncRNAs from pairwise comparison "I vs. abstract: Long noncoding RNAs (lncRNAs) have been extensively explored over the past decade, including mice and humans. However, their impact on the transdifferentiation of canine bone marrow mesenchymal stem cells (cBMSCs) into insulin-producing cells (IPCs) is largely unknown. In this study, we used a three-step induction procedure to induce cBMSCs into IPCs, and samples (two biological replicates each) were obtained after each step; the samples consisted of “BMSCs” (B), “stage 1” (S1), “stage 2” (S2), “stage 3” (S3), and “islets” (I). After sequencing, 15,091 lncRNAs were identified, and we screened 110, 41, 23, and 686 differentially expressed lncRNAs (p(adjusted) < 0.05) in B vs. S1, S1 vs. S2, S2 vs. S3, and I vs. S3 pairwise comparisons, respectively. In lncRNA target prediction, there were 166,623 colocalized targets and 2,976,362 correlated targets. Gene Ontology (GO) analysis showed that binding represented the main molecular functions of both the cis- and trans-modes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that the insulin signaling pathway, Rap1 signaling pathway, tight junctions, MAPK signaling pathway, and cell cycle were enriched for these relative genes. The expression of lncRNAs was verified using qRT-PCR. This study provides a lncRNA catalog for future research concerning the mechanism of the transdifferentiation of cBMSCs into IPCs. url: https://doi.org/10.3390/ijms21155549 doi: 10.3390/ijms21155549 id: cord-003158-mhlqnj52 author: Wang, Qi title: Adapted HCV JFH1 variant is capable of accommodating a large foreign gene insert and allows lower level HCV replication and viral production date: 2018-07-13 words: 5186.0 sentences: 291.0 pages: flesch: 56.0 cache: ./cache/cord-003158-mhlqnj52.txt txt: ./txt/cord-003158-mhlqnj52.txt summary: Previous studies have demonstrated that the HCV JFH1 NS5A C-terminal is a flexible region which is capable of accommodating foreign gene inserts (such as EGFP, 720bp and Rennilla luciferase [Rluc] , 930bp) and still permit HCV replication and viral production (18, 19, (24) (25) (26) (27) (28) (29) . In this study, we used the JFH1-AM120 as a vector to explore if infectious reporter virus would be produced following insertion of LacZ gene that was three time larger than Rluc, into the NS5A C-terminus. This result provided evidence that fusion protein of NS5A and β-galactosidase can be co-expressed in Huh7.5 cells after transfection of JFH1-AM120-LacZ RNA. Our results demonstrate that the LacZ reporter gene can be inserted into the NS5A C-terminus of HCV JFH1-AM120 and will express the predicted NS5A-LacZ fusion protein, which can be detected by western blotting three days after RNA transfection of cells. abstract: Infectious HCV carrying reporter genes have further applications in understanding the HCV life cycle including replication, viral assembly and release. In this study, a full-length 3039bp LacZ gene was inserted into the derivative of JFH1-AM120 to develop an additional reporter virus. The results showed that the recombinant reporter virus JFH1-AM120-LacZ can replicate and produce lower titers of infectious virus. However, insertion of the LacZ gene in the C-terminal region of the NS5A in HCV JFH1-AM120-LacZ decreased viral replication and dramatically impaired the production of infectious viral particles. Moreover, the JFH1-AM120-LacZ reporter virus lost the LacZ gene after serial passage. Nevertheless, the JFH1-AM120-LacZ reporter virus displayed the entire life cycle of HCV, from replication to production of infectious virus, in Huh7.5 cells. This study demonstrates that the NS5A region of HCV JFH1-AM120 has the capacity to accommodate large foreign genes up to 3,039 bp and suggests that other relatively large gene inserts can be accommodated at this site. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097470/ doi: 10.7150/ijbs.27411 id: cord-296250-7ln7p715 author: Wang, Sheng-Fan title: The pharmacological development of direct acting agents for emerging needed therapy against severe acute respiratory syndrome coronavirus-2 date: 2020-05-20 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was quickly identified as the causal pathogen leading to the outbreak of SARS-like illness all over the world. As the SARS-CoV-2 infection pandemic proceeds, many efforts are being dedicated to the development of diverse treatment strategies. Increasing evidence showed potential therapeutic agents directly acting against SARS-CoV-2 virus, such as interferon, RNA-dependent RNA polymerase inhibitors, protease inhibitors, viral entry blockers, neuraminidase inhibitor, vaccine, antibody agent targeting the SARS-CoV-2 RNA genome, natural killer cells, and nucleocytoplasmic trafficking inhibitor. To date, several direct anti-SARS-CoV-2 agents have demonstrated promising in vitro and clinical efficacy. This article reviews the current and future development of direct acting agents against SARS-CoV-2. url: https://www.ncbi.nlm.nih.gov/pubmed/32433345/ doi: 10.1097/jcma.0000000000000353 id: cord-354394-zojhdnlu author: Wang, Wei-Kung title: Detection of SARS-associated Coronavirus in Throat Wash and Saliva in Early Diagnosis date: 2004-07-17 words: 3972.0 sentences: 175.0 pages: flesch: 56.0 cache: ./cache/cord-354394-zojhdnlu.txt txt: ./txt/cord-354394-zojhdnlu.txt summary: We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 10(2) to 5.93 x 10(6) copies/mL) and saliva (7.08 x 10(3) to 6.38 x 10(8) copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four patients, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis. Using a quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) assay and fractionation experiment, we investigated the load of SARS-CoV in these samples and different components of the throat wash. As shown in Table 1 , SARS-CoV RNA was detected in the cell-associated component of the throat wash from all 16 specimens examined. abstract: The severe acute respiratory syndrome–associated coronavirus (SARS-CoV) is thought to be transmitted primarily through dispersal of droplets, but little is known about the load of SARS-CoV in oral droplets. We examined oral specimens, including throat wash and saliva, and found large amounts of SARS-CoV RNA in both throat wash (9.58 x 10(2) to 5.93 x 10(6) copies/mL) and saliva (7.08 x 10(3) to 6.38 x 10(8) copies/mL) from all specimens of 17 consecutive probable SARS case-patients, supporting the possibility of transmission through oral droplets. Immunofluorescence study showed replication of SARS-CoV in the cells derived from throat wash, demonstrating the possibility of developing a convenient antigen detection assay. This finding, with the high detection rate a median of 4 days after disease onset and before the development of lung lesions in four patients, suggests that throat wash and saliva should be included in sample collection guidelines for SARS diagnosis. url: https://www.ncbi.nlm.nih.gov/pubmed/15324540/ doi: 10.3201/eid1007.031113 id: cord-306688-po4p1466 author: Wang, X. title: Brome Mosaic Virus date: 2008-07-30 words: 4563.0 sentences: 177.0 pages: flesch: 41.0 cache: ./cache/cord-306688-po4p1466.txt txt: ./txt/cord-306688-po4p1466.txt summary: Among other advances, BMV was used to define the first ribosome binding sites in eukaryotic mRNAs, and to produce the first template-selective eukaryotic viral RNA-dependent RNA polymerase extract, the first infectious transcripts from cloned RNA virus cDNA, the first engineered RNA virus expression vectors expressing foreign genes, the first definition of subgenomic mRNA synthesis pathways and determinants, and the first demonstration of higher eukaryotic viral replication in yeast. In parallel to in vitro systems, cultured plant protoplasts provided a valuable substrate for in vivo replication studies due to their ability to be infected or transfected with nearly 100% efficiency with virions, virion RNAs, or in vitro transcripts from cloned viral cDNAs. For BMV, barley protoplast systems developed and refined by the groups of Okuno and Furusawa, Hall and others in the late 1970s have allowed studies of all aspects of BMV RNA replication, subgenomic RNA synthesis, progeny RNA encapsidation, and the like. abstract: Brome mosaic virus (BMV) is an isometric, nonenveloped positive-strand RNA virus and a well-studied, representative member of the alphavirus-like superfamily of human, animal, and plant viruses. BMV has been extensively studied as a model for viral RNA replication, gene expression, virus–host interactions, recombination, and encapsidation. Through contributions by many different groups, these studies have not only advanced understanding of BMV, but have also revealed insights and principles extending to many other viruses and to general cellular biology. Among other advances, BMV was used to define the first ribosome binding sites in eukaryotic mRNAs, and to produce the first template-selective eukaryotic viral RNA-dependent RNA polymerase extract, the first infectious transcripts from cloned RNA virus cDNA, the first engineered RNA virus expression vectors expressing foreign genes, the first definition of subgenomic mRNA synthesis pathways and determinants, and the first demonstration of higher eukaryotic viral replication in yeast. BMV has also contributed many insights into virion assembly, virus–host interactions, RNA recombination, and RNA replication, including parallels in the replication of positive-strand RNA, reverse-transcribing, and dsRNA viruses. This article reviews the major features of the virus and selected aspects of these and other advances with BMV. url: https://www.sciencedirect.com/science/article/pii/B9780123744104005604 doi: 10.1016/b978-012374410-4.00560-4 id: cord-257693-rnchfjbe author: Wang, Yeming title: Factors Associated With Prolonged Viral Shedding in Patients With Avian Influenza A(H7N9) Virus Infection date: 2018-04-10 words: 3987.0 sentences: 212.0 pages: flesch: 42.0 cache: ./cache/cord-257693-rnchfjbe.txt txt: ./txt/cord-257693-rnchfjbe.txt summary: Observational studies have reported that prolonged influenza viral shedding in the respiratory tract is associated with severe outcomes of patients with seasonal influenza [10] and that early initiation of antiviral treatment with neuraminidase inhibitors (NAIs) for patients infected with 2009 pandemic influenza A(H1N1) virus (A[H1N1] pdm09) has a survival benefit [11] [12] [13] [14] [15] [16] [17] . We conducted a retrospective, multicenter study of 478 hospitalized patients with laboratory-confirmed A(H7N9) infection who were identified during April 2013-March 2017 to assess the impact of different NAI treatment strategies and corticosteroid treatment on the duration of A(H7N9) shedding. In a multivariable model that included available data from 478 patients, the time from illness onset to antiviral treatment (HR, 0.90 [95% CI, .91-.96]) and systemic corticosteroid administration (HR, 0.62 [95% CI, .50-.77]) were independent factors associated with the duration of A(H7N9) RNA shedding (Table 2 and Figure 4 ). abstract: BACKGROUND. Data are limited on the impact of neuraminidase inhibitor (NAI) treatment on avian influenza A(H7N9) virus RNA shedding. METHODS. In this multicenter, retrospective study, data were collected from adults hospitalized with A(H7N9) infection during 2013–2017 in China. We compared clinical features and A(H7N9) shedding among patients with different NAI doses and combination therapies and evaluated factors associated with A(H7N9) shedding, using Cox proportional hazards regression. RESULTS. Among 478 patients, the median age was 56 years, 71% were male, and 37% died. The median time from illness onset to NAI treatment initiation was 8 days (interquartile range [IQR], 6–10 days), and the median duration of A(H7N9) RNA detection from onset was 15.5 days (IQR, 12–20 days). A(H7N9) RNA shedding was shorter in survivors than in patients who died (P < .001). Corticosteroid administration (hazard ratio [HR], 0.62 [95% confidence interval {CI}, .50-.77]) and delayed NAI treatment (HR, 0.90 [95% CI, .91-.96]) were independent risk factors for prolonged A(H7N9) shedding. There was no significant difference in A(H7N9) shedding duration between NAI combination treatment and monotherapy (P = .65) or between standard-dose and double-dose oseltamivir treatment (P = .70). CONCLUSIONS. Corticosteroid therapy and delayed NAI treatment were associated with prolonged A(H7N9) RNA shedding. NAI combination therapy and double-dose oseltamivir treatment were not associated with a reduced A(H7N9) shedding duration as compared to standard-dose oseltamivir. url: https://academic.oup.com/jid/article-pdf/217/11/1708/24789949/jiy115.pdf doi: 10.1093/infdis/jiy115 id: cord-289248-6mx4o0eb author: Wang, Yilong title: Enhancement of safety and immunogenicity of the Chinese Hu191 measles virus vaccine by alteration of the S-adenosylmethionine (SAM) binding site in the large polymerase protein date: 2018-05-01 words: 7018.0 sentences: 388.0 pages: flesch: 59.0 cache: ./cache/cord-289248-6mx4o0eb.txt txt: ./txt/cord-289248-6mx4o0eb.txt summary: These two mutants grew to high titer in Vero cells, were genetically stable, and were significantly more attenuated in vitro and in vivo compared to the parental rMV-Hu191 vaccine strain. We next compared the replication kinetics of the rMV-Hu191 mutants and the parental virus in Vero cells in the time course of 120 h after infection (Fig. 5 ). These data suggest that rMVs carrying mutations in the SAM binding site were more attenuated in Vero cells than the parental MV vaccine strain. In this study, we successfully generated two recombinant measles viruses with amino acid substitutions in the SAM binding site of L protein and examined the effects of these mutations on viral replication, safety, and immunogenicity. We generated two recombinant MV-Hu191 carrying mutations in the SAM binding site, which not only grew to high titer in Vero cells and were genetically stable but also were significantly more attenuated and immunogenic compared to the currently used Chinese MV vaccine strain. abstract: The live-attenuated measles virus (MV) vaccine based on the Hu191 strain has played a significant role in controlling measles in China. However, it has considerable adverse effects that may cause public health burden. We hypothesize that the safety and efficacy of MV vaccine can be improved by altering the S-adeno- sylmethionine (SAM) binding site in the conserved region VI of the large polymerase protein. To test this hypothesis, we established an efficient reverse genetics system for the rMV-Hu191 strain and generated two recombinant MV-Hu191 carrying mutations in the SAM binding site. These two mutants grew to high titer in Vero cells, were genetically stable, and were significantly more attenuated in vitro and in vivo compared to the parental rMV-Hu191 vaccine strain. Importantly, both MV-Hu191 mutants triggered a higher neutralizing antibody than rMV-Hu191 vaccine and provided complete protection against MV challenge. These results demonstrate its potential for an improved MV vaccine candidate. url: https://doi.org/10.1016/j.virol.2018.02.022 doi: 10.1016/j.virol.2018.02.022 id: cord-285290-l7mnq4yb author: Warner, Katherine Deigan title: Principles for targeting RNA with drug-like small molecules date: 2018-07-06 words: 7564.0 sentences: 400.0 pages: flesch: 49.0 cache: ./cache/cord-285290-l7mnq4yb.txt txt: ./txt/cord-285290-l7mnq4yb.txt summary: Here, we discuss principles for discovering small-molecule drugs that target RNA and argue that the overarching challenge is to identify appropriate target structures – namely in disease-causing RNAs that have high information content, and consequently appropriate ligand binding pockets. In our view, successful targeting of RNA in therapeutically useful ways with small molecules requires three distinct components: (1) identification of RNAs and RNA motifs with disease-related function, (2) use of screening approaches and libraries likely to identify drug-like molecules with appropriate pharmacological properties and (3) identification of and focus on RNA motifs with sufficient structural sophistication that make it likely that high affinity and specificity in small-molecule binding can be achieved. (1) a therapeutically compelling RNA target, (2) a screening approach that will identify drug-like lead molecules with appropriate pharmacological properties and (3) the identification of RNA motifs with sufficient information content such that high-specificity and high-potency binding to a high-quality pocket is achieved. abstract: RNA molecules are essential for cellular information transfer and gene regulation, and RNAs have been implicated in many human diseases. Messenger and non-coding RNAs contain highly structured elements, and evidence suggests that many of these structures are important for function. Targeting these RNAs with small molecules offers opportunities to therapeutically modulate numerous cellular processes, including those linked to “undruggable” protein targets. Despite this promise, there is currently only a single class of human-designed small molecules that target RNA used clinically – the linezolid antibiotics. A growing number of small-molecule RNA ligands are being identified, however, leading to burgeoning interest in the field. Here, we discuss principles for discovering small-molecule drugs that target RNA and argue that the overarching challenge is to identify appropriate target structures – namely in disease-causing RNAs that have high information content, and consequently appropriate ligand binding pockets. If focus is placed on such druggable binding sites in RNA, extensive knowledge of the kinds of molecules that comprise conventional drugs could then enable small-molecule drug discovery for RNA targets to become (only) roughly as difficult as for protein targets. url: https://doi.org/10.1038/nrd.2018.93 doi: 10.1038/nrd.2018.93 id: cord-316503-wtmmewiz author: Warren, Travis K. title: Advanced morpholino oligomers: A novel approach to antiviral therapy date: 2012-02-14 words: 6825.0 sentences: 315.0 pages: flesch: 40.0 cache: ./cache/cord-316503-wtmmewiz.txt txt: ./txt/cord-316503-wtmmewiz.txt summary: Phosphorodiamidate morpholino oligomers (PMOs) are synthetic antisense oligonucleotide analogs that are designed to interfere with translational processes by forming base-pair duplexes with specific RNA sequences. Peptide conjugated PMOs (PPMOs; Fig. 2 ), which include positively charged amino acid residues such as arginine, have been viewed as particularly promising transporters and have shown efficacy in multiple in vivo models of viral infection (Enterlein et al., 2006; Paessler et al., 2008; Stein, 2008; Swenson et al., 2009) . While PPMOs are efficacious in multiple in vivo models of viral infections, PPMOs are more poorly tolerated in vivo compared to neutral-charge PMOs. In mice, dose-dependent reductions in weight, behavioral alterations, and mild liver histopathology were observed following repeat administration of 200-300 lg doses of a PMO conjugated to an arginine-rich peptide (Deas et al., 2007) . abstract: Phosphorodiamidate morpholino oligomers (PMOs) are synthetic antisense oligonucleotide analogs that are designed to interfere with translational processes by forming base-pair duplexes with specific RNA sequences. Positively charged PMOs (PMOplus™) are effective for the postexposure protection of two fulminant viral diseases, Ebola and Marburg hemorrhagic fever in nonhuman primates, and this class of antisense agent may also have possibilities for treatment of other viral diseases. PMOs are highly stable, are effective by a variety of routes of administration, can be readily formulated in common isotonic delivery vehicles, and can be rapidly designed and synthesized. These are properties which may make PMOs good candidates for use during responses to emerging or reemerging viruses that may be insensitive to available therapies or for use during outbreaks, especially in regions that lack a modern medical infrastructure. While the efficacy of sequence-specific therapies can be limited by target-site sequence variations that occur between variants or by the emergence of resistant mutants during infections, various PMO design strategies can minimize these impacts. These strategies include the use of promiscuous bases such as inosine to compensate for predicted base-pair mismatches, the use of sequences that target conserved sites between viral strains, and the use of sequences that target host products that viruses utilize for infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22353544/ doi: 10.1016/j.antiviral.2012.02.004 id: cord-275602-cog4nma0 author: Watkins, Kevin title: Emerging Infectious Diseases: a Review date: 2018-06-22 words: 4672.0 sentences: 278.0 pages: flesch: 49.0 cache: ./cache/cord-275602-cog4nma0.txt txt: ./txt/cord-275602-cog4nma0.txt summary: SUMMARY: In addition to the aforementioned pathogens, the Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, Nipah virus, New Delhi metallo-ß-lactamase-1 Enterobacteriaceae, Rift Valley Fever virus, and Crimean-Congo Hemorrhagic Fever virus are reviewed. In 1992, an expert committee that produced the Institute of Medicine report on emerging infections defined them as "new, reemerging, or drug-resistant infections whose incidence in humans has increased within the past two decades or whose incidence threatens to increase in the near future." Additionally, six major contributors to these diseases were presented and included changes in human demographics and behavior, advances in technology and changes in industry practices, economic development and changes in land-use patterns, dramatic increases in volume and speed of international travel and commerce, microbial adaptation and change, and breakdown of public health capacity [1] . The World Health Organization has prioritized a number of infectious diseases as requiring urgent need for research and development given the concern for potential of severe outbreaks. abstract: PURPOSE OF REVIEW: This review highlights some of the recent concerning emerging infectious diseases, a number of them specifically that the World Health Organization has categorized as priorities for research. RECENT FINDINGS: Emerging and reemerging infectious diseases account for significant losses in not only human life, but also financially. There are a number of contributing factors, most commonly surrounding human behavior, that lead to disease emergence. Zoonoses are the most common type of infection, specifically from viral pathogens. The most recent emerging diseases in the USA are Emergomyces canadensis, the Heartland virus, and the Bourbon virus. SUMMARY: In addition to the aforementioned pathogens, the Severe Acute Respiratory Syndrome, Middle East Respiratory Syndrome, Nipah virus, New Delhi metallo-ß-lactamase-1 Enterobacteriaceae, Rift Valley Fever virus, and Crimean-Congo Hemorrhagic Fever virus are reviewed. These pathogens are very concerning with a high risk for potential epidemic, ultimately causing both significant mortality and financial costs. Research should be focused on monitoring, prevention, and treatment of these diseases. url: https://doi.org/10.1007/s40138-018-0162-9 doi: 10.1007/s40138-018-0162-9 id: cord-103853-ar09nzmw author: Wayment-Steele, Hannah K. title: RNA secondary structure packages ranked and improved by high-throughput experiments date: 2020-05-31 words: 4328.0 sentences: 201.0 pages: flesch: 42.0 cache: ./cache/cord-103853-ar09nzmw.txt txt: ./txt/cord-103853-ar09nzmw.txt summary: 20 In this work, we evaluate the performance of commonly-used packages capable of making thermodynamic predictions in two tasks that have been crowdsourced on Eterna and are emerging as central to RNA characterization and design: 1) predicting chemical reactivity data through calculating probabilities that nucleotides are unpaired, and 2) predicting relative stabilities of multiple structural states that underlie the functions of riboswitch molecules, a task that involves predicting affinities of both small molecules and proteins of interest. We evaluated commonly used secondary structure modeling packages in their ability to make thermodynamic predictions on a compilation of large datasets of diverse synthetic molecules from Eterna, which we termed EternaBench ( Figure 1A ). We trained models with a variety of combinations of data types to explore interactions in multitask training (Table 1) and evaluated performance on held-out test sets for single-structure prediction accuracy, chemical mapping prediction accuracy, and riboswitch fold change prediction. abstract: The computer-aided study and design of RNA molecules is increasingly prevalent across a range of disciplines, yet little is known about the accuracy of commonly used structure prediction packages in real-world tasks. Here, we evaluate the performance of current packages using EternaBench, a dataset comprising 23 in vitro structure mapping and 11 riboswitch activity datasets involving 18,509 synthetic sequences from the crowdsourced RNA design project Eterna. We find that CONTRAfold and RNAsoft, packages with parameters derived through statistical learning, achieve consistently higher accuracy than more widely used packages like the ViennaRNA software, which derive parameters primarily from thermodynamic experiments. Motivated by these results, we develop a multitask-learning-based model, EternaFold, which demonstrates improved performance that generalizes to diverse external datasets, including complete viral genomes probed in vivo and synthetic designs modeling mRNA vaccines. url: https://doi.org/10.1101/2020.05.29.124511 doi: 10.1101/2020.05.29.124511 id: cord-328947-3l9ydspz author: Webb, L. G. title: Chikungunya virus antagonizes cGAS-STING mediated type-I interferon responses by degrading cGAS date: 2020-10-15 words: 9857.0 sentences: 544.0 pages: flesch: 51.0 cache: ./cache/cord-328947-3l9ydspz.txt txt: ./txt/cord-328947-3l9ydspz.txt summary: CHIKV is no exception, the type-I interferon (IFN) response has been demonstrated to be key in controlling CHIKV infection [21] [22] [23] [24] [25] [26] and primary sensing of the virus is via the pattern recognition receptor (PRR) retinoic acid-inducible gene I (RIG-I)-mitochondrial antiviral signaling protein (MAVS) axis [24, 26] . The lack of cGAS degradation seen in the exogenous expression system when compared to the infected cells shows that although there is a clear interaction of cGAS with nsP4, the degradation of cGAS observed is not mediated by the non-structural proteins of CHIKV, but must require other viral or host factors. Chikungunya virus inhibits DNA sensing by degrading cGAS both mock and infected cells by 4 hpi suggesting that the stress produced during the process of infection (mock or CHIKV) in HFF-1s stimulates increased translation at early timepoints ( Fig 4D, lanes 2 and 5) . abstract: Chikungunya virus (CHIKV) is a mosquito-borne alphavirus known to cause epidemics resulting in predominantly symptomatic infections, which in rare cases cause long term debilitating arthritis and arthralgia. Significant progress has been made in understanding the roles of canonical RNA sensing pathways in the host recognition of CHIKV; however, less is known regarding antagonism of CHIKV by cytosolic DNA sensing pathways like that of cyclic GMP-AMP synthase (cGAS) and Stimulator of Interferon Genes (STING). With the use of cGAS or STING null cells we demonstrate that the pathway restricts CHIKV replication in fibroblasts and immune cells. We show that DNA accumulates in the cytoplasm of infected cells and that CHIKV blocks DNA dependent IFN-β transcription. This antagonism of DNA sensing is via an early autophagy-mediated degradation of cGAS and expression of the CHIKV capsid protein is sufficient to induce cGAS degradation. Furthermore, we identify an interaction of CHIKV nsP1 with STING and map the interaction to 23 residues in the cytosolic loop of the adaptor protein. This interaction stabilizes the viral protein and increases the level of palmitoylated nsP1 in cells. Together, this work supports previous publications highlighting the relevance of the cGAS-STING pathway in the early detection of (+)ssRNA viruses and provides direct evidence that CHIKV interacts with and antagonizes cGAS-STING signaling. url: https://doi.org/10.1371/journal.ppat.1008999 doi: 10.1371/journal.ppat.1008999 id: cord-280130-ewqe9edq author: Weber, Friedemann title: Viral suppression of the interferon system date: 2007-01-27 words: 4298.0 sentences: 224.0 pages: flesch: 39.0 cache: ./cache/cord-280130-ewqe9edq.txt txt: ./txt/cord-280130-ewqe9edq.txt summary: In most nucleated body cells, viral infections activate transcription of the ''''classic'''' IFN-b gene [1] by a signaling chain which is initiated by the RNA sensors RIG-I and MDA-5, which in turn act trough the adaptor IPS-1 and the kinases TBK-1 and IKK-3 to activate the transcription factor IRF-3 (see reviews by P. Many RNA and DNA viruses therefore express proteins which bind this key molecule to avoid both IFN induction and activation of dsRNA-dependent antiviral enzymes [7, 8] . Binding of the influenza virus NS1 protein to double-stranded RNA inhibits the activation of the protein kinase that phosphorylates the elF-2 translation initiation factor Ebola virus VP35 protein binds double-stranded RNA and inhibits alpha/beta interferon production induced by RIG-I signaling Double-stranded RNA binding of influenza B virus nonstructural NS1 protein inhibits protein kinase R but is not essential to antagonize production of alpha/beta interferon abstract: Type I interferons (IFN-α/β) were originally discovered by their strong and direct antiviral activity [A. Isaacs, J. Lindenmann, Virus interference. I. The interferon, Proc. R. Soc. Lond. B Biol. Sci. 147 (1957) 258–267]. (see review by J. Lindenmann on p. 719, in this issue). Nevertheless, only very recently it was entirely realized that viruses would not succeed without efficient tools to undermine this potent host defense system. Current investigations are revealing an astonishing variety of viral IFN antagonistic strategies targeting virtually all parts of the IFN system, often in a highly specific manner. Viruses were found to interfere with induction of IFN synthesis, IFN-induced signaling events, the antiviral effector proteins, or simply shut off the host cell macromolecule synthesis machinery to avoid booting of the antiviral host defense. Here, we will describe a few well-characterized examples to illustrate the sophisticated and often multi-layered anti-IFN mechanisms employed by viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/17336442/ doi: 10.1016/j.biochi.2007.01.005 id: cord-019051-gtruu1op author: Weber, Olaf title: The role of viruses in the etiology and pathogenesis of common cold date: 2009-11-10 words: 12321.0 sentences: 734.0 pages: flesch: 44.0 cache: ./cache/cord-019051-gtruu1op.txt txt: ./txt/cord-019051-gtruu1op.txt summary: Viruses with an established role in common cold are rhinoviruses, adenoviruses, parainfluenza viruses, coronaviruses and the respiratory syncytial virus, and these are reviewed in greater detail here. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex and it is safe to say, not fully understood for each and every virus that is linked to respiratory tract infection. RSV infection is assumed to be frequently misdiagnosed, particularly in adults [56] , because the symptoms are similar to those caused by other respiratory viruses like influenza. Human parainfluenza viruses (HPIV) are important causes of respiratory diseases in infants and children. HMPV is thought to be the second or third cause of severe acute respiratory tract infection in children, just ranking behind RSV and influenza virus [146, 148] . Retinoic acid-inducible gene I mediates early Antiviral Response and Toll-like receptor 3 expression in respiratory syncytial virus-infected airway epithelial cells abstract: Numerous viruses are able to cause respiratory tract infections. With the availability of new molecular techniques, the number of pathogens detected in specimens from the human respiratory tract has increased. Some of these viral infections have the potential to lead to severe systemic disease. Other viruses are limited to playing a role in the pathogenesis of the common cold syndrome. This chapter focuses on the viral pathogens that are linked to common cold. It is not the intention to comprehensively review all the viruses that are able to cause respiratory tract infections—this would go beyond the scope of this book. The list of viruses that are briefly reviewed here includes rhinoviruses, respiratory syncytial virus, parainfluenza virus, adenovirus, metapneumovirus and coronavirus. Bocavirus is discussed as one example of a newly identified pathogen with a less established role in the etiology and pathogenesis of common cold. Influenza virus does not cause what is defined as common cold. However, influenza viruses are associated with respiratory disease and the clinical picture of mild influenza and common cold frequently overlaps. Therefore, influenza virus has been included in this chapter. It is important to note that a number of viruses are frequently co-detected with other viruses in humans with respiratory diseases. Therefore, the viral etiology and the role of viruses in the pathogenesis of common cold is complex, and numberous questions remain to be answered. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7124101/ doi: 10.1007/978-3-7643-9912-2_5 id: cord-295019-8tf8ah6g author: Weber, Wilfried title: Emerging biomedical applications of synthetic biology date: 2011-11-29 words: 9511.0 sentences: 475.0 pages: flesch: 36.0 cache: ./cache/cord-295019-8tf8ah6g.txt txt: ./txt/cord-295019-8tf8ah6g.txt summary: Synthetic mammalian transcription circuits consisting of a chimeric small-molecule-responsive transcription factor and a cognate synthetic promoter were originally designed for future gene-based therapies, and the aim was to adjust therapeutic transgene expression in mammalian cells in response to a pharmacologically active substance 34, 47, 49, 91 . When mammalian cells that are transgenic for the screening circuit are exposed to a compound library, they detect and modulate reporter gene expression in the presence of a non-toxic, cellpermeable and bioavailable molecule that has a classspecific core structure and corresponding drug activity (for example, antibiotic activity) (FIG. The availability of compact RNA sensor-actuators that are easy to design and to alter and that control transgene expression in response to intracellular levels of key proteins may also improve the ability to link metabolic disease states with gene-based therapeutic interventions. abstract: Synthetic biology aims to create functional devices, systems and organisms with novel and useful functions on the basis of catalogued and standardized biological building blocks. Although they were initially constructed to elucidate the dynamics of simple processes, designed devices now contribute to the understanding of disease mechanisms, provide novel diagnostic tools, enable economic production of therapeutics and allow the design of novel strategies for the treatment of cancer, immune diseases and metabolic disorders, such as diabetes and gout, as well as a range of infectious diseases. In this Review, we cover the impact and potential of synthetic biology for biomedical applications. url: https://www.ncbi.nlm.nih.gov/pubmed/22124480/ doi: 10.1038/nrg3094 id: cord-256940-yuja99jg author: Wei, Bo title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports date: 2020-07-20 words: 1994.0 sentences: 136.0 pages: flesch: 56.0 cache: ./cache/cord-256940-yuja99jg.txt txt: ./txt/cord-256940-yuja99jg.txt summary: title: Long-term positive severe acute respiratory syndrome coronavirus 2 ribonucleic acid and therapeutic effect of antivirals in patients with coronavirus disease: Case reports Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. However, some COVID-19 patients have been reported to have long-term positivity for SARS-CoV-2 ribonucleic acid (RNA). On April 5, after three consecutive negative nucleic acid test results, he was discharged and transferred to another hospital for further treatment of comorbidities. Thus, DNVr may be a potential antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. abstract: Coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a pandemic. We herein report four COVID-19 cases with long-term positive viral ribonucleic acid (RNA) for about 61 days. Despite treatment with recombinant human interferon, convalescent plasma from COVID-19 patients, arbidol, etc., nucleic acid results were still positive for SARS-CoV-2. After treatment with ritonavir-boosted danoprevir (DNVr, 100/100 mg, once daily), all four patients showed two to three consecutive negative SARS-CoV-2 RNA and were thus discharged from hospital. Therefore, DNVr may be a potentially effective antiviral for COVID-19 patients with long-term positive SARS-CoV-2 RNA. url: https://doi.org/10.1590/0037-8682-0372-2020 doi: 10.1590/0037-8682-0372-2020 id: cord-337976-c2auspti author: Weiss, Susan R. title: Coronaviruses SD and SK share extensive nucleotide homology with murine coronavirus MHV-A59, more than that shared between human and murine coronaviruses date: 1983-04-30 words: 3818.0 sentences: 267.0 pages: flesch: 61.0 cache: ./cache/cord-337976-c2auspti.txt txt: ./txt/cord-337976-c2auspti.txt summary: A cDNA probe representing the genome of mouse hepatitis virus (MHV) strain A59 (MHV-A59) was used to measure nucleotide sequence homologies among murine and human coronaviruses and the SD and SK coronaviruses isolated by Burks et al. Since SD and SK were isolated by inoculation of multiple sclerosis (MS) central nervous system (CNS) tissue into mice or cultured mouse cells, it is important to determine their relationships to other murine and human coronavirus isolates. Some strains of HCV such as 0C43, are antigenically related to murine coronaviruses such as MHV strain JHM (McIntosh, 1974; Gerdes et al., 1981a, b) and may be grown in the brains of suckling mice (McIntosh et al., 1967) . We have further compared murine and human coronaviruses and SD and SK by using molecular hybridization of virus-specific RNA with cDNA probes. RNA extracted either from brain homogenates of OC43-infected suckling mice or from HRT cells infected with OC43 shows homology with A59 cDNA when assayed by blot hybridization. abstract: A cDNA probe representing the genome of mouse hepatitis virus (MHV) strain A59 (MHV-A59) was used to measure nucleotide sequence homologies among murine and human coronaviruses and the SD and SK coronaviruses isolated by Burks et al. Since SD and SK were isolated by inoculation of multiple sclerosis (MS) central nervous system (CNS) tissue into mice or cultured mouse cells, it is important to determine their relationships to other murine and human coronavirus isolates. Our results indicate that SD and SK share almost complete nucleotide homology (approximately 90%) with MHV-A59 and generate subgenomic RNAs of the same sizes as MHV-A59. The human coronavirus (HCV) strains tested show less homology with MHV-A59. The immunologically unrelated HCV-229 E shows no nucleotide homology with MHV-A59. The immunologically crossreactive HCV-OC43 shows nucleotide homology with MHV-A59 by blot hybridization but not when hybridized in solution and assayed by S1 nuclease digestion. url: https://api.elsevier.com/content/article/pii/S0042682283800221 doi: 10.1016/s0042-6822(83)80022-1 id: cord-321938-pda4a5n7 author: Weisshoff, Hardy title: Aptamer BC 007 - Efficient binder of spreading-crucial SARS-CoV-2 proteins date: 2020-11-02 words: 5076.0 sentences: 266.0 pages: flesch: 57.0 cache: ./cache/cord-321938-pda4a5n7.txt txt: ./txt/cord-321938-pda4a5n7.txt summary: We therefore checked whether a clinically developed aptamer, BC 007, which is currently in phase 2 of clinical testing for a different indication, would also be able to efficiently bind DNA-susceptible peptide structures from SARS-CoV-2-spreading crucial proteins, such as the receptor binding domain (RBD) of the spike protein and the RNA dependent RNA polymerase of SARS-CoV-2 (re-purposing). In the Spike protein of SARS-CoV-2, several sequences which are highly susceptible to interaction with DNA (multiple amino acids with positive charged side chains) were identified, in particular at the angiotensin I-converting enzyme 2 (ACE2)-receptor binding domain (RBD): YRLFRK (SARS-CoV-2 specific from protein data bank (PDB) data base entry PBD ID: 6VXX, source: [23] ), as well as NRKRISN (PBD ID: 6VXX) and KIKRMK (PDB ID: 5X5B source: [24] ). This enabled us to exploit NMR-spectroscopy to investigate whether the selected peptide-sequences from SARS-CoV-2 proteins bind to this clinically advanced aptamer (BC 007), forcing it into its well described quadruple structure just by molecular interaction. abstract: Corona virus disease 2019 (COVID-19) is a respiratory disease caused by a new coronavirus (SARS-CoV-2) which causes significant morbidity and mortality. The emergence of this novel and highly pathogenic SARS-CoV-2 and its rapid international spread poses a serious global public health emergency. To date 32,174,627 cases, of which 962,613 (2.99%) have died, have been reported (https://www.who.int/westernpacific/health-topics/coronavirus, accessed 23 Sep 2020). The outbreak was declared a Public Health Emergency of International Concern on 30 January 2020. There are still not many SARS-CoV-2-specific and effective treatments or vaccines available. A second round of infection is obviously unavoidable. Aptamers had already been at the centre of interest in the fight against viruses before now. The selection and development of a new aptamer is, however, a time-consuming process. We therefore checked whether a clinically developed aptamer, BC 007, which is currently in phase 2 of clinical testing for a different indication, would also be able to efficiently bind DNA-susceptible peptide structures from SARS-CoV-2-spreading crucial proteins, such as the receptor binding domain (RBD) of the spike protein and the RNA dependent RNA polymerase of SARS-CoV-2 (re-purposing). Indeed, several such sequence-sections have been identified. In particular for two of these sequences, BC 007 showed specific binding in a therapy-relevant concentration range, as shown in Nuclear magnetic resonance (NMR)- and Circular dicroism (CD)-spectroscopy and isothermal titration calorimetry (ITC). The excellent clinical toxicity and tolerability profile of this substance opens up an opportunity for rapid clinical testing of its COVID-19 effectiveness. url: https://www.sciencedirect.com/science/article/pii/S2405844020322647 doi: 10.1016/j.heliyon.2020.e05421 id: cord-346267-l08ld2cy author: Wertheim, Joel O. title: Purifying Selection Can Obscure the Ancient Age of Viral Lineages date: 2011-06-24 words: 6414.0 sentences: 327.0 pages: flesch: 47.0 cache: ./cache/cord-346267-l08ld2cy.txt txt: ./txt/cord-346267-l08ld2cy.txt summary: Over longer periods of evolutionary time (i.e., along long internal branches on a phylogenetic tree), evidence of evolution at the nucleotide level could be lost, which could bias tMRCA estimates towards younger dates (i.e., underestimate the length of these branches). The results presented here demonstrate that not accounting for purifying selection may bias tMRCA estimation in RNA viruses towards more recent dates, and a degree of correction can be realized by employing more realistic codon-based substitution models, capable of partially accounting for the biasing effect of purifying selection. Using BMCMC analysis, we inferred the substitution rate and root age under a standard nucleotide substitution model (GTR + Γ 4 ) for each of our three viral data sets: MeV/RPV/PPRV nucleoprotein, EBOV glycoprotein, and AIV neuraminidase (table 1) . The nucleotide substitution model (GTR + Γ 4 ) underestimated the length of branches simulated under empirical (IFEL) selection regimes inferred from the three viral data sets ( fig. abstract: Statistical methods for molecular dating of viral origins have been used extensively to infer the time of most common recent ancestor for many rapidly evolving pathogens. However, there are a number of cases, in which epidemiological, historical, or genomic evidence suggests much older viral origins than those obtained via molecular dating. We demonstrate how pervasive purifying selection can mask the ancient origins of recently sampled pathogens, in part due to the inability of nucleotide-based substitution models to properly account for complex patterns of spatial and temporal variability in selective pressures. We use codon-based substitution models to infer the length of branches in viral phylogenies; these models produce estimates that are often considerably longer than those obtained with traditional nucleotide-based substitution models. Correcting the apparent underestimation of branch lengths suggests substantially older origins for measles, Ebola, and avian influenza viruses. This work helps to reconcile some of the inconsistencies between molecular dating and other types of evidence concerning the age of viral lineages. url: https://www.ncbi.nlm.nih.gov/pubmed/21705379/ doi: 10.1093/molbev/msr170 id: cord-258595-bk35vxlr author: Westhaus, Sandra title: Detection of SARS-CoV-2 in raw and treated wastewater in Germany – Suitability for COVID-19 surveillance and potential transmission risks date: 2020-08-18 words: 4965.0 sentences: 305.0 pages: flesch: 57.0 cache: ./cache/cord-258595-bk35vxlr.txt txt: ./txt/cord-258595-bk35vxlr.txt summary: Inoculation of differentiated Caco-2 cells for ten days with purified and concentrated wastewater (P2, P5, P11, and P12) did not result in the production of infectious SARS-CoV-2 particles (data not shown), which suggests that treated sewage appears to be non-infectious even though viral RNA fragments can be detected. Inter-comparing these nine catchment areas, we plotted the estimated cumulative and the acute prevalence against the measured SARS-CoV-2 load (Figure 8 ), the latter calculated from RT-qPCR measured M-gene copy concentration ( Figure 4 ) and the actual wastewater flow Q actual on the day of sampling (Table 2) . In contrast, plotting the incidence against SARS-CoV-2 concentration did not yield a conclusive correlation (not shown), likely because the precision of the qPCR employed was not sufficient to discriminate relatively minor differences in the incidence prevailing in the studied catchment areas at the time of sampling, ranging from 30 to 174 cases per 100,000 residents (less than an order of magnitude, Figure 8C and D). abstract: Abstract Wastewater-based monitoring of the spread of the new SARS-CoV-2 virus, also referred to as wastewater-based epidemiology (WBE), has been suggested as a tool to support epidemiology. An extensive sampling campaign, including nine municipal wastewater treatment plants, has been conducted in different cities of the Federal State of North Rhine-Westphalia (Germany) on the same day in April 2020, close to the first peak of the corona crisis. Samples were processed and analysed for a set of SARS-CoV-2-specific genes, as well as pan-genotypic gene sequences also covering other coronavirus types, using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Additionally, a comprehensive set of chemical reference parameters and bioindicators was analysed to characterize the wastewater quality and composition. Results of the RT-qPCR based gene analysis indicate the presence of SARS-CoV-2 genetic traces in different raw wastewaters. Furthermore, selected samples have been sequenced using Sanger technology to confirm the specificity of the RT-qPCR and the origin of the coronavirus. A comparison of the particle-bound and the dissolved portion of SARS-CoV-2 virus genes shows that quantifications must not neglect the solid-phase reservoir. The infectivity of the raw wastewater has also been assessed by viral outgrowth assay with a potential SARS-CoV2- host cell line in vitro, which were not infected when exposed to the samples. This first evidence suggests that wastewater might be no major route for transmission to humans. Our findings draw attention to the need for further methodological and molecular assay validation for enveloped viruses in wastewater. url: https://api.elsevier.com/content/article/pii/S0048969720352797 doi: 10.1016/j.scitotenv.2020.141750 id: cord-349839-s32d3di2 author: Westhof, Eric title: RNA pseudoknots date: 1992-06-30 words: 3427.0 sentences: 185.0 pages: flesch: 59.0 cache: ./cache/cord-349839-s32d3di2.txt txt: ./txt/cord-349839-s32d3di2.txt summary: In the folding of a single-stranded RNA molecule, there are only three ways in which two base-paired segments can be related to each other: two consecutive hairpins; two helices separated by an internal bulge; and, pseudoknots [1]. The first two motifs can be represented as two-dimensional graphs without self-intersections whereas pseudoknots cannot, as they are fundamentally three-dimensional structures in which the four base-paired strands alternate along the sequence of the RNA molecule. The three types of ''classic'' pseudoknots with co-axial stacking of the two base-paired helices and with single-stranded segments crossing the RNA grooves. The third pseudoknot involves the 530 stem-loop structure [19] , which is known to be important for the binding of tRNA to the ribosomal A site [20] , and was recently shown to be essential for ribosomal function [21.o] . abstract: Abstract RNA pseudoknots result from Watson-Crick base pairing involving a stretch of bases located between paired strands and a distal single-stranded region. Recently, significant advances in our understanding of their structural and functional aspects have been accomplished. At the structural level, modelling and NMR studies have shown that a defined subset of pseudoknots may be considered as tertiary motifs in RNA foldings. At the functional level, there is evidence that the realm of functions encompassed by RNA pseudoknots extends from the control of translation in prokaryotes, retroviruses and coronaviruses to the control of catalytic activity in ribozymes and the control of replication in some plant viruses. url: https://www.sciencedirect.com/science/article/pii/0959440X9290221R doi: 10.1016/0959-440x(92)90221-r id: cord-286243-ddpemgqt author: Whitaker, Amy M. title: APE1: A skilled nucleic acid surgeon date: 2018-11-30 words: 5842.0 sentences: 274.0 pages: flesch: 41.0 cache: ./cache/cord-286243-ddpemgqt.txt txt: ./txt/cord-286243-ddpemgqt.txt summary: One such factor is the multifunctional enzyme human apurinic/apyrimidinic endonuclease 1 (APE1), known best for its DNA backbone cleavage activity at AP sites during base excision repair (BER). Abbreviations: 1-nt, 1-nucleotide; 5OHU, 5-hydroxy-2′-deoxyuridine; 8-oxoG, 8-oxoGuanine; AP, apurinic/apyrimidinic; APE1, human apurinic/apyrimidinic endonuclease 1; APE2, apurinic/apyrimidinic endonuclease 2; BER, base excision repair; DHT, 5,6-dihydrothymidine; DHU, 5,6-dihydro-2′-deoxyuridine; dRP, deoxyribonucleotide-phosphate; IR, ionizing radiation; NIR, nucleotide incision repair; pBQ-C, benzetheno exocyclic adduct of cytosine; PG, phosphoglycolate; PNK, polynucleotide kinase; PUA, α,β-unsaturated aldehyde; ROS, reactive oxygen species; THF, tetrahydrofuran; Tdp1, tyrosyl-DNA phosphodiesterase 1; XRCC1, X-ray repair cross-complementing protein 1 ⁎ Corresponding author. The BER pathway requires the coordinated activity of at least five enzymes including: (1) a DNA glycosylase capable of excising the modified base; (2) an AP-endonuclease, such as APE1, to generate a nick at the lesion site; (3) DNA polymerase β, which performs both lyase and DNA synthesis activities to remove the 5′ dRP (deoxyribonucleotide-phosphate) and fill the resulting gap; and, finally (4) DNA ligase III and (5) XRCC1 (X-ray repair cross-complementing protein 1) scaffolding to seal the nick and complete the repair, (Fig. 1) . abstract: Abstract Before a deleterious DNA lesion can be replaced with its undamaged counterpart, the lesion must first be removed from the genome. This process of removing and replacing DNA lesions is accomplished by the careful coordination of several protein factors during DNA repair. One such factor is the multifunctional enzyme human apurinic/apyrimidinic endonuclease 1 (APE1), known best for its DNA backbone cleavage activity at AP sites during base excision repair (BER). APE1 preforms AP site incision with surgical precision and skill, by sculpting the DNA to place the cleavage site in an optimal position for nucleophilic attack within its compact protein active site. APE1, however, has demonstrated broad surgical expertise, and applies its DNA cleavage activity to a wide variety of DNA and RNA substrates. Here, we discuss what is known and unknown about APE1 cleavage mechanisms, focusing on structural and mechanistic considerations. Importantly, disruptions in the biological functions associated with APE1 are linked to numerous human maladies, including cancer and neurodegenerative diseases. The continued elucidation of APE1 mechanisms is required for rational drug design towards novel and strategic ways to target its associated repair pathways. url: https://www.ncbi.nlm.nih.gov/pubmed/30170830/ doi: 10.1016/j.dnarep.2018.08.012 id: cord-272871-gu9ptt9y author: White, K.Andrew title: Defective RNAs of clover yellow mosaic virus encode nonstructural/coat protein fusion products date: 1991-08-31 words: 4609.0 sentences: 241.0 pages: flesch: 60.0 cache: ./cache/cord-272871-gu9ptt9y.txt txt: ./txt/cord-272871-gu9ptt9y.txt summary: Abstract A small group of 1.2-kb RNAs present on polyribosoes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Figure 2 shows Northern blots of polyribosomal RNA extracted from CYMV-infected tissue containing the 1.2-kb RNAs. The 7.0-kb gRNA is identified by all probes (Fig. 2 , lanes a, c, e, g, i, and k; probes 1 to 6), but the 1 .O-kb sgRNA encoding coat protein hybridizes only to probes corresponding to the 3'' region of the gRNA (Fig. 2 , lanes i and k; probes 5 and 6). The majority of the sequence of the prototype 1.2-kb RNA (Fig. 4) and of additional 1.2-kb RNAs is identical WHITE, BANCROFT, AND MACKIE with the corresponding region of CYMV gRNA reported by Sit et al. abstract: Abstract A small group of 1.2-kb RNAs present on polyribosoes from clover yellow mosaic virus (CYMV)-infected tissue contains sequences from the genomic RNA (gRNA) of CYMV and is encapsidated by CYMV coat protein. Some features of these RNAs suggest that they are similar to defective interfering (DI) RNAs, and would be the first to be reported for the potexvirus group. The prototype 1.2-kb RNA is 1172 nucleotides in length excluding a probable poly(A) tail and is composed of two noncontiguous regions corresponding to 757 nucleotides of the 5′ and 415 nucleotides of the 3′ terminal of CYMV's gRNA. The sequence of the prototype 1.2-kb RNA reveals that the two terminal gRNA regions present in this RNA encode a single open reading frame (ORF) joining the N-terminus of the 191-kDa nonstructural product and the C-terminus of the coat protein to form a 35-kDa 191-kDa/coat protein fusion product. The coding properties of this prototype RNA have been confirmed by translation in vitro of native and synthetic transcripts of the 1.2-kb RNAs, both of which direct the synthesis of the anticipated 35-kDa product which reacts with anti-CYMV antiserum. Three additional 1.2-kb RNA species, each of which contains a unique junction site, have been characterized. In all cases, a fusion ORF encoding a 191-kDa/coat protein fusion product is encoded on the RNA. The presence of a fusion ORF in all members of the 1.2-kb RNA species analyzed suggests that maintenance of this ORF may be important for the survival of this class of RNA within the plant. This coding strategy represents a novel property of plant virus defective RNAs. url: https://www.sciencedirect.com/science/article/pii/004268229190977J doi: 10.1016/0042-6822(91)90977-j id: cord-332006-if46jycd author: Whitehead, Kathryn A. title: Knocking down barriers: advances in siRNA delivery date: 2009 words: 6655.0 sentences: 391.0 pages: flesch: 42.0 cache: ./cache/cord-332006-if46jycd.txt txt: ./txt/cord-332006-if46jycd.txt summary: Three years later, Tuschl and co-workers published their celebrated proof-of-principle experiment demonstrating that synthetic small interfering RNA (siRNA) could achieve sequence-specific gene knockdown in a mammalian cell line 2 . Toxicity of certain cationic lipid particles has been reported both in vitro and in vivo [76] [77] [78] , and certain synthetic agents have been found to induce a gene signature of their own that might increase the off-target effects of siRNA 79, 80 . Tumour growth in a mouse model of metastatic Ewing''s sarcoma was shown to be inhibited by the systemic delivery of nanoparticles formed by cyclodextrin, the targeting ligand transferrin, and siRNA specific for the EWS-FLI1 fusion gene commonly associated with the condition. Toxicogenomics of non-viral drug delivery systems for RNAi: potential impact on siRNA-mediated gene silencing activity and specificity abstract: In the 10 years that have passed since the Nobel prize-winning discovery of RNA interference (RNAi), billions of dollars have been invested in the therapeutic application of gene silencing in humans. Today, there are promising data from ongoing clinical trials for the treatment of age-related macular degeneration and respiratory syncytial virus. Despite these early successes, however, the widespread use of RNAi therapeutics for disease prevention and treatment requires the development of clinically suitable, safe and effective drug delivery vehicles. Here, we provide an update on the progress of RNAi therapeutics and highlight novel synthetic materials for the encapsulation and intracellular delivery of nucleic acids. url: https://www.ncbi.nlm.nih.gov/pubmed/19180106/ doi: 10.1038/nrd2742 id: cord-338358-ppjxo2di author: Whitworth, Kristin M. title: Zygote injection of CRISPR/Cas9 RNA successfully modifies the target gene without delaying blastocyst development or altering the sex ratio in pigs date: 2016-10-15 words: 4959.0 sentences: 267.0 pages: flesch: 55.0 cache: ./cache/cord-338358-ppjxo2di.txt txt: ./txt/cord-338358-ppjxo2di.txt summary: title: Zygote injection of CRISPR/Cas9 RNA successfully modifies the target gene without delaying blastocyst development or altering the sex ratio in pigs Pairs of CRISPR guide RNAs that flanked the start codon and polyadenylated Cas9 were co-injected into the cytoplasm of zygotes and cultured in vitro to the blastocyst stage. In a previous study, CRISPR/Cas9 RNA injection of pig zygotes resulted in 100 % of the piglets having biallelic DNA edits of the targeted CD163 or CD1D gene (Whitworth et al. Zygote injection with CRISPR/Cas9 guide RNA was used to efficiently (100 %) create pigs with a biallelic edit of the TMPRSS2 gene for use as a biomedical model (Fig. 2e, f) . The sex ratio measured in the resulting blastocysts and piglets was not significantly affected by in vitro culture or CRISPR/Cas9 RNA injection. abstract: The CRISPR/Cas9 genome editing tool has increased the efficiency of creating genetically modified pigs for use as biomedical or agricultural models. The objectives were to determine if DNA editing resulted in a delay in development to the blastocyst stage or in a skewing of the sex ratio. Six DNA templates (gBlocks) that were designed to express guide RNAs that target the transmembrane protease, serine S1, member 2 (TMPRSS2) gene were in vitro transcribed. Pairs of CRISPR guide RNAs that flanked the start codon and polyadenylated Cas9 were co-injected into the cytoplasm of zygotes and cultured in vitro to the blastocyst stage. Blastocysts were collected as they formed on days 5, 6 or 7. PCR was performed to determine genotype and sex of each embryo. Separately, embryos were surgically transferred into recipient gilts on day 4 of estrus. The rate of blastocyst development was not significantly different between CRISPR injection embryos or the non-injected controls at day 5, 6 or 7 (p = 0.36, 0.09, 0.63, respectively). Injection of three CRISPR sets of guides resulted in a detectable INDEL in 92–100 % of the embryos analyzed. There was not a difference in the number of edits or sex ratio of male to female embryos when compared between days 5, 6 and 7 to the controls (p > 0.22, >0.85). There were 12 resulting piglets and all 12 had biallelic edits of TMRPSS2. Zygote injection with CRISPR/Cas9 continues to be a highly efficient tool to genetically modify pig embryos. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11248-016-9989-6) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s11248-016-9989-6 doi: 10.1007/s11248-016-9989-6 id: cord-267124-8efdzlc0 author: Wichmann, Dominic title: Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study date: 2020-05-06 words: 4062.0 sentences: 240.0 pages: flesch: 50.0 cache: ./cache/cord-267124-8efdzlc0.txt txt: ./txt/cord-267124-8efdzlc0.txt summary: In response to the pandemic spread of SARS-CoV-2, the authorities of the German federal state of Hamburg ordered mandatory autopsies in all patients dying with a diagnosis of COVID-19 confirmed by polymerase chain reaction (PCR). During autopsy, tissue samples for histology were taken from the following organs: heart, lungs, liver, kidneys, spleen, pancreas, brain, prostate and testes (in males), ovaries (in females), small bowel, saphenous vein, common carotid artery, pharynx, and muscle. In this autopsy study of 12 consecutive patients who died of COVID-19, we found a high incidence of deep venous thrombosis (58%). In studies that examined deceased patients with COVID-19 without relying on autopsy, no increased rates of pulmonary embolism were observed clinically. To our knowledge, only 3 case reports have been published on patients with COVID-19 who have undergone complete autopsy and a few more in which only lung tissue was examined (7, 8) . abstract: BACKGROUND: The new coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS–CoV-2), has caused more than 210 000 deaths worldwide. However, little is known about the causes of death and the virus's pathologic features. OBJECTIVE: To validate and compare clinical findings with data from medical autopsy, virtual autopsy, and virologic tests. DESIGN: Prospective cohort study. SETTING: Autopsies performed at a single academic medical center, as mandated by the German federal state of Hamburg for patients dying with a polymerase chain reaction–confirmed diagnosis of COVID-19. PATIENTS: The first 12 consecutive COVID-19–positive deaths. MEASUREMENTS: Complete autopsy, including postmortem computed tomography and histopathologic and virologic analysis, was performed. Clinical data and medical course were evaluated. Results: Median patient age was 73 years (range, 52 to 87 years), 75% of patients were male, and death occurred in the hospital (n = 10) or outpatient sector (n = 2). Coronary heart disease and asthma or chronic obstructive pulmonary disease were the most common comorbid conditions (50% and 25%, respectively). Autopsy revealed deep venous thrombosis in 7 of 12 patients (58%) in whom venous thromboembolism was not suspected before death; pulmonary embolism was the direct cause of death in 4 patients. Postmortem computed tomography revealed reticular infiltration of the lungs with severe bilateral, dense consolidation, whereas histomorphologically diffuse alveolar damage was seen in 8 patients. In all patients, SARS–CoV-2 RNA was detected in the lung at high concentrations; viremia in 6 of 10 and 5 of 12 patients demonstrated high viral RNA titers in the liver, kidney, or heart. LIMITATION: Limited sample size. CONCLUSION: The high incidence of thromboembolic events suggests an important role of COVID-19–induced coagulopathy. Further studies are needed to investigate the molecular mechanism and overall clinical incidence of COVID-19–related death, as well as possible therapeutic interventions to reduce it. PRIMARY FUNDING SOURCE: University Medical Center Hamburg-Eppendorf. url: https://www.ncbi.nlm.nih.gov/pubmed/32374815/ doi: 10.7326/m20-2003 id: cord-320921-eumuid3r author: Widagdo, W. title: Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits date: 2019-04-24 words: 4829.0 sentences: 239.0 pages: flesch: 51.0 cache: ./cache/cord-320921-eumuid3r.txt txt: ./txt/cord-320921-eumuid3r.txt summary: Our data indicate that despite relatively high viral RNA levels produced, low levels of infectious virus are excreted in the upper respiratory tract of rabbits as compared to dromedary camels, thus resulting in a lack of viral transmission. Besides dromedary camels, other animal species, i.e. llamas, alpacas, and pigs have been shown to be susceptible and develop upper respiratory tract infection upon experimental intranasal MERS-CoV inoculation [9] [10] [11] . We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). We found that rabbits inoculated with the MERS-CoV EMC strain and those with the Qatar15 strain developed an equally mild infection and shed similar levels of viral RNA in their nasal and throat swabs (Figure 3 ). abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) transmission from dromedaries to humans has resulted in major outbreaks in the Middle East. Although some other livestock animal species have been shown to be susceptible to MERS-CoV, it is not fully understood why the spread of the virus in these animal species has not been observed in the field. In this study, we used rabbits to further characterize the transmission potential of MERS-CoV. In line with the presence of MERS-CoV receptor in the rabbit nasal epithelium, high levels of viral RNA were shed from the nose following virus inoculation. However, unlike MERS-CoV-infected dromedaries, these rabbits did not develop clinical manifestations including nasal discharge and did shed only limited amounts of infectious virus from the nose. Consistently, no transmission by contact or airborne routes was observed in rabbits. Our data indicate that despite relatively high viral RNA levels produced, low levels of infectious virus are excreted in the upper respiratory tract of rabbits as compared to dromedary camels, thus resulting in a lack of viral transmission. url: https://www.ncbi.nlm.nih.gov/pubmed/31022948/ doi: 10.3390/v11040381 id: cord-291677-zcbyhsf1 author: Wilamowski, M. title: Methylation of RNA Cap in SARS-CoV-2 captured by serial crystallography date: 2020-08-16 words: 5348.0 sentences: 308.0 pages: flesch: 56.0 cache: ./cache/cord-291677-zcbyhsf1.txt txt: ./txt/cord-291677-zcbyhsf1.txt summary: To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We conducted serial synchrotron crystallography (SSX) experiments at 297 K to test whether low radiation dose could help uncover the structure of Nsp10/16 in a complex with Cap-1. The SARS-CoV-2 Nsp10/16 2′-O MTase complex provides a molecular arrangement for binding of the mRNA Cap-0 and subsequent methylation of the first transcribed nucleotide. The further development of SSX and implementation of time-resolved SSX crystallography is an approach that could visualize chemical processes and protein molecular dynamics -such as of the transfer of the methyl group catalyzed by Nsp10/16 2′O-MTase from SARS-CoV-2. Crystal structure and functional analysis of the SARS-coronavirus RNA cap 2′-o-methyltransferase nsp10/nsp16 complex abstract: The genome of the SARS-CoV-2 coronavirus contains 29 proteins, of which 15 are nonstructural. Nsp10 and Nsp16 form a complex responsible for the capping of mRNA at the 5′ terminus. In the methylation reaction the S-adenosyl-L-methionine serves as the donor of the methyl group that is transferred to Cap-0 at the first transcribed nucleotide to create Cap-1. The presence of Cap-1 makes viral RNAs mimic the host transcripts and prevents their degradation. To investigate the 2′-O methyltransferase activity of SARS-CoV-2 Nsp10/16, we applied fixed-target serial synchrotron crystallography (SSX) which allows for physiological temperature data collection from thousands of crystals, significantly reducing the x-ray dose while maintaining a biologically relevant temperature. We determined crystal structures of Nsp10/16 that revealed the states before and after the methylation reaction, for the first time illustrating coronavirus Nsp10/16 complexes with the m7GpppAm2′-O Cap-1, where 2′OH of ribose is methylated. We compare these structures with structures of Nsp10/16 at 297 K and 100 K collected from a single crystal. This data provide important mechanistic insight and can be used to design small molecules that inhibit viral RNA maturation making SARS-CoV-2 sensitive to host innate response. url: https://doi.org/10.1101/2020.08.14.251421 doi: 10.1101/2020.08.14.251421 id: cord-302047-vv5gpldi author: Willemsen, Anouk title: On the stability of sequences inserted into viral genomes date: 2019-11-14 words: 12557.0 sentences: 598.0 pages: flesch: 43.0 cache: ./cache/cord-302047-vv5gpldi.txt txt: ./txt/cord-302047-vv5gpldi.txt summary: Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Viruses genera covered in relevant studies Conclusions of this review All viruses • Inserted sequences are often unstable and rapidly lost upon passaging of an engineered virus • The position at which a sequence is integrated in the genome can be important for stability • Sequence stability is not an intrinsic property of genomes because demographic parameters, such as population size and bottleneck size, can have important effects on sequence stability • The multiplicity of cellular infection affects sequence stability, and can in some cases directly affect whether there is selection for deletion variants • Deletions are not the only class of mutations that can reduce the cost of inserted sequences, although they are the most common I: dsDNA abstract: Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prove to be unstable over time and are rapidly lost, limiting heterologous protein expression. Although virologists are aware that inserted sequences can be unstable, processes leading to insert instability are rarely considered from an evolutionary perspective. Here, we review experimental work on the stability of inserted sequences over a broad range of viruses, and we present some theoretical considerations concerning insert stability. Different virus genome organizations strongly impact insert stability, and factors such as the position of insertion can have a strong effect. In addition, we argue that insert stability not only depends on the characteristics of a particular genome, but that it will also depend on the host environment and the demography of a virus population. The interplay between all factors affecting stability is complex, which makes it challenging to develop a general model to predict the stability of genomic insertions. We highlight key questions and future directions, finding that insert stability is a surprisingly complex problem and that there is need for mechanism-based, predictive models. Combining theoretical models with experimental tests for stability under varying conditions can lead to improved engineering of viral modified genomes, which is a valuable tool for understanding genome evolution as well as for biotechnological applications, such as gene therapy. url: https://www.ncbi.nlm.nih.gov/pubmed/31741748/ doi: 10.1093/ve/vez045 id: cord-268763-s16n7f17 author: Williams, J. G. title: Identification of Three Endotypes in Pediatric Acute Respiratory Distress Syndrome by Nasal Transcriptomic Profiling date: 2020-05-02 words: 4791.0 sentences: 270.0 pages: flesch: 48.0 cache: ./cache/cord-268763-s16n7f17.txt txt: ./txt/cord-268763-s16n7f17.txt summary: The sequences from these specimens was used for downstream analysis (Figure 1) Assessing Nasal Specimen Similarity 64 nasal brushing specimens from 15 PARDS and 10 control subjects collected on study days 1, 3, 7, and 14, were analyzed by DESeq2. In comparing Group A, B, and C subjects, only disease severity (PELOD2) was statistically significant (Supplemental Table 1 ), and for individual specimens, PARDS classification (None, Mild, Moderate, or Severe), and the presence of direct lung injury, a viral or combined viral/bacterial cause of ARDS were significantly different between groups A, B, and C (Supplemental Table 2 ). Interferon-γ and tumor necrosis factor-related signaling were notable in Group B ( in conjunction with our findings that the only clinical variables that differentiated specimens from groups B and C from A were severity of lung injury and a viral cause of ARDS, and that viruses were the most common trigger of ARDS in both groups B and C, these data demonstrate that nasal epithelial transcriptomics can identify three distinct endotypes in PARDS: Endotypes A, B, and C. abstract: Acute respiratory distress syndrome (ARDS) and pediatric ARDS (PARDS) can be triggered by multiple pulmonary and non-pulmonary insults and are the source of substantial morbidity and mortality. The nasal epithelium is similar to that of the lower conducting airways and nasal transcriptomic profiling identifies disease and endotypes in lung cancer, COPD, and asthma. We conducted a prospective trial of testing whether this technique could identify PARDS endotypes in 26 control and 25 PARDS subjects <18 admitted to the PICU extracting RNA from inferior turbinate brushings on days 1, 3, 7, and 14. Standard RNA processing and mRNA-seq yielded ~25% usable specimens and a modified, low-input RNA protocol yielded 95% usable specimens. Sixty-four low-input specimens from 10 control and 15 PARDS subjects were used for initial analysis. Control and some PARDS subjects clustered together in both by-day and combined analysis into Groups A while some day 1, 3, and 7 specimens from the same subjects clustered into Groups B and C with specimens from these subjects moving to Group A with PARDS resolution. In multivariate analysis, the only clinical variables predictive of Group B or C status was severity of lung injury or viral PARDS trigger. Compared to Group A, Group B had upregulation of innate immune processes and group C had upregulation of cilia-associated processes. Analysis of the 15 specimens processed and analyzed by standard techniques identified the same processes as differentiating Groups A, B, and C. Mortality appeared to be higher in group B (25%) and C subjects (28.6%) compared to A subject (5%, p=0.1). Our findings demonstrate three distinct PARDS endotypes which may be useful for prognostic and therapeutic enrichment. ClinicalTrials.gov Identifier NCT03539783 url: https://doi.org/10.1101/2020.04.28.20083451 doi: 10.1101/2020.04.28.20083451 id: cord-000269-v4jochbe author: Wittekindt, Nicola E. title: Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics date: 2010-10-18 words: 5886.0 sentences: 314.0 pages: flesch: 44.0 cache: ./cache/cord-000269-v4jochbe.txt txt: ./txt/cord-000269-v4jochbe.txt summary: cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. The microbial community of mule deer lymph nodes Detection of protein-coding and ribosomal RNA transcripts provides strong support for the presence of viable and replicating microorganisms. As an alternative approach to identifying bacterial microorganisms present in lymph node tissue, we utilized amplicon DNA library sequencing technology. abstract: The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956653/ doi: 10.1371/journal.pone.0013432 id: cord-340325-0oh40b6r author: Witzigmann, Dominik title: Lipid nanoparticle technology for therapeutic gene regulation in the liver date: 2020-07-02 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Hereditary genetic disorders, cancer, and infectious diseases of the liver affect millions of people around the globe and are a major public health burden. Most contemporary treatments offer limited relief as they generally aim to alleviate disease symptoms. Targeting the root cause of diseases originating in the liver by regulating malfunctioning genes with nucleic acid-based drugs s holds great promise as a therapeutic approach. However, employing nucleic acid therapeutics in vivo is challenging due to their unfavorable characteristics. Lipid nanoparticle (LNP) delivery technology is a revolutionary development that has enabled clinical translation of gene (editing) therapies. LNPs can deliver siRNA, mRNA, DNA, or gene-editing complexes, providing opportunities to treat hepatic diseases by silencing pathogenic genes, expressing therapeutic proteins, or correcting genetic defects. Here we discuss the state-of-the-art LNP technology for hepatic gene therapy including formulation design parameters, production methods, preclinical development and clinical translation. url: https://www.sciencedirect.com/science/article/pii/S0169409X20300727?v=s5 doi: 10.1016/j.addr.2020.06.026 id: cord-327660-p1b07b4t author: Wolf, Yuri I. title: Origins and Evolution of the Global RNA Virome date: 2018-11-27 words: 13927.0 sentences: 658.0 pages: flesch: 45.0 cache: ./cache/cord-327660-p1b07b4t.txt txt: ./txt/cord-327660-p1b07b4t.txt summary: The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) . abstract: Viruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas −RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy. url: https://www.ncbi.nlm.nih.gov/pubmed/30482837/ doi: 10.1128/mbio.02329-18 id: cord-276364-zyw5aukk author: Wong, Ho Him title: Manipulation of autophagy by (+) RNA viruses date: 2019-08-08 words: 6884.0 sentences: 360.0 pages: flesch: 33.0 cache: ./cache/cord-276364-zyw5aukk.txt txt: ./txt/cord-276364-zyw5aukk.txt summary: Over the past few decades, a growing body of research has defined the critical role of this pathway in facilitating infection by numerous +RNA RNA viruses, including poliovirus (PV) [7, 8] , Coxsackievirus B3 (CVB3) [9, 10] , CVB4 [11] , Enterovirus 71 (EV71) [12] , Human rhinovirus (HRV) [13] , Foot-and-mouth disease virus (FMDV) [14] , encephalomyocarditis virus (EMCV) [15] , Dengue virus (DENV) [16, 17] , Zika virus (ZIKV) [18, 19] , Hepatitis C virus (HCV) [20] , Mouse hepatitic virus (MHV), Newcastle disease virus (NDV) [21] , Severe and acute respiratory syndrome coronavirus (SARS-CoV) [22] , Chikungunya virus (ChikV) [23] , and Japanese encephalitis virus (JEV) [24] . Delineating the process of viral assembly from replication is technically challenging, especially since both processes would very likely Induces formation of autophagosome-like double-membrane liposomes [112] Summary of Interactions between proteins from positive strand RNA viruses and host autophagy machinery. abstract: Autophagy is an evolutionarily conserved process central to host metabolism. Among its major functions are conservation of energy during starvation, recycling organelles, and turnover of long-lived proteins. Besides, autophagy plays a critical role in removing intracellular pathogens and very likely represents a primordial intrinsic cellular defence mechanism. More recent findings indicate that it has not only retained its ability to degrade intracellular pathogens, but also functions to augment and fine tune antiviral immune responses. Interestingly, viruses have also co-evolved strategies to manipulate this pathway and use it to their advantage. Particularly intriguing is infection-dependent activation of autophagy with positive stranded (+)RNA virus infections, which benefit from the pathway without succumbing to lysosomal degradation. In this review we summarise recent data on viral manipulation of autophagy, with a particular emphasis on +RNA viruses and highlight key unanswered questions in the field that we believe merit further attention. url: https://www.sciencedirect.com/science/article/pii/S1084952118302222 doi: 10.1016/j.semcdb.2019.07.013 id: cord-319501-a2x1hvkk author: Wong, Lok-Yin Roy title: A molecular arms race between host innate antiviral response and emerging human coronaviruses date: 2016-01-15 words: 7759.0 sentences: 460.0 pages: flesch: 51.0 cache: ./cache/cord-319501-a2x1hvkk.txt txt: ./txt/cord-319501-a2x1hvkk.txt summary: Particularly, the host pathogen recognition receptors and the signal transduction pathways to mount an effective antiviral response against SARS and MERS coronavirus infection are discussed. This suggests SARS-CoV N may interfere with RNA recognition by host immune sensors such as RIG-I and MDA5 thus achieving suppressive role in IFN production. Our group demonstrated that MERS-CoV ORF4a interacts with PACT, a cellular dsRNA-binding protein that optimally activates RIG-Iand MDA5-induced type I IFN production, in an RNAdependent manner (Siu et al., 2014c) . Infection with SARS-CoV and MERS-CoV has been accompanied with suppression of innate immune response, most notably with the suppression of type I IFN production and signaling pathways. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells Middle East respiratory syndrome coronavirus 4a protein is a double-stranded RNA-binding protein that suppresses pact-induced activation of RIG-I and MDA5 in the innate antiviral response abstract: Coronaviruses have been closely related with mankind for thousands of years. Communityacquired human coronaviruses have long been recognized to cause common cold. However, zoonotic coronaviruses are now becoming more a global concern with the discovery of highly pathogenic severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses causing severe respiratory diseases. Infections by these emerging human coronaviruses are characterized by less robust interferon production. Treatment of patients with recombinant interferon regimen promises beneficial outcomes, suggesting that compromised interferon expression might contribute at least partially to the severity of disease. The mechanisms by which coronaviruses evade host innate antiviral response are under intense investigations. This review focuses on the fierce arms race between host innate antiviral immunity and emerging human coronaviruses. Particularly, the host pathogen recognition receptors and the signal transduction pathways to mount an effective antiviral response against SARS and MERS coronavirus infection are discussed. On the other hand, the counter-measures evolved by SARS and MERS coronaviruses to circumvent host defense are also dissected. With a better understanding of the dynamic interaction between host and coronaviruses, it is hoped that insights on the pathogenesis of newly-identified highly pathogenic human coronaviruses and new strategies in antiviral development can be derived. [Image: see text] url: https://doi.org/10.1007/s12250-015-3683-3 doi: 10.1007/s12250-015-3683-3 id: cord-343963-99rd3o79 author: Wong, Mun-Teng title: Emerging roles of interferon-stimulated genes in the innate immune response to hepatitis C virus infection date: 2014-12-29 words: 17253.0 sentences: 1074.0 pages: flesch: 42.0 cache: ./cache/cord-343963-99rd3o79.txt txt: ./txt/cord-343963-99rd3o79.txt summary: 13, 14 Upon infection by viruses such as HCV, viral RNA is first sensed by cellular pattern recognition receptors (PRRs), and the PRR-mediated recruitment of adaptor proteins and the activation of downstream signaling lead to IFN production. First, we briefly discuss the signaling triggered by the retinoic acid-inducible gene 1-like receptor (RLR) and the Toll-like receptor (TLR), which leads to type I IFN synthesis and IFN-mediated signaling pathway activation, resulting in the expression of a variety of effector ISGs. We also summarize the strategies that HCV uses to escape IFN antiviral surveillance. 156 demonstrated that HCVinduced SG formation is IFN-and PKR-dependent and is inversely correlated with the induction of ISG proteins, such as myxovirus resistance gene A (MxA) and Ub-like (UBL)specific protease 18 (USP18), in HCV-infected cells without affecting the mRNA levels of these ISGs. Furthermore, the SG proteins TIA-1, TIAR and G3BP1 have been shown to play a critical role in HCV replication and infectious virus production. abstract: Infection with hepatitis C virus (HCV), a major viral cause of chronic liver disease, frequently progresses to steatosis and cirrhosis, which can lead to hepatocellular carcinoma. HCV infection strongly induces host responses, such as the activation of the unfolded protein response, autophagy and the innate immune response. Upon HCV infection, the host induces the interferon (IFN)-mediated frontline defense to limit virus replication. Conversely, HCV employs diverse strategies to escape host innate immune surveillance. Type I IFN elicits its antiviral actions by inducing a wide array of IFN-stimulated genes (ISGs). Nevertheless, the mechanisms by which these ISGs participate in IFN-mediated anti-HCV actions remain largely unknown. In this review, we first outline the signaling pathways known to be involved in the production of type I IFN and ISGs and the tactics that HCV uses to subvert innate immunity. Then, we summarize the effector mechanisms of scaffold ISGs known to modulate IFN function in HCV replication. We also highlight the potential functions of emerging ISGs, which were identified from genome-wide siRNA screens, in HCV replication. Finally, we discuss the functions of several cellular determinants critical for regulating host immunity in HCV replication. This review will provide a basis for understanding the complexity and functionality of the pleiotropic IFN system in HCV infection. Elucidation of the specificity and the mode of action of these emerging ISGs will also help to identify novel cellular targets against which effective HCV therapeutics can be developed. url: https://www.ncbi.nlm.nih.gov/pubmed/25544499/ doi: 10.1038/cmi.2014.127 id: cord-335067-tg66h99q author: Woolhouse, Mark E.J. title: Ecological and taxonomic variation among human RNA viruses date: 2013-03-19 words: 1395.0 sentences: 88.0 pages: flesch: 59.0 cache: ./cache/cord-335067-tg66h99q.txt txt: ./txt/cord-335067-tg66h99q.txt summary: The realisation that many newly discovered and/or emerging pathogens have zoonotic origins has prompted much interest in the nature of the non-human reservoirs and biological characteristics that enable pathogens to jump between host species. 1 Here, we focus on an important group of pathogens -RNA viruses -and consider how taxonomic diversity and various aspects of ecological diversity -host range, route of infection and transmissibility -are related to one another. 2 We catalogue ICTV-recognised RNA virus species for which we can find convincing evidence of natural human infection in the peer-reviewed scientific literature (see Ref. 3 for more methodological details). Our procedure reveals a total of 158 human infective RNA virus species from 47 genera and 17 families (with one genus unassigned to a family). The overlap is also illustrated in that 47 out of 60 recognised mammal virus genera contain human infective species, as do 17 out of 19 families. There are 68 species of vector-borne RNA virus that can infect humans. abstract: Only a minority of RNA viruses that can infect humans are capable of spreading in human populations independently of a zoonotic reservoir. This is especially true of vector-borne RNA viruses; the majority of these are not transmissible (via the vector) between humans at all. Understanding the biology underlying this observation will help us evaluate the public health risk associated with novel vector-borne RNA viruses. url: https://api.elsevier.com/content/article/pii/S1386653213000802 doi: 10.1016/j.jcv.2013.02.019 id: cord-266921-x9q7dwc4 author: Worrall, Jonathan AR title: Information available at cut rates: structure and mechanism of ribonucleases date: 2006-12-26 words: 4616.0 sentences: 222.0 pages: flesch: 49.0 cache: ./cache/cord-266921-x9q7dwc4.txt txt: ./txt/cord-266921-x9q7dwc4.txt summary: The exoribonuclease RNase II is representative of an extensive enzyme family found in all three domains of life, whose members play roles in the maturation, turn-Structure and mechanism of ribonucleases Worrall and Luisi 131 Whereas DEAD-box helicases use the free energy of ATP binding and hydrolysis to disrupt secondary structure, RNase R transduces the favourable free energy of RNA backbone hydrolysis into mechanical work that translates the single-stranded substrate further into the catalytic pocket, much like a ratchet. Crystal structures of the core of the exosomes from the archaea Sulfolobus solfataricus and Archaeoglobus fulgidus have recently become available, revealing a hexameric ring comprising two types of RNase-PH-like subunits, known as Rrp41 and Rrp42 (rRNA-processing proteins 41 and 42; see Figure 4a ) [36 ,37 ,38 ] . Structure of Escherichia coli RNase E catalytic domain and its implications for RNA turnover and processing abstract: Ribonucleases are counterweights in the balance of gene expression and are also involved in the maturation of functional RNA. Recent structural data reveal how ribonucleases recognize and cleave targets, in most cases with the catalytic assistance of metal cofactors. Many of these enzymes are ‘processive’, in that they make multiple scissions following the binding of substrates; crystallographic data can account for this solution behaviour. These data not only explain how ribonucleases turn over transcripts, but also provide hints about how they often play dual roles in quality control checks on structured RNA. url: https://www.sciencedirect.com/science/article/pii/S0959440X06002119 doi: 10.1016/j.sbi.2006.12.001 id: cord-337673-1nau263l author: Wu, Chang-Jer title: Antiviral applications of RNAi for coronavirus date: 2006-01-24 words: 4329.0 sentences: 253.0 pages: flesch: 52.0 cache: ./cache/cord-337673-1nau263l.txt txt: ./txt/cord-337673-1nau263l.txt summary: Recently, small interfering RNA (siRNA) has shown promise in the protection from viral invasion, as it can inhibit the expression of viral antigens and accessory genes as well as control the transcription and replication of the viral genome. Genes encoding vital proteins in reproducing SARS-CoV virions can be chosen for chemotherapeutic intervention (e.g., those coding for S, 3C-like protease [3CLpro], RNA-dependent RNA polymerase and possibly other gene products involved in viral-protein-mediated processes) [81] first demonstrated that siRNA was able to silence the replicase of SARS-CoV (1a region of the genome) and that this approach was effective in vitro against SARS-CoV. [82] subsequently observed that vector-based siRNAs could inhibit the replication of SARS-CoV, and showed that expression in the plasmid, pSUPER, of siRNAs specifically targeting viral RNA polymerases could block the cytopathic effects of SARS-CoV on Vero cells. [86] showed that three chemically synthesised siRNA duplexes targeting viral RNA polymerases, and one targeting the S gene potently inhibited SARS-CoV infection and replication in fetal rhesus kidney cells (FRhK-4) . abstract: Until the appearance of severe acute respiratory syndrome (SARS), caused by the SARS coronavirus (SARS-CoV) in early 2003, coronavirus infection was not considered to be serious enough to be controlled by either vaccination or specific antiviral therapy. It is now believed that the availability of antiviral drugs effective against SARS-CoV will be crucial for the control of future SARS outbreaks. Recently, RNA interference has been successfully used as a more specific and efficient method for gene silencing. RNA interference induced by small interfering RNA can inhibit the expression of viral antigens and so provides a new approach to the therapy of pathogenic viruses. This review provides an overview of current information on coronavirus and the application of small interfering RNA in viral therapeutics, with particular reference to SARS-CoV. url: https://www.ncbi.nlm.nih.gov/pubmed/16433589/ doi: 10.1517/13543784.15.2.89 id: cord-010762-c01wgg4v author: Wu, Jiqin title: A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase date: 2020-05-01 words: 9021.0 sentences: 382.0 pages: flesch: 50.0 cache: ./cache/cord-010762-c01wgg4v.txt txt: ./txt/cord-010762-c01wgg4v.txt summary: Previously reported NS5 structures represented by those from the Japanese encephalitis virus (JEV) and Dengue virus serotype 3 (DENV3) exhibit two apparently different global conformations, defining two sets of intra-molecular MTase-RdRP interactions. Data from in vitro polymerase assays further demonstrate that perturbing the JEV-mode but not the DENV3-mode intra-molecular interactions inhibits catalysis only at initiation, while the cell-based virological analysis suggests that both modes of interactions are important for virus proliferation. NS5 constructs bearing mutations specifically probing two modes of MTase-RdRP intra-molecular interfaces were tested in in vitro polymerase assays, and only the JEV-mode interface related mutants inhibited polymerase initiation primarily through a three-fold reduction in the Michaelis constant of the initiating NTP (K M, NTP ), while polymerase EC properties were not much affected by mutations probing both modes of interactions. abstract: The flaviviruses pose serious threats to human health. Being a natural fusion of a methyltransferase (MTase) and an RNA-dependent RNA polymerase (RdRP), NS5 is the most conserved flavivirus protein and an important antiviral target. Previously reported NS5 structures represented by those from the Japanese encephalitis virus (JEV) and Dengue virus serotype 3 (DENV3) exhibit two apparently different global conformations, defining two sets of intra-molecular MTase-RdRP interactions. However, whether these NS5 conformations are conserved in flaviviruses and their specific functions remain elusive. Here we report two forms of DENV serotype 2 (DENV2) NS5 crystal structures representing two conformational states with defined analogies to the JEV-mode and DENV3-mode conformations, respectively, demonstrating the conservation of both conformation modes and providing clues for how different conformational states may be interconnected. Data from in vitro polymerase assays further demonstrate that perturbing the JEV-mode but not the DENV3-mode intra-molecular interactions inhibits catalysis only at initiation, while the cell-based virological analysis suggests that both modes of interactions are important for virus proliferation. Our work highlights the role of MTase as a unique intra-molecular initiation factor specifically only through the JEV-mode conformation, providing an example of conformation-based crosstalk between naturally fused protein functional modules. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219791/ doi: 10.1371/journal.ppat.1008484 id: cord-327997-noqbcxua author: Wu, Kevin E. title: RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus date: 2020-06-20 words: 7201.0 sentences: 377.0 pages: flesch: 42.0 cache: ./cache/cord-327997-noqbcxua.txt txt: ./txt/cord-327997-noqbcxua.txt summary: We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus, and that the 5'' and 3'' viral untranslated regions contain the strongest, most distinct localization signals. As previously discussed, since much of the APEX-seq mitochondrial data used to train RNA-GPS actually consists of nuclear-encoded transcripts likely picked up as the APEX-COX4 fusion protein is transported to the mitochondria, we hypothesize that our predicted mitochondrial residency is alluding to similarity in localization pathways, rather than localization destination. To further validate the robustness of these results, we also trained a different predictive algorithm (a recurrent neural network, see STAR Methods for additional details) on the APEX-seq data and performed a similar set of experiments, comparing SARS-CoV-2 dominant subcellular residency predictions to human and coronavirus baselines ( Figure S3A /B). abstract: Abstract/Summary SARS-CoV-2 genomic and subgenomic RNA (sgRNA) transcripts hijack the host cell's machinery. Subcellular localization of its viral RNA could thus play important roles in viral replication and host antiviral immune response. We perform computational modeling of SARS-CoV-2 viral RNA subcellular residency across eight subcellular neighborhoods. We compare hundreds of SARS-CoV-2 genomes to the human transcriptome and other coronaviruses. We predict the SARS-CoV-2 RNA genome and sgRNAs to be enriched towards the host mitochondrial matrix and nucleolus, and that the 5’ and 3’ viral untranslated regions contain the strongest, most distinct localization signals. We interpret the mitochondrial residency signal as an indicator of intracellular RNA trafficking with respect to double-membrane vesicles, a critical stage in the coronavirus life cycle. Our computational analysis serves as a hypothesis generation tool to suggest models for SARS-CoV-2 biology and inform experimental efforts to combat the virus. A record of this paper’s Transparent Peer Review process is included in the Supplemental Information. url: https://www.sciencedirect.com/science/article/pii/S2405471220302374?v=s5 doi: 10.1016/j.cels.2020.06.008 id: cord-348799-qu4zin3o author: Wu, Nannan title: The interferon stimulated gene 20 protein (ISG20) is an innate defense antiviral factor that discriminates self versus non-self translation date: 2019-10-10 words: 11391.0 sentences: 520.0 pages: flesch: 48.0 cache: ./cache/cord-348799-qu4zin3o.txt txt: ./txt/cord-348799-qu4zin3o.txt summary: This lack of specificity was not present in cells however, given that the ectopic expression of ISG20 did not lead to the indiscriminate degradation of cellular RNAs (ribosomal as well as small nucleolar RNAs previously shown to be associated to ISG20 [2] ), nor of an Hepatitis C virus (HCV)-derived Luciferase reporter mRNA produced in vitro and then transfected into cells (S4C and S4D Fig) , suggesting that in cells the RNase activity of ISG20 is tightly controlled. Self mimicry allows the escape of target genes'' mRNAs from the effects of ISG20 VSV infection and ectopic DNA or RNA transfection do not bear much in common apart from the fact that both represent artificial injections into the cell of non-self genetic material from without. To further determine whether ISG20 acted on translation initiation and more specifically through specific initiation factors (eIFs), capped and polyadenylated mRNAs coding luciferase under the control of several 5'' untranslated regions (5'' UTRs) were generated in vitro and directly transfected in ISG20-expressing cells (Fig 3D) . abstract: ISG20 is a broad spectrum antiviral protein thought to directly degrade viral RNA. However, this mechanism of inhibition remains controversial. Using the Vesicular Stomatitis Virus (VSV) as a model RNA virus, we show here that ISG20 interferes with viral replication by decreasing protein synthesis in the absence of RNA degradation. Importantly, we demonstrate that ISG20 exerts a translational control over a large panel of non-self RNA substrates including those originating from transfected DNA, while sparing endogenous transcripts. This activity correlates with the protein’s ability to localize in cytoplasmic processing bodies. Finally, these functions are conserved in the ISG20 murine ortholog, whose genetic ablation results in mice with increased susceptibility to viral infection. Overall, our results posit ISG20 as an important defense factor able to discriminate the self/non-self origins of the RNA through translation modulation. url: https://doi.org/10.1371/journal.ppat.1008093 doi: 10.1371/journal.ppat.1008093 id: cord-354824-7fdcu2f0 author: Wu, Renyi title: An Update on Current Therapeutic Drugs Treating COVID-19 date: 2020-05-11 words: 9652.0 sentences: 504.0 pages: flesch: 42.0 cache: ./cache/cord-354824-7fdcu2f0.txt txt: ./txt/cord-354824-7fdcu2f0.txt summary: Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients. This estimated 20% of patients developing more severe disease with SARS-CoV-2 infection are most likely due to genetics, epigenetics, and or other factors, with dampened innate immune response to fight the virus coupled with enhanced viral load leading to cytokine storm, severe inflammatory/oxidative stress response, and severe lung injury secondary to ARDS. Chloroquine can inhibit the entry of SARS-CoV-2 and prevent virus-cell fusion by interfering with glycosylation of ACE2 receptor and its binding with spike protein, suggesting that chloroquine treatment might be more effective in the early stage of infection, before COVID-19 reduces ACE2 expression and activity [30, 38, 39] . Chloroquine diphosphate in two different dosages as adjunctive therapy of hospitalized patients with severe respiratory syndrome in the context of coronavirus (SARS-CoV-2) infection: Preliminary safety results of a randomized, doubleblinded, phase IIb clinical trial (CloroCovid-19 Study) abstract: The current pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has presented unprecedented challenges to the healthcare systems in almost every country around the world. Currently, there are no proven effective vaccines or therapeutic agents against the virus. Current clinical management includes infection prevention and control measures and supportive care including supplemental oxygen and mechanical ventilatory support. Evolving research and clinical data regarding the virologic SARS-CoV-2 suggest a potential list of repurposed drugs with appropriate pharmacological effects and therapeutic efficacies in treating COVID-19 patients. In this review, we will update and summarize the most common and plausible drugs for the treatment of COVID-19 patients. These drugs and therapeutic agents include antiviral agents (remdesivir, hydroxychloroquine, chloroquine, lopinavir, umifenovir, favipiravir, and oseltamivir), and supporting agents (Ascorbic acid, Azithromycin, Corticosteroids, Nitric oxide, IL-6 antagonists), among others. We hope that this review will provide useful and most updated therapeutic drugs to prevent, control, and treat COVID-19 patients until the approval of vaccines and specific drugs targeting SARS-CoV-2. url: https://doi.org/10.1007/s40495-020-00216-7 doi: 10.1007/s40495-020-00216-7 id: cord-264678-wt0lvhfl author: Wu, Tzong-Yuan title: IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico date: 2009-05-27 words: 5333.0 sentences: 306.0 pages: flesch: 58.0 cache: ./cache/cord-264678-wt0lvhfl.txt txt: ./txt/cord-264678-wt0lvhfl.txt summary: To develop the IRES search system, it will be necessary to screen the database of virus sequences by the prediction of secondary structure to identify the candidate IRES element in the virus genome, especially those positive strand viruses with 5'' untranslated regions. Enterovirus IRES domain IV [25] , was first selected as a target to compare with the whole genome sequences from four different viruses (Enterovirus 71 (U22521), Bovine Enterovirus (NC_001859), Human Rhinovirus (NC_001617) and Hepatitis C virus (NC_004102) [26] [27] [28] ) were downloaded into IRSS and ran UTR2SQ.pl program to proceed RNA secondary structure prediction (see Figure 1 ). First, the IRSS search capability is evaluated while virus genomes sequences were substituted for the entire UTRdb. The known IRES element which was used for RNA comparison was selected such as HCV IRES domain III structure for example. abstract: BACKGROUND: Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements. RESULTS: We designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters. CONCLUSION: IRSS is freely available at this website . In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies. url: https://doi.org/10.1186/1471-2105-10-160 doi: 10.1186/1471-2105-10-160 id: cord-342117-r2chpw7y author: Wu, Xinwei title: Inhibitory effect of small interfering RNA on dengue virus replication in mosquito cells date: 2010-10-14 words: 2928.0 sentences: 191.0 pages: flesch: 59.0 cache: ./cache/cord-342117-r2chpw7y.txt txt: ./txt/cord-342117-r2chpw7y.txt summary: The antiviral effect of siRNA was evaluated by measurement of cell survival rate using the MTT method and viral RNA was quantitated with real-time RT-PCR. CONCLUSIONS: Our data showed that synthetic siRNA against the DEN-1 membrane glycoprotein precursor gene effectively inhibited DEN-1 viral RNA replication and increased C6/36 cell survival rate. Therefore, in this study, we designed and synthesized 21 nt siRNAs against the DEN-I viral PrM gene, and investigated their inhibition effects of dengue virus replication in transfected C6/36 cells. These data indicate that siRNA against DEN viral genome can effectively inhibit viral RNA replication in the C6/36 cells, protect host cell from viral attack, suggesting its potential role in prevention and treatment of dengue fever. Our data showed that synthetic siRNA against the DEN membrane glycoprotein precursor gene effectively inhibited DEN viral RNA replication and increased C6/36 cell survival rate. Inhibition of viral gene expression and replication in mosquito cells by dsRNA-triggered RNA interference abstract: BACKGROUND: Dengue viruses (DENs) are the wildest transmitted mosquito-borne pathogens throughout tropical and sub-tropical regions worldwide. Infection with DENs can cause severe flu-like illness and potentially fatal hemorrhagic fever. Although RNA interference triggered by long-length dsRNA was considered a potent antiviral pathway in the mosquito, only limited studies of the value of small interfering RNA (siRNA) have been conducted. RESULTS: A 21 nt siRNA targeting the membrane glycoprotein precursor gene of DEN-1 was synthesized and transfected into mosquito C6/36 cells followed by challenge with DEN. The stability of the siRNA in cells was monitored by flow cytometry. The antiviral effect of siRNA was evaluated by measurement of cell survival rate using the MTT method and viral RNA was quantitated with real-time RT-PCR. The presence of cells containing siRNA at 0.25, 1, 3, 5, 7 days after transfection were 66.0%, 52.1%, 32.0%, 13.5% and 8.9%, respectively. After 7 days incubation with DEN, there was reduced cytopathic effect, increased cell survival rate (76.9 ± 4.5% vs 23.6 ± 14.6%) and reduced viral RNA copies (Ct value 19.91 ± 0.63 vs 14.56 ± 0.39) detected in transfected C6/36 cells. CONCLUSIONS: Our data showed that synthetic siRNA against the DEN-1 membrane glycoprotein precursor gene effectively inhibited DEN-1 viral RNA replication and increased C6/36 cell survival rate. siRNA may offer a potential new strategy for prevention and treatment of DEN infection. url: https://www.ncbi.nlm.nih.gov/pubmed/20946645/ doi: 10.1186/1743-422x-7-270 id: cord-255607-dbexsugq author: Wu, Yang title: Porcine Epidemic Diarrhea Virus nsp15 Antagonizes Interferon Signaling by RNA Degradation of TBK1 and IRF3 date: 2020-05-31 words: 6410.0 sentences: 357.0 pages: flesch: 48.0 cache: ./cache/cord-255607-dbexsugq.txt txt: ./txt/cord-255607-dbexsugq.txt summary: Our preliminary results revealed that endogenous TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3), the key components in the IFN signaling pathway were downregulated in PEDV infected IPEC-J2 cells by iTRAQ analysis. Moreover, PEDV nsp15 can directly degrade the RNA levels of TBK1 and IRF3 dependent on its EndoU activity to suppress IFN production and constrain the induction of IFN stimulated genes (ISGs), by which PEDV antagonizes the host innate response to facilitate its replication. Previous studies suggest that PEDV can restrain host innate immune response by different strategies, such as by degradation or cleavage of key factors essential the IFN signaling pathway [25, 26] , competitive interaction between viral encoded proteins and modulators for IFN production [27, 28] , or localization changes of antiviral components [29] . abstract: Porcine epidemic diarrhea virus (PEDV) causes a porcine disease associated with swine epidemic diarrhea. The type I interferon (IFN-I or IFN α/β) is a key mediator of innate antiviral response during virus infection. Different antagonistic strategies have been identified and determined as to how PEDV infection inhibits the host’s IFN responses to escape the host innate immune pathway, but the pathogenic mechanisms of PEDV infection are not fully elucidated. Our preliminary results revealed that endogenous TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3), the key components in the IFN signaling pathway were downregulated in PEDV infected IPEC-J2 cells by iTRAQ analysis. In this study, we screened nsp15 as the most important viral encoded protein involved in TBK1 and IRF3 reduction. Endoribonuclease (EndoU) activity has been well determined for coronavirus nsp15. Three residues (H226, H241, and K282) of PEDV nsp15 were identified as critical amino acids for PEDV EndoU but not D265, which was not well correlated with published results of other coronaviruses, such as severe acute respiratory syndrome virus (SARS-CoV). Moreover, PEDV nsp15 can directly degrade the RNA levels of TBK1 and IRF3 dependent on its EndoU activity to suppress IFN production and constrain the induction of IFN stimulated genes (ISGs), by which PEDV antagonizes the host innate response to facilitate its replication. Collectively, these results have confirmed that PEDV nsp15 was capable of subverting the IFN response by the RNA degradation of TBK1 and IRF3. url: https://doi.org/10.3390/v12060599 doi: 10.3390/v12060599 id: cord-354529-k8p2u7iq author: Wu, Yongran title: Patients with Prolonged Positivity of SARS-CoV-2 RNA Benefit from Convalescent Plasma Therapy: A Retrospective Study date: 2020-08-31 words: 3753.0 sentences: 223.0 pages: flesch: 57.0 cache: ./cache/cord-354529-k8p2u7iq.txt txt: ./txt/cord-354529-k8p2u7iq.txt summary: Clinical information of patients was collected from the electronic medical information system of Jinyintan Hospital, including the following factors: demographic data; date of symptom onset, admission, first CP infusion and discharge; laboratory data before and after infusion of CP, including white blood cell count, neutrophil count, lymphocyte count, liver and kidney function test, and inflammatory factors such as high sensitive C-reaction protein (HsCRP); results of SARS-CoV-2 test and cycle threshold value (Ct value) of quantitative reverse transcription-polymerase chain reaction; patients'' status and treatments before or after the CP therapy, including the vital signs, anti-virus therapy, oxygen therapy, and other treatments; total volume dose of CP; pulmonary imaging examination data; information on complications such as transfusion-related adverse reactions. Clinical Benefit and Outcome of Patients with Prolonged Positivity of SARS-CoV-2 RNA after CP Therapy As shown in Table 3 , the median and interquartile ranged total volume of CP transfusion was 400 (200-400) mL in EN group and 400 (400-800) mL in LN group. abstract: Convalescent plasma therapy has been implemented in a few cases of severe coronavirus disease 2019. No report about convalescent plasma therapy in treating patients with prolonged positivity of SARS-CoV-2 RNA has been published. In this study, we conducted a retrospective observational study in 27 patients with prolonged positivity of SARS-CoV-2 RNA, the clinical benefit of convalescent plasma therapy were analyzed. qRT-PCR test of SARS-CoV-2 RNA turned negative (≤ 7 days) in a part of patients (early negative group, n = 15) after therapy, others (late negative group, n = 12) turned negative in more than 7 days. Pulmonary imaging improvement was confirmed in 7 patients in early negative group and 8 in late negative group after CP therapy. Viral load decreased in early negative group compared with late negative group at day 3, 5, 7 after implementing convalescent plasma therapy. Patients in early negative group had a shorter median length of hospital stay. In conclusion, convalescent plasma therapy might help eliminate virus and shorten length of hospital stay in patients with prolonged positivity of SARS-CoV-2 RNA. url: https://www.ncbi.nlm.nih.gov/pubmed/32865701/ doi: 10.1007/s12250-020-00281-8 id: cord-304044-i1ikf96b author: Wu, Yue title: Inhibition of white spot syndrome virus in Litopenaeus vannamei shrimp by sequence-specific siRNA date: 2007-10-03 words: 4733.0 sentences: 304.0 pages: flesch: 58.0 cache: ./cache/cord-304044-i1ikf96b.txt txt: ./txt/cord-304044-i1ikf96b.txt summary: Here, we described specific silencing of five white spot syndrome virus (WSSV) genes in Litopenaeus vannamei in vivo with sequence-specific siRNAs. These genes included DNA polymerase (dnapol), ribonucleotide reductase small subunit (rr2), thymidine kinase and thymidylate kinase (tk-tmk), vp24 and vp28. control for interference action of siRNAs. Delivery of the selected sequence-specific siRNAs resulted in increase of survival rate of shrimp infected by WSSV, as compared to the virus injected controls (Fig. 1) . To examine if treatment of specific and mutant siRNAs resulted in a reduced expression level of the selected WSSV genes in shrimp in vivo, semiquantitative and highly sensitive RT-PCR analyses were used to compare the relative silencing effects. The results showed that sequence-specific siRNAs significantly inhibited replication of WSSV relative to that of positive controls and the mutant siRNA injected group at 24 h during experiment (Fig. 3) . Our data strongly indicated that sequence-specific siRNAs significantly inhibited expression of target genes and viral replication to protect shrimp from WSSV. abstract: RNA interference (RNAi) is a sequence-specific, post-transcriptional process of mRNA degradation. Here, we described specific silencing of five white spot syndrome virus (WSSV) genes in Litopenaeus vannamei in vivo with sequence-specific siRNAs. These genes included DNA polymerase (dnapol), ribonucleotide reductase small subunit (rr2), thymidine kinase and thymidylate kinase (tk-tmk), vp24 and vp28. At 6 days post-challenged, the relative survival rates of shrimp injected with siDNApol, siRR2, siTK-TMK, siVP24 and siVP28 (siRNAs for dnapol, rr2, tk-tmk, vp24 and vp28 genes) reached 50%, 50%, 66%, 33% and 33%, respectively. Specific siRNAs of the five WSSV genes could result in suppression of the target genes and a significant reduction in the viral proliferation. In negative controls, sequence-independent siRNA (mutant siRNA) could not inhibit expression of these five genes or viral replication. Consequently, injection of sequence-dependent siRNA could induce anti-WSSV activity in shrimp. These results suggest that siRNA can suppress WSSV efficiently in shrimp, and it may provide a potential approach to the therapy of aquaculture viral disease. url: https://api.elsevier.com/content/article/pii/S0044848607005200 doi: 10.1016/j.aquaculture.2007.06.029 id: cord-324212-aqp73hi9 author: Wyszko, Eliza title: Leadzyme formed in vivo interferes with tobacco mosaic virus infection in Nicotiana tabacum date: 2006-10-09 words: 4458.0 sentences: 298.0 pages: flesch: 60.0 cache: ./cache/cord-324212-aqp73hi9.txt txt: ./txt/cord-324212-aqp73hi9.txt summary: We identified a leadzyme substrate target sequence in genomic tobacco mosaic virus RNA and designed a 16‐mer oligoribonucleotide capable of forming a specific leadzyme motif with a five‐nucleotide catalytic loop. We identified a leadzyme substrate target sequence in genomic tobacco mosaic virus RNA and designed a 16-mer oligoribonucleotide capable of forming a specific leadzyme motif with a five-nucleotide catalytic loop. To achieve this goal, we analyzed the inhibition of tobacco mosaic virus (TMV) as a model system for inhibiting viral infections caused by positive single-stranded RNA (+)ssRNA viruses. In this article, we show that exogenous ssRNA with sequence complementarity binds the target site in TMV RNA to form a leadzyme motif, and in the presence of a catalytic amount of Pb 2+ , cleaves viral (+)ssRNA. Control assays, with 16-nucleotide catalytic RNA only or Pb 2+ applied in the presence of TMV, were performed to demonstrate the specificity of leadzyme cleavage. abstract: We developed a new method for inhibiting tobacco mosaic virus infection in tobacco plants based on specific RNA hydrolysis induced by a leadzyme. We identified a leadzyme substrate target sequence in genomic tobacco mosaic virus RNA and designed a 16‐mer oligoribonucleotide capable of forming a specific leadzyme motif with a five‐nucleotide catalytic loop. The synthetic 16‐mer RNA was applied with nontoxic, catalytic amount of lead to infected tobacco leaves. We observed inhibition of tobacco mosaic virus infection in tobacco leaves in vivo due to specific tobacco mosaic virus RNA cleavage effected by leadzyme. A significant reduction in tobacco mosaic virus accumulation was observed even when the leadzyme was applied up to 2 h after inoculation of leaves with tobacco mosaic virus. This process, called leadzyme interference, is determined by specific recognition and cleavage of the target site by the RNA catalytic strand in the presence of Pb(2+). url: https://www.ncbi.nlm.nih.gov/pubmed/17032353/ doi: 10.1111/j.1742-4658.2006.05497.x id: cord-331802-wo462anq author: Xia, Hongjie title: Human Enterovirus Nonstructural Protein 2C(ATPase) Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone date: 2015-07-28 words: 9410.0 sentences: 440.0 pages: flesch: 50.0 cache: ./cache/cord-331802-wo462anq.txt txt: ./txt/cord-331802-wo462anq.txt summary: Herein, we report that the nonstructural protein 2C(ATPase) of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. Herein, we report that although bacterially expressed EV71 2C ATPase did not exhibit any RNA remodeling activity, eukaryotically expressed EV71 2C ATPase functions not only as an RNA helicase that unwinds RNA helices from 3 0 to 5 0 in an ATP-dependent manner but also as an RNA chaperone that destabilizes helices from either direction and facilitates strand annealing and complex RNA structure formation independently of ATP. abstract: RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2C(ATPase) of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2C(ATPase) middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2C(ATPase) facilitated EV71 RNA synthesis in vitro; when 2C(ATPase) helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2C(ATPase)-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2C(ATPase) are also conserved in coxsackie A virus 16 (CAV16), another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2C(ATPase), and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings increase our understanding of enteroviruses and the two types of RNA remodeling activities. url: https://www.ncbi.nlm.nih.gov/pubmed/26218680/ doi: 10.1371/journal.ppat.1005067 id: cord-262844-qeheeqe3 author: Xia, Xuhua title: Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense date: 2020-04-14 words: 3305.0 sentences: 204.0 pages: flesch: 53.0 cache: ./cache/cord-262844-qeheeqe3.txt txt: ./txt/cord-262844-qeheeqe3.txt summary: The zinc finger antiviral protein (ZAP, known as ZC3HAV1 in mammals or hZAP in human), a key component in mammalian interferon-mediated immune response, binds specifically to CpG dinucleotides in viral RNA genomes via its RNA-binding domain (Meagher et al., 2019) . If a coronavirus infects a different host tissue with different ZAP abundance, then its RNA genome will experience different selection pressure against its CpG. The most striking pattern in Fig. 1 is an isolated but dramatic shift in the lineage leading to BatCoV RaTG13 which was reported (Zhou et al., 2020) (Theys et al., 2018) , but also in experimentally CpG dinucleotide-enriched viral genomes (Antzin-Anduetza et al., 2017; Burns et al., 2009; Fros et al., 2017; Trus et al., 2019; Tulloch et al., 2014; Wasson et al., 2017) . To search for a mammalian host with the potential to select viral lineages with low Poder, 2011; Pratelli, 2006) , have genomic ICpG and GC% values similar to those observed in SARS-CoV-2 and BatCoV RaTG13 (Fig. 3A) . abstract: Wild mammalian species, including bats, constitute the natural reservoir of Betacoronavirus (including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues provide different cellular environments, especially different antiviral and RNA modification activities that can alter RNA modification signatures observed in the viral RNA genome. The zinc finger antiviral protein (ZAP) binds specifically to CpG dinucleotides and recruits other proteins to degrade a variety of viral RNA genomes. Many mammalian RNA viruses have evolved CpG deficiency. Increasing CpG dinucleotides in these low-CpG viral genomes in the presence of ZAP consistently leads to decreased viral replication and virulence. Because ZAP exhibits tissue-specific expression, viruses infecting different tissues are expected to have different CpG signatures, suggesting a means to identify viral tissue-switching events. I show that SARS-CoV-2 has the most extreme CpG deficiency in all known Betacoronavirus genomes. This suggests that SARS-CoV-2 may have evolved in a new host (or new host tissue) with high ZAP expression. A survey of CpG deficiency in viral genomes identified a virulent canine coronavirus (Alphacoronavirus) as possessing the most extreme CpG deficiency, comparable to that observed in SARS-CoV-2. This suggests that the canine tissue infected by the canine coronavirus may provide a cellular environment strongly selecting against CpG. Thus, viral surveys focused on decreasing CpG in viral RNA genomes may provide important clues about the selective environments and viral defenses in the original hosts. url: https://www.ncbi.nlm.nih.gov/pubmed/32289821/ doi: 10.1093/molbev/msaa094 id: cord-278436-job4854r author: Xie, Mao-Hua title: A phage RNA-binding protein binds to a non-cognate structured RNA and stabilizes its core structure date: 2009-01-09 words: 3380.0 sentences: 196.0 pages: flesch: 60.0 cache: ./cache/cord-278436-job4854r.txt txt: ./txt/cord-278436-job4854r.txt summary: Recent studies suggest that some RNA-binding proteins facilitate the folding of non-cognate RNAs. Here, we report that bacteriophage MS2 coat protein (MS2 CP) bound and promoted the catalytic activity of Candida group I ribozyme. This mechanism is similar to that of the yeast mitochondrial tyrosyl-tRNA synthetase on other group I introns, suggesting that different RNA-binding proteins may use common mechanisms to support RNA structures. Interestingly, CYT 18 also stimulates the activity of several non-cognate group I introns [12] , questioning the specificity of the action of RNA-binding proteins. In this study, the protein-protected RNA cloning (PRC) method has been developed to successfully identify the MS2-binding site on the Candida group I ribozyme RNA. In summary, the finding of MS2 CP binding of the P5ab-P5 structure of the Candida group I ribozyme suggests that this phage protein can interact with a bulged RNA paired region connected to an asymmetric internal loop containing three adenines. abstract: Recent studies suggest that some RNA-binding proteins facilitate the folding of non-cognate RNAs. Here, we report that bacteriophage MS2 coat protein (MS2 CP) bound and promoted the catalytic activity of Candida group I ribozyme. Cloning of the MS2-bound RNA segments showed that this protein primarily interacts with the P5ab–P5 structure. Ultraviolet cross-linking and the T1 footprinting assay further showed that MS2 binding stabilized tertiary interactions, including the conserved L9–P5 interaction, and led to a more compact core structure. This mechanism is similar to that of the yeast mitochondrial tyrosyl-tRNA synthetase on other group I introns, suggesting that different RNA-binding proteins may use common mechanisms to support RNA structures. url: https://www.sciencedirect.com/science/article/pii/S0006291X08021153 doi: 10.1016/j.bbrc.2008.10.160 id: cord-268122-74nj66vb author: Xie, Na title: NAD(+) metabolism: pathophysiologic mechanisms and therapeutic potential date: 2020-10-07 words: 32037.0 sentences: 1955.0 pages: flesch: 39.0 cache: ./cache/cord-268122-74nj66vb.txt txt: ./txt/cord-268122-74nj66vb.txt summary: The NAD + decline during normal aging results in oxidative damage, metabolic disorder, circadian rhythm abnormalities, and mitochondrial dysfunction through regulating signaling pathways, such as p53, NF-κB, PGC-1α and HIF-1α, by sirtuins and PARPs. NAD + and its metabolites function as crucial regulators to maintain cellular redox homeostasis through replenishing the reducing power or modulating the activity of NAD + -consuming enzymes including sirtuins and PARPs. However, disequilibrium of NAD + metabolism could disturb physiological processes, including mitochondria function, circadian rhythm, inflammation, DNA repair and metabolism, leading to aging-associated dysfunction and cancer. c The deduced NAD + levels in kidney are attributed to the decreased expression of enzymes in NAD + de novo synthesis and increased consumption by DNA damage activated PARPs. NAD + depletion inhibits the SIRT1/PGC1α mediated mitochondrial quality control, ATP production and NAD + de novo biosynthesis. abstract: Nicotinamide adenine dinucleotide (NAD(+)) and its metabolites function as critical regulators to maintain physiologic processes, enabling the plastic cells to adapt to environmental changes including nutrient perturbation, genotoxic factors, circadian disorder, infection, inflammation and xenobiotics. These effects are mainly achieved by the driving effect of NAD(+) on metabolic pathways as enzyme cofactors transferring hydrogen in oxidation-reduction reactions. Besides, multiple NAD(+)-dependent enzymes are involved in physiology either by post-synthesis chemical modification of DNA, RNA and proteins, or releasing second messenger cyclic ADP-ribose (cADPR) and NAADP(+). Prolonged disequilibrium of NAD(+) metabolism disturbs the physiological functions, resulting in diseases including metabolic diseases, cancer, aging and neurodegeneration disorder. In this review, we summarize recent advances in our understanding of the molecular mechanisms of NAD(+)-regulated physiological responses to stresses, the contribution of NAD(+) deficiency to various diseases via manipulating cellular communication networks and the potential new avenues for therapeutic intervention. url: https://doi.org/10.1038/s41392-020-00311-7 doi: 10.1038/s41392-020-00311-7 id: cord-003596-6dg7i06i author: Xiong, Qingqing title: Biomedical applications of mRNA nanomedicine date: 2018-07-27 words: 12783.0 sentences: 666.0 pages: flesch: 36.0 cache: ./cache/cord-003596-6dg7i06i.txt txt: ./txt/cord-003596-6dg7i06i.txt summary: The rise of mRNA nanomedicines is rapidly advancing their applications in a wide range of biomedical fields, such as vaccination, protein-replacement therapy, gene editing, and cell reprogramming and engineering. The four major biomedical applications of mRNA nanomedicine include: 1) nanovaccines derived from antigen-encoded mRNA for the activation of the immune system; 2) proteinreplacement therapy for the treatment of genetic disorder diseases and cancer due to the mutation or loss of protein expression; 3) gene-editing achieved by the co-delivery of Cas9-encoded mRNA and gRNA; and 4) cell programming and engineering through the introduction of mRNA encoding for transcript factors or other functional molecules. In other studies, SAM vaccines encoding influenza antigens were successfully delivered to DCs by chitosan-nanoparticles and PEI-based polyplexes, which were also reported to successfully induce humoral and cellular immune responses in mice [145, 146] . Phosphorothioate cap analogs increase stability and translational efficiency of RNA vaccines in immature dendritic cells and induce superior immune responses in vivo abstract: As an attractive alternative to plasmid DNA, messenger RNA (mRNA) has recently emerged as a promising class of nucleic acid therapeutics for biomedical applications. Advances in addressing the inherent shortcomings of mRNA and in the development of nanoparticle-based delivery systems have prompted the development and clinical translation of mRNA-based medicines. In this review, we discuss the chemical modification strategies of mRNA to improve its stability, minimize immune responses, and enhance translational efficacy. We also highlight recent progress in nanoparticle-based mRNA delivery. Considerable attention is given to the increasingly widespread applications of mRNA nanomedicine in the biomedical fields of vaccination, protein-replacement therapy, gene editing, and cellular reprogramming and engineering. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472920/ doi: 10.1007/s12274-018-2146-1 id: cord-329618-kywhulpc author: Xu, Cheng title: A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells date: 2016-05-23 words: 8323.0 sentences: 426.0 pages: flesch: 55.0 cache: ./cache/cord-329618-kywhulpc.txt txt: ./txt/cord-329618-kywhulpc.txt summary: To elucidate the effect of type I IFN on the Jak/stat pathway in salmonid alphavirus subtype 3 (SAV3) infected macrophage/dendritic like TO-cells derived from Atlantic salmon (Salmo salar L) headkidney leukocytes, we used a differential transcriptome analysis by RNA-seq and the Kyoto encyclopedia of genes and genomes (KEGGs) pathway analysis to generate a repertoire of de novo assembled genes from type I IFN treated and non-treated TO-cells infected with SAV3. CONCLUSION: Data presented in this study shows that SAV3 infection downregulates several genes of the Jak/stat pathway, which could be an immune evasion strategy, used to block the transcription of antiviral genes that would interfere with SAV3 replication in TO-cells. Hence, in this study we used the KEGG pathway analysis software which is a third generation PT based software to identify networks of genes that form the Jak/stat signaling pathway from a de novo assembled transcriptome with the aim to better understand the modulation of genes expressed by TO cells infected with SAV3. abstract: BACKGROUND: The Janus kinase (Jak) and signaling transducer activator of transcription (Stat) pathway mediates the signaling of genes required for cellular development and homeostasis. To elucidate the effect of type I IFN on the Jak/stat pathway in salmonid alphavirus subtype 3 (SAV3) infected macrophage/dendritic like TO-cells derived from Atlantic salmon (Salmo salar L) headkidney leukocytes, we used a differential transcriptome analysis by RNA-seq and the Kyoto encyclopedia of genes and genomes (KEGGs) pathway analysis to generate a repertoire of de novo assembled genes from type I IFN treated and non-treated TO-cells infected with SAV3. RESULTS: Concurrent SAV3 infection with type I IFN treatment of TO-cells suppressed SAV3 structural protein (SP) expression by 2log(10) at 2 days post infection compared to SAV3 infection without IFN treatment which paved way to evaluating the impact of type I IFN on expression of Jak/stat pathway genes in SAV3 infected TO-cells. In the absence of type I IFN treatment, SAV3 downregulated several Jak/stat pathway genes that included type I and II receptor genes, Jak2, tyrosine kinase 2 (Tyk2), Stat3 and Stat5 pointing to possible failure to activate the Jak/stat signaling pathway and inhibition of signal transducers caused by SAV3 infection. Although the suppressor of cytokine signaling (SOCS) genes 1 and 3 were upregulated in the IFN treated cells, only SOCS3 was downregulated in the SAV3 infected cells which points to inhibition of SOCS3 by SAV3 infection in TO-cells. CONCLUSION: Data presented in this study shows that SAV3 infection downregulates several genes of the Jak/stat pathway, which could be an immune evasion strategy, used to block the transcription of antiviral genes that would interfere with SAV3 replication in TO-cells. Overall, we have shown that combining de novo assembly with pathway based transcriptome analyses provides a contextual approach to understanding the molecular networks of genes that form the Jak/stat pathway in TO-cells infected by SAV3. url: https://doi.org/10.1186/s12864-016-2739-6 doi: 10.1186/s12864-016-2739-6 id: cord-335614-qh98622y author: Xu, Puzhi title: A Multi-Omics Study of Chicken Infected by Nephropathogenic Infectious Bronchitis Virus date: 2019-11-16 words: 6543.0 sentences: 352.0 pages: flesch: 41.0 cache: ./cache/cord-335614-qh98622y.txt txt: ./txt/cord-335614-qh98622y.txt summary: These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout. The results of PCA and OPLA-DA analysis showed that there was an obvious separation between the content of the Con and Dis groups, revealing significant changes in the concentrations of metabolites in the kidney induced by NIBV infection. In addition, the transcriptomic analysis showed that NIBV infection also activated the RIG-I-like receptor signalling pathway (Figure 3f , signal 2), which included the transcriptional upregulation of genes such as MDA5, IPS-1, TRAF3, and IκB. In the present study, the ABCG2 mRNA was downregulated in the model group chicken kidneys, partially explaining the significantly increased uric acid levels caused by NIBV infection. abstract: Chicken gout resulting from nephropathogenic infectious bronchitis virus (NIBV) has become a serious kidney disease problem in chicken worldwide with alterations of the metabolic phenotypes in multiple metabolic pathways. To investigate the mechanisms in chicken responding to NIBV infection, we examined the global transcriptomic and metabolomic profiles of the chicken’s kidney using RNA-seq and GC–TOF/MS, respectively. Furthermore, we analyzed the alterations in cecal microorganism composition in chickens using 16S rRNA-seq. Integrated analysis of these three phenotypic datasets further managed to create correlations between the altered kidney transcriptomes and metabolome, and between kidney metabolome and gut microbiome. We found that 2868 genes and 160 metabolites were deferentially expressed or accumulated in the kidney during NIBV infection processes. These genes and metabolites were linked to NIBV-infection related processes, including immune response, signal transduction, peroxisome, purine, and amino acid metabolism. In addition, the comprehensive correlations between the kidney metabolome and cecal microbial community showed contributions of gut microbiota in the progression of NIBV-infection. Taken together, our research comprehensively describes the host responses during NIBV infection and provides new clues for further dissection of specific gene functions, metabolite affections, and the role of gut microbiota during chicken gout. url: https://doi.org/10.3390/v11111070 doi: 10.3390/v11111070 id: cord-342800-62jklwiy author: Xu, Shuqin title: mRNA Vaccine Era—Mechanisms, Drug Platform and Clinical Prospection date: 2020-09-09 words: 13579.0 sentences: 706.0 pages: flesch: 43.0 cache: ./cache/cord-342800-62jklwiy.txt txt: ./txt/cord-342800-62jklwiy.txt summary: The RNActive ® vaccine platform designed by CureVac used co-delivered RNA and protamine complex as the adjuvant to induce Th1 T cell responses, and naked, unmodified, and sequence-optimized mRNA as the antigen to develop mRNA vaccines [54] . used LNP to deliver self-amplified RNA vaccines, which caused the mRNA expression level in mice to be significantly higher than that of naked mRNA, CD4 + , and CD8 + T cell immune responses were also effectively induced. Overall development steps of those vaccines are (1) constructing the core antigen-encoding mRNA sequence optimized or combined based on selected antigen(s) from the target pathogen; (2) trying and choosing a proper combination of mRNA construction type, adjuvants, carrier materials and the route of administration; (3) detecting in vivo expression of the encoded antigen and the level of elicited immune responses; (4) providing research and demonstrations of immune induction mechanisms. abstract: Messenger ribonucleic acid (mRNA)-based drugs, notably mRNA vaccines, have been widely proven as a promising treatment strategy in immune therapeutics. The extraordinary advantages associated with mRNA vaccines, including their high efficacy, a relatively low severity of side effects, and low attainment costs, have enabled them to become prevalent in pre-clinical and clinical trials against various infectious diseases and cancers. Recent technological advancements have alleviated some issues that hinder mRNA vaccine development, such as low efficiency that exist in both gene translation and in vivo deliveries. mRNA immunogenicity can also be greatly adjusted as a result of upgraded technologies. In this review, we have summarized details regarding the optimization of mRNA vaccines, and the underlying biological mechanisms of this form of vaccines. Applications of mRNA vaccines in some infectious diseases and cancers are introduced. It also includes our prospections for mRNA vaccine applications in diseases caused by bacterial pathogens, such as tuberculosis. At the same time, some suggestions for future mRNA vaccine development about storage methods, safety concerns, and personalized vaccine synthesis can be found in the context. url: https://www.ncbi.nlm.nih.gov/pubmed/32916818/ doi: 10.3390/ijms21186582 id: cord-254903-g9ropt9c author: Xu, Xiaofeng title: Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data date: 2020-09-16 words: 3280.0 sentences: 179.0 pages: flesch: 61.0 cache: ./cache/cord-254903-g9ropt9c.txt txt: ./txt/cord-254903-g9ropt9c.txt summary: RESULTS: In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China''s Yunnan Province in 2016. In the present study, we identified a new MGTV strain Yunnan2016 detected in Amblyomma testudinarium ticks [17] and aimed to achieve the following research goals: (1) establish a method to generate the full-length genome sequence of an RNA virus using sRNA-seq data; (2) determine the feasibility of using the sRNA-seq based method in the detection of viruses in a small tick; and (3) provide a high-quality and well-curated reference genome for future studies on MGTV, JMTV, KITV and GXTV. abstract: BACKGROUND: In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported. RESULTS: In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. CONCLUSIONS: To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography. url: https://www.ncbi.nlm.nih.gov/pubmed/32938401/ doi: 10.1186/s12864-020-07060-5 id: cord-352200-i05h8csb author: Xu, Yi title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus date: 2012-04-27 words: 5286.0 sentences: 278.0 pages: flesch: 47.0 cache: ./cache/cord-352200-i05h8csb.txt txt: ./txt/cord-352200-i05h8csb.txt summary: title: Transcriptome and Comparative Gene Expression Analysis of Sogatella furcifera (Horváth) in Response to Southern Rice Black-Streaked Dwarf Virus METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. As a whole, 81388 distinct unigenes have been identified and the results indicated that SRBSDV infection can potentially perturb primary metabolism and the ubiquitin-proteasome pathway of WBPH and activate immune regulatory systems, such as RNA interfering, autophagy and antimicrobial peptide production. However, some unigenes were obtained only from viruliferous or non-viruliferous samples (data not shown) and we believe these differences may be caused by distinctions that arise from long-term ecological adaptation to virus infection. In addition, GO analysis also showed a similar distribution of gene functions for non-viruliferous and viruliferous WBPH (Figure 4 ), indicating that the number of genes expressed in each GO category was not significantly affected by SRBSDV infection. abstract: BACKGROUND: The white backed planthopper (WBPH), Sogatella furcifera (Horváth), causes great damage to many crops by direct feeding or transmitting plant viruses. Southern rice black-streaked dwarf virus (SRBSDV), transmitted by WBPH, has become a great threat to rice production in East Asia. METHODOLOGY/PRINCIPAL FINDINGS: By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of WBPH and profiled the alternation of gene expression in response to SRBSDV infection in transcriptional level. Over 25 million reads of high-quality DNA sequences and 81388 different unigenes were generated using Illumina technology from both viruliferous and non-viruliferous WBPH. WBPH has a very similar gene ontological distribution to other two closely related rice planthoppers, Nilaparvata lugens and Laodelphax striatellus. 7291 microsatellite loci were also predicted which could be useful for further evolutionary analysis. Furthermore, comparative analysis of the two transcriptomes generated from viruliferous and non-viruliferous WBPH provided a list of candidate transcripts that potentially were elicited as a response to viral infection. Pathway analyses of a subset of these transcripts indicated that SRBSDV infection may perturb primary metabolism and the ubiquitin-proteasome pathways. In addition, 5.5% (181 out of 3315) of the genes in cell cytoskeleton organization pathway showed obvious changes. Our data also demonstrated that SRBSDV infection activated the immunity regulatory systems of WBPH, such as RNA interference, autophagy and antimicrobial peptide production. CONCLUSIONS/SIGNIFICANCE: We employed massively parallel pyrosequencing to collect ESTs from viruliferous and non-viruliferous samples of WBPH. 81388 different unigenes have been obtained. We for the first time described the direct effects of a Reoviridae family plant virus on global gene expression profiles of its insect vector using high-throughput sequencing. Our study will provide a road map for future investigations of the fascinating interactions between Reoviridae viruses and their insect vectors, and provide new strategies for crop protection. url: https://www.ncbi.nlm.nih.gov/pubmed/22558400/ doi: 10.1371/journal.pone.0036238 id: cord-273487-nfgjz6f9 author: Xu, Zaikun title: The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles date: 2012-11-10 words: 5354.0 sentences: 286.0 pages: flesch: 56.0 cache: ./cache/cord-273487-nfgjz6f9.txt txt: ./txt/cord-273487-nfgjz6f9.txt summary: Loss of DDX56 helicase activity did not affect expression of WNV capsid protein (Fig. 4A ) nor its secretion from infected cells in the form of virus particles (Fig. 5A ). Data in Fig. 5B show that virus particles isolated from infected cells expressing helicase dead mutants D166N and E167Q contained 3-4 times less genomic RNA than those isolated from non-silencing cells or cells expressing RNAi-resistant wild type DDX56. Data in Fig. 6 show that in transfected or infected cells, the WNV capsid does not bind to the DEAD box helicase-containing region of DDX56 (DDX56-NT-myc), but rather, the C-terminal part of the protein, which was produced in cells expressing DDX56-CT-myc. The helicase activity of DDX56 is not essential for replication or assembly of WNV virions per se but our data indicate that it is critical for infectivity of virus particles. abstract: Although flaviviruses encode their own helicases, evidence suggests that cellular helicases are also required for replication and/or assembly of these viruses. By and large, the mechanisms of action for viral and cellular helicases are not known. Moreover, in some cases, enzymatic activity is not even required for their roles in virus biology. Recently, we showed that expression of the host nucleolar helicase DDX56 is important for infectivity of West Nile virus (WNV) particles. In the present study, we demonstrate that the helicase activity of this enzyme is essential for its role in assembly of infectious WNV virions. Over-expression of the capsid-binding region of DDX56 also reduces infectivity of WNV suggesting that interaction of DDX56 and capsid protein is an important step in the virion assembly pathway. To our knowledge, this is the first study showing that enzymatic activity of a cellular helicase is critical for infectivity of flaviviruses. url: https://api.elsevier.com/content/article/pii/S0042682212003923 doi: 10.1016/j.virol.2012.08.011 id: cord-007181-qpahuqld author: YOGO, Yoshiaki title: Polyadenylate in the Virion RNA of Mouse Hepatitis Virus date: 1977-10-17 words: 2058.0 sentences: 122.0 pages: flesch: 59.0 cache: ./cache/cord-007181-qpahuqld.txt txt: ./txt/cord-007181-qpahuqld.txt summary: Sedimentation Analysis-PH]Virion RNA dissolved in 0.1 ml NET was layered on a 15-30% sucrose gradient in NET containing 0.3% SDS, then sedimented at 48,000 rpm for 90 min at room temperature in an SW 50.1 rotor. Isolation of Poly(A)-fHJAdenosine-or P''P]labeled MH virion RNA containing 50 (ig of carrier tRNA was digested with a combination of ribonuclease A (2//g) and Tl (50 units The hydrolysate was neutralized with HC1O, at 0°C and the precipitate was removed by centrifugation. We therefore extracted RNA from [*H]uridine-labeled MH virions with phenol/chloroform as well as 1 % SDS, and RNA''s obtained by both methods were compared by sucrose gradient centrifugation. To isolate poly(A), [''HJadenosine-labeled total virion RNA was digested with a combination of ribonuclease A and Tl. The digest was adjusted to 0.3 M NaCl-0.001 M EDTA-0.02 M Tris-HCl (pH 7.5)-7 M urea and applied to a DEAE-Sephadex column equilibrated with the same buffer. abstract: Mouse hepatitis (MH) virus was grown in SR-CDF1-DBT, a mouse cell line, and purified by ammonium sulfate precipitation and by density gradient centrifugation. Extraction of RNA from purified virions with 1% SDS and sedimentation analysis of the RNA revealed a major 50S component and two minor components. Treatment of virions with phenol/chloroform also produced the 50S component, although its yield was lower. MH virion RNA can bind to a poly(U)-fiberglass filter, indicating that MH virion RNA contains poly(A). A poly(A)-like fragment was isolated by digestion with ribonuclease A [EC 3.1.4.22] and T1 [EC 3.1.4.8] and by DEAE-Sephadex column chromatography. Analysis of the fragment for base composition showed it to be an adenine-rich material. Its chain length was about 90 nucleotides, as determined by ion-exchange chromatography and gel electrophoresis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109782/ doi: 10.1093/oxfordjournals.jbchem.a131782 id: cord-014908-jys1y0k9 author: Yadav, Rakesh title: Trends and Perspectives of Biosensors for Food and Environmental Virology date: 2010-05-19 words: 5113.0 sentences: 259.0 pages: flesch: 32.0 cache: ./cache/cord-014908-jys1y0k9.txt txt: ./txt/cord-014908-jys1y0k9.txt summary: Unluckily, the PCR-based tools do not persistently amplify nucleic acids if viruses are found in infected food or environmental samples at critically low level. Another successful innovative biosensor with combined microfluidics and biosensing capabilities, furnish real time and automated affinity bioanalysis (e.g. for antigen-antibody assays) through surface plasmon resonance (SPR)-based original optical transduction mechanism. Since molecular recognition trait is central in the biosensing systems, all the structural components can be targeted to device a biosensor for detection of the specific virion particles present in food and environment samples. Molecular nanotechnology-based new nanostructures/nanomaterials such as aptamers are capable for developing highly specific biosensor for target elements detection. DNA-based biosensors have great applications in food and environmental analysis including determination of the pathogenic bacteria , and virus DNA sequence such as that of SARS virus (Abad-Valle et al. Quartz crystal microbalance (QCM)-based piezoelectric sensors can detect the hybridized viral DNA and also the capsid protein-ligand interactions. abstract: Food and environmental virology has become a very important and interesting area of research because of food safety and public health concerns. During the last few decades, increasing foodborne diseases and environmental generated illnesses are considered to be highly challenging issues. Biosensor technology holds great promise for the healthcare market, and the security sector. Similar to clinical diagnostic tools, biosensors are being developed for the rapid, reliable, yet inexpensive identification and enumeration of pathogenic viruses which are adulterating environment, food and feed commodities. In this modern era, bio-and nano-technologies play a pivotal role in virological diagnostics of food industry, environmental and veterinary samples. This review covers the recent advances and future prospects of nanotechnology-based bioanalytical microsystems for food and environmental virology. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7090531/ doi: 10.1007/s12560-010-9034-5 id: cord-340554-7cwp2xbw author: Yamasaki, Satoshi title: ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow date: 2019-03-06 words: nan sentences: nan pages: flesch: nan cache: txt: summary: abstract: Recent progress in molecular biology has revealed that many non-coding RNAs regulate gene expression or catalyze biochemical reactions in tumors, viruses and several other diseases. The tertiary structure of RNA molecules and RNA–RNA/protein interaction sites are of increasing importance as potential targets for new medicines that treat a broad array of human diseases. Current RNA drugs are split into two groups: antisense RNA molecules and aptamers. In this report, we present a novel workflow to predict RNA tertiary structures and RNA–RNA/protein interactions using the KNIME environment, which enabled us to assemble a combination of RNA-related analytical tools and databases. In this study, three analytical workflows for comprehensive structural analysis of RNA are introduced: (1) prediction of the tertiary structure of RNA; (2) prediction of the structure of RNA–RNA complexes and analysis of their interactions; and (3) prediction of the structure of RNA–protein complexes and analysis of their interactions. In an RNA–protein case study, we modeled the tertiary structure of pegaptanib, an aptamer drug, and performed docking calculations of the pegaptanib-vascular endothelial growth factor complex using a fragment of the interaction site of the aptamer. We also present molecular dynamics simulations of the RNA–protein complex to evaluate the affinity of the complex by mutating bases at the interaction interface. The results provide valuable information for designing novel features of aptamer-protein complexes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s10822-019-00195-y) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/30840170/ doi: 10.1007/s10822-019-00195-y id: cord-000794-l565gha4 author: Yan, Huan title: Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus date: 2012-11-13 words: 13364.0 sentences: 698.0 pages: flesch: 54.0 cache: ./cache/cord-000794-l565gha4.txt txt: ./txt/cord-000794-l565gha4.txt summary: Here, by using near zero distance photo-cross-linking and tandem affinity purification, we revealed that the receptor-binding region of pre-S1 specifically interacts with sodium taurocholate cotransporting polypeptide (NTCP), a multiple transmembrane transporter predominantly expressed in the liver. Photoreactive ligand peptides for identification of interacting protein(s) of pre-S1 domain of L envelope protein To identify the pre-S1 interacting molecule(s), we employed a photo-cross-linking approach using a synthetic peptide derived from the native pre-S1 peptide with particular residues replaced by eLife digest Liver diseases related to the human hepatitis B virus (HBV) kill about 1 million people every year, and more than 350 million people around the world are infected with the virus. In this study, by employing a unique approach of tandem affinity purification combined with MS analysis against a Tupaia hepatocyte proteome database established by deep sequencing, we revealed that the liver bile acid transporter, NTCP, specifically interacts with a key region in the pre-S1 domain of the HBV envelope L protein. abstract: Human hepatitis B virus (HBV) infection and HBV-related diseases remain a major public health problem. Individuals coinfected with its satellite hepatitis D virus (HDV) have more severe disease. Cellular entry of both viruses is mediated by HBV envelope proteins. The pre-S1 domain of the large envelope protein is a key determinant for receptor(s) binding. However, the identity of the receptor(s) is unknown. Here, by using near zero distance photo-cross-linking and tandem affinity purification, we revealed that the receptor-binding region of pre-S1 specifically interacts with sodium taurocholate cotransporting polypeptide (NTCP), a multiple transmembrane transporter predominantly expressed in the liver. Silencing NTCP inhibited HBV and HDV infection, while exogenous NTCP expression rendered nonsusceptible hepatocarcinoma cells susceptible to these viral infections. Moreover, replacing amino acids 157–165 of nonfunctional monkey NTCP with the human counterpart conferred its ability in supporting both viral infections. Our results demonstrate that NTCP is a functional receptor for HBV and HDV. DOI: http://dx.doi.org/10.7554/eLife.00049.001 url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485615/ doi: 10.7554/elife.00049 id: cord-013280-kczj24se author: Yang, Bo title: Molecular Mechanisms of Immune Escape for Foot-and-Mouth Disease Virus date: 2020-09-04 words: 11293.0 sentences: 608.0 pages: flesch: 46.0 cache: ./cache/cord-013280-kczj24se.txt txt: ./txt/cord-013280-kczj24se.txt summary: Viral capsid protein VP1 and leading protein L pro can inhibit the production of interferon (IFN) and innate immune response by interacting with soluble resistance-related calcium-binding protein (sorcin) or host transcription factor ADNP [12, 13] . Viral capsid protein VP1 and leading protein L pro can inhibit the production of interferon (IFN) and innate immune response by interacting with soluble resistance-related calcium-binding protein (sorcin) or host transcription factor ADNP [12, 13] . FMDV VP1 interacts with host ribosomal protein SA (RPSA) to continually activate the MAPK signal pathway and promote virus replication by inhibiting the RPSA-mediated function [59] (Figure 2 , Table 1 ). It interacts with the VISA protein to inhibit the formation of VISA-regulated complex, thereby inhibiting the dimerization and phosphorylation of IRF3, inhibiting the expression of antiviral genes induced by IFN-β, and promoting FMDV replication [60] (Figure 2 , Table 1 ). abstract: Foot-and-mouth disease virus (FMDV) causes a highly contagious vesicular disease in cloven-hoofed livestock that results in severe consequences for international trade, posing a great economic threat to agriculture. The FMDV infection antagonizes the host immune responses via different signaling pathways to achieve immune escape. Strategies to escape the cell immune system are key to effective infection and pathogenesis. This review is focused on summarizing the recent advances to understand how the proteins encoded by FMDV antagonize the host innate and adaptive immune responses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7558374/ doi: 10.3390/pathogens9090729 id: cord-319649-d6dqr03e author: Yang, Jie title: A cypovirus VP5 displays the RNA chaperone-like activity that destabilizes RNA helices and accelerates strand annealing date: 2013-12-05 words: 7876.0 sentences: 375.0 pages: flesch: 53.0 cache: ./cache/cord-319649-d6dqr03e.txt txt: ./txt/cord-319649-d6dqr03e.txt summary: Here, we expressed VP5 from type 5 Helicoverpa armigera cypovirus (HaCPV-5) in a eukaryotic system and determined that this VP5 possesses RNA chaperone-like activity, which destabilizes RNA helices and accelerates strand annealing independent of ATP. In this study, we expressed HaCPV-5 VP5 in a eukaryotic expression system and determined that this CPV VP5 possesses an RNA chaperone-like activity to ATP-independently destabilize RNA helices and accelerate strand annealing. Moreover, we found that HaCPV-5 VP5 could facilitate the transcription initiation of an alternative polymerase (i.e. reverse transcriptase) through a CPV panhandle-structured RNA template, thereby strongly suggesting a direct role of the RNA chaperone activity of VP5 in the initiation of cypoviral dsRNA replication. In the family Reoviridae, CPV VP5 may not be the only RNA chaperone, as rotavirus nonstructural protein 2 (NSP2), which is a multifunctional enzyme involved in rotaviral dsRNA replication, was previously shown to contain ATP-independent nucleic acid helix-destabilizing activity (45) . abstract: For double-stranded RNA (dsRNA) viruses in the family Reoviridae, their inner capsids function as the machinery for viral RNA (vRNA) replication. Unlike other multishelled reoviruses, cypovirus has a single-layered capsid, thereby representing a simplified model for studying vRNA replication of reoviruses. VP5 is one of the three major cypovirus capsid proteins and functions as a clamp protein to stabilize cypovirus capsid. Here, we expressed VP5 from type 5 Helicoverpa armigera cypovirus (HaCPV-5) in a eukaryotic system and determined that this VP5 possesses RNA chaperone-like activity, which destabilizes RNA helices and accelerates strand annealing independent of ATP. Our further characterization of VP5 revealed that its helix-destabilizing activity is RNA specific, lacks directionality and could be inhibited by divalent ions, such as Mg(2+), Mn(2+), Ca(2+) or Zn(2+), to varying degrees. Furthermore, we found that HaCPV-5 VP5 facilitates the replication initiation of an alternative polymerase (i.e. reverse transcriptase) through a panhandle-structured RNA template, which mimics the 5′-3′ cyclization of cypoviral positive-stranded RNA. Given that the replication of negative-stranded vRNA on the positive-stranded vRNA template necessitates the dissociation of the 5′-3′ panhandle, the RNA chaperone activity of VP5 may play a direct role in the initiation of reoviral dsRNA synthesis. url: https://www.ncbi.nlm.nih.gov/pubmed/24319147/ doi: 10.1093/nar/gkt1256 id: cord-308884-erofmh39 author: Yang, Seung Won title: Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation date: 2018-01-08 words: 11025.0 sentences: 560.0 pages: flesch: 53.0 cache: ./cache/cord-308884-erofmh39.txt txt: ./txt/cord-308884-erofmh39.txt summary: authors: Yang, Seung Won; Jang, Yo Han; Kwon, Soon Bin; Lee, Yoon Jae; Chae, Wonil; Byun, Young Ho; Kim, Paul; Park, Chan; Lee, Young Jae; Kim, Choon Kang; Kim, Young Seok; Choi, Seong Il; Seong, Baik Lin It should be noted that specificity of the antibody response to a reporter protein relative to the RID docking protein was not appreciably different regardless of the origin of an RID and the animal species to be immunized (compare Fig. 5A with 5D for eGFP and Fig. 5B with 5F for the HAgD), probably as a result of high homology (;80%) in an amino acid sequence between the murine and rabbit counterparts. D) ELISA data showing that according to the number of boosts, high-titer antibodies in serum samples from mice (n = 5) immunized with mRID-HAgD (20 mg/mouse) bound to the PR8 (H1N1) virus (10 4 PFU/well). abstract: A novel protein-folding function of RNA has been recognized, which can outperform previously known molecular chaperone proteins. The RNA as a molecular chaperone (chaperna) activity is intrinsic to some ribozymes and is operational during viral infections. Our purpose was to test whether influenza hemagglutinin (HA) can be assembled in a soluble, trimeric, and immunologically activating conformation by means of an RNA molecular chaperone (chaperna) activity. An RNA-interacting domain (RID) from the host being immunized was selected as a docking tag for RNA binding, which served as a transducer for the chaperna function for de novo folding and trimeric assembly of RID-HA1. Mutations that affect tRNA binding greatly increased the soluble aggregation defective in trimer assembly, suggesting that RNA interaction critically controls the kinetic network in the folding/assembly pathway. Immunization of mice resulted in strong hemagglutination inhibition and high titers of a neutralizing antibody, providing sterile protection against a lethal challenge and confirming the immunologically relevant HA conformation. The results may be translated into a rapid response to a new influenza pandemic. The harnessing of the novel chaperna described herein with immunologically tailored antigen-folding functions should serve as a robust prophylactic and diagnostic tool for viral infections.—Yang, S. W., Jang, Y. H., Kwon, S. B., Lee, Y. J., Chae, W., Byun, Y. H., Kim, P., Park, C., Lee, Y. J., Kim, C. K., Kim, Y. S., Choi, S. I., Seong, B. L. Harnessing an RNA-mediated chaperone for the assembly of influenza hemagglutinin in an immunologically relevant conformation. url: https://www.ncbi.nlm.nih.gov/pubmed/29295864/ doi: 10.1096/fj.201700747rr id: cord-280616-9mwr6a4x author: Yang, Ying title: Small non-coding RNAs-based bone regulation and targeting therapeutic strategies date: 2017-11-15 words: 16961.0 sentences: 828.0 pages: flesch: 36.0 cache: ./cache/cord-280616-9mwr6a4x.txt txt: ./txt/cord-280616-9mwr6a4x.txt summary: reported a mechanosensitive miRNA, hsa-miR-103a-3p, that exhibited negative effects on Runx2 during cyclic mechanical stretch (CMS)induced osteoblastogenesis, leading to decreased bone formation both in vitro and in vivo (Zuo et al., 2015) . To understand whether other effective paracrine pathways exist in the interaction between the two cell types, Li and colleagues conducted miRNA-mediated osteoclast-directed osteoblastic bone formation in ovariectomized (OVX) mice, indicating that inhibition of osteoclast-derived exosomal mmu-miR-214-3p induced significantly suppressed osteoclastogenesis (Li et al., 2016b) . In addition, Krzeszinski and colleagues found that mmu-miR-34a-5p knockout and heterozygous mice exhibited elevated bone resorption and reduced bone mass by targeting transforming growth factor-b-induced factor 2 (Tgif2), indicating that miR-34a-5p was a critical osteoclast suppressor and a potential therapeutic strategy to combat osteoporosis, and could exert both anti-catabolic and anabolic effects compared to current drugs that are solely anticatabolic (Krzeszinski et al., 2014) . abstract: Small non-coding RNAs, which are 20–25 nucleotide ribonucleic acids, have emerged as an important transformation in the biological evolution over almost three decades. microRNAs (miRNAs) and short interfering RNAs (siRNAs) are two significant categories of the small RNAs that exert important effects on bone endocrinology and skeletology. Therefore, clarifying the expression and function of these important molecules in bone endocrine physiology and pathology is of great significance for improving their potential therapeutic value for metabolism-associated bone diseases. In the present review, we highlight the recent advances made in understanding the function and molecular mechanism of these small non-coding RNAs in bone metabolism, especially their potentially therapeutic values in bone-related diseases. url: https://www.sciencedirect.com/science/article/pii/S0303720716304877 doi: 10.1016/j.mce.2016.11.018 id: cord-255795-su7f5ges author: Yelin, Idan title: Evaluation of COVID-19 RT-qPCR test in multi-sample pools date: 2020-03-27 words: 2262.0 sentences: 113.0 pages: flesch: 55.0 cache: ./cache/cord-255795-su7f5ges.txt txt: ./txt/cord-255795-su7f5ges.txt summary: Here, testing a pooling approach for the standard RT-qPCR test, we find that a single positive sample can be detected even in pools of up to 32 samples, with an estimated false negative rate of 10%. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close integral groups, such as hospital departments, army units, or factory shifts. Here, we test the ability of the standard RT-qPCR test for detecting a single positive sample within a pool of negative samples. Pooling clinical RNA samples, we tested previously confirmed positive samples alone and combined with an increasing number of previously confirmed negative samples and found that positive samples can still be well observed in pools of up to 32 samples, and possibly even 64 with additional PCR cycles. We found that a single clinical sample with SARS-CoV-2 RNA can be consistently detected in a pool of up to 32 samples. abstract: The recent emergence of SARS-CoV-2 lead to a current pandemic of unprecedented levels. Though diagnostic tests are fundamental to the ability to detect and respond, many health systems are already experiencing shortages of reagents associated with this test. Here, testing a pooling approach for the standard RT-qPCR test, we find that a single positive sample can be detected even in pools of up to 32 samples, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles. As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close integral groups, such as hospital departments, army units, or factory shifts. url: https://doi.org/10.1101/2020.03.26.20039438 doi: 10.1101/2020.03.26.20039438 id: cord-323668-evzzfu04 author: Yin, Zhixin title: lncRNA expression signatures in response to enterovirus 71 infection date: 2013-01-11 words: 3493.0 sentences: 208.0 pages: flesch: 50.0 cache: ./cache/cord-323668-evzzfu04.txt txt: ./txt/cord-323668-evzzfu04.txt summary: To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. These findings suggest the widespread differential expression of lncRNAs in response to 0006 virus infection and their involvement in regulating the host response, including innate immunity [19] . Further analysis resulted in 313 differentially expressed lncRNAs and nearby coding gene pairs (distance < 300 kb) for each comparison between mock-and EV71-infected cells (Table S7) . In the present study, using Arraystar microarray analysis, we identified the differentially expressed lncRNAs in RD cells after EV71 infection, together with nearby differentially expressed mRNA pairs. They also observed the down-regulation of several genes encoding proteins involved in host RNA synthesis in EV71-infected SF268 cells. [19] performed functional enrichment analysis on the nearby protein-coding genes of differentially expressed lncRNAs in SARS-CoV infected mouse. abstract: Abstract Outbreaks of hand, foot, and mouth disease caused by enterovirus 71 (EV71) have become considerable threats to the health of infants and young children. To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. We observed the differential expression of more than 4800 lncRNAs during infection. Further analysis showed 160 regulated enhancer-like lncRNA and nearby mRNA pairs, as well as 313 regulated Rinn’s lncRNA [M. Guttman I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen, T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn, E.S. Lander. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458 (2009) 223–227, A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B.E. Bernstein, A. van Oudenaarden, A. Regev, E.S. Lander, J.L. Rinn. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106 (2009) 11667–11672] and nearby mRNA pairs. The results provided information for further research on the prevention and treatment of EV71 infection, as well as on distinguishing severe and mild EV71 cases. url: https://api.elsevier.com/content/article/pii/S0006291X12022917 doi: 10.1016/j.bbrc.2012.11.101 id: cord-266521-vovas81d author: Yokobayashi, Yohei title: Aptamer-based and aptazyme-based riboswitches in mammalian cells date: 2019-06-22 words: 3228.0 sentences: 155.0 pages: flesch: 43.0 cache: ./cache/cord-266521-vovas81d.txt txt: ./txt/cord-266521-vovas81d.txt summary: In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. While the ribozyme was not specifically regulated by a small molecule via an aptamer, this work paved the way for the subsequent riboswitches that employ allosterically regulated ribozymes (aptazymes) embedded in the 5 0 and/or 3 0 UTR to chemically regulate gene expression in mammalian cells (Figure 1a ) [13] [14] [15] [16] . A new mode of engineered RNA-based gene regulation in mammalian cells was demonstrated by controlling the accessibility of a miRNA target site by aptamer-ligand interaction abstract: Molecular recognition by RNA aptamers has been exploited to control gene expression in response to small molecules in mammalian cells. These mammalian synthetic riboswitches offer attractive features such as small genetic size and lower risk of immunological complications compared to protein-based transcriptional gene switches. The diversity of gene regulatory mechanisms that involve RNA has also inspired the development of mammalian riboswitches that harness various regulatory mechanisms. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting. url: https://api.elsevier.com/content/article/pii/S1367593118302023 doi: 10.1016/j.cbpa.2019.05.018 id: cord-252485-cxi3cr15 author: Yoshida, Asuka title: IFN-β-inducing, unusual viral RNA species produced by paramyxovirus infection accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner date: 2015-08-04 words: 7074.0 sentences: 306.0 pages: flesch: 50.0 cache: ./cache/cord-252485-cxi3cr15.txt txt: ./txt/cord-252485-cxi3cr15.txt summary: We and other groups have recently reported that recombinant viruses of Sendai virus (SeV), a prototype of the family Paramyxoviridae, in which the C proteins are knocked-out or mutated, generate dsRNA in infected cells at levels similar to the production of IFN-β (Takeuchi et al., 2008; Irie et al., 2010) . These unusual RNAs exhibited distinct properties in infected cells in terms of encapsidation with the viral N protein and subcellular distribution with SG marker proteins and RLRs. Our results suggest that RNA-typedependent mechanisms recognize and accumulate virus-derived, IFN-β-inducible, unusual RNAs into specific compartment to trigger the production of IFN-β, and that SeV may evade detection by the host innate immune system by preventing the production of these RNA species. Since the naked cbDI genomes have been reported readily to form an ideal structure as the RIG-I ligands of 5 -triphosphated, blunt-ended dsRNA (Kolakofsky, 1976) , these results indicated that the major IFN-β-inducing viral RNA species produced in the cells infected with CNT was encapsidated cbDI genomes, whereas those for SeV-4C(-) and NDV were not. abstract: The interferon (IFN) system is one of the most important defensive responses of mammals against viruses, and is rapidly evoked when the pathogen-associated molecular patterns (PAMPs) of viruses are sensed. Non-self, virus-derived RNA species have been identified as the PAMPs of RNA viruses. In the present study, we compared different types of IFN-β-inducing and -non-inducing viruses in the context of Sendai virus infection. We found that some types of unusual viral RNA species were produced by infections with IFN-β-inducing viruses and accumulated into distinct cytoplasmic structures in an RNA-type-dependent manner. One of these structures was similar to the so-called antiviral stress granules (avSGs) formed by an infection with IFN-inducing viruses whose C proteins were knocked-out or mutated. Non-encapsidated, unusual viral RNA harboring the 5′-terminal region of the viral genome as well as RIG-I and typical SG markers accumulated in these granules. Another was a non-SG-like inclusion formed by an infection with the Cantell strain; a copyback-type DI genome, but not an authentic viral genome, specifically accumulated in the inclusion, whereas RIG-I and SG markers did not. The induction of IFN-β was closely associated with the production of these unusual RNAs as well as the formation of the cytoplasmic structures. url: https://doi.org/10.3389/fmicb.2015.00804 doi: 10.3389/fmicb.2015.00804 id: cord-282372-nmii30mc author: Youk, Jeonghwan title: Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection date: 2020-07-10 words: 5124.0 sentences: 294.0 pages: flesch: 53.0 cache: ./cache/cord-282372-nmii30mc.txt txt: ./txt/cord-282372-nmii30mc.txt summary: Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Although basic molecular mechanisms in SARS-CoV-2 infection have been identified [5] [6] [7] [8] , most findings have been obtained from experiments using non-physiological cell lines 9 , model animals, such as transgenic mice expressing human angiotensin-converting enzyme 2 (ACE2) 10 , ferrets 11 and golden hamsters 12 , or from observation in clinical cohorts 13 and/or inference from in-silico computational methods [14] [15] [16] . Immunostaining for double-stranded viral RNA (dsRNA) and nucleocapsid protein (NP) of SARS-CoV-2 identified widespread viral infection in hAT2 cells co-expressing pro-SFTPC and ACE2 in hAOs ( Fig. 2a and 2b; Extended Data Fig. 3) . abstract: Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which is the cause of a present global pandemic, infects human lung alveolar cells (hACs). Characterising the pathogenesis is crucial for developing vaccines and therapeutics. However, the lack of models mirroring the cellular physiology and pathology of hACs limits the study. Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Further tracing of viral mutations acquired during transmission identifies full infection of individual cells effectively from a single viral entry. Our study provides deep insights into the pathogenesis of SARS-CoV-2, and the application of long-term 3D hAT2 cultures as models for respiratory diseases. url: https://doi.org/10.1101/2020.07.10.194498 doi: 10.1101/2020.07.10.194498 id: cord-002238-fyztb8d9 author: Young, D. F. title: Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family date: 2016-09-29 words: 7727.0 sentences: 344.0 pages: flesch: 51.0 cache: ./cache/cord-002238-fyztb8d9.txt txt: ./txt/cord-002238-fyztb8d9.txt summary: We have previously shown that IFIT1 is primarily responsible for the antiviral action of interferon (IFN) alpha/beta against parainfluenza virus type 5 (PIV5), selectively inhibiting the translation of PIV5 mRNAs. Here we report that while PIV2, PIV5, and mumps virus (MuV) are sensitive to IFIT1, nonrubulavirus members of the paramyxoviridae such as PIV3, Sendai virus (SeV), and canine distemper virus (CDV) are resistant. Despite their limited genetic information, the majority of paramyxoviruses encode small multifunctional accessory proteins that function to aid virus multiplication and block cellular antiviral defense mechanisms; typically, these proteins can block both the production of, and the signaling response to, interferons (IFNs) (for reviews, see references 3, 4, 5, 6, and 7). These results therefore show that MuV Enders is sensitive to IFIT1 but SeV and CDV are not, the weak inhibition of SeV and CDV protein synthesis observed in A549 and A549/shIFIT1 cells pretreated with IFN presumably being due to the action of other ISGs induced by IFN. abstract: We have previously shown that IFIT1 is primarily responsible for the antiviral action of interferon (IFN) alpha/beta against parainfluenza virus type 5 (PIV5), selectively inhibiting the translation of PIV5 mRNAs. Here we report that while PIV2, PIV5, and mumps virus (MuV) are sensitive to IFIT1, nonrubulavirus members of the paramyxoviridae such as PIV3, Sendai virus (SeV), and canine distemper virus (CDV) are resistant. The IFIT1 sensitivity of PIV5 was not rescued by coinfection with an IFIT1-resistant virus (PIV3), demonstrating that PIV3 does not specifically inhibit the antiviral activity of IFIT1 and that the inhibition of PIV5 mRNAs is regulated by cis-acting elements. We developed an in vitro translation system using purified human IFIT1 to further investigate the mechanism of action of IFIT1. While the translations of PIV2, PIV5, and MuV mRNAs were directly inhibited by IFIT1, the translations of PIV3, SeV, and CDV mRNAs were not. Using purified human mRNA-capping enzymes, we show biochemically that efficient inhibition by IFIT1 is dependent upon a 5′ guanosine nucleoside cap (which need not be N7 methylated) and that this sensitivity is partly abrogated by 2′O methylation of the cap 1 ribose. Intriguingly, PIV5 M mRNA, in contrast to NP mRNA, remained sensitive to inhibition by IFIT1 following in vitro 2′O methylation, suggesting that other structural features of mRNAs may influence their sensitivity to IFIT1. Thus, surprisingly, the viral polymerases (which have 2′-O-methyltransferase activity) of rubulaviruses do not protect these viruses from inhibition by IFIT1. Possible biological consequences of this are discussed. IMPORTANCE Paramyxoviruses cause a wide variety of diseases, and yet most of their genes encode structural proteins and proteins involved in their replication cycle. Thus, the amount of genetic information that determines the type of disease that paramyxoviruses cause is relatively small. One factor that will influence disease outcomes is how they interact with innate host cell defenses, including the interferon (IFN) system. Here we show that different paramyxoviruses interact in distinct ways with cells in a preexisting IFN-induced antiviral state. Strikingly, all the rubulaviruses tested were sensitive to the antiviral action of ISG56/IFIT1, while all the other paramyxoviruses tested were resistant. We developed novel in vitro biochemical assays to investigate the mechanism of action of IFIT1, demonstrating that the mRNAs of rubulaviruses can be directly inhibited by IFIT1 and that this is at least partially because their mRNAs are not correctly methylated. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5044818/ doi: 10.1128/jvi.01056-16 id: cord-000293-pc4x5e24 author: Yu, Chien-Hung title: Stimulation of ribosomal frameshifting by antisense LNA date: 2010-08-06 words: 3901.0 sentences: 194.0 pages: flesch: 49.0 cache: ./cache/cord-000293-pc4x5e24.txt txt: ./txt/cord-000293-pc4x5e24.txt summary: The requirements for À1 ribosomal frameshifting are the presence of a slippery heptanucleotide sequence X XXY YYZ (where X can be A, U, G or C; Y can be A or U; and Z does not equal Y; the spaces indicate the original reading frame) (8) followed by a downstream structural element, such as a pseudoknot, a hairpin or an antisense oligonucleotide duplex [for reviews, see (9) ]. We and others have demonstrated that small RNA oligonucleotides are able to mimic the function of frameshifter pseudoknots or hairpins by redirecting ribosomes into new reading frames (27, 28) . These results demonstrate that LNA modifications indeed enhance the antisense-induced frameshifting efficiency probably due to higher thermodynamic stability and RNA-like structural properties. In addition to RNA oligonucleotides, we demonstrated that LNA/DNA mix-mers are also capable of stimulating efficient À1 ribosomal frameshifting in contrast to DNA oligonucleotides. Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of À1 ribosomal frameshifting abstract: Programmed ribosomal frameshifting is a translational recoding mechanism commonly used by RNA viruses to express two or more proteins from a single mRNA at a fixed ratio. An essential element in this process is the presence of an RNA secondary structure, such as a pseudoknot or a hairpin, located downstream of the slippery sequence. Here, we have tested the efficiency of RNA oligonucleotides annealing downstream of the slippery sequence to induce frameshifting in vitro. Maximal frameshifting was observed with oligonucleotides of 12–18 nt. Antisense oligonucleotides bearing locked nucleid acid (LNA) modifications also proved to be efficient frameshift-stimulators in contrast to DNA oligonucleotides. The number, sequence and location of LNA bases in an otherwise DNA oligonucleotide have to be carefully manipulated to obtain optimal levels of frameshifting. Our data favor a model in which RNA stability at the entrance of the ribosomal tunnel is the major determinant of stimulating slippage rather than a specific three-dimensional structure of the stimulating RNA element. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001050/ doi: 10.1093/nar/gkq650 id: cord-000482-wifs97yy author: Yu, Chien-Hung title: Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting date: 2011-07-29 words: 4774.0 sentences: 223.0 pages: flesch: 55.0 cache: ./cache/cord-000482-wifs97yy.txt txt: ./txt/cord-000482-wifs97yy.txt summary: −1 Programmed ribosomal frameshifting (PRF) in synthesizing the gag-pro precursor polyprotein of Simian retrovirus type-1 (SRV-1) is stimulated by a classical H-type pseudoknot which forms an extended triple helix involving base–base and base–sugar interactions between loop and stem nucleotides. In short, pDUAL-HIV(0) was digested by KpnI and BamHI, followed by insertion of complementary oligonucleotides to clone the SRV-1 gag-pro pseudoknot, various hairpins as shown in Figures 2C and 5, and a negative control (NC) which formed no apparent secondary structure downstream of the slippery sequence. These data support the notion that downstream structures serve as barriers to stall translating ribosomes to stimulate frameshifting, and demonstrate that there is a correlation between the thermodynamic stability of a hairpin and its frameshift inducing capacity. In the present study, a 12 bp hairpin derivative of the SRV-1 gag-pro pseudoknot with a calculated stability of À26.9 kcal/mol was capable of inducing 22% of frameshifting, which is only 1.4-fold . abstract: −1 Programmed ribosomal frameshifting (PRF) in synthesizing the gag-pro precursor polyprotein of Simian retrovirus type-1 (SRV-1) is stimulated by a classical H-type pseudoknot which forms an extended triple helix involving base–base and base–sugar interactions between loop and stem nucleotides. Recently, we showed that mutation of bases involved in triple helix formation affected frameshifting, again emphasizing the role of the triple helix in −1 PRF. Here, we investigated the efficiency of hairpins of similar base pair composition as the SRV-1 gag-pro pseudoknot. Although not capable of triple helix formation they proved worthy stimulators of frameshifting. Subsequent investigation of ∼30 different hairpin constructs revealed that next to thermodynamic stability, loop size and composition and stem irregularities can influence frameshifting. Interestingly, hairpins carrying the stable GAAA tetraloop were significantly less shifty than other hairpins, including those with a UUCG motif. The data are discussed in relation to natural shifty hairpins. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203594/ doi: 10.1093/nar/gkr579 id: cord-002676-zwkl1ywk author: Yu, Dong-Shan title: The lifecycle of the Ebola virus in host cells date: 2017-06-15 words: 5322.0 sentences: 287.0 pages: flesch: 45.0 cache: ./cache/cord-002676-zwkl1ywk.txt txt: ./txt/cord-002676-zwkl1ywk.txt summary: However, the mechanisms of EBOV lifecycle in host cells, including viral entry, membrane fusion, RNP formation, GP-tetherin interaction, and VP40-inner leaflet association remain poorly understood. Then, the Tyro3 protein kinase (TAM) family, including Axl, Dtk, and Mer, which widely expressed in many cell types, span the plasma membrane and contain intracellular tyrosine kinase domains, are facilitate EBOV GP-dependent attachment [39, 40] . In addition, folate receptor-α (FR-α) was reported to be a co-receptor in binding cells that expressed MARV or EBOV GP, mediated syncytia formation triggered by GP, and facilitated cellular entry of the virus [28] . After the virus has been internalized into the endosome, fusion induced by cleaved GP is fundamentally independent of pH, which indicated an unidentified host cell factor critical for filovirus entry is sensitive to an acidic pH [56] . Host Cell Plasma Membrane Phosphatidylserine Regulates the Assembly and Budding of Ebola Virus abstract: Ebola haemorrhagic fever causes deadly disease in humans and non-human primates resulting from infection with the Ebola virus (EBOV) genus of the family Filoviridae. However, the mechanisms of EBOV lifecycle in host cells, including viral entry, membrane fusion, RNP formation, GP-tetherin interaction, and VP40-inner leaflet association remain poorly understood. This review describes the biological functions of EBOV proteins and their roles in the lifecycle, summarizes the factors related to EBOV proteins or RNA expression throughout the different phases, and reviews advances with regards to the molecular events and mechanisms of the EBOV lifecycle. Furthermore, the review outlines the aspects remain unclear that urgently need to be solved in future research. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589696/ doi: 10.18632/oncotarget.18498 id: cord-260452-js4nr4d8 author: Yu, Junyang title: Activation and Role of NACHT, LRR, and PYD Domains-Containing Protein 3 Inflammasome in RNA Viral Infection date: 2017-10-31 words: 4082.0 sentences: 222.0 pages: flesch: 34.0 cache: ./cache/cord-260452-js4nr4d8.txt txt: ./txt/cord-260452-js4nr4d8.txt summary: Both the pathogen-associated molecule pattern derived from virions and intracellular stress molecules involved in the process of viral infection lead to activation of the NLRP3 inflammasome, which in turn triggers inflammatory responses for antiviral defense and tissue healing. IL-1β and IL-18 serve to activate myriad downstream cell responses, and orchestrate innate and adaptive immunity through MyD88/IRAK4/TRAF6-mediated NF-κB signaling and the JNK/p38 mitogen-activated protein kinase pathways (60-63), which may represent key events for the NLRP3 inflammasome-dependent antiviral defense. In BV-2 mouse microglia cells infected by Japanese encephalitis virus, the NLRP3 inflammasome induces production of IL-1β and IL-18 rapidly (within 3 h of exposure) and of TNF-α, CCL2, and IL-6 later (within 6 h after exposure) (40) ; the findings suggest that the NLRP3dependent protective inflammatory response is a very early phase innate immune response against RNA viral infection. abstract: NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome activation and effects during ribonucleic acid (RNA) viral infection are the focus of a wide range of research currently. Both the pathogen-associated molecule pattern derived from virions and intracellular stress molecules involved in the process of viral infection lead to activation of the NLRP3 inflammasome, which in turn triggers inflammatory responses for antiviral defense and tissue healing. However, aberrant activation of the NLRP3 inflammasome can instead support viral pathogenesis and promote disease progression. Here, we summarize and expound upon the recent literature describing the molecular mechanisms underlying the activation and effects of the NLRP3 inflammasome in RNA viral infection to highlight how it provides protection against RNA viral infection. url: https://doi.org/10.3389/fimmu.2017.01420 doi: 10.3389/fimmu.2017.01420 id: cord-012032-zolowuhj author: Yu, Peifa title: 2’-Fluoro-2’-deoxycytidine inhibits murine norovirus replication and synergizes MPA, ribavirin and T705 date: 2020-08-08 words: 3499.0 sentences: 197.0 pages: flesch: 45.0 cache: ./cache/cord-012032-zolowuhj.txt txt: ./txt/cord-012032-zolowuhj.txt summary: To further examine the antiviral effects, another murine macrophage cell line, J774A.1, was used, and a similar inhibitory effect of 2''-FdC on MNV-1 replication was observed, with decreased viral RNA and NS1/2 protein expression ( Supplementary Fig. 1 ). As shown in Fig. 3D and E, the viral NS1/2 protein expression and viral titers were further decreased when the antivirals were used in combination, supporting the synergistic antiviral effects of 2''-FdC with MPA, ribavirin, or T705 against MNV replication. The combined effect of 2''-FdC and ribavirin on viral replication was analyzed using a qRT-PCR assay (n = 2-4) and mathematical modeling using MacSynergy. RAW264.7 cells were infected with MNV-1 at an MOI of 1 for 1 h and then left untreated or treated with 2''-FdC and MPA, ribavirin, or T705 at the indicated concentrations for 20 h, alone or in combination. abstract: Noroviruses are the main causative agents of acute viral gastroenteritis worldwide. However, no vaccine or specific antiviral treatment is available, imposing a heavy global health burden. The nucleoside analogue 2’-fluoro-2’-deoxycytidine (2’-FdC) has been reported to have broad antiviral activity. Here, we report that 2’-FdC significantly inhibits murine norovirus replication in macrophages. This effect was partially reversed by exogenous supplementation of cytidine triphosphate. The combination of 2’-FdC with mycophenolic acid, ribavirin or favipiravir (T705) exerts synergistic antiviral effects. These results indicate that 2’-FdC is a potential candidate for antiviral drug development against norovirus infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s00705-020-04759-4) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414258/ doi: 10.1007/s00705-020-04759-4 id: cord-342902-y1v8wzxq author: Yuan, Shuofeng title: Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters date: 2020-10-07 words: 5692.0 sentences: 291.0 pages: flesch: 45.0 cache: ./cache/cord-342902-y1v8wzxq.txt txt: ./txt/cord-342902-y1v8wzxq.txt summary: Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. We found that co-application of clofazimine and remdesivir impacts SARS-CoV-2 replication in a manner that extends beyond the additive combinatorial activity predicted by the Bliss independence model (maximal Bliss Synergy Score of 44.28; Figure 5a , Extended Data Figure 2) , and indicates these two drugs harbor a synergistic antiviral relationship. abstract: COVID-19 pandemic is the third zoonotic coronavirus (CoV) outbreak of the century after severe acute respiratory syndrome (SARS) in 2003 and Middle East respiratory syndrome (MERS) since 2012. Treatment options for CoVs are largely lacking. Here, we show that clofazimine, an anti-leprosy drug with a favorable safety and pharmacokinetics profile, possesses pan-coronaviral inhibitory activity, and can antagonize SARS-CoV-2 replication in multiple in vitro systems, including the human embryonic stem cell-derived cardiomyocytes and ex vivo lung cultures. The FDA-approved molecule was found to inhibit multiple steps of viral replication, suggesting multiple underlying antiviral mechanisms. In a hamster model of SARS-CoV-2 pathogenesis, prophylactic or therapeutic administration of clofazimine significantly reduced viral load in the lung and fecal viral shedding, and also prevented cytokine storm associated with viral infection. Additionally, clofazimine exhibited synergy when administered with remdesivir. Since clofazimine is orally bioavailable and has a comparatively low manufacturing cost, it is an attractive clinical candidate for outpatient treatment and remdesivir-based combinatorial therapy for hospitalized COVID-19 patients, particularly in developing countries. Taken together, our data provide evidence that clofazimine may have a role in the control of the current pandemic SARS-CoV-2, endemic MERS-CoV in the Middle East, and, possibly most importantly, emerging CoVs of the future. url: https://doi.org/10.21203/rs.3.rs-86169/v1 doi: 10.21203/rs.3.rs-86169/v1 id: cord-351489-tzmev77c author: Yuan, Shuofeng title: Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19) date: 2020-06-10 words: 5002.0 sentences: 238.0 pages: flesch: 40.0 cache: ./cache/cord-351489-tzmev77c.txt txt: ./txt/cord-351489-tzmev77c.txt summary: They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. In this primary screening, chloroquine, lopinavir, and remdesivir which were recently reported to have anti-SARS-CoV-2 activity, exhibited about 1.3-2.0 log10 copies/mL reduction in viral RNA load ( Figure 1 ). In comparison, recombinant IFN-β demonstrated the most potent anti-SARS-CoV-2 activity, with Avonex (IFN-β1a), Rebif (IFN-β1a), and Betaferon (IFN-β1b) each achieving about 3 log10 copies/mL reduction in viral load. In our primary screening using a fixed antiviral agent concentration and virus inoculum, we identified recombinant IFNs and lipogenesis modulators to be the most potent anti-SARS-CoV-2 agents among 22 broad-spectrum antivirals. abstract: The ongoing Coronavirus Disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) signals an urgent need for an expansion in treatment options. In this study, we investigated the anti-SARS-CoV-2 activities of 22 antiviral agents with known broad-spectrum antiviral activities against coronaviruses and/or other viruses. They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. Betaferon (interferon-β1b) exhibited the most potent anti-SARS-CoV-2 activity in viral antigen expression, viral load reduction, and plaque reduction assays among the recombinant interferons. The lipogenesis modulators 25-hydroxycholesterol and AM580 exhibited EC(50) at low micromolar levels and selectivity indices of >10.0. Combinational use of these host-based antiviral agents with virus-based antivirals to target different processes of the SARS-CoV-2 replication cycle should be evaluated in animal models and/or clinical trials. url: https://www.ncbi.nlm.nih.gov/pubmed/32532085/ doi: 10.3390/v12060628 id: cord-252466-usrpodjx author: Yun, Nadezhda E. title: Pathogenesis of Lassa Fever date: 2012-10-09 words: 5668.0 sentences: 290.0 pages: flesch: 40.0 cache: ./cache/cord-252466-usrpodjx.txt txt: ./txt/cord-252466-usrpodjx.txt summary: Apparently, failure to develop the cellular immune response that would control dissemination of LASV, which is indicated by high serum virus titers, combined with disseminated replication in tissues and absence of neutralizing antibodies, leads to the development of fatal Lassa fever [64] . Downregulation of immune responses caused by LASV infection demonstrated in vitro is also in agreement with the results of clinical observations showing that fatal outcome of Lassa fever correlates with low levels or absence of interleukin (IL) 8 and IFN inducible protein 10 (IP-10) in circulation [70] . These data indicate that T cells are essential for rapid resolution of LASV infection; however, if the host fails to control virus replication due to inadequate activation of the immune system, T lymphocytes may play a key role in Lassa fever pathogenesis. abstract: Lassa virus, an Old World arenavirus (family Arenaviridae), is the etiological agent of Lassa fever, a severe human disease that is reported in more than 100,000 patients annually in the endemic regions of West Africa with mortality rates for hospitalized patients varying between 5-10%. Currently, there are no approved vaccines against Lassa fever for use in humans. Here, we review the published literature on the life cycle of Lassa virus with the specific focus put on Lassa fever pathogenesis in humans and relevant animal models. Advancing knowledge significantly improves our understanding of Lassa virus biology, as well as of the mechanisms that allow the virus to evade the host’s immune system. However, further investigations are required in order to design improved diagnostic tools, an effective vaccine, and therapeutic agents. url: https://doi.org/10.3390/v4102031 doi: 10.3390/v4102031 id: cord-005378-u2bbgn8k author: Yun, Sang-Im title: Overview: Replication of porcine reproductive and respiratory syndrome virus date: 2013-12-19 words: 6583.0 sentences: 349.0 pages: flesch: 49.0 cache: ./cache/cord-005378-u2bbgn8k.txt txt: ./txt/cord-005378-u2bbgn8k.txt summary: Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that causes significant losses in the pig industry, is one of the most important animal pathogens of global significance. Similarly, mutagenesis studies have shown that EAV NSP1 (which contains a tandem of the PCPα and PCPβ domains, with PCPα having lost its enzymatic activity) is involved in regulating the accumulation of minusstrand templates to control the relative abundance of viral mRNAs, thereby coordinating genome replication, subgenomic mRNA synthesis, and virus production (Tijms et al., 2001 (Tijms et al., , 2007 Nedialkova et al., 2010) . Structure and cleavage specificity of the chymotrypsin-like serine protease (3CLSP/nsp4) of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Identification of the CD163 protein domains involved in infection of the porcine reproductive and respiratory syndrome virus abstract: Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that causes significant losses in the pig industry, is one of the most important animal pathogens of global significance. Since the discovery of the virus, significant progress has been made in understanding its epidemiology and transmission, but no adequate control measures are yet available to eliminate infection with this pathogen. The genome replication of PRRSV is required to reproduce, within a few hours of infection, the millions of progeny virions that establish, disseminate, and maintain infection. Replication of the viral RNA genome is a multistep process involving a replication complex that is formed not only from components of viral and cellular origin but also from the viral genomic RNA template; this replication complex is embedded within particular virus-induced membrane vesicles. PRRSV RNA replication is directed by at least 14 replicase proteins that have both common enzymatic activities, including viral RNA polymerase, and also unusual and poorly understood RNA-processing functions. In this review, we summarize our current understanding of PRRSV replication, which is important for developing a successful strategy for the prevention and control of this pathogen. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7091224/ doi: 10.1007/s12275-013-3431-z id: cord-332844-2se4d1yp author: Yun, Sang-Im title: Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses date: 2015-12-29 words: 4793.0 sentences: 233.0 pages: flesch: 52.0 cache: ./cache/cord-332844-2se4d1yp.txt txt: ./txt/cord-332844-2se4d1yp.txt summary: Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase. Generation of an infectious cDNA clone is a key step in developing a reverse genetics system for RNA viruses, especially for positive-strand RNA viruses, because its genome acts as viral mRNA that is translated into proteins by host cell ribosomes. abstract: Reverse genetics, an approach to rescue infectious virus entirely from a cloned cDNA, has revolutionized the field of positive-strand RNA viruses, whose genomes have the same polarity as cellular mRNA. The cDNA-based reverse genetics system is a seminal method that enables direct manipulation of the viral genomic RNA, thereby generating recombinant viruses for molecular and genetic studies of both viral RNA elements and gene products in viral replication and pathogenesis. It also provides a valuable platform that allows the development of genetically defined vaccines and viral vectors for the delivery of foreign genes. For many positive-strand RNA viruses such as Japanese encephalitis virus (JEV), however, the cloned cDNAs are unstable, posing a major obstacle to the construction and propagation of the functional cDNA. Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase. url: https://www.ncbi.nlm.nih.gov/pubmed/26780115/ doi: 10.3791/53164 id: cord-005060-n901y2d4 author: ZHANG, Feiyun title: Complete Nucleotide Sequence of Ryegrass Mottle Virus : A New Species of the Genus Sobemovirus date: 2001 words: 2602.0 sentences: 173.0 pages: flesch: 62.0 cache: ./cache/cord-005060-n901y2d4.txt txt: ./txt/cord-005060-n901y2d4.txt summary: The largest ORF 2 encodes a polyprotein of 947 amino acids (103.6 kDa), which codes for a serine protease and an RNA-dependent RNA polymerase. The genome sequence of sobernoviruses has been determined in Southern bean mosaic virus (SBMV)''2,24), CfMV8315), Rice yellow mottle virus (RYMV)") and Lucerne transient streak virus (LTSV, accession number U31286). However, the con-served sequence, WAG + E/D rich sequence is detected in the region, and putative E/S cleavage sites are present on both sides of the region : proteolytic cleavage would result in a protein of 9 kDa. Possibly, the VPg of RGMoV is located between the protease and the RNA-dependent RNA polymerase domains in the same order as in the SBMV ORF 222) (Fig. 3) . In the RGMoV RNA sequence, no ORF corresponds to the second largest product of 68 kDa. The putative replicase of CfMV is translated as part of a single polyprotein by -1 ribosomal frameshifting between two overlapping ORFs having a coding capacity for 60.9 kDa and 56.3 kDa proteins7J8). abstract: The genome of Ryegrass mottle virus (RGMoV) comprises 4210 nucleotides. The genomic RNA contains four open reading frames (ORFs). The largest ORF 2 encodes a polyprotein of 947 amino acids (103.6 kDa), which codes for a serine protease and an RNA-dependent RNA polymerase. The viral coat protein is encoded on ORF 4 present at the 3′-proximal region. Other ORFs 1 and 3 encode the predicted 14.6 kDa and 19.8 kDa proteins of unknown function. The consensus signal for frameshifting, heptanucleotide UUUAAAC and a stem-loop structure just downstream is in front of the AUG codon of ORF 3. Analysis of the in vitro translation products of RGMoV RNA suggests that the 68 kDa protein may represent a fusion protein of ORF 2-ORF 3 produced by frameshifting. The protease region of the polyprotein and coat protein have a low similarity with that of the sobemoviruses (approximately 25% amino acid identity), while the RNA-dependent RNA polymerase region has particularly strong similarity (54 to 60% of more than 350 amino acid residues). The sequence similarities of RGMoV to the sobemoviruses, together with the characteristic genome organization indicate that RGMoV is a new species of the genus Sobemovirus. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088213/ doi: 10.1007/pl00012989 id: cord-265139-x7g3jcjm author: Zaiou, Mohamed title: The Emerging Role and Promise of Circular RNAs in Obesity and Related Metabolic Disorders date: 2020-06-16 words: 8180.0 sentences: 440.0 pages: flesch: 41.0 cache: ./cache/cord-265139-x7g3jcjm.txt txt: ./txt/cord-265139-x7g3jcjm.txt summary: There is also growing evidence that circRNAs are closely linked to non-alcoholic fatty liver disease (NAFLD), a disorder that is caused by a plethora of factors including hepatic lipid accumulation, adipose tissue and mitochondrial dysfunction, a high-fat diet, obesity, a chronic inflammatory state, insulin resistance (IR), and genetic and epigenetic factors [48, 55] . In addition to classical epigenetic modifications, a variety of ncRNAs have been uncovered in different cells and organs including adipose tissues, many of which are involved in the regulation of adipogenesis and other metabolic processes implying their role in the etiology of obesity [69] . Emerging evidence from in vitro and in vivo animal studies suggest that circRNAs are expressed in adipose tissues and may modulate adipogenesis and lipid metabolism. Collectively, the results from the above studies demonstrate that several circRNAs are differentially expressed in adipose tissue and support a significant role of these RNA species in the regulatory networks of adipogenesis. abstract: Circular RNAs (circRNAs) are genome transcripts that are produced from back-splicing of specific regions of pre-mRNA. These single-stranded RNA molecules are widely expressed across diverse phyla and many of them are stable and evolutionary conserved between species. Growing evidence suggests that many circRNAs function as master regulators of gene expression by influencing both transcription and translation processes. Mechanistically, circRNAs are predicted to act as endogenous microRNA (miRNA) sponges, interact with functional RNA-binding proteins (RBPs), and associate with elements of the transcriptional machinery in the nucleus. Evidence is mounting that dysregulation of circRNAs is closely related to the occurrence of a range of diseases including cancer and metabolic diseases. Indeed, there are several reports implicating circRNAs in cardiovascular diseases (CVD), diabetes, hypertension, and atherosclerosis. However, there is very little research addressing the potential role of these RNA transcripts in the occurrence and development of obesity. Emerging data from in vitro and in vivo studies suggest that circRNAs are novel players in adipogenesis, white adipose browning, obesity, obesity-induced inflammation, and insulin resistance. This study explores the current state of knowledge on circRNAs regulating molecular processes associated with adipogenesis and obesity, highlights some of the challenges encountered while studying circRNAs and suggests some perspectives for future research directions in this exciting field of study. url: https://doi.org/10.3390/cells9061473 doi: 10.3390/cells9061473 id: cord-338812-q24jycgk author: Zakaryan, H. title: Nuclear remodelling during viral infections date: 2011-04-28 words: 4462.0 sentences: 226.0 pages: flesch: 37.0 cache: ./cache/cord-338812-q24jycgk.txt txt: ./txt/cord-338812-q24jycgk.txt summary: At present, we know that the nucleus contains the chromatin territories that mainly consist of DNA-protein complexes, as well as several distinct interchromosomal compartments (bodies) that support molecular activities, including replication, transcription and processing of nucleic acids (Fig. 1) . For many years the classical view of these components focused on their crucial role for the biogenesis of ribosomal subunits, but proteomic analysis of human nucleoli showed the presence of about 4500 nucleolar proteins with different functions, thus revealing the multifunctional nature of the nucleolus (Ahmad et al., 2009) . The previous decade of extensive studies implicated PML NBs in stress response (Maul et al., 1995) , gene regulation (Zhong et al., 2000) , oncogenesis (Salomoni and Pandolfi, 2002) , cell senescence (Bischof et al., 2002) , DNA damage repair (Dellaire and Bazett-Jones, 2004) , apoptosis (Takahashi et al., 2004) as well as in antiviral defence mechanisms (Everett and Chelbi-Alix, 2007) . abstract: Because of their limited coding capacity, viruses are not able to encode all proteins that are required for their replication. Therefore, they depend on a wide variety of cellular functions and structures, such as the host cell nucleus. It has been shown that DNA, as well as RNA viruses, exploit the nucleus because it provides essential machinery for viral replication. On the other hand, the nucleus undergoes significant remodelling during viral usurpation or exploitation. Moreover, it is becoming increasingly clear that some subnuclear structures, such as promyelocytic leukaemia nuclear bodies, act as an antiviral defence mechanism, and several viruses antagonize this intracellular defence by modifying subnuclear structures. This article reviews the main alterations that take place in nucleus during viral infections. url: https://www.ncbi.nlm.nih.gov/pubmed/21501365/ doi: 10.1111/j.1462-5822.2011.01596.x id: cord-277547-2vim1wno author: Zandi, Keivan title: Antiviral activity of four types of bioflavonoid against dengue virus type-2 date: 2011-12-28 words: 4381.0 sentences: 247.0 pages: flesch: 52.0 cache: ./cache/cord-277547-2vim1wno.txt txt: ./txt/cord-277547-2vim1wno.txt summary: In the present study, antiviral activity of four types of bioflavonoid against dengue virus type -2 (DENV-2) in Vero cell was evaluated. Daidzein showed a weak anti-dengue activity with IC(50 )= 142.6 μg mL(-1 )when the DENV-2 infected cells were treated after virus adsorption. Although there was no significant direct virucidal activity against DENV-2 by quercetin, continuous treatment of cells from 5 h before virus infection up to 4 days post-infection exhibited anti-dengue activity with IC 50 = 28.9 μg mL -1 (Figure 3a) . There was no significant change in the antiviral activity of daidzein when cells were treated continuously from 5 h before virus infection up to 4 days post infection comparing to its anti-dengue activity for postadsorption treatment (Figure 1 ). To investigate which of the many flavonoids could affect DENV infection, in the present study, we examined the potential effects of quercetin, naringin, hesperetin and daidzein on dengue virus infection of Vero cells. abstract: BACKGROUND: Dengue is a major mosquito-borne disease currently with no effective antiviral or vaccine available. Effort to find antivirals for it has focused on bioflavonoids, a plant-derived polyphenolic compounds with many potential health benefits. In the present study, antiviral activity of four types of bioflavonoid against dengue virus type -2 (DENV-2) in Vero cell was evaluated. Anti-dengue activity of these compounds was determined at different stages of DENV-2 infection and replication cycle. DENV replication was measured by Foci Forming Unit Reduction Assay (FFURA) and quantitative RT-PCR. Selectivity Index value (SI) was determined as the ratio of cytotoxic concentration 50 (CC(50)) to inhibitory concentration 50 (IC(50)) for each compound. RESULTS: The half maximal inhibitory concentration (IC(50)) of quercetin against dengue virus was 35.7 μg mL(-1 )when it was used after virus adsorption to the cells. The IC(50 )decreased to 28.9 μg mL(-1 )when the cells were treated continuously for 5 h before virus infection and up to 4 days post-infection. The SI values for quercetin were 7.07 and 8.74 μg mL(-1), respectively, the highest compared to all bioflavonoids studied. Naringin only exhibited anti-adsorption effects against DENV-2 with IC(50 )= 168.2 μg mL(-1 )and its related SI was 1.3. Daidzein showed a weak anti-dengue activity with IC(50 )= 142.6 μg mL(-1 )when the DENV-2 infected cells were treated after virus adsorption. The SI value for this compound was 1.03. Hesperetin did not exhibit any antiviral activity against DENV-2. The findings obtained from Foci Forming Unit Reduction Assay (FFURA) were corroborated by findings of the qRT-PCR assays. Quercetin and daidzein (50 μg mL(-1)) reduced DENV-2 RNA levels by 67% and 25%, respectively. There was no significant inhibition of DENV-2 RNA levels with naringin and hesperetin. CONCLUSION: Results from the study suggest that only quercetin demonstrated significant anti-DENV-2 inhibitory activities. Other bioflavonoids, including daidzein, naringin and hesperetin showed minimal to no significant inhibition of DENV-2 virus replication. These findings, together with those previously reported suggest that select group of bioflavonoids including quercetin and fisetin, exhibited significant inhibitory activities against dengue virus. This group of flavonoids, flavonol, could be investigated further to discover the common mechanisms of inhibition of dengue virus replication. url: https://www.ncbi.nlm.nih.gov/pubmed/22201648/ doi: 10.1186/1743-422x-8-560 id: cord-328460-thx9zh11 author: Zanoli, Laura Maria title: Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices date: 2012-12-27 words: 8972.0 sentences: 407.0 pages: flesch: 36.0 cache: ./cache/cord-328460-thx9zh11.txt txt: ./txt/cord-328460-thx9zh11.txt summary: Miniaturized isothermal amplification systems will be then illustrated including nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), multiple displacement amplification (MDA) and recombinase polymerase amplification (RPA). In addition, the use of droplet-based microfluidic systems for PCR enables the amplification and the analysis of individual target sequences to be performed in a significantly lower time as a consequence of a higher thermal cycling speed. These include nucleic acid sequence-based amplification (NASBA), loop-mediated amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), recombinase polymerase amplification (RPA) and multiple displacement amplification (MDA) [7] . Unlike other electrochemical techniques [56], based on the immobilization of an oligonucleotide probe onto an electrode, hybridization of a complementary target sequence, and transduction of the hybridization event [57], the microfluidic detection of LAMP amplicons [55] does not require probe immobilization and bacteria detection can be accomplished in a single chamber without DNA extraction and purification steps, since the used isothermal temperature (66 °C) provides enough thermal shock to lyse the E. abstract: Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed. url: https://doi.org/10.3390/bios3010018 doi: 10.3390/bios3010018 id: cord-319906-s7kzp795 author: Zemla, Adam T title: StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase date: 2011-06-02 words: 7496.0 sentences: 303.0 pages: flesch: 40.0 cache: ./cache/cord-319906-s7kzp795.txt txt: ./txt/cord-319906-s7kzp795.txt summary: When for a given reference structure a structure-based search is performed on a set of proteins from the Protein Data Bank (PDB), StralSV identifies all structurally similar fragments from that set, evaluates the calculated structure-based alignments between the query (reference) motif (designated "segment" in this work) and the detected structure fragments, and quantifies the observed sequence variability at each residue position on the query structure. (For an illustration of a "span", see additional file 1: StralSV-RdRp_Suppl_Figure 1.docx.) All residue-residue pairs that are contained within a span''s alignment are used to calculate the sequence variability data at the corresponding position in the query structure. The qualified hits (structure fragments from PDB with detected local similarities to the query structure) for six selected sequence positions (positional hits) of polio RdRp (positions identified in Figure 3 ) were categorized and quantified based on SCOP (Structure Classification of Proteins database; version 1.75, June 2009 release) identifiers [32] . abstract: BACKGROUND: Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. RESULTS: Here we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses. CONCLUSIONS: StralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/. url: https://www.ncbi.nlm.nih.gov/pubmed/21635786/ doi: 10.1186/1471-2105-12-226 id: cord-030654-8yxa1r1c author: Zhang, Changhui title: Structural basis for the multimerization of nonstructural protein nsp9 from SARS-CoV-2 date: 2020-08-20 words: 4281.0 sentences: 289.0 pages: flesch: 62.0 cache: ./cache/cord-030654-8yxa1r1c.txt txt: ./txt/cord-030654-8yxa1r1c.txt summary: This structure was revealed to be a horseshoe-like tetramer, which may play an essential role in nsp9 oligomerization and in the regulation of viral nucleic acid binding during the replication of the virus. The initial structure solved by molecular replacement showed that six SARS-CoV-2 nsp9 protomers form an OB-fold cluster in an asymmetric unit ( Supplementary Fig. 1a ). To obtain more information about the protein interfaces and the likely biological assemblies of the OB-fold cluster, we calculated the structure of SARS-CoV-2 nsp9 using PDBe-PISA [27] . These three contact surfaces in interface I b/c contribute a hydrophobic base with eight hydrogen bonds and one salt bridge, making the SARS-CoV-2 nsp9 tetramer extremely stable in the crystal structure. In this present study, we observed the nucleic acid-binding ability of SARS-CoV-2 nsp9, using the electrophoretic mobility The molecules in these two interfaces are shown as cartoons and colored and labeled as in Fig. 2a . abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of a potentially fatal disease named coronavirus disease 2019 (COVID-19), has raised significant public health concerns globally. To date, the COVID-19 pandemic has caused millions of people to be infected with SARS-CoV-2 worldwide. It has been known since the 2003 SARS epidemic that coronaviruses (CoVs) have large RNA genomes, the replication of which requires an RNA-dependent RNA replication/transcription complex. CoV nonstructural proteins (Nsps) play pivotal roles in the assembly of this complex and associated enzymatic functions in virus genomic replication. Several smaller nonenzymatic Nsps assist with RNA-dependent RNA polymerase function. In this study, we determined the structure of SARS-CoV-2 nonstructural protein 9 (nsp9), an RNA-binding protein that is essential for CoV replication. Its homotetrameric structure with two stable dimeric interfaces provids a structural basis for understanding the mechanisms of RNA-binding protein self-assembly, which may be essential for the regulation of viral RNA replication and transcription. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7438161/ doi: 10.1186/s43556-020-00005-0 id: cord-104162-fe51v2pt author: Zhang, Chiyu title: Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy date: 2020-11-02 words: 3745.0 sentences: 208.0 pages: flesch: 49.0 cache: ./cache/cord-104162-fe51v2pt.txt txt: ./txt/cord-104162-fe51v2pt.txt summary: Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. Assays of the base order-dependent component of the folding energy have shown that a highly conserved region, in otherwise rapidly mutating HIV-1 genomes, associates with an RNA structure corresponding, not to a protein-encoding function, but to an RNA packaging signal. This high GC% value can obscure the contribution of the base order-dependent component of the folding energy, which provides a sensitive indicator of local intraspecies pressures for the conservation of function within a population (i.e. a mutated organism is eliminated by natural selection so no longer can be assayed for function in the population). abstract: Base order, not composition, best reflects local evolutionary pressure for folding of single-stranded nucleic acids. The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 “Achilles heel,” the signal can be targeted by a recently described antiviral compound (NSC 260594) or by synthetic oligonucleotides. Thus, a conserved base-order-rich region of HIV-1 may facilitate therapeutic attack. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e.g. NSP3, ORF3a), we suggest that their nucleic acid level functions – such as the ribosomal frameshifting element (FSE) that facilitates differential expression of 1a and 1ab polyproteins – can be considered potential “Achilles heels” for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The region of the FSE scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein. url: https://doi.org/10.1101/2020.10.22.343673 doi: 10.1101/2020.10.22.343673 id: cord-274049-3gw65kpu author: Zhang, Han title: CRISPR Editing in Biological and Biomedical Investigation date: 2017-05-31 words: 6583.0 sentences: 333.0 pages: flesch: 40.0 cache: ./cache/cord-274049-3gw65kpu.txt txt: ./txt/cord-274049-3gw65kpu.txt summary: © 2017 Wiley Periodicals, Inc. nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), have enabled the manipulation of genes by targeting DNA double-stranded breaks (DSBs) via non-homologous end-joining (NHEJ) or homology-directed repair (HDR) pathways [Rudin et al., 1989; Rouet et al., 1994; Choulika et al., 1995; Bibikova et al., 2002; Moscou and Bogdanove, 2009 ]. Overall, these studies empower a broader range of disease modeling applications via CRISPR-Cas9-mediated genome engineering, allowing researchers to uncover fundamental mechanisms in disease initiation, maintenance and procession, and explore the therapeutic potential of the CRISPR-Cas9 system to correct disease-causing mutations. Owing to its ability to completely disrupt target genes and the simplicity of designing potent sgRNAs, the CRISPR-Cas9 system has been extended to large-scale loss-of-function (LOF) genome screens in human cells [Koike-Yusa et al., 2014; Shalem et al., 2014; Wang et al., 2014; Zhou et al., 2014] . Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease abstract: The revolutionary technology for genome editing known as the clustered regularly interspaced short palindromic repeat (CRISPR)‐CRISPR‐associated protein 9 (Cas9) system has sparked advancements in biological and biomedical research. The scientific breakthrough of the development of CRISPR‐Cas9 technology has allowed us to recapitulate human diseases by generating animal models of interest ranging from zebrafish to non‐human primates. The CRISPR‐Cas9 system can also be used to delineate the mechanisms underlying the development of human disorders and to precisely correct disease‐causing mutations. Repurposing this technology enables wider applications in transcriptome and epigenome manipulation and holds promise to reach the clinic. In this review, we highlight the latest advances of the CRISPR‐Cas9 system in different platforms and discuss the hurdles and challenges this technology is facing. J. Cell. Biochem. 118: 4152–4162, 2017. © 2017 Wiley Periodicals, Inc. url: https://www.ncbi.nlm.nih.gov/pubmed/28467679/ doi: 10.1002/jcb.26111 id: cord-310192-8x37nx4s author: Zhang, Huaqun title: Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy date: 2019-04-25 words: 7235.0 sentences: 355.0 pages: flesch: 43.0 cache: ./cache/cord-310192-8x37nx4s.txt txt: ./txt/cord-310192-8x37nx4s.txt summary: In this review, we will give a broad overview of different methods for structure determination and discuss some recent advancements in both sample preparation and data acquisition that have advanced the study of large RNAs by nuclear magnetic resonance (NMR) spectroscopy. Base-pairing, hydrogen bonding, nucleotide accessibility and other secondary structure-related characteristics, can be obtained by treating RNAs with specific chemical reagents (typically dimethyl sulfate [DMS] and/or one or more SHAPE reagents) and probing for the sites of modification by sequencing (Cordero, Kladwang, VanLang, & Das, 2012; Merino, Wilkinson, Coughlan, & Weeks, 2005; Tian & Das, 2016; Weeks, 2010) . Traditionally, these studies have been applied to relatively small RNAs. The ability to site-specifically incorporate 13 C labels within an RNA ribose and/or base makes NMR spectroscopy a powerful tool for dynamics studies of large RNAs, expanding the types of experiments that can be conducted and simplifying analysis (see data acquisition and analysis advancements below). abstract: The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high‐resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry. Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs. RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems. url: https://doi.org/10.1002/wrna.1541 doi: 10.1002/wrna.1541 id: cord-274773-3jhka8wl author: Zhang, Jialin title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge date: 2019-09-30 words: 3943.0 sentences: 207.0 pages: flesch: 51.0 cache: ./cache/cord-274773-3jhka8wl.txt txt: ./txt/cord-274773-3jhka8wl.txt summary: title: Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5‐day‐old neonatal piglets from virulent challenge High levels of IgG antibodies and NA were also detected in the serum of neonatal piglets born to immunized sows, which suggests that the antibodies were successfully transferred through the colostrum and milk. The protective efficacy of passive immunity elicited by the inactivated PDCoV vaccine against challenge with a highly pathogenic virulent strain in neonatal piglets born to immunized sows was investigated. These results suggest that within the first week, IgG antibodies in colostrum and milk of immunized sows could provide protection for piglets against TGEV virulent challenge. Moreover, high levels of IgG antibodies and NA responses were detected in serum, which protected the piglets against virulent PDCoV challenge. Pathogenicity of porcine deltacoronavirus (PDCoV) strain NH and immunization of pregnant sows with an inactivated PDCoV vaccine protects 5-day-old neonatal piglets from virulent challenge abstract: In this study, the pathogenicity of porcine deltacoronavirus (PDCoV) strain NH (passage 10, P10) was evaluated. We found that PDCoV strain NH is enteropathogenic in 5‐day‐old pigs. Pathogenicity experiments provided a challenge model for studying the protection efficiency of passive immunity. In order to investigate the protective efficacy of passive immunity in newborn piglets, pregnant sows were vaccinated with either a PDCoV‐inactivated vaccine at the Houhai acupoint (n = 5) or DMEM as a negative control (n = 2) using a prime/boost strategy 20 and 40 days before delivery. PDCoV spike (S)‐specific IgG and neutralizing antibody (NA) responses were detected in immunized sows and piglets born to immunized sows. PDCoV spike (S)‐specific sIgA was also detected in the colostrum and milk of immunized sows. Five days post‐farrowing, piglets were orally challenged with PDCoV strain NH (10(5) TCID(50)/piglet). Severe diarrhoea, high levels of viral RNA copies and substantial intestinal villus atrophy were detected in piglets born to unimmunized sows. Only 4 of 31 piglets (12.9%) born to immunized sows in the challenge group displayed mild to moderate diarrhoea, lower viral RNA copies and minor intestinal villi damage compared to piglets born to unimmunized sows post‐challenge. Mock piglets exhibited no typical clinical symptoms. The challenge experiment results indicated that the inactivated PDCoV vaccine exhibited 87.1% protective efficacy in the piglets. These findings suggest that the inactivated PDCoV vaccine has the potential to be an effective vaccine, providing protection against virulent PDCoV. url: https://doi.org/10.1111/tbed.13369 doi: 10.1111/tbed.13369 id: cord-300884-rqfxe0x1 author: Zhang, Jianqiang title: Genomic characterization of equine coronavirus date: 2007-12-05 words: 6804.0 sentences: 378.0 pages: flesch: 56.0 cache: ./cache/cord-300884-rqfxe0x1.txt txt: ./txt/cord-300884-rqfxe0x1.txt summary: Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). In contrast to the replicase proteins which are directly translated from the genomic RNA, coronavirus structural and accessory proteins are expressed from a nested set of 3′ coterminal subgenomic (sg) mRNAs that also possess a common 5′ leader sequence derived from the 5′ end of the genome (Pasternak et al., 2006; Sawicki et al., 2007) . Following multiple alignments with the S proteins of other group 2a coronaviruses, a potential cleavage recognition sequence (RRQRR) was identified at residues 764-768 which would predict a cleavage between amino acids 768 and 769, separating the ECoV S protein into S1 and S2 subunits (Fig. 1) . abstract: The complete genome sequence of the first equine coronavirus (ECoV) isolate, NC99 strain was accomplished by directly sequencing 11 overlapping fragments which were RT–PCR amplified from viral RNA. The ECoV genome is 30,992 nucleotides in length, excluding the polyA tail. Analysis of the sequence identified 11 open reading frames which encode two replicase polyproteins, five structural proteins (hemagglutinin esterase, spike, envelope, membrane, and nucleocapsid) and four accessory proteins (NS2, p4.7, p12.7, and I). The two replicase polyproteins are predicted to be proteolytically processed by three virus-encoded proteases into 16 non-structural proteins (nsp1–16). The ECoV nsp3 protein had considerable amino acid deletions and insertions compared to the nsp3 proteins of bovine coronavirus, human coronavirus OC43, and porcine hemagglutinating encephalomyelitis virus, three group 2 coronaviruses phylogenetically most closely related to ECoV. The structure of subgenomic mRNAs was analyzed by Northern blot analysis and sequencing of the leader–body junction in each sg mRNA. url: https://www.sciencedirect.com/science/article/pii/S0042682207004655 doi: 10.1016/j.virol.2007.06.035 id: cord-344782-ond1ziu5 author: Zhang, Jing title: Identification of a novel nidovirus as a potential cause of large scale mortalities in the endangered Bellinger River snapping turtle (Myuchelys georgesi) date: 2018-10-24 words: 6003.0 sentences: 280.0 pages: flesch: 49.0 cache: ./cache/cord-344782-ond1ziu5.txt txt: ./txt/cord-344782-ond1ziu5.txt summary: Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Following the detection of the novel virus, in November 2015 (about 6 months after the cessation of the outbreak) an intensive survey of the parts of the river where affected turtles had been detected [2] was undertaken by groups of biologists and ecologists and samples collected from a wide range of aquatic species and some terrestrial animals (n = 360) to establish the size of the remaining population and whether any other animals were carrying this virus. BRV, as a novel nidovirus, was isolated from tissues of diseased animals, very high levels of viral RNA were detected in tissues with marked pathological changes and in situ hybridisation assays demonstrated the presence of specific viral RNA in lesions in kidneys and eye tissue-two of the main affected organs. abstract: In mid-February 2015, a large number of deaths were observed in the sole extant population of an endangered species of freshwater snapping turtle, Myuchelys georgesi, in a coastal river in New South Wales, Australia. Mortalities continued for approximately 7 weeks and affected mostly adult animals. More than 400 dead or dying animals were observed and population surveys conducted after the outbreak had ceased indicated that only a very small proportion of the population had survived, severely threatening the viability of the wild population. At necropsy, animals were in poor body condition, had bilateral swollen eyelids and some animals had tan foci on the skin of the ventral thighs. Histological examination revealed peri-orbital, splenic and nephric inflammation and necrosis. A virus was isolated in cell culture from a range of tissues. Nucleic acid sequencing of the virus isolate has identified the entire genome and indicates that this is a novel nidovirus that has a low level of nucleotide similarity to recognised nidoviruses. Its closest relatives are nidoviruses that have recently been described in pythons and lizards, usually in association with respiratory disease. In contrast, in the affected turtles, the most significant pathological changes were in the kidneys. Real time PCR assays developed to detect this virus demonstrated very high virus loads in affected tissues. In situ hybridisation studies confirmed the presence of viral nucleic acid in tissues in association with pathological changes. Collectively these data suggest that this virus is the likely cause of the mortalities that now threaten the survival of this species. Bellinger River Virus is the name proposed for this new virus. url: https://doi.org/10.1371/journal.pone.0205209 doi: 10.1371/journal.pone.0205209 id: cord-012784-c74jr4ga author: Zhang, Le-le title: Identification of nagilactone E as a protein synthesis inhibitor with anticancer activity date: 2020-02-11 words: 4879.0 sentences: 265.0 pages: flesch: 48.0 cache: ./cache/cord-012784-c74jr4ga.txt txt: ./txt/cord-012784-c74jr4ga.txt summary: We previously reported that nagilactone E (NLE), a dinorditerpenoid isolated from Podocarpus nagi, possessed anticancer effects against lung cancer cells in vitro. To better understand the potential biological processes associated with the effects of NLE in lung cancer A549 cells, GO analysis was performed using the online DAVID 6.8 bioinformatics resource. To clarify the mechanisms underlying the anticancer effect of NLE in A549 lung cancer cells, we further analyzed the DEGs using the CMap dataset. As shown in Fig. 4a , the mRNA levels of NRF2, p21, STAT3, and ATF4 were upregulated after NLE treatment, which was consistent with the results obtained by RNA-seq analysis. Thereafter, the inhibitory effect of NLE on de novo protein synthesis in A549 cells was further confirmed using the Click-iT assay. CMap dataset analysis supported NLE as a protein synthesis inhibitor, which was further confirmed by the Click-iT assay. abstract: Norditerpenoids and dinorditerpenoids represent diterpenoids widely distributed in the genus Podocarpus with notable chemical structures and biological activities. We previously reported that nagilactone E (NLE), a dinorditerpenoid isolated from Podocarpus nagi, possessed anticancer effects against lung cancer cells in vitro. In this study we investigated the in vivo effect of NLE against lung cancer as well as the underlying mechanisms. We administered NLE (10 mg·kg(−1)·d(−1), ip) to CB-17/SCID mice bearing human lung cancer cell line A549 xenograft for 3 weeks. We found that NLE administration significantly suppressed the tumor growth without obvious adverse effects. Thereafter, RNA sequencing (RNA-seq) analysis was performed to study the mechanisms of NLE. The effects of NLE on A549 cells have been illustrated by GO and pathway enrichment analyses. CMap dataset analysis supported NLE to be a potential protein synthesis inhibitor. The inhibitory effect of NLE on synthesis of total de novo protein was confirmed in Click-iT assay. Using the pcDNA3-RLUC-POLIRES-FLUC luciferase assay we further demonstrated that NLE inhibited both cap-dependent and cap-independent translation. Finally, molecular docking revealed the low-energy binding conformations of NLE and its potential target RIOK2. In conclusion, NLE is a protein synthesis inhibitor with anticancer activity. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470872/ doi: 10.1038/s41401-019-0332-7 id: cord-287275-vwyny1vt author: Zhang, Meng-Jia title: Genomic characterization and pathogenicity of porcine deltacoronavirus strain CHN-HG-2017 from China date: 2018-10-30 words: 5181.0 sentences: 267.0 pages: flesch: 56.0 cache: ./cache/cord-287275-vwyny1vt.txt txt: ./txt/cord-287275-vwyny1vt.txt summary: In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. In addition, it has been reported that newborn piglets inoculated with two recent Chinese PDCoV isolates, named CHN-HN-2014 and CHN-GD-2016, developed clear clinical signs, including severe diarrhea, vomiting, and dehydration [21, 22] . Analysis of the genomic sequence suggested that CHN-HG-2017 is a potential recombinant virus derived from Chinese and Vietnam PDCoV strains. To confirm that virus propagation had occurred, the infectivity of the plaque-purified CHN-HG-2017 strain in LLC-PK1 cells was tested by IFA and western blot with an mAb against the PDCoV N protein. Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014 abstract: Porcine deltacoronavirus (PDCoV) was first detected in Hong Kong and has recently spread to many countries around the world. PDCoV causes acute diarrhea and vomiting in pigs, resulting in significant economic losses in the global pork industry. In this study, a Chinese PDCoV strain, designated CHN-HG-2017, was isolated from feces of a suckling piglet with severe watery diarrhea on a farm located in central China. Subsequently, the virus was identified by an indirect immunofluorescence assay and electron microscopy. A nucleotide sequence alignment showed that the whole genome of CHN-HG-2017 is 97.6%-99.1% identical to other PDCoV strains. Analysis of potential recombination sites showed that CHN-HG-2017 is a possible recombinant originating from the strains CH/SXD1/2015 and Vietnam/HaNoi6/2015. Furthermore, the pathogenicity of this recombinant PDCoV strain was investigated in 5-day-old piglets by oral inoculation. The challenged piglets developed typical symptoms, such as vomiting, anorexia, diarrhea and lethargy, from 1 to 7 days post-inoculation (DPI). Viral shedding was detected in rectal swabs until 14 DPI in the challenged piglets. Interestingly, high titers of virus-neutralizing antibodies in sera were detected at 21 DPI. Tissues of small intestines from CHN-HG-2017-infected piglets at 4 DPI displayed significant macroscopic and microscopic lesions with clear viral antigen expression. Our analysis of the full genome sequence of a recombinant PDCoV and its virulence in suckling piglets might provide new insights into the pathogenesis of PDCoV and facilitate further investigation of this newly emerged pathogen. url: https://doi.org/10.1007/s00705-018-4081-6 doi: 10.1007/s00705-018-4081-6 id: cord-298820-nogoqyxl author: Zhang, Qi title: Transcriptome altered by latent human cytomegalovirus infection on THP-1 cells using RNA-seq date: 2016-12-05 words: 4670.0 sentences: 261.0 pages: flesch: 45.0 cache: ./cache/cord-298820-nogoqyxl.txt txt: ./txt/cord-298820-nogoqyxl.txt summary: Here, we profiled the expression of mRNAs and long noncoding RNAs (lncRNAs) in THP-1 cells using the emerging RNA-seq to investigate the transcriptional changes during HCMV latent infection. These studies identified a subset of differently expressed genes, which are involved in a variety of biological functions including innate immunity response, inflammation pathway, cell cycle regulation, cellular metabolism and cell adhesion, during lytic HCMV infection. The present study adopted RNA-seq to identify global changes of mRNAs and lncRNAs in host cell during HCMV experimental latent infection of THP-1 cells, in an attempt to derive insights into the mechanism underlying alterations in response to infection. In this study, we profiled the expression of mRNAs and lncRNAs in host cell using the emerging RNA-seq to investigate the transcriptional changes in HCMV latent infection. abstract: Human cytomegalovirus (HCMV) has been recognized as a cause of severe, sometimes life-threatening disease in congenitally infected newborns as well as in immunocompromised individuals. However, the molecular mechanisms of the host-virus interaction remain poorly understood. Here, we profiled the expression of mRNAs and long noncoding RNAs (lncRNAs) in THP-1 cells using the emerging RNA-seq to investigate the transcriptional changes during HCMV latent infection. At 4 days post HCMV infection, a total of 169,008,624 sequence reads and 180,616 transcripts were obtained, respectively. Of these transcripts, 1,354 noncoding genes and 12,952 protein-coding genes were observed in Refseq database. Differential gene expression analysis identified 2,153 differentially expressed genes (DEGs) between HCMV-infected and mock-infected THP-1 cells, including 1,098 up-regulated genes and 1,055 down-regulated genes. These regulated genes were involved in pathways of apoptosis, inflammatory response and cell cycle progression, all of which may be implicated in viral pathogenesis. In addition, 646 lncRNAs (208 known lncRNAs and 438 novel lncRNAs) were upregulated and 424 (140 known and 284 novel) were downregulated in infected THP-1 cells. These findings have provided a dynamic scenario of DE candidate genes and lncRNAs at the virus-host interface and clearly warrant further experimental investigation associated with HCMV infection. url: https://api.elsevier.com/content/article/pii/S0378111916307302 doi: 10.1016/j.gene.2016.09.014 id: cord-274785-9jgg8ukr author: Zhang, Qiang title: Viral Regulation of RNA Granules in Infected Cells date: 2019-04-29 words: 7384.0 sentences: 458.0 pages: flesch: 47.0 cache: ./cache/cord-274785-9jgg8ukr.txt txt: ./txt/cord-274785-9jgg8ukr.txt summary: TIA/G3BP/PABP-specific stress granules (SG) and GW182/DCP-specific RNA processing bodies (PB) are two major distinguishable RNA granules in somatic cells and contain various ribosomal subunits, translation factors, scaffold proteins, RNA-binding proteins, RNA decay enzymes and helicases to exclude mRNAs from the cellular active translational pool. The process of SG formation can be artificially divided into the following steps ( Fig. 2) : (1) accumulation of stalled translation initiation complexes ) in response to various types of stress; (2) the RNA-binding proteins such as RAS-GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and T cell-restricted intracellular antigen 1 (TIA1) bind mRNAs and aggregate to nucleate SG formation. SG proteins (eIF4G, eIF3, PABP) are selectively sequestered within Ebola virus inclusion bodies and co-localize with viral RNA to form inclusion body-bound granules, which are functionally and structurally different from canonical SG, probably leading to inhibit the antiviral role of SG (Nelson et al. Interaction of TIA-1/TIAR with West Nile and dengue virus products in infected cells interferes with stress granule formation and processing body assembly abstract: RNA granules are cytoplasmic, microscopically visible, non-membrane ribo-nucleoprotein structures and are important posttranscriptional regulators in gene expression by controlling RNA translation and stability. TIA/G3BP/PABP-specific stress granules (SG) and GW182/DCP-specific RNA processing bodies (PB) are two major distinguishable RNA granules in somatic cells and contain various ribosomal subunits, translation factors, scaffold proteins, RNA-binding proteins, RNA decay enzymes and helicases to exclude mRNAs from the cellular active translational pool. Although SG formation is inducible due to cellular stress, PB exist physiologically in every cell. Both RNA granules are important components of the host antiviral defense. Virus infection imposes stress on host cells and thus induces SG formation. However, both RNA and DNA viruses must confront the hostile environment of host innate immunity and apply various strategies to block the formation of SG and PB for their effective infection and multiplication. This review summarizes the current research development in the field and the mechanisms of how individual viruses suppress the formation of host SG and PB for virus production. url: https://www.ncbi.nlm.nih.gov/pubmed/31037644/ doi: 10.1007/s12250-019-00122-3 id: cord-327024-1k5jucae author: Zhang, Qingshui title: Isolation and characterization of an astrovirus causing fatal visceral gout in domestic goslings date: 2018-04-19 words: 4167.0 sentences: 213.0 pages: flesch: 47.0 cache: ./cache/cord-327024-1k5jucae.txt txt: ./txt/cord-327024-1k5jucae.txt summary: 18 reported the detection of avian nephritis virus infection in Croatian goose flocks and provided evidence that this AstV was associated with stunting and prehatching mortality of goose embryos. To determine the potential genetic mutation(s) that might occur during the goose embryo passage, the initial virus genome was sequenced using the total RNA extracted from the clinical case tissue homogenate. When the samples were tested by RT-PCR for virus shedding evaluation, the AAstV specific RNA was sequentially detected from the cloacal swabs of infected goslings from 2 to 12 dpi (Fig. 6 ). To evaluate the potential adaptive mutation (s) of the virus that might occur during the process of goose embryo passage, we sequenced the complete genome of initial virus using the total RNA extracted from the clinical case tissue homogenate of kidney, spleen, and liver using the method described above. abstract: Astroviruses are recognized as a leading cause of gastroenteritis in humans and animals. They are also associated with extra-intestinal diseases, such as hepatitis in ducklings, nephritis in chickens, and encephalitis in cattle. In February 2017, a fatal infection of goslings characterized by visceral urate deposition was reported in the Shandong province, China. Our systematic investigation led to the isolation of an astrovirus, designated AAstV/Goose/CHN/2017/SD01, and similar disease was reproduced by experimental infection of healthy goslings, fulfilling Koch’s postulates. The isolated astrovirus replicated well and resulted in 100% mortality of goose embryos. Complete genome sequence analysis revealed that the isolate was genetically distinct from known astroviruses and closely related to members of the avastrovirus genogroup II. Experimental infection showed that the isolate was highly pathogenic in goslings, causing clinical signs, growth repression and in many cases mortality. Histopathological examination indicated that lesions occurred mainly in the kidneys of infected birds. However, virus-specific genomic RNA was detected in all representative tissues, and virus shedding was detected up to 12 days after inoculation, suggesting that the isolate was able to spread systemically and replicate efficiently in vivo. Collectively, our study demonstrates, for the first time, the etiological role of a genetically distinct astrovirus in the fatal infection of goslings. url: https://www.ncbi.nlm.nih.gov/pubmed/29674726/ doi: 10.1038/s41426-018-0074-5 id: cord-321155-dty18esg author: Zhang, Rongxin title: Whole genome identification of potential G-quadruplexes and analysis of the G-quadruplex binding domain for SARS-CoV-2 date: 2020-06-05 words: 4927.0 sentences: 331.0 pages: flesch: 57.0 cache: ./cache/cord-321155-dty18esg.txt txt: ./txt/cord-321155-dty18esg.txt summary: We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. To get the potential G-quadruplexes in the SARS-CoV-2 genome, we took the strategy described as follows ( Fig. 2A) : (i) Predicting the PG4s with three software independently. To further characterize the potential canonical secondary structures competitive with Gquadruplexes, the landscape of thermodynamic stability of the SARS-CoV-2 genome was depicted by using ΔG°z-score [55] . The distributions of loop length between the SARS-CoV-2 PG4s and the human two-quartet Gquadruplexes did not show discrepancies (Fig. S1 , Wilcoxon test, p-value = 0.4552). Recent research revealed that the G-quadruplexes in human UTRs (Untranslated Regions) are under selective pressures [58] , and some coronaviruses on bats and pangolins are closely related to SARS-CoV-2. Thus, we started to explore whether the SARS-CoV-2 genome contains the protein-coding sequence similar to SUD and whether SARS-CoV-2 retains the ability to bind RNA G-quadruplexes. abstract: The Coronavirus Disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) quickly become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about G-quadruplexes on the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes both in the positive and negative-sense viral stands. The identified potential G-quadruplexes exhibits similar features to the G-quadruplexes detected in the human transcriptome. Within some bat and pangolin related beta coronaviruses, the G-quartets rather than the loops are under heightened selective constraints. We also found that the SUD-like sequence is retained in the SARS-CoV-2 genome, while some other coronaviruses that can infect humans are depleted. Further analysis revealed that the SARS-CoV-2 SUD-like sequence is almost conserved among 16,466 SARS-CoV-2 samples. And the SARS-CoV-2 SUDcore-like dimer displayed similar electrostatic potential pattern to the SUD dimer. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, we hope our fundamental research could provide new insights for the SARS-CoV-2 drug discovery. url: https://doi.org/10.1101/2020.06.05.135749 doi: 10.1101/2020.06.05.135749 id: cord-329707-89zyu8bl author: Zhang, Xue title: Inhibition of SARS-CoV Gene Expression by Adenovirus-Delivered Small Hairpin RNA date: 2006-11-30 words: 3212.0 sentences: 210.0 pages: flesch: 54.0 cache: ./cache/cord-329707-89zyu8bl.txt txt: ./txt/cord-329707-89zyu8bl.txt summary: We constructed recombinant adenoviral vectors that can express shRNAs, which inhibited the expression of SARS-CoV genes effectively in mammalian cells. METHODS: In this study, we designed several plasmids that express small hairpin RNA molecules (shRNA) specifically targeting to the genes encoding for the SARS-CoV nucleocapsid (N) protein and envelope (E) protein, respectively. The effects of adenovirus-delivered small hairpin RNA on SARS-CoV gene expression were determined by RT-PCR, Western blot, and luciferase activity assays. RESULTS: The levels of viral mRNAs and viral proteins of the targets were significantly decreased or completely inhibited in cell lines after being infected with the recombinant adenoviruses that expressed specific shRNA molecules. CONCLUSIONS: Since many cell types can be efficiently infected by adenovirus, recombinant adenoviruses could serve as an alternative powerful tool for shRNA delivery and for gene suppression, especially when the targeted cells are resistant to transfection by DNA or RNA. abstract: OBJECTIVE: Severe acute respiratory syndrome (SARS) is a highly contagious and lethal disease caused by a new type of coronavirus, SARS-associated coronavirus (SARS-CoV). Currently, there is no efficient treatment and prevention for this disease. We constructed recombinant adenoviral vectors that can express shRNAs, which inhibited the expression of SARS-CoV genes effectively in mammalian cells. METHODS: In this study, we designed several plasmids that express small hairpin RNA molecules (shRNA) specifically targeting to the genes encoding for the SARS-CoV nucleocapsid (N) protein and envelope (E) protein, respectively. Effective shRNA molecules to the viral genes were screened and identified, and then constructed into adenovirus vectors. The effects of adenovirus-delivered small hairpin RNA on SARS-CoV gene expression were determined by RT-PCR, Western blot, and luciferase activity assays. RESULTS: The levels of viral mRNAs and viral proteins of the targets were significantly decreased or completely inhibited in cell lines after being infected with the recombinant adenoviruses that expressed specific shRNA molecules. CONCLUSIONS: Since many cell types can be efficiently infected by adenovirus, recombinant adenoviruses could serve as an alternative powerful tool for shRNA delivery and for gene suppression, especially when the targeted cells are resistant to transfection by DNA or RNA. With availability of high titers of adenoviruses and uniform and rapid infection, this approach would have foreseeable wide applications both in experimental biology and molecular medicine. url: https://www.ncbi.nlm.nih.gov/pubmed/17139181/ doi: 10.1159/000097391 id: cord-258286-lodjcj8c author: Zhang, Xuming title: Expression of Interferon-γ by a Coronavirus Defective-Interfering RNA Vector and Its Effect on Viral Replication, Spread, and Pathogenicity date: 1997-07-07 words: 5866.0 sentences: 296.0 pages: flesch: 54.0 cache: ./cache/cord-258286-lodjcj8c.txt txt: ./txt/cord-258286-lodjcj8c.txt summary: Previous studies have shown that immunocoma large plaque variant derived from the parental JHM petent mice infected with MHV exhibited increased exstrain (Stohlman et al., 1982) ; the small plaque variant pression of a number of cytokines, including IL-1, IL-6, DS (Stohlman et al., 1982) ; the neutralization-escape mu-TNF-a, and IFN-g, in the CNS at the time of viral cleartant 2.2-V-1 (Fleming et al., 1987; Wang et al., 1992) , and ance (Pearce et al., 1994) . The expressed IFNg exhibited antiviral activity, prevented virus spread in layers of DBT cells grown at approximately 70% confluence in 60-mm petri dishes were infected with MHV at vitro, and altered viral pathogenesis in mice. Expression of IFN-g using an MHV DI RNA vector cell metabolism prior to infection or it may be that interferon acts at an early stage of viral replication. abstract: Abstract A defective-interfering (DI) RNA of the murine coronavirus mouse hepatitis virus (MHV) was developed as a vector for expressing interferon-γ (IFN-γ). The murine IFN-γ gene was cloned into the DI vector under the control of an MHV transcriptional promoter and transfected into MHV-infected cells. IFN-γ was secreted into culture medium as early as 6 hr posttransfection and reached a peak level (up to 180 U/ml) at 12 hr posttransfection. The DI-expressed IFN-γ (DE-IFN-γ) exhibited an antiviral activity comparable to that of recombinant IFN-γ and was blocked by a neutralizing monoclonal antibody against IFN-γ. Treatment of macrophages with DE-IFN-γ selectively induced the expression of the cellular inducible nitric oxide synthase and the IFN-γ-inducing factor (IGIF) but did not affect the amounts of the MHV receptor mRNA. Antiviral activity was detected only when cells were pretreated with IFN-γ for 24 hr prior to infection; no inhibition of virus replication was detected when cells were treated with IFN-γ during or after infection. Furthermore, addition of IFN-γ together with MHV did not prevent infection, but appeared to prevent subsequent viral spread. MHV variants with different degrees of neurovirulence in mice had correspondingly different levels of sensitivities to IFN-γ treatmentin vitro,with the most virulent strain being most resistant to IFN-γ treatment. Infection of susceptible mice with DE-IFN-γ-containing virus caused significantly milder disease, accompanied by more pronounced mononuclear cell infiltrates into the CNS and less virus replication, than that caused by virus containing a control DI vector. This study thus demonstrates the feasibility and usefulness of this MHV DI vector for expressing cytokines and may provide a model for studying the role of cytokines in MHV pathogenesis. url: https://api.elsevier.com/content/article/pii/S0042682297985986 doi: 10.1006/viro.1997.8598 id: cord-263302-z5uhrta5 author: Zhang, Xuming title: Identification of a Noncanonical Signal for Transcription of a Novel Subgenomic mRNA of Mouse Hepatitis Virus: Implication for the Mechanism of Coronavirus RNA Transcription date: 2000-12-05 words: 7944.0 sentences: 411.0 pages: flesch: 58.0 cache: ./cache/cord-263302-z5uhrta5.txt txt: ./txt/cord-263302-z5uhrta5.txt summary: Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). Further sequencing on cDNA clones derived from JHM2c mRNAs by reserve transcription-polymerase chain reaction (RT-PCR) has shown that the leader-body joining sites in subgenomic mRNA2-1 are more heterogeneous . When it was placed in front of the chloramphenicol acetyl-transferase (CAT) gene in the defective-interfering (DI) RNA-CAT reporter plasmid, the IG5-1, which is devoid of any known IRES sequence, can direct the synthesis of a subgenomic CAT-containing mRNA and expression of the CAT activity, thus confirming that the IG5-1 serves as a promoter for transcription of a subgenomic mRNA. To identify the minimal sequence required for subgenomic mRNA transcription, three deletions within the 140-nt sequence were made by PCR, and the deletion fragments were cloned into the DI RNA-CAT reporter vector in place of the wild-type, full-length (140-nt) se, and MHV-1 (F), respectively. abstract: Abstract Subgenomic RNA transcription of coronaviruses involves the interaction between the leader (or antileader) and the intergenic (IG) sequences. However, it is not clear how these two sequences interact with each other. In this report, a previously unrecognized minor species of subgenomic mRNA, termed mRNA5–1, was identified in cells infected with mouse hepatitis virus (MHV) strains JHM2c, JHM(2), JHM(3), A59, and MHV-1. Sequence analysis revealed that the leader-body fusion site of the mRNA is located at approximately 150 nucleotides (nt) downstream of the consensus IG sequence for mRNA 5 and did not have sequence homology with any known IG consensus sequences. To determine whether this sequence functions independently as a promoter, we cloned a 140-nt sequence (from ≈70 nt upstream to ≈70 nt downstream of the fusion site) from viral genomic RNA and placed it in front of a reporter gene in the defective-interfering (DI) RNA-chloramphenicol acetyltransferase (CAT) reporter vector. Transfection of the reporter RNA into MHV-infected cells resulted in synthesis of a CAT-specific subgenomic mRNA detected by reverse transcription-polymerase chain reaction (RT-PCR). The strength of this promoter was similar to that of the IG7 (for mRNA 7) as measured by the CAT activity. Deletion analysis showed that the sequence as few as 13 nt was sufficient to initiate mRNA transcription, while mutations within the 13-nt abolished mRNA transcription. In vitro translation study confirmed that the envelope (E) protein was translated from mRNA5–1, which encodes the open reading frame (ORF) 5b at its 5′-end, indicating that mRNA5–1 is a functional message. Furthermore, when the ORF5b was replaced with the CAT gene and placed in the DI in the context of viral mini-genome, CAT was expressed not only from the first ORF of mRNA5–1 but also from the second and third ORF of mRNA5 and genomic DI RNA, respectively, suggesting that more than one mechanism is involved in regulation of ORF5b expression. Our findings thus support the notion that base-pairing between the leader (or antileader) and the IG is not the sole mechanism in subgenomic RNA transcription. url: https://api.elsevier.com/content/article/pii/S0042682200906378 doi: 10.1006/viro.2000.0637 id: cord-267532-5rnqd9mb author: Zhang, Xuming title: Expression of Hemagglutinin/Esterase by a Mouse Hepatitis Virus Coronavirus Defective–Interfering RNA Alters Viral Pathogenesis date: 1998-03-01 words: 6892.0 sentences: 357.0 pages: flesch: 55.0 cache: ./cache/cord-267532-5rnqd9mb.txt txt: ./txt/cord-267532-5rnqd9mb.txt summary: HEor CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. In the present study, we used this DI RNA vector system to express the viral HE gene in the CNS of mice in the presence of an HE-deficient helper virus. To determine the basis for the reduction in mortality following A59-DE-HE infection compared to other viruses ( Fig. 2) , virus titers in the brains of mice infected with A59-DE-HE were initially compared to mice infected with the parental A59 or A59-DE-CAT at 6 days p.i. Based on the survival of most mice infected with A59-DE-HE, reduced viral replication in the CNS was anticipated. IL-6 mRNA was also increased in the CNS of mice infected with A59-DE-HE virus (Fig. 5B) ; however, no differences were detected in the liver between the two groups. abstract: Abstract A defective-interfering (DI) RNA of mouse hepatitis virus (MHV) was developed as a vector for expressing MHV hemagglutinin/esterase (HE) protein. The virus containing an expressed HE protein (A59-DE-HE) was generated by infecting cells with MHV-A59, which does not express HE, and transfecting thein vitro-transcribed DI RNA containing the HE gene. A similar virus (A59-DE-CAT) expressing the chloramphenicol acetyltransferase (CAT) was used as a control. These viruses were inoculated intracerebrally into mice, and the role of the HE protein in viral pathogenesis was evaluated. Results showed that all mice infected with parental A59 or A59-DE-CAT succumbed to infection by 9 days postinfection (p.i.), demonstrating that inclusion of the DI did not by itself alter pathogenesis. In contrast, 60% of mice infected with A59-DE-HE survived infection. HE- or CAT-specific subgenomic mRNAs were detected in the brains at days 1 and 2 p.i. but not later, indicating that the genes in the DI vector were expressed only in the early stage of viral infection. No significant difference in virus titer or viral antigen expression in brains was observed between A59-DE-HE- and A59-DE-CAT-infected mice, suggesting that virus replication in brain was not affected by the expression of HE. However, at day 3 p.i. there was a slight increase in the extent of inflammatory cell infiltration in the brains of the A59-DE-HE-infected mice. Surprisingly, virus titers in the livers of A59-DE-HE-infected mice were 3 log10lower than that of the A59-DE-CAT-infected mice at day 6 p.i. Also, substantially less necrosis and viral antigen were detected in the livers of the A59-DE-HE-infected mice. This may account for the reduced mortality of these mice. The possible contribution of the host immune system to this difference in pathogenesis was analyzed by comparing the expression of four cytokines. Results showed that both tumor necrosis factor-α and interleukin-6 mRNAs increased in the brains of the A59-DE-HE-infected mice at day 2 p.i., whereas interferon-γ and interleukin-1α mRNAs were similar between A59-DE-HE- and A59-DE-CAT-infected mice. These data suggest that the transient expression of HE protein enhances an early innate immune response, possibly contributing to the eventual clearance of virus from the liver. This study indicates the feasibility of the DI expression system for studying roles of viral proteins during MHV infection. url: https://api.elsevier.com/content/article/pii/S0042682297989935 doi: 10.1006/viro.1997.8993 id: cord-343632-cv3qgno3 author: Zhang, Yinhua title: Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP date: 2020-02-29 words: 2344.0 sentences: 143.0 pages: flesch: 49.0 cache: ./cache/cord-343632-cv3qgno3.txt txt: ./txt/cord-343632-cv3qgno3.txt summary: Here we report a method to identify SARS-CoV-2 (COVID-19) virus RNA from purified RNA or cell lysis using loop-mediated isothermal amplification (LAMP) using a visual, colorimetric detection. Here we describe a molecular diagnostic approach for SARS-CoV-2 RNA detection using loop-mediated isothermal amplification (LAMP) and simple visual detection of amplification for potential use in rapid, field applications. This study describes testing and validation of 5 sets LAMP primers targeting two fragments of the SARS-CoV-2 genome using short (~300bp) RNA fragments made with in vitro transcription and RNA samples from patients. https://doi.org/10.1101/2020.02.26.20028373 doi: medRxiv preprint With current diagnostic methods, e.g. RT-qPCR, purified RNA is used in the input. Although a small number of samples were tested here, the colorimetric LAMP assay enables reliable SARS-CoV-2 detection without sophisticated instrumentation, matching the RT-qPCR performance in field and point-of-care settings. /2020 In conclusion, colorimetric LAMP provides a simple, rapid method for SARS-CoV-2 RNA detection. abstract: The ability to detect an infectious agent in a widespread epidemic is crucial to the success of quarantine efforts in addition to sensitive and accurate screening of potential cases of infection from patients in a clinical setting. Enabling testing outside of sophisticated laboratories broadens the scope of control and surveillance efforts, but also requires robust and simple methods that can be used without expensive instrumentation. Here we report a method to identify SARS-CoV-2 (COVID-19) virus RNA from purified RNA or cell lysis using loop-mediated isothermal amplification (LAMP) using a visual, colorimetric detection. This test was additionally verified using RNA samples purified from respiratory swabs collected from COVID-19 patients in Wuhan, China with equivalent performance to a commercial RT-qPCR test while requiring only heating and visual inspection. This simple and sensitive method provides an opportunity to facilitate virus detection in the field without a requirement for complex diagnostic infrastructure. url: https://doi.org/10.1101/2020.02.26.20028373 doi: 10.1101/2020.02.26.20028373 id: cord-257652-ndt8f812 author: Zhang, Yong-Zhen title: The diversity, evolution and origins of vertebrate RNA viruses date: 2018-08-13 words: 4249.0 sentences: 171.0 pages: flesch: 40.0 cache: ./cache/cord-257652-ndt8f812.txt txt: ./txt/cord-257652-ndt8f812.txt summary: In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. However, following the extensive use of PCR and the Sanger sequencing methods for virus identification over the past decade, the number of RNA viruses sampled from lower vertebrates has steadily increased [28] , with notable examples being arenavirus and paramyxoviruses in reptiles [29] , and novirhabdoviruses and other RNA viruses from fish [30] , although these numbers were still very limited compared to the viruses described in birds and mammals. abstract: Despite a substantial increase in our knowledge of the biodiversity and evolution of vertebrate RNA viruses, far less is known about the diversity, evolution and origin of RNA viruses across the diverse phylogenetic range of viruses, and particularly in healthy animals that are often only rarely utilized for virological sampling. Fortunately, recent advances in virus discovery using metagenomic approaches are beginning to reveal a multitude of RNA viruses in vertebrates other than birds and mammals. In particular, fish harbor a remarkable array of RNA viruses, including the relatives of important pathogens. In addition, despite frequent cross-species transmission, the RNA viruses in vertebrates generally follow the evolutionary history of their hosts, which began in the oceans and then moved to terrestrial habitats over timescales covering hundreds of millions of years. url: https://api.elsevier.com/content/article/pii/S1879625718300622 doi: 10.1016/j.coviro.2018.07.017 id: cord-333515-llqpfhwg author: Zhao, Juanjuan title: Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019 date: 2020-03-03 words: 3575.0 sentences: 230.0 pages: flesch: 56.0 cache: ./cache/cord-333515-llqpfhwg.txt txt: ./txt/cord-333515-llqpfhwg.txt summary: Their serial plasma samples (n = 535) collected during the hospitalization period were tested for total antibodies (Ab), IgM and IgG against SARS-CoV-2 using immunoassays. To mitigate this knowledge gap, and to provide scientific analysis on the benefit of antibody testing when used in combination with the current RNA testing, this study investigates the dynamics of total antibody (Ab), IgM and IgG antibody against SARS-CoV-2 in serial blood samples collected from 173 confirmed COVID-19 patients and provides discussion on the clinical value of antibody testing. A total of 535 plasma samples collected during the hospitalization period of the 173 patients were tested for antibodies against SARS-CoV-2. In addition to the diagnosis value of Ab test, our study revealed a strong positive correlation between clinical severity and antibody titer since 2-week after illness onset, for the first time in COVID-19 patients. abstract: Summary Background The novel coronavirus SARS-CoV-2 is a newly emerging virus. The antibody response in infected patient remains largely unknown, and the clinical values of antibody testing have not been fully demonstrated. Methods A total of 173 patients with confirmed SARS-CoV-2 infection were enrolled. Their serial plasma samples (n = 535) collected during the hospitalization period were tested for total antibodies (Ab), IgM and IgG against SARS-CoV-2 using immunoassays. The dynamics of antibodies with the progress and severity of disease was analyzed. Findings Among 173 patients, the seroconversion rate for Ab, IgM and IgG was 93.1% (161/173), 82.7% (143/173) and 64.7% (112/173), respectively. Twelve patients who had not seroconverted were those only blood samples at the early stage of illness were collected. The seroconversion sequentially appeared for Ab, IgM and then IgG, with a median time of 11, 12 and 14 days, respectively. The presence of antibodies was < 40% among patients in the first 7 days of illness, and then rapidly increased to 100.0%, 94.3% and 79.8% for Ab, IgM and IgG respectively since day 15 after onset. In contrast, the positive rate of RNA decreased from 66.7% (58/87) in samples collected before day 7 to 45.5% (25/55) during days 15 to 39. Combining RNA and antibody detections significantly improved the sensitivity of pathogenic diagnosis for COVID-19 patients (p < 0.001), even in early phase of 1-week since onset (p = 0.007). Moreover, a higher titer of Ab was independently associated with a worse clinical classification (p = 0.006). Interpretation The antibody detection offers vital clinical information during the course of SARS-CoV-2 infection. The findings provide strong empirical support for the routine application of serological testing in the diagnosis and management of COVID-19 patients. url: https://doi.org/10.1101/2020.03.02.20030189 doi: 10.1101/2020.03.02.20030189 id: cord-328686-5ik5em5a author: Zhao, L. title: First study on surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: Post-lockdown date: 2020-08-21 words: 1606.0 sentences: 110.0 pages: flesch: 61.0 cache: ./cache/cord-328686-5ik5em5a.txt txt: ./txt/cord-328686-5ik5em5a.txt summary: In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint From the findings of this study, during the middle risk period, positive samples were detected both in 83 municipal and hospital wastewater systems. . https://doi.org/10.1101/2020.08.19.20172924 doi: medRxiv preprint Although SARS-CoV-2 RNA surveillance in wastewaters is a useful WBE drive, the public health risk associated 109 with water cycle is unclear since viral particles infectivity in sewage and faeces is yet to be determined in 110 addition to its probable fecal-oral transmission. abstract: Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community. Congruently, SARS-CoV-2 virus, the etiologic agent of COVID-19, has been demonstrated to infect the gastrointestinal tissues, and be shed in feces. In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, ground water, and soil samples of municipal and hospital wastewater systems and related environment in Wuhan during the COVID-19 middle and low risk periods, and the viral RNA copies quantified using RT-qPCR. From the findings of this study, during the middle risk period, one influent sample and three secondary treatment effluents collected from Waste Water Treatment Plant 2 (WWTP2), as well as two influent samples from wastewater system of Hospital 2 were SARS-CoV-2 RNA positive. One sludge sample collected from Hospital 4; which was obtained during low risk period, was positive for SARS-CoV-2 RNA. These study findings demonstrate the significance of WBE in continuous surveilling and monitoring of SARS-CoV-2 at the community level, even when the COVID19 prevalence is low. Therefore, the application of WBE is principally useful in tracking the level of infections in communities and the risk assessment of the secondary environment. url: https://doi.org/10.1101/2020.08.19.20172924 doi: 10.1101/2020.08.19.20172924 id: cord-011803-9122f1zc author: Zhao, Yang title: The RNA quality control pathway nonsense-mediated mRNA decay targets cellular and viral RNAs to restrict KSHV date: 2020-07-03 words: 8355.0 sentences: 493.0 pages: flesch: 50.0 cache: ./cache/cord-011803-9122f1zc.txt txt: ./txt/cord-011803-9122f1zc.txt summary: Collectively, our study describes an intricate relationship between cellular targets of an RNA quality control pathway and KSHV lytic gene expression, and demonstrates that NMD can function as a cell intrinsic restriction mechanism acting upon DNA viruses. EJCs are deposited at the exon-exon junction, thus we determined whether the EJC component eukaryotic translation initiation factor 4A3 (eIF4A3) is associated with spliced KSHV RNAs. To test EJC association with KSHV transcripts we performed eIF4A3 formaldehyde crosslinking RNA immunoprecipitation (fRIP) coupled to reverse transcription quantitative PCR (RT-qPCR) on lytic iSLK.219 and TREx-BCBL-RTA cells (Fig. 1g, h) . Leveraging p-UPF1 fRIP-seq we identified NMD targets transcriptome-wide in both latent and lytic PEL cells and targets include both host and viral RNAs. Remarkably, the mRNA encoding RTA, the master transcription factor governing KSHV reactivation, is targeted by NMD via its 3′UTR and silencing of UPF1 is sufficient to potentiate RTA-mediated transactivation. abstract: Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved RNA decay mechanism that has emerged as a potent cell-intrinsic restriction mechanism of retroviruses and positive-strand RNA viruses. However, whether NMD is capable of restricting DNA viruses is not known. The DNA virus Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi’s sarcoma and primary effusion lymphoma (PEL). Here, we demonstrate that NMD restricts KSHV lytic reactivation. Leveraging high-throughput transcriptomics we identify NMD targets transcriptome-wide in PEL cells and identify host and viral RNAs as substrates. Moreover, we identified an NMD-regulated link between activation of the unfolded protein response and transcriptional activation of the main KSHV transcription factor RTA, itself an NMD target. Collectively, our study describes an intricate relationship between cellular targets of an RNA quality control pathway and KSHV lytic gene expression, and demonstrates that NMD can function as a cell intrinsic restriction mechanism acting upon DNA viruses. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334219/ doi: 10.1038/s41467-020-17151-2 id: cord-291754-1zxztadu author: Zhao, Ye title: Successful establishment of a reverse genetic system for QX-type infectious bronchitis virus and technical improvement of the rescue procedure date: 2019-10-15 words: 6848.0 sentences: 344.0 pages: flesch: 54.0 cache: ./cache/cord-291754-1zxztadu.txt txt: ./txt/cord-291754-1zxztadu.txt summary: In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. To compare the in vitro replication of the rescued virus rYN and its parental strain YN on CEK cells, 200 μl PBS containing 10 3.0 TCID 50 of rYN or YN virus were inoculated onto the CEK cells in 24-well plates, and 200 μl supernatants from three wells from each group were harvested at the time points of 6, 12, 24, 36, 48, and 60 hpi for a real-time PCR detection assay for IBV N gene as described above. Collectively, these results demonstrate the successful rescue of the pathogenic IBV strain YN from cloned cDNA by using electroporation of full-length IBV in vitro transcripts into N-protein expressing cells and subsequent virus amplification in the allantoic cavities of ECE. abstract: In this study, a pathogenic avian infectious bronchitis virus (IBV) QX-type strain YN was successfully rescued by vaccinia virus based reverse genetic technology. Ten fragments contiguously spanning the complete IBV genome were amplified and cloned into the vaccinia virus genome by homologous recombination. The full-length genomic cDNA was transcribed in vitro, and its transcript was transfected into BHK-21/N cells that could stably express IBV N protein. At 48 h post transfection, the culture medium was harvested and inoculated into 10-day-old specific-pathogen-free embryonated chicken eggs to replicate the rescued virus. This strategy was chosen to facilitate the rescue procedure and to ensure that the recombinant rYN virus will not require any cell culture adaptations. After only one in ovo passage, the recombinant YN virus (rYN) was successfully recovered and confirmed to possess the introduced silent marker mutation in its genome. Biological characteristics of rYN such as the EID(50), TCID(50), replication in ovo, and replication kinetcs in vitro were tested and all were similar to its parental strain YN. Our findings demonstrate the successful construction of highly-pathogenic QX-type IBV using a modified rescue procedure, allowing for future studies of the molecular biology and pathogenicity of IBV field strains. url: https://www.ncbi.nlm.nih.gov/pubmed/31430502/ doi: 10.1016/j.virusres.2019.197726 id: cord-290802-761wqgbe author: Zhao, Zheng title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery date: 2020-09-18 words: 3890.0 sentences: 237.0 pages: flesch: 51.0 cache: ./cache/cord-290802-761wqgbe.txt txt: ./txt/cord-290802-761wqgbe.txt summary: title: Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus. In sum, structurally, SARS-CoV-2 has high global/ core structural similarity to the RDRP catalytic domains of all other RNA viruses, which provides an opportunity for structure-based COVID-19 drug design and repurposing, noting that keys differences lie in the subtle details. According to the similarity of functionsite interaction fingerprints over all complexes, it was possible to divide the binding modes into four classes, where each class contains multiple PDB structures from different kinds of viruses (Table 1) . abstract: [Image: see text] The coronavirus disease of 2019 (COVID-19) pandemic speaks to the need for drugs that not only are effective but also remain effective given the mutation rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To this end, we describe structural binding-site insights for facilitating COVID-19 drug design when targeting RNA-dependent RNA polymerase (RDRP), a common conserved component of RNA viruses. We combined an RDRP structure data set, including 384 RDRP PDB structures and all corresponding RDRP–ligand interaction fingerprints, thereby revealing the structural characteristics of the active sites for application to RDRP-targeted drug discovery. Specifically, we revealed the intrinsic ligand-binding modes and associated RDRP structural characteristics. Four types of binding modes with corresponding binding pockets were determined, suggesting two major subpockets available for drug discovery. We screened a drug data set of 7894 compounds against these binding pockets and presented the top-10 small molecules as a starting point in further exploring the prevention of virus replication. In summary, the binding characteristics determined here help rationalize RDRP-targeted drug discovery and provide insights into the specific binding mechanisms important for containing the SARS-CoV-2 virus. url: https://www.ncbi.nlm.nih.gov/pubmed/32946692/ doi: 10.1021/acs.jproteome.0c00623 id: cord-273711-bxijla09 author: Zhao, Zhixun title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells date: 2012-02-17 words: 4172.0 sentences: 242.0 pages: flesch: 53.0 cache: ./cache/cord-273711-bxijla09.txt txt: ./txt/cord-273711-bxijla09.txt summary: title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells When Vero cells were transfected with shRNA expression vectors (p61/GFP, p70/GFP, p165/GFP and p296/GFP) and then infected with GTPV, GTPV-ORF095-70 was found to be the most effective inhibition site in decreasing cytopathic effect (CPE) induced by GTPV. These results suggest that the siRNA generated by in vitro transcription effectively and specifically inhibit the expression of GTPV ORF095 conserved regions in BHK-21 cells. To investigate whether or not knockout of ORF095 relieves cytopathic effect (CPE) induced by GTPV, Vero cells were transfected by plasmids expressing ORF095 protein-targeted shRNAs (p61/GFP, p70/GFP, p165/GFP and p296/GFP), respectively. Therefore, ORF095 gene is a good target to suppress GTPV replication by RNAi. In conclusion, this study demonstrates that vector-based shRNA methodology can effectively inhibit GTPV replication on Vero cells. RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells abstract: BACKGROUND: Goatpox is an economically important disease in goat and sheep-producing areas of the world. Many vaccine strategies developed to control the disease are not yet completely successful. Hairpin expression vectors have been used to induce gene silencing in a large number of studies on viruses. However, none of these studies has been attempted to study GTPV. In the interest of exploiting improved methods to control goat pox, it is participated that RNAi may provide effective protection against GTPV. In this study we show the suppression of Goatpox virus (GTPV) replication via knockdown of virion core protein using RNA interference. RESULTS: Four short interfering RNA (siRNA) sequences (siRNA-61, siRNA-70, siRNA-165 and siRNA-296) against a region of GTPV ORF095 were selected. Sense and antisense siRNA-encoding sequences separated by a hairpin loop sequence were designed as short hairpin RNA (shRNA) expression cassettes under the control of a human U6 promoter. ORF095 amplicon was generated using PCR, and then cloned into pEGFP-N1 vector, named as p095/EGFP. p095/EGFP and each of the siRNA expression cassettes (p61, p70, p165 and p296) were co-transfected into BHK-21 cells. Fluorescence detection, flow cytometric analysis, retro transcription PCR (RT-PCR) and real time PCR were used to check the efficiency of RNAi. The results showed that the ORF095-specific siRNA-70 effectively down-regulated the expression of ORF095. When Vero cells were transfected with shRNA expression vectors (p61/GFP, p70/GFP, p165/GFP and p296/GFP) and then infected with GTPV, GTPV-ORF095-70 was found to be the most effective inhibition site in decreasing cytopathic effect (CPE) induced by GTPV. The results presented here indicated that DNA-based siRNA could effectively inhibit the replication of GTPV (approximately 463. 5-fold reduction of viral titers) on Vero cells. CONCLUSIONS: This study demonstrates that vector-based shRNA methodology can effectively inhibit GTPV replication on Vero cells. Simultaneously, this work represents a strategy for controlling goatpox, potentially facilitating new experimental approaches in the analysis of both viral and cellular gene functions during of GTPV infection. url: https://www.ncbi.nlm.nih.gov/pubmed/22340205/ doi: 10.1186/1743-422x-9-48 id: cord-025181-eg108wcd author: Zheng, Zhihang title: Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate date: 2020-05-25 words: 5919.0 sentences: 340.0 pages: flesch: 59.0 cache: ./cache/cord-025181-eg108wcd.txt txt: ./txt/cord-025181-eg108wcd.txt summary: In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. Further, we compared the infectivity of these two viral variants in a self-limited infection model, in which type I IFN receptor of wild-type Balb/c mice had been transiently blocked before infection, and found only the virus strain exhibiting larger plaque size caused infectious viral particles in sera. We have recently developed a ZIKV infection model in Balb/c mice with transient blockage of type I IFN Fig. 2 Phylogenetic analysis of DENV-2 1D4-5-SP and DENV-2 8H2-7-LP with representative serotype-2 dengue viruses of different genotypes isolated from different geographical regions. abstract: Dengue virus (DENV) is a single-stranded RNA virus transmitted by mosquitoes in tropical and subtropical regions. It causes dengue fever, dengue hemorrhagic fever and dengue shock syndrome in patients. Each year, 390 million people are estimated to be infected by four serotypes of dengue virus, creating a great burden on global public health and local economy. So far, no antiviral drug is available for dengue disease, and the newly licensed vaccine is far from satisfactory. One large obstacle for dengue vaccine and drug development is the lack of suitable small animal models. Although some DENV infection models have been developed, only a small number of viral strains can infect immunodeficient mice. In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. This study not only offers new small animal models of dengue viral infection, but also provides new viral variants for further investigations on dengue viral pathogenesis. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246292/ doi: 10.1007/s12250-020-00229-y id: cord-351520-c5fi2uoh author: Zhong, Bo title: Regulation of virus-triggered type I interferon signaling by cellular and viral proteins date: 2010-02-01 words: 10571.0 sentences: 637.0 pages: flesch: 46.0 cache: ./cache/cord-351520-c5fi2uoh.txt txt: ./txt/cord-351520-c5fi2uoh.txt summary: Recently, we and others identified a new adapter protein called mediator of IRF3 activation (MITA, also known as STING), which plays a critical role in virus-induced type I IFN expression (Ishikawa and Barber, 2008; Zhong et al., 2008) . abstract: Host pattern recognition receptors (PRRs) recognize invading viral pathogens and initiate a series of signaling cascades that lead to the expression of type I interferons (IFNs) and inflammatory cytokines. During the past decade, significant progresses have been made to characterize PRRs such as Toll-like receptors (TLRs) and RIG-I-like receptors (RLRs) and elucidate the molecular mechanisms of TLR- and RLR-mediated signaling. To avoid excessive and harmful immune effects caused by over-activation of these signaling pathways, host cells adopt a number of strategies to regulate them. In addition, invading viruses also employ a variety of mechanisms to inhibit the production of type I IFNs, thereby evading the supervision and clearance by the host. In this review, we briefly summarize the TLR- and RLR-mediated type I IFN signaling and then focus on the mechanisms by which host cellular and viral components regulate the expression of type I IFNs. url: https://doi.org/10.1007/s11515-010-0013-x doi: 10.1007/s11515-010-0013-x id: cord-013171-wgn529rc author: Zhong, Yi title: STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway date: 2020-09-16 words: 6746.0 sentences: 410.0 pages: flesch: 50.0 cache: ./cache/cord-013171-wgn529rc.txt txt: ./txt/cord-013171-wgn529rc.txt summary: title: STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway They extended this analysis to multiple cell types of diverse origin, including human embryonic STAU1 selectively regulates the expression of inflammatory and immune response genes and alternative splicing of the nerve growth factor receptor signaling pathway carcinoma stem cells (NT2), mouse neural progenitor cells (N2A), human retinal epithelial cells (ARPE19), and primary mouse embryonic fibroblasts (MEFs). RASEs detected by qPCR were consistent with those by RNA-seq, which demonstrated that STAU1 may play a significant regulatory role in the AS of ''nerve growth factor receptor signaling pathway''. In addition, the AS of multiple genes was also regulated by STAU1, and the main enriched pathways not only include ''retrograde transport'' and ''muscle cell differentiation'', but also the ''nerve growth factor receptor signaling pathway''. abstract: Double-stranded RNA-binding protein Staufen homolog 1 (STAU1) is a highly conserved multifunctional double-stranded RNA-binding protein, and is a key factor in neuronal differentiation. RNA sequencing was used to analyze the overall transcriptional levels of the upregulated cells by STAU1 and control cells, and select alternative splicing (AS). It was determined that the high expression of STAU1 led to changes in the expression levels of a variety of inflammatory and immune response genes, including IFIT2, IFIT3, OASL, and CCL2. Furthermore, STAU1 was revealed to exert a significant regulatory effect on the AS of genes related to the ‘nerve growth factor receptor signaling pathway’. This is of significant importance for neuronal survival, differentiation, growth, post-damage repair, and regeneration. In conclusion, overexpression of STAU1 was associated with immune response and regulated AS of pathways related to neuronal growth and repair. In the present study, the whole transcriptome of STAU1 expression was first analyzed, which laid a foundation for further understanding the key functions of STAU1. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551455/ doi: 10.3892/or.2020.7769 id: cord-294363-bv6xa8v8 author: Zhou, Hong title: Potential Therapeutic Targets and Promising Drugs for Combating SARS‐CoV‐2 date: 2020-05-05 words: 8902.0 sentences: 456.0 pages: flesch: 46.0 cache: ./cache/cord-294363-bv6xa8v8.txt txt: ./txt/cord-294363-bv6xa8v8.txt summary: Several studies demonstrated angiotensin converting enzyme 2 (ACE2) as an important therapeutic target of SARS-CoV-2 entry and infection, and many potential targets were subsequently proposed, such as the spike (S) protein and transmembrane serine protease 2 (TMPRSS2). Therefore, accelerating research for potential therapeutic target confirmation, promising drug discovery, and clinical verification development will speed up efforts to combat SARS-CoV-2. In addition to inhibiting the virus directly, ASOs are also expected to target the disease-related proteins involved in the inflammatory cytokine storm process, which could be considered a promising therapeutic strategy for combating SARS-CoV-2 . Although many strategies have been used to block the attachment, entry, replication and release processes to inhibit SARS-CoV-2 infection, how to prevent viral evasion from host immune responses and virus-induced cytopathic effects is considered one of the most urgent problems that need to be solved in SARS-CoV-2-induced pneumonia-associated respiratory syndrome (PARS) patients. abstract: As of April 9, 2020, a novel coronavirus (SARS‐CoV‐2) had caused 89,931 deaths and 1,503,900 confirmed cases worldwide, which indicates an increasingly severe and uncontrollable situation. Initially, little was known about the virus. As research continues, we have learned the genome structure, epidemiological and clinical characteristics and pathogenic mechanisms of SARS‐CoV‐2. Based on these discoveries, identifying potential targets involved in the processes of virus pathogenesis is urgently needed, and discovering or developing promising drugs based on potential targets is the most pressing need. Therefore, we summarize the potential therapeutic targets involved in virus pathogenesis and discuss the advancements, possibilities and significance of promising drugs based on these targets for treating SARS‐CoV‐2. This review will facilitate the identification of potential targets and provide promising clues for drug development that can be translated into clinical applications for combating SARS‐CoV‐2. url: https://www.ncbi.nlm.nih.gov/pubmed/32368792/ doi: 10.1111/bph.15092 id: cord-284549-edliu3it author: Zhou, Hui title: Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells date: 2019-11-27 words: 4697.0 sentences: 289.0 pages: flesch: 62.0 cache: ./cache/cord-284549-edliu3it.txt txt: ./txt/cord-284549-edliu3it.txt summary: In this study, we screened all the nonstructural proteins of HCV and found that HCV NS2 could suppress RNAi induced either by small hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) in mammalian cells. In this study, we uncovered that HCV nonstructural NS2 protein possessed a potent in vitro VSR activity that suppressed the RNAi induced by short hairpin RNA (shRNA) and siRNA in mammalian cells. Our results showed that the reversal effect of EGFP silencing could be observed at 48 hpt (Fig. 2C) , indicating that the VSR activity was dependent on the expression level of HCV NS2 protein. To investigate whether HCV NS2 can inhibit this step, small RNAs harvested from HEK293T cells co-expressing EGFP-specific shRNA together with NS2 were subjected to Northern blotting with a DIG-labeled RNA probe targeting EGFP siRNA produced from shRNA by Dicer. abstract: RNAi interference (RNAi) is an evolutionarily conserved post-transcriptional gene silencing mechanism and has been well recognized as an important antiviral immunity in eukaryotes. Numerous viruses have been shown to encode viral suppressors of RNAi (VSRs) to antagonize antiviral RNAi. Hepatitis C virus (HCV) is a medically important human pathogen that causes acute and chronic hepatitis. In this study, we screened all the nonstructural proteins of HCV and found that HCV NS2 could suppress RNAi induced either by small hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) in mammalian cells. Moreover, we demonstrated that NS2 could suppress RNAi via its direct interaction with double-stranded RNAs (dsRNAs) and siRNAs, and further identified that the cysteine 184 of NS2 is required for the RNAi suppression activity through a serial of point mutation analyses. Together, our findings uncovered that HCV NS2 can act as a VSR in vitro, thereby providing novel insights into the life cycle and virus-host interactions of HCV. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12250-019-00182-5) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12250-019-00182-5 doi: 10.1007/s12250-019-00182-5 id: cord-344410-yo9libo0 author: Zhou, Yan title: Mutational analysis of the SDD sequence motif of a PRRSV RNA-dependent RNA polymerase date: 2011-09-16 words: 5856.0 sentences: 295.0 pages: flesch: 57.0 cache: ./cache/cord-344410-yo9libo0.txt txt: ./txt/cord-344410-yo9libo0.txt summary: A core palm structure containing the four motifs (A-D) found in all classes of polymerases [1] is present in the C-terminal region of nsp9; therefore, it is possible to identify RdRp catalytic activity by testing whether the conserved SDD motif (at residues 3050 to 3052 of nsp9) itself is essential for virus replication (Figure 1) . To study the impact of mutations in the SDD motif on PRRSV transcription, RT-PCR analysis of the sg mRNA7s was performed on the total RNAs obtained from mock-transfected BHK-21 cells and cells transfected with pMDD, pSAD, pSED, pSND, pSGD, pSDA, pSDE, pSDN, pSGA, pGND, pGDD, and pAPRRS, using a forward primer located in the leader region and a reverse primer in ORF7. The mutant PRRSV full-length cDNA clones pMDD, pSAD, pSED, pSND, pSGD, pSDA, pSDE, pSDN, pGDN, and pSGA carrying mutations specifying the SDD motif in the viral replicase (Table 1) , were transfected into BHK-21 cells and failed to produce sg mRNA7s (Figure 2) . abstract: The subgenomic mRNA transcription and genomic replication of the porcine reproductive and respiratory syndrome virus (PRRSV) are directed by the viral replicase. The replicase is expressed in the form of two polyproteins and is subsequently processed into smaller nonstructural proteins (nsps). nsp9, containing the viral replicase, has characteristic sequence motifs conserved among the RNA-dependent RNA polymerases (RdRp) of positive-strand (PS) RNA viruses. To test whether the conserved SDD motif can tolerate other conserved motifs of RNA viruses and the influence of every residue on RdRp catalytic activity, many amino acids substitutions were introduced into it. Only one nsp9 substitution, of serine by glycine (S3050G), could rescue mutant viruses. The rescued virus was genetically stable. Alteration of either aspartate residue was not tolerated, destroyed the polymerase activity, and abolished virus transcription, but did not eliminate virus replication. We also found that the SDD motif was essentially invariant for the signature sequence of PRRSV RdRp. It could not accommodate other conserved motifs found in other RNA viral polymerases, except the GDD motif, which is conserved in all the other PS RNA viruses. These findings indicated that nidoviruses are evolutionarily related to other PS RNA viruses. Our studies support the idea that the two aspartate residues of the SDD motif are critical and essential for PRRSV transcription and represent a sequence variant of the GDD motif in PS RNA viruses. url: https://www.ncbi.nlm.nih.gov/pubmed/21922433/ doi: 10.1007/s11427-011-4216-4 id: cord-323973-wszo9s3d author: Zhu, Hanliang title: The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond date: 2020-07-20 words: 9784.0 sentences: 493.0 pages: flesch: 50.0 cache: ./cache/cord-323973-wszo9s3d.txt txt: ./txt/cord-323973-wszo9s3d.txt summary: [9] The analysis of larger volumes of biological fluids with a low viral load is likely to reduce the risk of false-negative results, but microfluidic point-of-care (POC) devices are typically unable to handle mL-scale volumes in a short time due to the requirement of slow flow rates. [15] The PCR test on samples prepared from blood and urine specimens is capable of detecting the virus in the early stages of the disease, resulting in early diagnosis and subsequent isolation of infected patients to block transmission. The total reaction time depends on a series of parameters, such as the chip size, the PCR master mix volume determining the value of C, the thermal conductivity of the substrate (G), and the temperature cycling rate. A number of fully integrated systems have so far been developed, starting with the non-portable GenExpert from Cepheid, which was first utilized for anthrax detection by the United States Postal Service, [64] and then with different primers to perform HIV and tuberculosis diagnostics in South Africa. abstract: Infectious diseases, such as the most recent case of COVID-19, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfilling this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis. url: https://api.elsevier.com/content/article/pii/S0165993620302132 doi: 10.1016/j.trac.2020.115984 id: cord-035110-5lkzhjfh author: Zhu, Le title: Isolation and characterization of exosomes for cancer research date: 2020-11-10 words: 14672.0 sentences: 743.0 pages: flesch: 34.0 cache: ./cache/cord-035110-5lkzhjfh.txt txt: ./txt/cord-035110-5lkzhjfh.txt summary: Another study reported that triple-negative breast cancer (TNBC) cells can activate stromal cells by releasing exosomes containing unshielded RNAs that mimic viral components to co-opt anti-viral immune responses, thereby promoting tumor growth [115] . Furthermore, CAF-derived exosomes contain intact metabolites, including amino acids, lipids, and TCA-cycle intermediates, which are internalized by prostate cancer cells to promote tumor growth [122] . EGFR carried in exosomes secreted from gastric cancer cells can be delivered to the liver and integrated into the plasma membrane of liver stromal cells, thus favoring the development of a liver-like microenvironment and promoting liver-specific metastasis [147] . In addition, abundant studies have demonstrated that tumor-derived exosomes can modulate the cell biology of MDSCs, including increasing their expansion, promoting their activation, and enhancing their immunosuppressive function [162] . Tumor-associated macrophages-derived exosomes promote the migration of gastric cancer cells by transfer of functional Apolipoprotein E abstract: Exosomes are a subset of extracellular vesicles that carry specific combinations of proteins, nucleic acids, metabolites, and lipids. Mounting evidence suggests that exosomes participate in intercellular communication and act as important molecular vehicles in the regulation of numerous physiological and pathological processes, including cancer development. Exosomes are released by various cell types under both normal and pathological conditions, and they can be found in multiple bodily fluids. Moreover, exosomes carrying a wide variety of important macromolecules provide a window into altered cellular or tissue states. Their presence in biological fluids renders them an attractive, minimally invasive approach for liquid biopsies with potential biomarkers for cancer diagnosis, prediction, and surveillance. Due to their biocompatibility and low immunogenicity and cytotoxicity, exosomes have potential clinical applications in the development of innovative therapeutic approaches. Here, we summarize recent advances in various technologies for exosome isolation for cancer research. We outline the functions of exosomes in regulating tumor metastasis, drug resistance, and immune modulation in the context of cancer development. Finally, we discuss prospects and challenges for the clinical development of exosome-based liquid biopsies and therapeutics. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652679/ doi: 10.1186/s13045-020-00987-y id: cord-310268-8q4tk6fd author: Zhu, Qinchang title: DNA Aptamers in the Diagnosis and Treatment of Human Diseases date: 2015-11-25 words: 8649.0 sentences: 411.0 pages: flesch: 47.0 cache: ./cache/cord-310268-8q4tk6fd.txt txt: ./txt/cord-310268-8q4tk6fd.txt summary: Nucleic acid aptamers are RNA and single-stranded (ss) DNA oligonucleotides with lengths typically ranging from 15 to 70 mers, which have the same level of target-binding affinity as monoclonal antibodies (the dissociation constant (K d ) usually ranges from 0.1 to 50 nM) [5, 6] . This SELEX is able to generate DNA aptamers that recognize the cell-surface or intracellular target protein in their native conformation, which shows great potential in cell-specific therapeutics and diagnostic applications [26] [27] [28] . Recently, modified cell-SELEX methods have been developed to select aptamers targeting specific cells like disease state cells and metastatic cells. In the era of personalized medicine, DNA aptamer-based therapeutics and diagnostics are believed to have great potential for extensive application because of their flexibility to specifically bind to any molecule targets. abstract: Aptamers have a promising role in the field of life science and have been extensively researched for application as analytical tools, therapeutic agents and as vehicles for targeted drug delivery. Compared with RNA aptamers, DNA aptamers have inherent advantages in stability and facility of generation and synthesis. To better understand the specific potential of DNA aptamers, an overview of the progress in the generation and application of DNA aptamers in human disease diagnosis and therapy are presented in this review. Special attention is given to researches that are relatively close to practical application. DNA aptamers are expected to have great potential in the diagnosis and treatment of human diseases. url: https://www.ncbi.nlm.nih.gov/pubmed/26610462/ doi: 10.3390/molecules201219739 id: cord-346138-ip42zcld author: Zhurakivska, Khrystyna title: An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens date: 2020-08-20 words: 3947.0 sentences: 211.0 pages: flesch: 56.0 cache: ./cache/cord-346138-ip42zcld.txt txt: ./txt/cord-346138-ip42zcld.txt summary: The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. Several authors therefore suppose an infection of the gastrointestinal tract by the virus (11, 24) , with its continuous elimination with the feces which has been reported to last from 1 to 12 days (24) and in some cases, viral RNA were detected in feces or anal swabs even after the respiratory tests became negative (11, 22, 24) . The reference method for testing positivity to SARS-CoV-2 infection is represented by the pharyngeal swab that is taken from the patient''s nasopharynx or oropharynx and, through an RT-PCR analyzed for the presence of viral RNA (8) . abstract: Coronavirus disease 2019 quickly spread in China and has, since March 2020 become a pandemic, causing hundreds of thousands of deaths worldwide. The causative agent was promptly isolated and named SARS-CoV-2. Scientific efforts are related to identifying the best clinical management of these patients, but also in understanding their infectivity in order to limit the spread of the virus. Aimed at identifying viral RNA in the various compartments of the organism of sick subjects, diagnostic tests are carried out. However, the accuracy of such tests varies depending on the type of specimen used and the time of illness at which they are performed. This review of the literature aims to summarize the preliminary findings reported in studies on Covid-19 testing. The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. It highlights that most patients already reach the peak of the viral load in the upper airways within the first days of displaying symptoms, which thereafter tend to decrease. This suggests that many patients may already be infectious before symptoms start to appear. url: https://www.ncbi.nlm.nih.gov/pubmed/32974267/ doi: 10.3389/fpubh.2020.00487 id: cord-349417-vn7q8wc4 author: Ziebuhr, John title: The Coronavirus Replicase: Insights into a Sophisticated Enzyme Machinery date: 2006 words: 3379.0 sentences: 179.0 pages: flesch: 45.0 cache: ./cache/cord-349417-vn7q8wc4.txt txt: ./txt/cord-349417-vn7q8wc4.txt summary: Activation of the coronavirus replication complex involves extensive proteolytic processing of the replicase polyproteins to produce 16 (in IBV: 15) mature products called nonstructural proteins (nsp) 1 to 16 (reviewed in Refs. The N-terminal regions of the coronavirus polyproteins, which are poorly conserved among the coronavirus groups I, II, and III, are cleaved at two (in IBV) or three sites (in all other coronaviruses) by one (IBV and SARS-CoV) or two zinc-finger-containing papain-like cysteine proteases called PL1 pro and PL2 pro . The observed pattern of conservation in different nidovirus families suggests a functional hierarchy for the newly identified RNA-processing activities, with the manganese ion-dependent uridylate-specific endoribonuclease, NendoU, playing a central role. Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity The nsp2 replicase proteins of murine hepatitis virus and severe acute respiratory syndrome coronavirus are dispensable for viral replication abstract: nan url: https://www.ncbi.nlm.nih.gov/pubmed/17037497/ doi: 10.1007/978-0-387-33012-9_1 id: cord-318478-fn0gcxbb author: Ziv, Omer title: The short- and long-range RNA-RNA Interactome of SARS-CoV-2 date: 2020-10-07 words: 5760.0 sentences: 343.0 pages: flesch: 56.0 cache: ./cache/cord-318478-fn0gcxbb.txt txt: ./txt/cord-318478-fn0gcxbb.txt summary: Available models for the RNA structure of SARS-CoV-2 and related viruses are largely confined to short-distance base-pairing which result in local folding of important cis-acting elements (Andrews et al., 2020; Huston et al., 2020; Kelly et al., 2020; Lan et al., 2020; Manfredonia et al., 2020; Ryder, 2020; Sanders et al., 2020; Sun et al., 2020) . In addition to the canonical UTR structures, we provide here a direct in vivo evidence for genome cyclization in SARS-CoV-2, mediated by long-range base-pairing between the 5′ and 3′ UTRs ( Figures 5B and S4B ). The long-distance RNA structure map for SARS-CoV-2 provides a practical starting point to dissect the regulation of discontinuous transcription, as it identifies cis-acting elements that interact with each other to create genome topologies that favour the synthesis of the ensemble of sgmRNAs. RNA viruses evolve sophisticated mechanisms to enhance the functional capacity of their size-restricted genomes and to regulate the expression levels of their replicase components. abstract: The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells, and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction - the FSE-arch - that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses, and will aid future efforts to develop antiviral strategies. url: https://doi.org/10.1101/2020.07.19.211110 doi: 10.1101/2020.07.19.211110 id: cord-035067-ic843wr9 author: de Almeida, Joana Ferro Machado title: COVID-19 and the gastrointestinal tract: what do we already know? date: 2020-11-05 words: 5453.0 sentences: 336.0 pages: flesch: 56.0 cache: ./cache/cord-035067-ic843wr9.txt txt: ./txt/cord-035067-ic843wr9.txt summary: Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools. Information on country of origin, mean age, different comorbidities, typical symptoms (fever, cough, and dyspnea, among others), gastrointestinal symptoms (diarrhea, nausea, vomiting, and abdominal pain), and the presence of viral RNA in feces, when cited, were included in this study for analysis. (19) According to the descriptive, cross-sectional, multicenter study (three hospitals in Hubei, China) by Pan et al., with 204 patients, in which 107 were male, mean age of 52.91±15.98 years, 103 (50.5%) reported some gastrointestinal symptom, such as lack of appetite (81; 78.6%), diarrhea (35; 34.0%), vomiting (4; 3.9%), and abdominal pain (2; 1.9%). (26) Cipriano et al., conducted a systematic review with six studies of patients from China, which points to the possibility of SARS-CoV-2 infection in the gastrointestinal tract and fecal-oral transmission. abstract: The new coronavirus disease pandemic is defining 2020, with almost 17.5 million infected individuals and 700 thousand deaths up to beginning of August. It is caused by SARS-CoV-2 and the transmission is through the respiratory tract. Those infected may be asymptomatic, present typical symptoms (fever, dry cough and dyspnea), gastrointestinal symptoms (diarrhea, nausea, vomiting and abdominal pain) and viral RNA in stools. The objective of this work was to review the literature related to the prevalence of gastrointestinal symptoms, and to check the possibility of fecal-oral transmission. We searched PubMed(®) database on COVID-19 and gastrointestinal tract and selected articles using the PRISMA method. We eliminated articles based on titles and abstracts, small number of patients and the mechanism of infection, leaving 14 studies. Comorbidities and laboratory alterations (elevation of hepatic aminotransferases and bilirubin) were related to worsening of the disease. The prevalence of gastrointestinal symptoms ranged from 6.8% to 61.3%, including diarrhea (8.14% to 33.7%), nausea/vomiting (1.53% to 26.4%), anorexia (12.1% to 40.0%) and abdominal pain (0% to 14.5%). The presence of viral RNA in stools was rarely tested, but positive in 0% to 48.1%. The gastrointestinal tract is affected by COVID-19, causing specific symptoms, laboratory alterations and viral presence in the feces. However, the results of prevalence and possibility of fecal-oral transmission were varied, requiring further studies for more assertive conclusions. It is important that healthcare professionals draw attention to this fact, since these changes can help make diagnosis and initiate early treatment. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7647386/ doi: 10.31744/einstein_journal/2020rw5909 id: cord-259233-smmhhroe author: de Armas‐Rillo, Laura title: Membrane dynamics associated with viral infection date: 2016-01-28 words: 7086.0 sentences: 374.0 pages: flesch: 40.0 cache: ./cache/cord-259233-smmhhroe.txt txt: ./txt/cord-259233-smmhhroe.txt summary: Several RNA viruses induce the formation of these autophagosome-like vesicles (also referred to as DMVs) to enhance viral replication and non-lytic egression, such as poliovirus and CVB3, HIV-1 and HCV. Indeed, autophagosome-like vesicles may represent a trafficking pathway for these viruses, connecting to multivesicular bodies (MVBs), and assuring virus assembly and budding at the cell surface while protecting them from intrinsic antiviral factors and immune responses. Trogocytosis involves the exchange of cell surface membrane patches that may contain receptor clusters associated to viral particles, while exosomes are vesicles formed from MVBs that could participate in viral infection and spreading between cells of the Alphavirus group of this family [12] , couple their RNA synthesis to endosome and lysosome membranes modified by the association of virus specific components. It remains unclear how proteins from distinct viruses and host cells use the same intracellular membrane compartments or events (e.g. autophagy) to achieve viral replication, without affecting important cellular processes. abstract: Viral replication and spreading are fundamental events in the viral life cycle, accounting for the assembly and egression of nascent virions, events that are directly associated with viral pathogenesis in target hosts. These processes occur in cellular compartments that are modified by specialized viral proteins, causing a rearrangement of different cell membranes in infected cells and affecting the ER, mitochondria, Golgi apparatus, vesicles and endosomes, as well as processes such as autophagic membrane flux. In fact, the activation or inhibition of membrane trafficking and other related activities are fundamental to ensure the adequate replication and spreading of certain viruses. In this review, data will be presented that support the key role of membrane dynamics in the viral cycle, especially in terms of the assembly, egression and infection processes. By defining how viruses orchestrate these events it will be possible to understand how they successfully complete their route of infection, establishing viral pathogenesis and provoking disease. © 2015 The Authors Reviews in Medical Virology Published by John Wiley & Sons, Ltd. url: https://www.ncbi.nlm.nih.gov/pubmed/26817660/ doi: 10.1002/rmv.1872 id: cord-354510-jlg5je0s author: de Carvalho, A. F. title: THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL date: 2020-06-20 words: 4112.0 sentences: 234.0 pages: flesch: 58.0 cache: ./cache/cord-354510-jlg5je0s.txt txt: ./txt/cord-354510-jlg5je0s.txt summary: Methods Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. 13 Here we describe the use of a simple, virus-inactivating and denaturing solution as part of a swab collection kit, aiming to decrease the infectious potential of the clinical sample and, at the same time, to preserve highly frail RNA molecules during transportation and short-term storage before testing. In order to increase personnel safety, to avoid losing collaborators due to infections by SARS-CoV-2, and at the same time to increase preservation of the RNA contained in clinical samples, we introduced the use of the guanidinecontaining solution as collection and transport media instead of commonly used viral transport media (VTM). abstract: Background Since the emergence of the COVID-19, health officials have struggled to devise strategies to counteract the speed of the pandemic's spread across the globe. It became imperative to implement accurate diagnostic tests for the detection of SARS-CoV-2 RNA on respiratory samples. In many places, however, besides the limited availability of test reagents, laboratory personnel face the challenge of adapting their working routines to manipulate highly infective clinical samples. Here, we proposed the use of a virus-inactivating solution as part of a sample collection kit to decrease the infectious potential of the collected material without affecting the integrity of RNA samples used in diagnostic tests based on RT-qPCR. Methods Nasopharyngeal and oropharyngeal swab samples were collected from SARS-CoV-2-infected patients and from laboratory personnel using a commercially available viral transport solution (VTM) and the denaturing solution (DS) described here. RNA extracted from all samples was tested by RT-qPCR using probes for viral and human genes. Exposure of laboratory personnel to infective viruses was also accessed using ELISA tests. Findings The use of the DS did not interfere with the detection of viral genome or the endogenous human mRNA, since similar results were obtained from samples collected with VTM or DS. In addition, all tests of laboratory personnel for the presence of viral RNA and IgG antibodies against SARS-CoV-2 were negative. Interpretation The methodology described here provides a strategy that allow high diagnostic accuracy as well as safe manipulation of clinical samples by those involved with diagnostic procedures. Funding: CAPES, FAPEMIG, CNPq, MCTIC, FIOCRUZ and the UK Global Challenges Research Fund (GCRF). url: https://doi.org/10.1101/2020.06.18.20134304 doi: 10.1101/2020.06.18.20134304 id: cord-256510-orr2roxz author: de Castro, Isabel Fernández title: Virus factories: biogenesis and structural design date: 2012-10-04 words: 5188.0 sentences: 259.0 pages: flesch: 43.0 cache: ./cache/cord-256510-orr2roxz.txt txt: ./txt/cord-256510-orr2roxz.txt summary: For example, transmission electron microscopy (TEM) of cells infected with coxsackievirus showed intracellular organized lattices (Fig. 1E) , very similar to those assembled by the viral RNA polymerase in vitro (Kemball et al., 2010) close relationship between self-interaction and replication activity is reported for viral polymerases of other viruses such as FHV (Dye et al., 2005) , hepatitis C virus (Qin et al., 2002) and RUBV (Risco et al., 2012) . For viral genome replication, the virus first assembles cytoplasmic mini-nuclei with attached mitochondria (Tolonen et al., 2001) ; virus morphogenesis then starts an aggresome-like structure (Risco et al., 2002) , where immature viruses assemble using an atypical membrane remodelling mechanism that has been characterized by ET (Chlanda et al., 2009) . Although we are beginning to understand how replication organelles are assembled, information is still limited about how cell organelles are recruited, about the mechanisms of macromolecular transport between compartments, and about the signals that regulate the major structural changes in the factory during distinct stages in the virus life cycle. abstract: Replication and assembly of many viruses occur in specific intracellular compartments known as ‘virus factories’. Our knowledge of the biogenesis and architecture of these unique structures has increased considerably in the last 10 years, due to technical advances in cellular, molecular and structural biology. We now know that viruses build replication organelles, which recruit cell and viral components in a macrostructure in which viruses assemble and mature. Cell membranes and cytoskeleton participate in the biogenesis of these scaffolds and mitochondria are present in many factories, where they might supply energy and other essential factors. New inter‐organelle contacts have been visualized within virus factories, whose structure is very dynamic, as it changes over time. There is increasing interest in identifying the factors involved in their biogenesis and functional architecture, and new microscopy techniques are helping us to understand how these complex entities are built and work. In this review, we summarize recent findings on the cell biology, biogenesis and structure of virus factories. url: https://www.ncbi.nlm.nih.gov/pubmed/22978691/ doi: 10.1111/cmi.12029 id: cord-269011-230p8rsf author: de Haan, Cornelis A.M. title: Molecular Interactions in the Assembly of Coronaviruses date: 2005-08-31 words: 22956.0 sentences: 1052.0 pages: flesch: 46.0 cache: ./cache/cord-269011-230p8rsf.txt txt: ./txt/cord-269011-230p8rsf.txt summary: Biochemical and theoretical studies led to a topological model for the MHV M protein Rottier et al., 1984 Rottier et al., , 1986 , in which the polypeptide spans the lipid bilayer three times, leaving a small amino-terminal domain (15-35 residues) in the lumen of intracellular organelles (or outside the virus), whereas the carboxyterminal half of the protein is located on the cytoplasmic side of the membrane (or inside the virion). Using a mutational approach including deletions, insertions, and substitutions, both the transmembrane domain and the cysteine-rich region immediately downstream thereof, but not the carboxy-terminal part of the cytoplasmic tail, were shown to be important for MHV S protein-induced cell-cell fusion (Bos et al., 1995; Chang and Gombold, 2001; Chang et al., 2000) The cleavage requirements of the S proteins for the biological activities of the coronavirus spike remain enigmatic. abstract: This chapter describes the interactions between the different structural components of the viruses and discusses their relevance for the process of virion formation. Two key factors determine the efficiency of the assembly process: intracellular transport and molecular interactions. Many viruses have evolved elaborate strategies to ensure the swift and accurate delivery of the virion components to the cellular compartment(s) where they must meet and form (sub) structures. Assembly of viruses starts in the nucleus by the encapsidation of viral DNA, using cytoplasmically synthesized capsid proteins; nucleocapsids then migrate to the cytosol, by budding at the inner nuclear membrane followed by deenvelopment, to pick up the tegument proteins. url: https://www.sciencedirect.com/science/article/pii/S0065352705640067 doi: 10.1016/s0065-3527(05)64006-7 id: cord-332992-8rmqg4rf author: de Vries, A. A. F. title: SARS-CoV-2/COVID-19: a primer for cardiologists date: 2020-07-15 words: 9182.0 sentences: 433.0 pages: flesch: 39.0 cache: ./cache/cord-332992-8rmqg4rf.txt txt: ./txt/cord-332992-8rmqg4rf.txt summary: Although SARS-CoV-2 particles/components have been detected in, for example, endothelial cells, the digestive tract and the liver, not all extrarespiratory manifestations of COVID-19 are necessarily caused by direct viral injury but may also be the consequence of the hypoxaemia, (hyper)inflammatory response, neuroendocrine imbalance and other pathophysiological changes induced by the airway infection [43] . Factors that may contribute to the thrombophilia observed in severely ill COVID-19 patients include the following: (1) a disturbed balance between pro-and anticoagulant activities due to excessive production of proinflammatory cytokines, activation of complement, formation of neutrophil extracellular traps and activation of platelets; (2) inflammation-related endothelial activation; (3) death of SARS-CoV-2-infected endothelial cells; (4) endothelial dysfunction caused by unbalanced angiotensin IIangiotensin II type-1 receptor signalling; (5) formation of prothrombotic antiphospholipid antibodies; (6) immobility-associated reduction of blood flow; (7) hypoxia due to respiratory impairment resulting from SARS-CoV-2-induced lung injury [79] [80] [81] . abstract: In the late autumn of 2019, a new potentially lethal human coronavirus designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, China. The pandemic spread of this zoonotic virus has created a global health emergency and an unprecedented socioeconomic crisis. The severity of coronavirus disease 2019 (COVID-19), the illness caused by SARS-CoV‑2, is highly variable. Most patients (~85%) develop no or mild symptoms, while others become seriously ill, some succumbing to disease-related complications. In this review, the SARS-CoV‑2 life cycle, its transmission and the clinical and immunological features of COVID-19 are described. In addition, an overview is presented of the virological assays for detecting ongoing SARS-CoV‑2 infections and the serological tests for SARS-CoV-2-specific antibody detection. Also discussed are the different approaches to developing a COVID-19 vaccine and the perspectives of treating COVID-19 with antiviral drugs, immunomodulatory agents and anticoagulants/antithrombotics. Finally, the cardiovascular manifestations of COVID-19 are briefly touched upon. While there is still much to learn about SARS-CoV‑2, the tremendous recent advances in biomedical technology and knowledge and the huge amount of research into COVID-19 raise the hope that a remedy for this disease will soon be found. COVID-19 will nonetheless have a lasting impact on human society. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12471-020-01475-1) contains supplementary material, which is available to authorized users. url: https://doi.org/10.1007/s12471-020-01475-1 doi: 10.1007/s12471-020-01475-1 id: cord-285676-4kgy20o9 author: de Vries, Antoine A.F. title: The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses date: 1997-02-28 words: 7980.0 sentences: 437.0 pages: flesch: 53.0 cache: ./cache/cord-285676-4kgy20o9.txt txt: ./txt/cord-285676-4kgy20o9.txt summary: The overlapping ORFs 1a and b found at the 58 end of the nidoviral genome are frequently referred to as the ''''polymerase gene.'''' However, there is little doubt that the processing of the encoded polyproteins yields proteins required for RNA synthesis as well as a number of products involved in other aspects of virus replication. The sequence conservation between the more closely related corona-and toroviruses is clustered in six domains, four of which are also found in the arterivirus POL1b: the ''''classical'''' RNA-dependent RNA polymerase (RdRp) and helicase (H) domains, which are also present in the polymerases of most other viruses, a zinc finger motif (zf), and a short region of 80-100 residues, which has not yet been identified in other viral polymerases and was called the ''''coronavirus-like'''' (CVL) domain (3) (motif 2 in Fig. 1b) . abstract: Abstract Viruses in the families Arteriviridae and Coronaviridae have enveloped virions which contain nonsegmented, positive-stranded RNA, but the constituent genera differ markedly in genetic complexity and virion structure. Nevertheless, there are striking resemblances among the viruses in the organization and expression of their genomes, and sequence conservation among the polymerase polyproteins strongly suggests that they have a common ancestry. On this basis, the International Committee on Taxonomy of Viruses recently established a new order, Nidovirales, to contain the two families. Here, the common traits and distinguishing features of the Nidovirales are reviewed. url: https://api.elsevier.com/content/article/pii/S1044577397901049 doi: 10.1006/smvy.1997.0104 id: cord-000083-3p81yr4n author: nan title: Poster Exhibition date: 2009-01-31 words: 112815.0 sentences: 7542.0 pages: flesch: 56.0 cache: ./cache/cord-000083-3p81yr4n.txt txt: ./txt/cord-000083-3p81yr4n.txt summary: R. China Background: The objective of this study was to evaluate the early virologic response for prediction of achievement of HBeAg seroconversion and hepatitis B virus (HBV) DNA negativity after two years of lamivudine treatment in chronic hepatitis B (CHB) patients. Methods: A total of 620 patients who tested positive for hepatitis B surface antigen and were referred to Chiba University Hospital between February 1985 and March 2008 were included in the study, and their following characteristics were analyzed: age, gender, the status of HBeAg, ALT, HBV-DNA level, and PLT. Methods: A total of 60 patients with chronic hepatitis B, 32 (53.3%) were HBeAg positive (group A) while 28(46.7%) were HBeAg negative (group B) were included in this study after meeting the following criteria: age 18 to 60 years, HBsAg positive for more than 6 months, serum HBV-DNA was >5 log(10) copies/mL and ALT more than two times the upper normal limit. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712310/ doi: 10.1007/s12072-009-9123-4 id: cord-001521-l36f1gp7 author: nan title: Oral and Poster Manuscripts date: 2011-04-08 words: 183363.0 sentences: 11362.0 pages: flesch: 53.0 cache: ./cache/cord-001521-l36f1gp7.txt txt: ./txt/cord-001521-l36f1gp7.txt summary: The IC 50 values determined in functional NI assays provide valuable information for detection of resistant viruses, but should not be used to draw direct correlations with drug concentrations needed to inhibit virus replication in the infected human host, as clinical data to support such inferences are inadequate. • Standardized reagents and protocols • Choice of detection technology • Simple instrumentation requirements • High sensitivity for use with low virus concentrations • Compatibility with batch-mode processing and largescale assay throughput • Broad specificity of influenza detection • Flexibility in assay format • Additional NA assay applications -cell-based viral assays, screening for new NIs, detection of NA from other organisms Functional neuraminidase inhibition assays enable detection of any resistance mutation and are extremely important in conjunction with sequence-based screening assays for global monitoring of virus isolates for NI resistance mutations, including known and new mutations. Such new assays need to include methods to measure local antibodies and virus-specific lymphocytes, especially in the case of live attenuated influenza vaccines, because of their potential to induce such broad-based immune responses. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313891/ doi: 10.1111/j.1750-2659.2011.00209.x id: cord-001835-0s7ok4uw author: nan title: Abstracts of the 29th Annual Symposium of The Protein Society date: 2015-10-01 words: 138514.0 sentences: 6150.0 pages: flesch: 40.0 cache: ./cache/cord-001835-0s7ok4uw.txt txt: ./txt/cord-001835-0s7ok4uw.txt summary: Altogether, these results indicate that, although PHDs might be more selective for HIF as a substrate as it was initially thought, the enzymatic activity of the prolyl hydroxylases is possibly influenced by a number of other proteins that can directly bind to PHDs. Non-natural aminoacids via the MIO-enzyme toolkit Alina Filip 1 , Judith H Bartha-V ari 1 , Gergely B an oczy 2 , L aszl o Poppe 2 , Csaba Paizs 1 , Florin-Dan Irimie 1 1 Biocatalysis and Biotransformation Research Group, Department of Chemistry, UBB, 2 Department of Organic Chemistry and Technology An attractive enzymatic route to enantiomerically pure to the highly valuable a-or b-aromatic amino acids involves the use of aromatic ammonia lyases (ALs) and aminomutases (AMs). Continuing our studies of the effect of like-charged residues on protein-folding mechanisms, in this work, we investigated, by means of NMR spectroscopy and molecular-dynamics simulations, two short fragments of the human Pin1 WW domain [hPin1(14-24); hPin1(15-23)] and one single point mutation system derived from hPin1(14-24) in which the original charged residues were replaced with non-polar alanine residues. abstract: nan url: https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/pro.2823 doi: 10.1002/pro.2823 id: cord-004534-jqm1hxps author: nan title: Abstract date: 2009-06-09 words: 139023.0 sentences: 6450.0 pages: flesch: 42.0 cache: ./cache/cord-004534-jqm1hxps.txt txt: ./txt/cord-004534-jqm1hxps.txt summary: HIV-1 to efficiently complete a replication cycle has to integrate its genome into the host cellular DNA.After HIV-1 enters target cells,neosynthesized viral DNA forms along with other proteins the pre-integration complex (PIC).PICs are then transported into the nucleus where integration,catalyzed by the viral integrase,takes place.HIV-1 viral particles engineered to incorporate integrase fused to EGFP have proven effective to study PICs within nuclei of infected cells.In this study we report the live imaging analysis of nuclear PIC dynamics obtained by time-lapse microscopy.Intranuclear trajectories of IN-EGFP-labeled PIC were collected in three dimensions and examined by both mean squared displacement (MSD) and cage diameter (CD) analysis.In CD the maximum distances measured between two positions occupied by a PIC in a time window of 2 minutes were calculated while in our MSD analysis 5-minute long trajectory segments were considered.Remarkably,MSD revealed the presence of an underlying active transport mechanism.To test the possible role of actin filaments,PIC nuclear trafficking was analyzed in cells treated with latrunculin B (actin polymerization inhibitor).Preliminary results suggest that the disruption of actin function impairs the active nuclear movement of PICs. Second harmonic generation microscopy reveals sarcomere contractile dynamics of cardiomyocytes N. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7079852/ doi: 10.1007/s00249-009-0478-1 id: cord-004584-bcw90f5b author: nan title: Abstracts: 8th EBSA European Biophysics Congress, August 23rd–27th 2011, Budapest, Hungary date: 2011-08-06 words: 106850.0 sentences: 5038.0 pages: flesch: 41.0 cache: ./cache/cord-004584-bcw90f5b.txt txt: ./txt/cord-004584-bcw90f5b.txt summary: Our goals are two-fold: (1) to monitor conformational changes in each domain upon its binding to specific ligands and then to correlate the observed changes with structural differences between the CRDs and (2) to investigate the interaction between the CRDs and lipid model membranes. Cholesterol-assisted lipid and protein interactions such as the integration into lipid nanodomains are considered to play a functional part in a whole range of membrane-associated processes, but their direct and non-invasive observation in living cells is impeded by the resolution limit of [200nm of a conventional far-field optical microscope. Therefore, to investigate the dynamic and complex membrane lateral organization in living cells, we have developed an original approach based on molecule diffusion measurements performed by fluorescence correlation spectroscopy at different spatial scales (spot variable FCS, svFCS) (1). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080017/ doi: 10.1007/s00249-011-0734-z id: cord-004879-pgyzluwp author: nan title: Programmed cell death date: 1994 words: 81677.0 sentences: 4465.0 pages: flesch: 51.0 cache: ./cache/cord-004879-pgyzluwp.txt txt: ./txt/cord-004879-pgyzluwp.txt summary: Furthermore kinetic experiments after complementation of HIV=RT p66 with KIV-RT pSl indicated that HIV-RT pSl can restore rate and extent of strand displacement activity by HIV-RT p66 compared to the HIV-RT heterodimer D66/D51, suggesting a function of the 51 kDa polypeptide, The mouse mammary tumor virus proviral DNA contains an open reading frame in the 3'' long terminal repeat which can code for a 36 kDa polypeptide with a putative transmembrane sequence and five N-linked glycosylation sites. To this end we used constructs encoding the c-fos (and c-jun) genes fused to the hormone-binding domain of the human estrogen receptor, designated c-FosER (and c-JunER), We could show that short-term activation (30 mins.) of c-FosER by estradiole (E2) led to the disruption of epithelial cell polarity within 24 hours, as characterized by the expression of apical and basolateral marker proteins. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7087532/ doi: 10.1007/bf02033112 id: cord-005147-mvoq9vln author: nan title: Autorenregister date: 2017-02-23 words: 86573.0 sentences: 4356.0 pages: flesch: 45.0 cache: ./cache/cord-005147-mvoq9vln.txt txt: ./txt/cord-005147-mvoq9vln.txt summary: Using whole-exome sequencing and trio-based de novo analysis, we identified a novel heterozygous de novo frameshift variant in the leukemia inhibitory factor receptor (LIFR) gene causing instability of the mRNA in a patient presenting with bilateral CAKUT and requiring kidney transplantation at one year of age. Loss of cdkl5 associated with deficient mammalian target of rapamycin (mTOR) signaling in mice and human cells We and other groups have shown that mutations in the X-linked cyclin-dependent kinase-like 5 (CDKL5) gene cause a severe neurodevelopmental disorder with clinical features including intellectual disability, early-onset intractable seizures and autism, that are closely related to those present in Rett syndrome (RTT) patients. Functional characterization of novel GNB1 mutations as a rare cause of global developmental delay Over the past years, prioritization strategies that combined the molecular predictors of sequence variants from exomes and genomes of patients with rare Mendelian disorders with computer-readable phenotype information became a highly effective method for detecting disease-causing mutations. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7088617/ doi: 10.1007/s11825-017-0126-6 id: cord-007890-bie1veti author: nan title: ECC-4 Abstracts date: 2002-04-16 words: 85992.0 sentences: 5665.0 pages: flesch: 50.0 cache: ./cache/cord-007890-bie1veti.txt txt: ./txt/cord-007890-bie1veti.txt summary: Effects of Interferon alpha plus ribavirine therapy on frequencies of HCV, HIV and CMV specific CD4-T-cell responses in peripheral blood of HIV/HCV coinfected patients after 6 months of treatment SoA9.5 Methods: Two groups of patients with chronic HCV infection were studied: 26 HIV coinfected progressors with antiretroviral therapy and 13 HIV-negative controls. In order to assess the local temporal trend of antibiotic sensitivity of the most common urinary tract bacterial pathogen, all urine-cultured Escherichia coli isolates were reviewed as to susceptibility profile, and specimen source (community-versus hospital-acquired infection). Methods: A total of 87 penicillin resistant clinical strains isolated from patients at Hacettepe Children''s Hospital, Ankara, Turkey between 1999 and 2001 were tested for their in vitro susceptibility to various antibiotics that are commonly used in the treatment of respiratory tract infections. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7126403/ doi: 10.1016/s0924-8579(02)00033-x id: cord-010092-uftc8inx author: nan title: Abstract of 29th Regional Congress of the ISBT date: 2019-06-07 words: 233304.0 sentences: 13171.0 pages: flesch: 54.0 cache: ./cache/cord-010092-uftc8inx.txt txt: ./txt/cord-010092-uftc8inx.txt summary: Prospective testing of blood donations in endemic areas of the U.S. revealed 0.38% of donors were positive for Babesia DNA or antibodies (Moritz, NEJM, 2016) Aims: -To report results of ongoing Babesia clinical trial -To explain significance of Babesia as a TT infection Methods: In cobas â Babesia for use on the cobas â 6800/8800 Systems, is a qualitative polymerase chain reaction nucleic acid amplification test, developed to detect in whole blood (WB) donor samples the 4 Babesia species that cause human disease: B. In sensitivity analyses, there were two discrepant results for HIV testing, three for HCV, and five for anti-HBc. Summary/Conclusions: Elecsys â infectious disease parameters on the cobas e 801 analyser demonstrate high specificity/sensitivity for screening first-time blood donor samples, with similar clinical performance to other commercially available assays. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169345/ doi: 10.1111/vox.12792 id: cord-014462-11ggaqf1 author: nan title: Abstracts of the Papers Presented in the XIX National Conference of Indian Virological Society, “Recent Trends in Viral Disease Problems and Management”, on 18–20 March, 2010, at S.V. University, Tirupati, Andhra Pradesh date: 2011-04-21 words: 35453.0 sentences: 1711.0 pages: flesch: 49.0 cache: ./cache/cord-014462-11ggaqf1.txt txt: ./txt/cord-014462-11ggaqf1.txt summary: Molecular diagnosis based on reverse transcription (RT)-PCR s.a. one step or nested PCR, nucleic acid sequence based amplification (NASBA), or real time RT-PCR, has gradually replaced the virus isolation method as the new standard for the detection of dengue virus in acute phase serum samples. Non-genetic methods of management of these diseases include quarantine measures, eradication of infected plants and weed hosts, crop rotation, use of certified virus-free seed or planting stock and use of pesticides to control insect vector populations implicated in transmission of viruses. The results of this study indicate that NS1 antigen based ELISA test can be an useful tool to detect the dengue virus infection in patients during the early acute phase of disease since appearance of IgM antibodies usually occur after fifth day of the infection. The studies showed high level of expression in case of constructed vector as compared to infected virus for the specific protein. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639731/ doi: 10.1007/s13337-011-0027-2 id: cord-014685-ihh30q6f author: nan title: Posters P788 - P999 date: 2005-09-21 words: 38354.0 sentences: 1784.0 pages: flesch: 45.0 cache: ./cache/cord-014685-ihh30q6f.txt txt: ./txt/cord-014685-ihh30q6f.txt summary: This study has attempted to analyse the structural properties of membrane peptides and proteins through the use of model systems that have been designed to mimic their natural counterparts: Podlubnaya 2 1 Institute of Theoretical and Experimental Biophysics RAS, 2 Pushchino State University Amyloid brils are formed by proteins or their peptides in the result of a conformational transition from alpha helix into beta-sheet structure. Analysis of the results of such studies indicate that folding of SNase fragments is dominated by developing the local and non-local nucleation sites from native-like secondary structures and by intensifying the longrange interactions of residues at nucleation sites with residues further removed in sequence. The results show that at different pH values the aggregation processes of both proteins follow different pathways determined by the variations in the native structure and by the details of the involved conformational changes. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7080055/ doi: 10.1007/s00249-005-0504-x id: cord-015237-8cxfa8wf author: nan title: Structure Watch date: 2005 words: 274.0 sentences: 23.0 pages: flesch: 66.0 cache: ./cache/cord-015237-8cxfa8wf.txt txt: ./txt/cord-015237-8cxfa8wf.txt summary: The solution structures of the four RNA-binding domains (RBDs) of polypyrimidine-tract-binding protein-1 (PTB1) in complex with RNA have now been solved by Oberstrass et al., leading to new models for the function of PTB1 as a repressor of alternative splicing. used NMR to look at the structure of RBD1-4 in complex with a 5′-CUCUCU-3′ oligonucleotide, which is a common feature of intronic regulatory sequences. Each RBD binds independently to one RNA molecule and recognizes a different consensus sequence within the oligonucleotide. The nucleotides interact with the flat β-sheet surface of each RBD but, unlike other RBD-RNA structures, the third β-strand is only weakly involved in RNA binding. A single PTB1 molecule can therefore bring two distant pyrimidine tracts into close proximity and induce RNA looping -a feature that has led to the proposal of various models for the function of this protein in alternative splicing. Structure of PTB bound to RNA: specific binding and implications for splicing regulation abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097638/ doi: 10.1038/nrm1780 id: cord-015394-uj7fe5y6 author: nan title: Scientific Abstracts date: 2008-12-23 words: 242330.0 sentences: 15267.0 pages: flesch: 52.0 cache: ./cache/cord-015394-uj7fe5y6.txt txt: ./txt/cord-015394-uj7fe5y6.txt summary: Studies involving immunohistochemical analysis of normal ovaries have shown that granulosa cells express significantly higher levels of the activator protein-1 (AP-1) transcription factor, cFos compared to theca cells, where cFos expression is virtually absent. Following acute hypoxia (0.5% O2) for one to six hours, RhoA mRNA, total protein and activation (RhoA-GTP) levels were analysed, using semi-quantitative PCRs and western blot, and compared to normoxic non-pregnant human uterine smooth muscle control cells. Since there is an urgent need for non-invasive methods for determination of fetal (F) and placental (P) function, this study was designed to evaluate the genes differently and commonly expressed in P tissue and leukocytes in maternal (M) and F circulation.Material and Methods. The current study: 1) localized IL-6 mRNA levels in preeclamptic versus normal decidual sections; 2) evaluated mechanisms regulating IL-6 synthesis by targeting intracellular signaling pathways with specific inhibitors; 3) identified potential IL-6 targets by immunolocalizing the IL-6 receptor (IL-6R) to specific cell types in placental bed biopsies. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104449/ doi: 10.1177/19337191080150020102 id: cord-020010-q58x6xb0 author: nan title: 19th ICAR Abstracts: date: 2006-03-13 words: 46663.0 sentences: 2181.0 pages: flesch: 44.0 cache: ./cache/cord-020010-q58x6xb0.txt txt: ./txt/cord-020010-q58x6xb0.txt summary: In the present study we reported the antiviral activity of neuraminidase inhibitor oseltamivir against lethal H5N1 influenza virus infection in ferrets, an appropriate animal model that closely resembles clinical signs of human influenza. Earl Kern 1 , Kathy Keith 2 , Robert Jordan 2 , Dennis Hruby 2 , Debra Quenelle 2 1 Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA; 2 SIGA Technologies, Inc., Corvallis, OR, USA Although cidofovir (CDV) has been approved as an investigational new drug for emergency treatment of smallpox, its lack of oral activity and dose limiting toxicity dictates a need for continued development of better therapeutic agents for this potential bioterror disease. The in vitro antiviral activity of one of the most selective compounds, i.e. CHI-033, was assessed by (i) MTS-based cytopathic effect assays, (ii) virus yield reduction assays, (iii) real-time quantitative PCR (RT-QPCR) and (iv) by monitoring viral antigen expression. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7133865/ doi: 10.1016/j.antiviral.2006.02.001 id: cord-020235-stcrozdw author: nan title: Abstracts of Papers Presented at the 38th Meeting of the Deutsche Gesellschaft für Hygiene und Mikrobiologie, Virology Section, Göttingen, 5.–8.10.1981 date: 2012-03-15 words: 13494.0 sentences: 843.0 pages: flesch: 58.0 cache: ./cache/cord-020235-stcrozdw.txt txt: ./txt/cord-020235-stcrozdw.txt summary: Hepatitis A virus (HAV) was isolated directly from human stool in diploid human fibroplasrs, Viral antigen was expressed only after 210 days of incubation of the infected cultures. Univ., 0-8700 Wiirzburg Effect of Measles (SSPE) Antiserum on Viral Surface Proteins and Hormone Receptor Activity in C6/SSPE Persistently Infected Cells BARRETT, P. Inst, of Genetics, Univ., 0-5000 Co logne Virus-Cell DNA Recombinants in Human Cells Lytically Infected by Ad2 NEUMANN, R., WEYER, U., and DOERFLER, W. In vitro, however, the gag-specific peptide sequences are cleaved off upon addition of the purified viral piS protease; in the case of the replication-defective, transforming avian sarcoma virus PRC II the cleaved nongag part has a ryrosine-phosphorylaring kinase activity similar to that described for the RSV src-gene product pp60 src . f. Virologie, Univ., D·6300 Giefen, 3 A protein of a molecular weight of about 38.000 d has been found to be phosphorylated 1 h after the onset of cell transformation by Rous sarcoma virus (RSV). abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134445/ doi: 10.1016/s0174-3031(82)80128-5 id: cord-022888-dnsdg04n author: nan title: Poster Sessions date: 2009-08-19 words: 188640.0 sentences: 9313.0 pages: flesch: 45.0 cache: ./cache/cord-022888-dnsdg04n.txt txt: ./txt/cord-022888-dnsdg04n.txt summary: Methods: Phospho-specific Western blot analyses were performed to verify the functionality of the different IFN-g pathway components, intra-and extracellular flow cytometry experiments were employed to determine the expression of antigen processing components and HLA class I cell surface antigens, quantitative real time-PCR experiments to confirm the absence of JAK2 and presence of pathway relevant molecules as well as, genomic PCR and chromosome typing technique to prove the deletion of JAK2. In order to accomplish these objectives we induced priming or tolerance of ovalbumin (OVA 323-339 peptide)-specific T cells from DO11.10 TCR transgenic mice in vitro or, following adoptive transfer of near physiologically relevant numbers of such cells into recipients, in vivo and correlated functional outcome (via proliferation and cytokine readout assays or antibody production) with E3 ubiquitin-protein ligases expression and the ubiquitination status of the TCR signalling machinery. abstract: No Abtract url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7163517/ doi: 10.1002/eji.200990224 id: cord-022940-atbjwpo5 author: nan title: Poster Sessions date: 2016-09-07 words: 241182.0 sentences: 12746.0 pages: flesch: 47.0 cache: ./cache/cord-022940-atbjwpo5.txt txt: ./txt/cord-022940-atbjwpo5.txt summary: We have studied the effect of inhibition of IRE1 (inositol requiring enzyme 1), which is a central mediator of endoplasmic reticulum stress and controls cell proliferation and tumor growth, on hypoxic regulation of the expression of different proliferation related genes in U87 glioma cells. Transient inhibition of Akt and mTOR protein kinase activation in tumor cells followed by reactivation of signaling pathway did not result in a time-dependent difference on EGFR, HER2 and HER3 expression levels. In our study we aimed to determine cytotoxic effect of RES in K562 human CML cell line and to evaluate the expressions of miRNAs that are associated with genetics of leukemia after treatment with RES; to investigate target genes of miRNAs which show significant expression alterations and molecular mechanisms of RES treatment. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164006/ doi: 10.1111/febs.13808 id: cord-023017-k6edtg58 author: nan title: AASLD Abstracts (pp. 282A–382A) date: 2006-02-10 words: 65796.0 sentences: 3553.0 pages: flesch: 51.0 cache: ./cache/cord-023017-k6edtg58.txt txt: ./txt/cord-023017-k6edtg58.txt summary: 14/55 (25%) patients in AC who did not discontinue by week 24 received ribavirin dose reduction in comparison to 31/108 ( The clinical outcome in response to combination therapy for treatment of chronic hepatitis C virus (HCV) infection appears to be different for Caucasian versus African American patients. Over the period of combination therapy, most patients in which serum virus titers were reduced to non detectable levels had significant increases in T cell responses to HCV proteins. CHRONIC Background: Recent large prospective trials demonstrated that the combination therapy of interferon (1FN)-alphalribavirin significantly increased the ratio of a sustained virological response in patients with chronic hepatitis C in comparison with IFN monotherapy, especially in patients with high HCV-RNA titer and genotype lb. Results: Patients with chronic HCV infection showed higher MxA gene expression levels than healthy controls, indicating that hepatitis C virus induces IFN production. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7165819/ doi: 10.1002/hep.1840380505 id: cord-023120-jcgf2401 author: nan title: Animal virus genetics date: 2004-06-18 words: 17801.0 sentences: 1474.0 pages: flesch: 67.0 cache: ./cache/cord-023120-jcgf2401.txt txt: ./txt/cord-023120-jcgf2401.txt summary: We suggest that, (1) c regions contain promotors for viral RNA synthesis, (2) cx contains a more efficient promotor than c" and (3) non-acute disease foliows the formation of critical viral-cell recombinants in which ( 2 ) The r e s u l t i n g CDNA i s f r a c t i o n a t e d and a l l fragments having a length g r e a t e r than 300 nucleotides are i s o l a t e d and c u t with a r e s t r i c t i o n endonuclease capable of d i g e s t i n g single-stranded DNA. Studies of the synthesis and processing of viral proteins in simian sarcoma associated virus (SSAV)infected and SSV(SSAV)transformed marmoset and human cell lines has demonstrated polyprotein precursors precipitable by anti-SSAV p30 and anti-SSAV gp70. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7166955/ doi: 10.1002/jss.400140505 id: cord-023208-w99gc5nx author: nan title: Poster Presentation Abstracts date: 2006-09-01 words: 70854.0 sentences: 3492.0 pages: flesch: 43.0 cache: ./cache/cord-023208-w99gc5nx.txt txt: ./txt/cord-023208-w99gc5nx.txt summary: In order to develop a synthetic protocol by an automated instrumentation, increasing yield, purity of the crude, and reaction time, a microwave-assisted solid phase peptide synthesis was validated comparing the use of the new generation of Triazine-Based Coupling Reagents (TBCRs) with a series of commonly used ones. Ubiquitinium is a well known mechanism in protein degredation of Eukaryotic cells ,in which many obsolte and corrupted three dimentional structure protein ,become marked by covalent attachment of ubuquitin through a multi-step enzymatic pathway.Ubiquitin is a small ,8.5 kDa peptide of 76 amino acid residues that targets such substrtes for proteolysis in proteasome .Recnt studies showed that an extra cellular ubiquitination process also taking place in the epididymes of humans and other animals marks protein on the surface of the defective sperm .it appears that structurally and functionally defective sperm become surface ubiquitinated by epididymal epithelial cells. This head-to-tailcyclized 14-amino-acid peptide contains one disulfide bridge and a lysine residue (Lys5) present in the P1 position, which is responsible for inhibitor specificity.As was reported by us and other groups, SFTI-1 analogues with one cycle only retain trypsin inhibitory activity. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7167816/ doi: 10.1002/psc.797 id: cord-023346-8sqbqjm1 author: nan title: MONDAY: POSTERS date: 2005-06-08 words: 130043.0 sentences: 7330.0 pages: flesch: 54.0 cache: ./cache/cord-023346-8sqbqjm1.txt txt: ./txt/cord-023346-8sqbqjm1.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169255/ doi: 10.1111/j.1423-0410.2005.00652.x id: cord-023354-f2ciho6o author: nan title: TUESDAY PLENARY SESSION 3 TUESDAY: POSTERS date: 2005-06-08 words: 130046.0 sentences: 7333.0 pages: flesch: 54.0 cache: ./cache/cord-023354-f2ciho6o.txt txt: ./txt/cord-023354-f2ciho6o.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169300/ doi: 10.1111/j.1423-0410.2005.00654.x id: cord-023364-ut56gczm author: nan title: EDUCATION DAY MONDAY: PLENARY SESSION 1 MONDAY: PARALLEL SESSIONS date: 2005-06-08 words: 130049.0 sentences: 7334.0 pages: flesch: 54.0 cache: ./cache/cord-023364-ut56gczm.txt txt: ./txt/cord-023364-ut56gczm.txt summary: • enhancement of automation/computerisation; • process control to provide an ''error-free pathway''; • (national) surveillance and trend analysis of results, preferably based on national working standards; • significantly increased sensitivity, especially from development of antigen/antibody ''combi'' assays (e.g. for HIV, and recently, for HCV); • awareness of HBsAg vaccine-escape mutants and design of assays to cope with this; • extension of range of agents and markers tested for (varies in different countries); • increasing range of assays available for testing donors with a relevant history of exposure to malaria or Chagas'' disease infection (for retrieval of otherwise wasted blood); • European Union''s in vitro diagnostics directive: this has caused some problems and reduced flexibility. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7169338/ doi: 10.1111/j.1423-0410.2005.00651.x id: cord-023608-w2g7v7g1 author: nan title: ISAR News date: 2017-10-20 words: 6059.0 sentences: 284.0 pages: flesch: 48.0 cache: ./cache/cord-023608-w2g7v7g1.txt txt: ./txt/cord-023608-w2g7v7g1.txt summary: ICAR retains its flavor and personality, providing an interdisciplinary forum at which investigators involved in basic, translational, and clinical research worldwide meet to review recent developments in all areas of antiviral research, drug and vaccine development. Additionally, satellite activities such as the Women in Science Roundtable, the Career Development Panel and the New Member and First Time Attendee luncheon (The Happy Hour) provided an opportunity to discuss other issues of relevance. With so many different competing conferences and meetings to attend and a long economic crisis of which scientific research did not escape, ISAR has gone through great financial efforts to continue supporting the participation of students, postdocs and young investigators. The TCFF Awards support the professional development of women with potential to make significant contributions to the field of Antiviral Research by providing funds to attend a conference, visit another laboratory, take a course, or acquire specialized training. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172721/ doi: 10.1016/s0166-3542(17)30664-2 id: cord-023770-ymxapsv6 author: nan title: Closteroviridae date: 2011-11-23 words: 3662.0 sentences: 197.0 pages: flesch: 53.0 cache: ./cache/cord-023770-ymxapsv6.txt txt: ./txt/cord-023770-ymxapsv6.txt summary: In general, capsid proteins and their homologs (CPm) show a significant degree of sequence conservation and the duplicate copies probably retain the general spatial folding and some crucial properties of the CPs. Notable exception are a group of ampeloviruses with the smallest genomes in the family [e.g. grapevine leafrollassociated virus 4 (GLRaV-4), GLRaV-5, GLRaV-6, GLRaV-9, pineapple mealybug wilt-associated virus 1(PMWaV-1) and PMWaV-3] which do not appear to possess CPm. The genome expression strategy is based on: (i) proteolytic processing of the polyprotein encoded by ORF1a; (ii) 1 Pos. ssRNA ribosomal frameshift for the expression of the RdRp domain encoded by ORF1b, a mechanism not found in other ()RNA plant viruses; (iii) expression of the downstream ORFs via the formation of a nested set of 3 co-terminal sub-genomic RNAs (sgRNAs). abstract: This chapter focuses on Closteroviridae family whose member genuses are Closterovirus, Ampelovirus, and Crinivirus. The virions are helically constructed filaments with a pitch of the primary helix in the range of 3.4–3.8 nm, containing about 10 protein subunits per turn of the helix and showing a central hole of 3–4 nm. The very flexuous and open structure of the particles is the most conspicuous trait of members of the family. The virions have a diameter of about 12 nm and their length ranges from 650 nm in case of species with fragmented genome, to over 2000 nm in case of species with monopartite genome. The fragility of virions and a tendency to end-to-end aggregation contribute to the fact that a range of lengths is often given for single viruses. The virions of several species are degraded by CsCl and are unstable in high salt concentration, resist moderately high temperatures and organic solvents, but are sensitive to RNase and chelation. Regardless of the genome type, monopartite or fragmented, virions contain a single molecule of linear, positive sense, single stranded RNA, constituting 5–6% of the particle weight. The structural proteins of most members of the family consist of a major CP and of a diverged copy of it denoted minor CP (CPm), with a size ranging from 22 to 46 kDa (CP) and 23 to 80 kDa (CPm). The members of the family have one of the largest genomes among plant viruses because of sequence duplication and acquisition of nonviral coding sequences such as protease, and HSP70 protein via RNA recombination. url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7173617/ doi: 10.1016/b978-0-12-384684-6.00085-9 id: cord-031907-ilhr3iu5 author: nan title: ISEV2020 Abstract Book date: 2020-07-15 words: 200999.0 sentences: 11528.0 pages: flesch: 44.0 cache: ./cache/cord-031907-ilhr3iu5.txt txt: ./txt/cord-031907-ilhr3iu5.txt summary: L.M., and the National Institutes of Health (R35GM119623) to T.R.G. The addition of a size exclusion chromatography step to various urinary extracellular vesicle concentrating methods reveals differences in the small RNA profile Introduction: Urinary extracellular vesicles (EVs) and their RNA cargo are a novel source of biomarkers for various diseases, however non-vesicular RNA (e.g. associated with proteins) is also present within urine. We then evaluated efficiency of heart targeting for eAAV9 or eAAV6 and standard AAV9 or AAV6 encoding for EGFP, mCherry or firefly luciferase in different human cell lines in vitro, in black mouse and in passive immunity nude mouse model in vivo using flow cytometry, confocal microscopy, Langendorff perfusion system and Methods: HLHS patients (n = 3) after Glenn procedure and swine (n = 3) after PAB were given RV injections of allogeneic/xenogeneic MSCs. Donor-specific, HLA-I+, exosomes were isolated from plasma. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480431/ doi: 10.1080/20013078.2020.1784511 id: cord-034648-vfqth54o author: nan title: WITHDRAWN date: 2020-10-12 words: 2000.0 sentences: 145.0 pages: flesch: 55.0 cache: ./cache/cord-034648-vfqth54o.txt txt: ./txt/cord-034648-vfqth54o.txt summary: To determine if gene expression changes were associated with changes in cellular response, transwell assays were performed to assess HTR-8 cell migration and invasion after exposure to 2.5% O 2 or 21% O 2 for 6hrs and 24hrs. Outcome parameters monitored were estradiol levels, follicle morphology and survival throughout the in vitro culture interval (IVC), germinal vesicle breakdown (GVBD), oocyte maturation to metaphase II stage, fertilization and development to blastocyst. Cell number in blastocysts was determined by Hoechst staining RESULTS: Pre-antral follicles measured 121.9 AE 40.9 mM with oocyte diameters of 61.1AE 4.1 mM at time of seeding. RESULTS: Based on scRNAseq data in non-human primate ovarian tissue, ACE2 and TMPRSS2 co-localize in a sub-population of oocytes in antral follicles (62% of cells, Pearson correlation¼0.37), but to a lesser extent in less mature oocytes and not at all in ovarian somatic cells. abstract: nan url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641335/ doi: 10.1016/j.fertnstert.2020.08.1019 id: cord-286711-nr6vnl9h author: nan title: Other viruses causing gastroenteritis date: 2003-12-31 words: 2186.0 sentences: 125.0 pages: flesch: 48.0 cache: ./cache/cord-286711-nr6vnl9h.txt txt: ./txt/cord-286711-nr6vnl9h.txt summary: Some of these viruses discussed in this chapter are toroviruses, picobirnaviruses, enteroviruses, human immunodeficiency virus (HIV), herpesviruses, and coronaviruses. Cytomegalovirus (CMV) and herpes simplex viruses, members of the Herpesviridae family, are found as the cause of colitis and esophagitis, mainly in HIV-infected patients. Besides the viruses producing the majority of human viral gastroenteritis (Sections II-V), other viruses infect more rarely, but are sometimes able to cause epidemics. HIV, the causative agent of the Acquired Immunodeficiency Syndrome (AIDS), is a member of the Lentivirus genus of the Retroviridae family. HIV, the causative agent of the Acquired Immunodeficiency Syndrome (AIDS), is a member of the Lentivirus genus of the Retroviridae family. Cytomegalovirus (CMV) and herpes simplex viruses, members of the Herpesviridae family, are found as the cause of colitis and oesophagitis, mainly in HIV-infected patients (Levinson and Bennets, 1985; Jacobson and Mills, 1988; Dieterich and Robinson, 1991; Theise et al. Enteric viruses and diarrhoea in HIV-infected patients abstract: Publisher Summary Besides the viruses producing the majority of human viral gastroenteritis, other viruses infect more rarely but are sometimes able to cause epidemics. In particular, they cause chronic infection in the immunocompromised. Some of these viruses discussed in this chapter are toroviruses, picobirnaviruses, enteroviruses, human immunodeficiency virus (HIV), herpesviruses, and coronaviruses. Toroviruses make up a genus of the Coronaviridae family. They are a well-described cause of diarrhea in calves and horses but may also infect sheep, goats, and pigs. Picobirnaviruses are related to members of the Birnaviridae family. They are found in the feces of HIV-infected patients with diarrhea more frequently than in HIV-infected patients without diarrhea, but a virus-specific immune response was not measurable. The genus Enterovirus is of the Picornaviridae family. All enteroviruses infect man via the gastrointestinal tract where they have their first site of replication, probably in lymphoid tissues of the pharynx and gut. HIV, the causative agent of the acquired immunodeficiency syndrome (AIDS), is a member of the Lentivirus genus of the Retroviridae family. Cytomegalovirus (CMV) and herpes simplex viruses, members of the Herpesviridae family, are found as the cause of colitis and esophagitis, mainly in HIV-infected patients. Coronavirus is another genus of the Coronaviridae family. Coronaviruses infect the respiratory and gastrointestinal tracts. They are a recognized cause of the common cold in man. url: https://api.elsevier.com/content/article/pii/S0168706903090372 doi: 10.1016/s0168-7069(03)09037-2 id: cord-327518-yilv9z2m author: nan title: Coronaviridae date: 2011-11-23 words: 7123.0 sentences: 351.0 pages: flesch: 49.0 cache: ./cache/cord-327518-yilv9z2m.txt txt: ./txt/cord-327518-yilv9z2m.txt summary: In coronaviruses, proteolytic processing results in the production of 15 (in viruses belonging to the species Avian coronavirus) or 16 mature products, commonly referred to as non-structural proteins (nsp''s) and numbered according to their position -from N-to C-terminus -in the viral polyproteins ( Figure 1 ). Apart from their relatively close phylogenetic relationship, the only general characteristics that would set them apart from other coronaviruses are (i) a unique type of nsp1, distinct in size and sequence from betacoronavirus nsp1 and without apparent counterpart in the gammacoronaviruses, and (ii) the presence of a commonly-shared accessory gene (designated ORF3 in most alphacoronavirus species, ORF3b and 3c in TGEV and in FCoV/CCoV, respectively) for a dispensable multi-spanning alphacoronavirus membrane protein (αmp). The structural proteins are expressed from three sg mRNA species that are 3 co-terminal with the genome and believed to be produced via a process of discontinuous minus-strand RNA synthesis similar to that of coronaviruses ( Figure 12 ). abstract: This chapter focuses on Coronaviridae family whose two subfamilies include Coronavirinae and Torovirinae. The member genera include Alphacoronavirus, Betacoronavirus, Gammacoronavirus, Torovirus, and Bafinivirus. The members of the family Coronaviridae are enveloped and positive stranded RNA viruses of three classes of vertebrates, which include corona- and toroviruses for mammals, coronaviruses for birds, and bafiniviruses for fishes. The nucleocapsids are helical and can be released from the virion by treatment with detergents. Where the coronavirus nucleocapsid appears to be loosely wound, those of the Torovirinae are distinctively tubular. The entire replication cycle takes place in the cytoplasm and involves the production of full-length and subgenome-sized (sg) minus-strand RNA intermediates with the viral genome serving both as mRNA for the replicase polyproteins and as a template for minus-strand synthesis. Members of the family Coronaviridae all seem to share two envelope protein species, the membrane (M) and spike (S) proteins. Similarities in size, predicted structures and presumed function(s) suggest a common ancestry, and the remote, but significant sequence similarities observed for toro-, bafini-, and (to lesser extent) coronavirus S proteins lend further support to this view. The replicase polyproteins of the Coronaviridae comprise a number of characteristic domains arranged in a conserved order. url: https://www.sciencedirect.com/science/article/pii/B9780123846846000689 doi: 10.1016/b978-0-12-384684-6.00068-9 id: cord-340489-yo3cp5vs author: nan title: KAPITEL 13 Infektionskrankheiten date: 2008-12-31 words: 26536.0 sentences: 3917.0 pages: flesch: 45.0 cache: ./cache/cord-340489-yo3cp5vs.txt txt: ./txt/cord-340489-yo3cp5vs.txt summary: Die Wirksamkeit von BVDU bei VZV-Infektionen (Varizellen und Zoster) immunkompromittierter Patienten ist durchaus sehr gut und vergleichbar der von i.v. verabreichtem Aciclovir, jedoch fällt die Nutzen-Risiko-Betrachtung insgesamt auch bei VZV-Therapie zu Gunsten von Aciclovir aus, da BVDU eher mutagen zu sein scheint und nicht zusammen mit 5-Fluorouracil (Zytostatikum) gegeben werden darf. In klinischen Studien konnte durch Anwendung von ACV bei EBV-Infektionen auch die Virusausscheidung deutlich vermindert werden, ein wesentlicher Einfluss auf den Krankheitsverlauf ließ sich nicht erreichen. Typisch für viele opportunistische Erreger ist, dass sie weit verbreitet sind und nach einer Primärinfektion, die bereits vor der HIV-Infektion stattfindet, zu latenten Infektionen führen. Die Prophylaxe von Infektionen bereits vor deren erstem Auftreten (Primärprophylaxe) oder nach der ersten Episode (Sekundärprophylaxe) ist weiterhin eine wichtige Aufgabe bei der Betreuung HIV-positiver Patienten, auch wenn opportunistische Infektionen durch die antiretrovirale Therapie insgesamt seltener geworden sind. abstract: Zur Orientierung Infektionskrankheiten werden durch Pathogene verursacht, die sich im Wirt vermehren: Ektoparasiten, Helminthen, Protozoen, Pilze, Bakterien, Viren, Prionen. Infektionskrankheiten können alle Organe bzw. Organsysteme befallen. Entstehung und Verlauf werden durch Faktoren beeinflusst, die sich grob einteilen lassen in Erreger- und Wirtsfaktoren. Die Kenntnis und richtige Einschätzung dieser Faktoren sind entscheidend für Diagnostik und Therapie dieser Erkrankungen. url: https://api.elsevier.com/content/article/pii/B9783437428319100130 doi: 10.1016/b978-3-437-42831-9.10013-0 id: cord-271701-tx0lqgff author: te Velthuis, Aartjan J.W. title: The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension date: 2011-10-29 words: 7357.0 sentences: 367.0 pages: flesch: 56.0 cache: ./cache/cord-271701-tx0lqgff.txt txt: ./txt/cord-271701-tx0lqgff.txt summary: Commonly, its core subunit is a single RNA-dependent RNA polymerase (RdRp) that drives the production of template strands for replication, new genome molecules, and-in many RNA virus groupsalso subgenomic (sg) mRNAs. This canonical RdRp is structurally conserved among RNA viruses and widely accepted to drive catalysis of phosphodiester bond formation via a well-established reaction mechanism involving two metal ions that are coordinated by aspartate residues in its motifs A and C (3) (4) (5) . Interestingly, both nsp8 and nsp(7+8) are able to extend the RNA primers beyond template length in the presence of heparin ( Figure 4D and Supplementary Figure S2B ), suggesting that these extensions result from terminal transferase activity and not from template switching, as was previously observed for poliovirus 3D pol (20) . Subsequent alanine substitution of the N-terminal D/ ExD/E motif, composed of D50 and D52 in SARS-CoV, greatly affected primer extension activity on the CU 10 template as shown in Figure 5C . abstract: Uniquely among RNA viruses, replication of the ∼30-kb SARS-coronavirus genome is believed to involve two RNA-dependent RNA polymerase (RdRp) activities. The first is primer-dependent and associated with the 106-kDa non-structural protein 12 (nsp12), whereas the second is catalysed by the 22-kDa nsp8. This latter enzyme is capable of de novo initiation and has been proposed to operate as a primase. Interestingly, this protein has only been crystallized together with the 10-kDa nsp7, forming a hexadecameric, dsRNA-encircling ring structure [i.e. nsp(7+8), consisting of 8 copies of both nsps]. To better understand the implications of these structural characteristics for nsp8-driven RNA synthesis, we studied the prerequisites for the formation of the nsp(7+8) complex and its polymerase activity. We found that in particular the exposure of nsp8's natural N-terminal residue was paramount for both the protein's ability to associate with nsp7 and for boosting its RdRp activity. Moreover, this ‘improved’ recombinant nsp8 was capable of extending primed RNA templates, a property that had gone unnoticed thus far. The latter activity is, however, ∼20-fold weaker than that of the primer-dependent nsp12-RdRp at equal monomer concentrations. Finally, site-directed mutagenesis of conserved D/ExD/E motifs was employed to identify residues crucial for nsp(7+8) RdRp activity. url: https://www.ncbi.nlm.nih.gov/pubmed/22039154/ doi: 10.1093/nar/gkr893 id: cord-286332-cdg4im5h author: van Beurden, Steven J. title: A reverse genetics system for avian coronavirus infectious bronchitis virus based on targeted RNA recombination date: 2017-06-12 words: 6995.0 sentences: 350.0 pages: flesch: 54.0 cache: ./cache/cord-286332-cdg4im5h.txt txt: ./txt/cord-286332-cdg4im5h.txt summary: Herein, the genomic part coding for the spike glycoprotein ectodomain was replaced by that of the coronavirus mouse hepatitis virus (MHV), allowing for the selection and propagation of recombinant mIBV in murine cells. This problem was solved by transfecting IBV genomic RNA into otherwise non-susceptible cells, exchanging the IBV spike gene by that of the mouse hepatitis virus (MHV) provided as part of a synthetic RNA, and by subsequently rescuing recombinant IBV from infected/ transfected cells in embryonated eggs (Fig. 1) . b Stage 1 in targeted RNA recombination: an interspecies chimeric murinized IBV with a MHV spike ectodomain (mIBV) is generated by a single recombination event of IBV genomic RNA with synthetic RNA transcribed from donor plasmid p-mIBV in the 3′-end region of the 1b gene (indicated by a black curved line). Upon transfection of synthetic rIBV donor RNA into mIBV-infected murine LR7 cells, subsequent infectious IBV virus particles could be rescued in ECE. abstract: BACKGROUND: Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens that causes severe economic losses in the poultry industry worldwide. Major advances in the study of the molecular biology of IBV have resulted from the development of reverse genetics systems for the highly attenuated, cell culture-adapted, IBV strain Beaudette. However, most IBV strains, amongst them virulent field isolates, can only be propagated in embryonated chicken eggs, and not in continuous cell lines. METHODS: We established a reverse genetics system for the IBV strain H52, based on targeted RNA recombination in a two-step process. First, a genomic and a chimeric synthetic, modified IBV RNA were co-transfected into non-susceptible cells to generate a recombinant chimeric murinized (m) IBV intermediate (mIBV). Herein, the genomic part coding for the spike glycoprotein ectodomain was replaced by that of the coronavirus mouse hepatitis virus (MHV), allowing for the selection and propagation of recombinant mIBV in murine cells. In the second step, mIBV was used as the recipient. To this end a recombination with synthetic RNA comprising the 3′-end of the IBV genome was performed by introducing the complete IBV spike gene, allowing for the rescue and selection of candidate recombinants in embryonated chicken eggs. RESULTS: Targeted RNA recombination allowed for the modification of the 3′-end of the IBV genome, encoding all structural and accessory genes. A wild-type recombinant IBV was constructed, containing several synonymous marker mutations. The in ovo growth kinetics and in vivo characteristics of the recombinant virus were similar to those of the parental IBV strain H52. CONCLUSIONS: Targeted RNA recombination allows for the generation of recombinant IBV strains that are not able to infect and propagate in continuous cell lines. The ability to introduce specific mutations holds promise for the development of rationally designed live-attenuated IBV vaccines and for studies into the biology of IBV in general. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-017-0775-8) contains supplementary material, which is available to authorized users. url: https://www.ncbi.nlm.nih.gov/pubmed/28606144/ doi: 10.1186/s12985-017-0775-8 id: cord-291860-dw1sfzqx author: van Boheemen, Sander title: Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients date: 2019-12-16 words: 5398.0 sentences: 276.0 pages: flesch: 40.0 cache: ./cache/cord-291860-dw1sfzqx.txt txt: ./txt/cord-291860-dw1sfzqx.txt summary: Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. Clinical sensitivity was analyzed using the optimized procedure, which in short consisted of total nucleic acid extraction, including internal controls (1:100 dilution); the adapted New England Biolabs Next library preparation protocol, including fragmentation with zinc, for combined RNA and DNA detection (see Library Preparation); and sequencing of 10 million reads (Illumina NextSeq 500). The Centrifuge default settings, with NCBI''s nucleotide database and assignment of sequence reads to a maximum of five labels per sequence, resulted in various spurious classifications ( Figure 4) [eg, Lassa virus ( Figure 5 ), evidently highly unlikely to be present in patient samples from the Netherlands with respiratory complaints]. abstract: Viruses are the main cause of respiratory tract infections. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of all potential pathogens. To apply mNGS in viral diagnostics, sensitive and simultaneous detection of RNA and DNA viruses is needed. Herein, were studied the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection. The sequencing protocol and bioinformatics analysis were designed and optimized, including exogenous internal controls. Subsequently, the protocol was retrospectively validated using 25 clinical respiratory samples. The developed protocol using Illumina NextSeq 500 sequencing showed high repeatability. Use of the National Center for Biotechnology Information’s RefSeq database as opposed to the National Center for Biotechnology Information’s nucleotide database led to enhanced specificity of classification of viral pathogens. A correlation was established between read counts and PCR cycle threshold value. Sensitivity of mNGS, compared with PCR, varied up to 83%, with specificity of 94%, dependent on the cutoff for defining positive mNGS results. Viral pathogens only detected by mNGS, not present in the routine diagnostic workflow, were influenza C, KI polyomavirus, cytomegalovirus, and enterovirus. Sensitivity and analytical specificity of this mNGS protocol were comparable to PCR and higher when considering off-PCR target viral pathogens. One single test detected all potential viral pathogens and simultaneously obtained detailed information on detected viruses. url: https://www.sciencedirect.com/science/article/pii/S1525157819304325 doi: 10.1016/j.jmoldx.2019.10.007 id: cord-289321-ahl46ql9 author: van Buuren, Nicholas title: Transmission genetics of drug-resistant hepatitis C virus date: 2018-03-28 words: 7817.0 sentences: 394.0 pages: flesch: 48.0 cache: ./cache/cord-289321-ahl46ql9.txt txt: ./txt/cord-289321-ahl46ql9.txt summary: Differential visualization of drug-resistant and -susceptible RNA genomes within cells revealed that resistant variants of NS3/4A protease and NS5A phosphoprotein are cis-dominant, ensuring their direct selection from complex environments. Our goal was to screen the HCV-encoded viral proteins that are current targets of antiviral compounds to determine the intracellular dominance relationships between drug-resistant and drug-susceptible genomes. To test whether susceptibility to NS5A inhibitors was dominant in the context of viral infections, we analyzed U, S, S + R and R cell populations by flow cytometry as previously performed for the NS3/4A inhibitor in Figure 3 . To test whether exogenously expressed drug-susceptible NS5A proteins could co-assemble with drug-resistant NS5A, we utilized the previously described HCV plasmid that expresses HA-tagged and GFP-tagged NS5A within the same polyprotein but does not support genome replication ( Figure 5A) . Failure of NS5A proteins to mix during infection is a likely explanation for the cis-dominance of drug resistance observed in cultured cells (Figure 4) . abstract: Antiviral development is plagued by drug resistance and genetic barriers to resistance are needed. For HIV and hepatitis C virus (HCV), combination therapy has proved life-saving. The targets of direct-acting antivirals for HCV infection are NS3/4A protease, NS5A phosphoprotein and NS5B polymerase. Differential visualization of drug-resistant and -susceptible RNA genomes within cells revealed that resistant variants of NS3/4A protease and NS5A phosphoprotein are cis-dominant, ensuring their direct selection from complex environments. Confocal microscopy revealed that RNA replication complexes are genome-specific, rationalizing the non-interaction of wild-type and variant products. No HCV antivirals yet display the dominance of drug susceptibility shown for capsid proteins of other viruses. However, effective inhibitors of HCV polymerase exact such high fitness costs for drug resistance that stable genome selection is not observed. Barriers to drug resistance vary with target biochemistry and detailed analysis of these barriers should lead to the use of fewer drugs. url: https://www.ncbi.nlm.nih.gov/pubmed/29589830/ doi: 10.7554/elife.32579 id: cord-299754-tgexahwd author: van Tol, Sarah title: The TRIMendous Role of TRIMs in Virus–Host Interactions date: 2017-08-22 words: 18211.0 sentences: 1015.0 pages: flesch: 41.0 cache: ./cache/cord-299754-tgexahwd.txt txt: ./txt/cord-299754-tgexahwd.txt summary: Downstream of the initial pattern recognition, TRIMs also influence the recruitment and interaction of adaptor molecules (stimulator of IFN genes (STING), mitochondrial antiviral signaling protein (MAVS), TGF-β-activated kinase 1(TAK1)/MAP3K7-binding protein (TAB) 2, Myeloid differentiation primary response gene 88 (MyD88), TIR-domain-containing adapterinducing interferon-β (TRIF), NF-κB essential modulator (NEMO), nucleosome assembly protein (NAP-1), and tumor necrosis factor (TNF) receptor-associated factors (TRAF) family memberassociated NF-κB activator (TANK)) and enzymes (TRAF3, TRAF6, TAK1, inhibitor of NF-κB (IκB) kinase (IKK) α,β,ε, TANK binding kinase 1 (TBK1)) to signaling complexes in order to activate transcription factors. Downstream of the initial pattern recognition, TRIMs also influence the recruitment and interaction of adaptor molecules (stimulator of IFN genes (STING), mitochondrial antiviral signaling protein (MAVS), TGF-β-activated kinase 1(TAK1)/MAP3K7-binding protein (TAB) 2, Myeloid differentiation primary response gene 88 (MyD88), TIR-domain-containing adapter-inducing interferon-β (TRIF), NF-κB essential modulator (NEMO), nucleosome assembly protein (NAP-1), and tumor necrosis factor (TNF) receptor-associated factors (TRAF) family member-associated NF-κB activator (TANK)) and enzymes (TRAF3, TRAF6, TAK1, inhibitor of NF-κB (IκB) kinase (IKK) α,β,ε, TANK binding kinase 1 (TBK1)) to signaling complexes in order to activate transcription factors. abstract: The innate antiviral response is integral in protecting the host against virus infection. Many proteins regulate these signaling pathways including ubiquitin enzymes. The ubiquitin-activating (E1), -conjugating (E2), and -ligating (E3) enzymes work together to link ubiquitin, a small protein, onto other ubiquitin molecules or target proteins to mediate various effector functions. The tripartite motif (TRIM) protein family is a group of E3 ligases implicated in the regulation of a variety of cellular functions including cell cycle progression, autophagy, and innate immunity. Many antiviral signaling pathways, including type-I interferon and NF-κB, are TRIM-regulated, thus influencing the course of infection. Additionally, several TRIMs directly restrict viral replication either through proteasome-mediated degradation of viral proteins or by interfering with different steps of the viral replication cycle. In addition, new studies suggest that TRIMs can exert their effector functions via the synthesis of unconventional polyubiquitin chains, including unanchored (non-covalently attached) polyubiquitin chains. TRIM-conferred viral inhibition has selected for viruses that encode direct and indirect TRIM antagonists. Furthermore, new evidence suggests that the same antagonists encoded by viruses may hijack TRIM proteins to directly promote virus replication. Here, we describe numerous virus–TRIM interactions and novel roles of TRIMs during virus infections. url: https://www.ncbi.nlm.nih.gov/pubmed/28829373/ doi: 10.3390/vaccines5030023 id: cord-315384-eqiokrub author: van der Hoek, Lia title: Croup Is Associated with the Novel Coronavirus NL63 date: 2005-08-23 words: 4403.0 sentences: 209.0 pages: flesch: 57.0 cache: ./cache/cord-315384-eqiokrub.txt txt: ./txt/cord-315384-eqiokrub.txt summary: The viral RNA was more prevalent in samples from outpatients (7.9%) than from hospitalised patients (3.2%, p = 0.003), and co-infection with either respiratory syncytial virus or parainfluenza virus 3 was observed frequently. The samples had been collected from hospitalised patients and outpatients from December 1999 to October 2001 in four different regions in Germany as part of the prospective population-based PRI.DE study and analysed for RNA from respiratory viruses. The samples had been collected from hospitalised patients and outpatients from December 1999 to October 2001 in four different regions in Germany as part of the prospective population-based PRI.DE study and analysed for RNA from respiratory viruses. To investigate the prevalence of HCoV-NL63 and its involvement in respiratory diseases, we now analysed 949 samples from the Paediatric Respiratory Infection in Germany (PRI.DE) study, a prospective population-based study on lower respiratory tract infections (LRTIs) in children under 3 y of age in Germany [8, 9] . abstract: BACKGROUND: The clinical relevance of infections with the novel human coronavirus NL63 (HCoV-NL63) has not been investigated systematically. We therefore determined its association with disease in young children with lower respiratory tract infection (LRTI). METHODS AND FINDINGS: Nine hundred forty-nine samples of nasopharyngeal secretions from children under 3 y of age with LRTIs were analysed by a quantitative HCoV-NL63-specific real-time PCR. The samples had been collected from hospitalised patients and outpatients from December 1999 to October 2001 in four different regions in Germany as part of the prospective population-based PRI.DE study and analysed for RNA from respiratory viruses. Forty-nine samples (5.2%), mainly derived from the winter season, were positive for HCoV-NL63 RNA. The viral RNA was more prevalent in samples from outpatients (7.9%) than from hospitalised patients (3.2%, p = 0.003), and co-infection with either respiratory syncytial virus or parainfluenza virus 3 was observed frequently. Samples in which only HCoV-NL63 RNA could be detected had a significantly higher viral load than samples containing additional respiratory viruses (median 2.1 × 10(6) versus 2.7 × 10(2) copies/ml, p = 0.0006). A strong association with croup was apparent: 43% of the HCoV-NL63-positive patients with high HCoV-NL63 load and absence of co-infection suffered from croup, compared to 6% in the HCoV-NL63-negative group, p < 0.0001. A significantly higher fraction (17.4%) of samples from croup patients than from non-croup patients (4.2%) contained HCoV-NL63 RNA. CONCLUSION: HCoV-NL63 infections occur frequently in young children with LRTI and show a strong association with croup, suggesting a causal relationship. url: https://www.ncbi.nlm.nih.gov/pubmed/16104827/ doi: 10.1371/journal.pmed.0020240 id: cord-347302-ylnb6qfl author: van der Schaar, Hilde M. title: Fat(al) attraction: Picornaviruses Usurp Lipid Transfer at Membrane Contact Sites to Create Replication Organelles date: 2016-03-22 words: 5330.0 sentences: 266.0 pages: flesch: 36.0 cache: ./cache/cord-347302-ylnb6qfl.txt txt: ./txt/cord-347302-ylnb6qfl.txt summary: Replication organelles (ROs) are membranous structures that not only harbor viral proteins but also contain a specific array of hijacked host factors that create a unique lipid microenvironment optimal for genome replication. Whatever function GBF1 plays in enterovirus replication, it might be related to the functioning rather than the formation of ROs, because poliovirus proteins expressed in the presence of BFA induced membrane rearrangements indistinguishable from those found in infected cells [43] . The Importance of MCSs for Controlling the Metabolism of Other Lipids in Infected Cells Besides mediating cholesterol/PI4P exchange, OSBP regulates the homeostasis of other lipids via MCSs. Notably, OSBP regulates the ceramide transfer protein (CERT)-dependent shuttling of ceramide (a precursor of sphingomyelin, a lipid that associates with cholesterol in membrane microdomains) from ER to trans-Golgi [70] . Since RO membranes are enriched in PI4P, ORP5 and/or ORP8 may also be recruited to ER-RO MCSs and transport phosphatidylserine to ROs, from where it may transition to the autophagosome-like DMVs. Enterovirus replication has been associated with alterations of other lipid metabolic pathways as well. abstract: All viruses that carry a positive-sense RNA genome (+RNA), such as picornaviruses, hepatitis C virus, dengue virus, and SARS- and MERS-coronavirus, confiscate intracellular membranes of the host cell to generate new compartments (i.e., replication organelles) for amplification of their genome. Replication organelles (ROs) are membranous structures that not only harbor viral proteins but also contain a specific array of hijacked host factors that create a unique lipid microenvironment optimal for genome replication. While some lipids may be locally synthesized de novo, other lipids are shuttled towards ROs. In picornavirus-infected cells, lipids are exchanged at membrane contact sites between ROs and other organelles. In this paper, we review recent advances in our understanding of how picornaviruses exploit host membrane contact site machinery to generate ROs, a mechanism that is used by some other +RNA viruses as well. url: https://api.elsevier.com/content/article/pii/S0966842X16000548 doi: 10.1016/j.tim.2016.02.017 id: cord-309043-dlmx12vt author: von Brunn, Albrecht title: Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome date: 2007-05-23 words: 6706.0 sentences: 341.0 pages: flesch: 52.0 cache: ./cache/cord-309043-dlmx12vt.txt txt: ./txt/cord-309043-dlmx12vt.txt summary: The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. There are reports that a number of MHV and SARS-CoV replicase proteins colocalize and eventually interact in cytoplasmic membrane bound complexes, in which viral RNA synthesis occurs [18, 19] . We therefore cloned the SARS-CoV ORFeome by recombinatorial cloning (GATEWAY technology) and performed a genome-wide analysis for viral protein interactions by yeast-two-hybrid (Y2H) matrix screen. To systematically study the subcellular localization of viral proteins within eukaryotic HeLa cells the SARS-CoV ORFs were transfected in eukaryotic vectors with either N-or C-terminal Flag tags and detected with an anti-Flag antibody. In this study we report the cloning of the complete ORFeome of SARS-CoV and the results of a matrix-based yeast two-hybrid screen of pairwise viral protein-protein interactions. abstract: The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural protein products. The functions of a large number of viral ORFs are poorly understood or unknown. In order to gain more insight into functions and modes of action and interaction of the different proteins, we cloned the viral ORFeome and performed a genome-wide analysis for intraviral protein interactions and for intracellular localization. 900 pairwise interactions were tested by yeast-two-hybrid matrix analysis, and more than 65 positive non-redundant interactions, including six self interactions, were identified. About 38% of interactions were subsequently confirmed by CoIP in mammalian cells. Nsp2, nsp8 and ORF9b showed a wide range of interactions with other viral proteins. Nsp8 interacts with replicase proteins nsp2, nsp5, nsp6, nsp7, nsp8, nsp9, nsp12, nsp13 and nsp14, indicating a crucial role as a major player within the replication complex machinery. It was shown by others that nsp8 is essential for viral replication in vitro, whereas nsp2 is not. We show that also accessory protein ORF9b does not play a pivotal role for viral replication, as it can be deleted from the virus displaying normal plaque sizes and growth characteristics in Vero cells. However, it can be expected to be important for the virus-host interplay and for pathogenicity, due to its large number of interactions, by enhancing the global stability of the SARS proteome network, or play some unrealized role in regulating protein-protein interactions. The interactions identified provide valuable material for future studies. url: https://www.ncbi.nlm.nih.gov/pubmed/17520018/ doi: 10.1371/journal.pone.0000459 id: cord-302830-5psqxxc8 author: Ávila‐Pérez, Ginés title: Ultrastructural characterization of membranous torovirus replication factories date: 2016-07-05 words: 9037.0 sentences: 426.0 pages: flesch: 51.0 cache: ./cache/cord-302830-5psqxxc8.txt txt: ./txt/cord-302830-5psqxxc8.txt summary: To characterize the torovirus RTCs, we generated specific sera for BEV M pro , Hel and RdRp, three key proteins in the formation and functioning of nidovirus RTCs, that were used in confocal and transmission electron microscopy (TEM) assays to analyse the location of viral components involved in BEV replication. It has been shown that in cells infected with different nidoviruses, virus-induced membrane reorganization produces characteristic DMVs, as well as other membranous structures, which have been related with the viral RNA replication and transcription processes. To investigate whether torovirus DMVs are the sites where replication and transcription occur, we obtained specific sera for the BEV M pro , Hel and RdRp, three key proteins in the formation and functioning of RTCs. All showed a high colocalization with each other and with newly synthesized RNAs. However, the dsRNA, widely used as a marker of RTC in several positive-strand RNA viruses, only showed a partial colocalization with the nsps. abstract: Plus‐stranded RNA viruses replicate in the cytosol of infected cells, in membrane‐bound replication complexes containing the replicase proteins, the viral RNA and host proteins. The formation of the replication and transcription complexes (RTCs) through the rearrangement of cellular membranes is currently being actively studied for viruses belonging to different viral families. In this work, we identified double‐membrane vesicles (DMVs) in the cytoplasm of cells infected with the equine torovirus Berne virus (BEV), the prototype member of the Torovirus genus (Coronaviridae family, Nidovirales order). Using confocal microscopy and transmission electron microscopy, we observed a close relationship between the RTCs and the DMVs of BEV. The examination of BEV‐infected cells revealed that the replicase proteins colocalize with each other and with newly synthesized RNA and are associated to the membrane rearrangement induced by BEV. However, the double‐stranded RNA, an intermediate of viral replication, is exclusively limited to the interior of DMVs. Our results with BEV resemble those obtained with other related viruses in the Nidovirales order, thus providing new evidence to support the idea that nidoviruses share a common replicative structure based on the DMV arranged clusters. url: https://doi.org/10.1111/cmi.12620 doi: 10.1111/cmi.12620 id: cord-278635-vwdxr1bl author: Świętoń, Edyta title: Low pathogenic avian influenza virus isolates with different levels of defective genome segments vary in pathogenicity and transmission efficiency date: 2020-08-28 words: 5432.0 sentences: 295.0 pages: flesch: 48.0 cache: ./cache/cord-278635-vwdxr1bl.txt txt: ./txt/cord-278635-vwdxr1bl.txt summary: In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). Virions containing highly deleted forms of genome segments (defective viral genes-DVGs) are able to replicate only in the presence and at the expense of fully infectious virus, hence the term "defective interfering particles" (DIPs) [4] . To evaluate the effect of DIPs on the course of infection with low pathogenic avian influenza virus (LPAIV), a comparison of pathogenicity of two virus stocks of H7N7 LPAIV with different levels of defective genomes was performed in turkeys and chickens. Infected birds received the same infectious dose of the virus but with different amount of DVGs. The semiquantitative analysis of defective particles was done by a combination of RT-PCR, real time RT-PCR and whole genome sequencing and indicated significantly higher amount of truncated gene segments in 95/95(DVG-high). abstract: Defective interfering particles (DIPs) of influenza virus are generated through incorporation of highly truncated forms of genome segments, mostly those coding polymerase complex proteins (PB2, PB1, PA). Such particles are able to replicate only in the presence of a virus with the complete genome, thus DIPs may alter the infection outcome by suppressing production of standard virus particles, but also by stimulating the immune response. In the present study we compared the clinical outcome, mortality and transmission in chickens and turkeys infected with the same infectious doses of H7N7 low pathogenic avian influenza virus containing different levels of defective gene segments (95/95(DVG-high) and 95/95(DVG-low)). No clinical signs, mortality or transmission were noted in SPF chickens inoculated with neither virus stock. Turkeys infected with 95/95(DVG-high) showed only slight clinical signs with no mortality, and the virus was transmitted only to birds in direct contact. In contrast, more severe disease, mortality and transmission to direct and indirect contact birds was observed in turkeys infected with 95/95(DVG-low). Apathy, lower water and food intake, respiratory system disorders and a total mortality of 60% were noted. Shedding patterns in contact turkeys indicated more efficient within- and between-host spread of the virus than in 95/95(DVG-high) group. Sequencing of virus genomes showed no mutations that could account for the observed differences in pathogenicity. The results suggest that the abundance of DIPs in the inoculum was the factor responsible for the mild course of infection and disrupted virus transmission. url: https://doi.org/10.1186/s13567-020-00833-6 doi: 10.1186/s13567-020-00833-6 ==== make-pages.sh questions [ERIC WAS HERE] parallel: Warning: Only enough available processes to run 15 jobs in parallel. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf parallel: Warning: or /proc/sys/kernel/pid_max may help. parallel: Warning: No more processes: Decreasing number of running jobs to 14. parallel: Warning: Raising ulimit -u or /etc/security/limits.conf may help. /data-disk/reader-compute/reader-cord/bin/list-questions.sh: fork: retry: No child processes /data-disk/reader-compute/reader-cord/bin/list-questions.sh: fork: retry: No child processes ==== make-pages.sh search /data-disk/reader-compute/reader-cord/bin/make-pages.sh: line 77: /data-disk/reader-compute/reader-cord/tmp/search.htm: No such file or directory Traceback (most recent call last): File "/data-disk/reader-compute/reader-cord/bin/tsv2htm-search.py", line 51, in with open( TEMPLATE, 'r' ) as handle : htm = handle.read() FileNotFoundError: [Errno 2] No such file or directory: '/data-disk/reader-compute/reader-cord/tmp/search.htm' ==== make-pages.sh topic modeling corpus Zipping study carrel