Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 48 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 3836 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 55 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 15 SARS 5 IBV 5 China 3 virus 3 codon 3 RVA 2 usage 2 strain 2 bat 2 ITA 2 CoV-2 2 ACE2 1 vp7 1 vp1 1 variant 1 protein 1 population 1 polish 1 pfu 1 model 1 korean 1 japanese 1 indian 1 hexon 1 genome 1 figure 1 bayesian 1 Zambia 1 USA 1 Taiwan 1 TMPRSS2 1 Sweden 1 Sudan 1 Rab1404 1 RNA 1 RBD 1 Pteropus 1 Poland 1 PEDV 1 PCR 1 ORF2 1 ORF 1 ON1 1 NL63 1 MRV 1 Leptospira 1 Lacroix 1 LHLJ/07VII 1 Korea 1 JEV Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 1457 virus 1041 strain 985 sequence 855 protein 756 % 632 gene 577 analysis 508 study 491 genome 456 cell 440 bat 418 host 416 coronavirus 378 infection 377 sample 373 codon 346 region 313 genotype 307 disease 305 mutation 302 population 294 epitope 270 vaccine 265 acid 248 usage 244 model 242 number 229 tree 227 recombination 221 type 218 amino 206 time 206 datum 205 method 201 r 198 evolution 192 group 191 bronchitis 190 c 189 rate 184 value 181 g 178 transmission 175 human 175 diversity 173 patient 171 lineage 167 dog 164 result 163 site Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 1997 al 1808 . 1596 et 666 SARS 363 CoV-2 329 RNA 301 China 294 Fig 266 IBV 214 CoV 200 PCR 187 S 118 C 116 Table 114 S1 111 CH 101 A 100 CoVs 94 HRSV 87 RT 86 USA 85 M 85 EV71 83 HIV 82 COVID-19 79 RVA 79 GenBank 78 FeKoV 77 ORF 75 NoVs 73 Borrelia 71 aa 70 Korea 70 Italy 69 ACE2 68 VP1 68 T 67 South 67 IFN 66 Leptospira 64 S2 64 MERS 62 QX 61 kobuvirus 61 Coronavirus 58 HIV-1 57 cK 53 PEDV 53 JEV 53 East Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 437 we 304 it 112 they 94 i 45 them 18 us 13 he 5 she 5 itself 3 ch/ 2 themselves 2 one 1 À0.516 1 you 1 rs12329760 1 ourselves 1 kx263307-kx263316 1 ifnβ1 1 her 1 h120 1 clustalx Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 5440 be 846 use 832 have 343 show 290 identify 285 find 251 base 226 include 215 isolate 202 detect 185 infect 173 indicate 165 report 163 suggest 149 cause 146 perform 136 reveal 135 associate 134 contain 131 obtain 128 follow 126 relate 126 do 126 determine 124 provide 118 estimate 113 analyze 110 observe 108 compare 107 bind 106 describe 105 predict 105 collect 97 emerge 90 consider 87 belong 86 result 85 represent 85 know 83 encode 77 accord 76 locate 73 give 72 involve 71 select 69 increase 69 affect 68 generate 67 support 67 share Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 418 human 350 viral 336 - 333 other 323 genetic 321 high 309 not 307 also 290 respiratory 284 different 280 phylogenetic 274 infectious 217 more 198 molecular 195 first 192 positive 189 nucleotide 187 however 186 most 174 only 160 genomic 154 novel 147 non 146 acute 145 evolutionary 145 complete 145 canine 143 further 142 like 141 such 141 similar 141 new 131 low 128 avian 122 specific 121 severe 121 respectively 116 same 109 synonymous 107 potential 105 multiple 104 immune 102 well 99 large 99 highly 97 major 97 important 96 single 95 structural 94 natural Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 64 high 52 most 19 Most 17 least 15 good 9 close 7 strong 7 low 7 large 5 long 5 late 5 great 5 early 3 near 1 simple 1 short 1 poor 1 old 1 big 1 ClustalW Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 134 most 13 least 4 well 1 worst 1 close Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 10 www.ncbi.nlm.nih.gov 7 dx 6 github.com 4 tree.bio.ed.ac.uk 3 www 3 dx.doi.org 3 blast.ncbi.nlm.nih.gov 2 www.ebi.ac.uk 1 xena.ucsc.edu 1 www.viprbrc.org 1 www.technelysium.com.au 1 www.phylogeny.fr 1 www.nitttrkol.ac.in 1 www.nhc.gov.cn 1 www.ncbi.nlm 1 www.ncbi 1 www.kazusa.or.jp 1 www.jalview.org 1 www.generunner.com 1 www.epicov.org 1 www.ddgpharmfac.net 1 www.cogconsortium.uk 1 www.cbs.dtu.dk 1 www.cbs 1 www.bioinformatics.babraham.ac.uk 1 web.expasy.org 1 virological.org 1 viralzone.expasy.org 1 tools.iedb.org 1 talk.ictvonline.org 1 spades.bioinf 1 sidirect2.rnai.jp 1 rotac.regatools.be 1 rega.kuleuven.be 1 nextstrain.org 1 multalin.toulouse.inra.fr 1 macman123.shinyapps.io 1 itol.embl.de 1 gtrnadb 1 genomes.urv.es 1 eurofinsgenomics.eu 1 doi.org 1 cov-glue.cvr.gla.ac.uk 1 blast.ncbi 1 beast.bio.ed.ac.uk 1 arxiv.org 1 aps.unmc.edu 1 abacus.gene.ucl.ac.uk Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 7 http://dx 3 http://www.ncbi.nlm.nih.gov 3 http://www 3 http://blast.ncbi.nlm.nih.gov/Blast.cgi 2 http://www.ncbi.nlm.nih.gov/orffinder/ 2 http://www.ncbi.nlm.nih.gov/ 2 http://www.ebi.ac.uk/fasta33 2 http://tree.bio.ed.ac.uk/software/ 2 http://github.com/CaioFreire/CUB 2 http://dx.doi.org/10.1016/j.meegid.2015.03 1 http://xena.ucsc.edu 1 http://www.viprbrc.org/ 1 http://www.technelysium.com.au/ 1 http://www.phylogeny.fr/documentation.cgi 1 http://www.nitttrkol.ac.in/indrajit/projects/COVID-Mutation-India/" 1 http://www.nhc.gov.cn/yzygj/s7653p/202003/46c9294a7dfe4cef80dc7f5912eb1989.s 1 http://www.ncbi.nlm.nih.gov/taxonomy/ 1 http://www.ncbi.nlm.nih.gov/gorf/gorf.html 1 http://www.ncbi.nlm.nih.gov/Genbank/ 1 http://www.ncbi.nlm 1 http://www.ncbi 1 http://www.kazusa.or.jp/codon/ 1 http://www.jalview.org/ 1 http://www.generunner.com 1 http://www.epicov.org 1 http://www.ddgpharmfac.net/vaxijen/ 1 http://www.cogconsortium.uk/data/ 1 http://www.cbs.dtu.dk/services/NetMHC/ 1 http://www.cbs 1 http://www.bioinformatics.babraham.ac.uk/ 1 http://web.expasy.org/protparam/ 1 http://virological.org/t/selection-analysis-of-gisaid-sars-cov-2data/448/3 1 http://viralzone.expasy.org/ 1 http://tree.bio.ed.ac.uk/ 1 http://tree.bio.ed.ac.uk 1 http://tools.iedb.org/conservancy/ 1 http://talk.ictvonline.org/taxonomy/ 1 http://spades.bioinf 1 http://sidirect2.rnai.jp 1 http://rotac.regatools.be 1 http://rega.kuleuven.be/cev/viralmetagenomics/virus-classification/ 1 http://nextstrain.org 1 http://multalin.toulouse.inra.fr/multalin/ 1 http://macman123.shinyapps.io/ugi-scov2-alignmentscreen/ 1 http://itol.embl.de/ 1 http://gtrnadb 1 http://github.com/nextstrain/ncov/tree/master/data 1 http://github.com/liampshaw/CoV-homoplasy-filtering 1 http://github.com/DamienFr/CoV-homoplasy 1 http://github.com/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 4 samples were positive 4 studies have also 3 analysis using maximum 3 bats are natural 3 rna was reverse 3 samples were also 3 sequences were more 3 strains were almost 2 bats are genetically 2 cells was as 2 china including yunnan 2 epitope binding efficiency 2 gene was closely 2 genome is also 2 genome is approximately 2 genomes were successfully 2 genotype was also 2 protein causes endoplasmic 2 samples showing hyper 2 samples were randomly 2 sequence is build 2 sequences were identical 2 strains cause disease 2 strains did not 2 strains were first 2 studies are necessary 2 study did not 2 study was also 2 virus are responsible 2 virus does not 2 virus was first 2 viruses do not 2 viruses were similar 1 % are attributable 1 % is suggestive 1 % were lower 1 . is widely 1 . used snp 1 . using pcr 1 . were highly 1 . were present 1 analyses reveal human 1 analyses showed significant 1 analysis are least 1 analysis does not 1 analysis has also 1 analysis identified only 1 analysis identified stronger 1 analysis is limited 1 analysis provides insight Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 1 china were not clear 1 coronavirus is not closely 1 gene is not variable 1 mutation is not necessarily 1 protein contained no aliphatic 1 protein is not essential 1 protein was not complete 1 samples were not able 1 sequences were not normally 1 strain does not directly 1 strains are not variant 1 virus is not essential 1 viruses are not simple A rudimentary bibliography -------------------------- id = cord-255141-55ho9av4 author = Abolnik, Celia title = Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus date = 2015-04-03 keywords = IBV; ORF summary = A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5′UTR did not alter the predicted secondary structure. Coronavirus accessory proteins are generally dispensable for virus replication, but they play vital roles in virulence and pathogenesis by affecting host innate immune responses, encoding pro-or anti-apoptotic activities, or by effecting other signalling pathways that influence disease outcomes (Susan & Julian, 2011) . Mapping of the receptor-binding domain and amino acids critical for attachment in the spike protein of avian coronavirus infectious bronchitis virus Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences doi = 10.1016/j.meegid.2015.03.033 id = cord-271818-bedfwdyt author = Afelt, Aneta title = Distribution of bat-borne viruses and environment patterns date = 2017-12-23 keywords = AOI; Cambodia; Lacroix summary = Viruses associated to synanthropic bat genera, such as Myotis or Scotophilus were associated to highly transformed habitats with human presence while viruses associated to fruit bat genera were correlated with natural environments with dense forest, grassland areas and regions of high elevation. Another conclusion from this analysis is the higher bat biodiversity observed in Cambodia associated to more anthropized environment than in LAO PDR where dense forest was predominant (Fig. 3) . The contributions of the environmental variables to the construction of this axis were the highest for elevation, SDI and grassland which were correlated on the negative side and connectivity, forest fragmentation, cropland cover, water cover, wetland cover and settlement cover which were distributed on the positive side (Fig. 4a) . The principal dimension of variability of the PCA opposed anthropogenic transformed lands on the positive side to more natural environments (i.e. forest, higher elevation areas and grassland areas, with low fragmentation) on the negative side (Fig. 4a) . doi = 10.1016/j.meegid.2017.12.009 id = cord-318577-04jsj9sb author = Bodnar, Livia title = Identification of a novel canine norovirus date = 2017-04-24 keywords = ITA summary = By screening a collection of fecal samples from young dogs from different European countries, noroviruses (NoVs) were found in 13/294 (4.4%) animals with signs of enteritis whilst they were not detected in healthy dogs (0/42). Interestingly, significant sequence variation has been found across different canine/feline NoV strains identified to date, allowing the classification of at least 4 genotypes from three distinct genogroups, i.e. GIV.2, GVI.1 and GVI.2 and GVII ( Table 1 ). In order to draw a more complete picture of NoV molecular epidemiology in dogs, in this study a collection of fecal specimens from diarrheic and healthy animals obtained from different European countries was screened using both broadly-reactive primers for caliciviruses and primers specific for NoVs. The sequence of a large portion of the genome at the 3′ end of two canine NoV strains was determined. doi = 10.1016/j.meegid.2017.04.020 id = cord-319399-r5hgfsxz author = Chakraborty, Supriyo title = Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach date = 2019-11-06 keywords = JEV; japanese summary = title: Japanese encephalitis virus: A multi-epitope loaded peptide vaccine formulation using reverse vaccinology approach The predicted epitopes identified in five proteins selected in this study could be promising for formulating a peptide vaccine against JEV and hence, could prevent the spread of JEV in affected individuals. In this study, the potential epitopes for peptide vaccine formulation were identified in five proteins of JEV namely E, prM, NS1, NS3 and NS5. In a study, the probable epitopes were identified from E6 protein of hrHPVs and these epitopes were reported to possess competence in preparing successful peptide vaccine against hrHPVs. Based on in silico approach, it was suggested Table 2a Immunogenicity (Ig) and number of aliphatic amino acids in T-cell epitopes of JEV (Hopp & Woods approach, 1981 The present study suggested that a multi-epitope-based peptide vaccine against JEV could be developed by combining the promising Bcell and T-cell epitopes found in E, prM, NS1, NS3 and NS5 proteins. doi = 10.1016/j.meegid.2019.104106 id = cord-266660-0wq77k6y author = Choi, Jong-Chul title = Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea date = 2014-06-19 keywords = PEDV; korean summary = title: Comparative genome analysis and molecular epidemiology of the reemerging porcine epidemic diarrhea virus strains isolated in Korea We detected three PEDV strains from ten small intestine samples from piglets with acute diarrhea and we determined the complete genome sequences of the reemerging Korean PEDV field isolates, except for the noncoding regions from both ends. This study aimed to determine the complete genome sequence of the reemerging Korean PEDV strain and to investigate their genetic relationship with other strains using comparative genome analysis and phylogenetic analysis. In addition, all available complete genome sequences of PEDV isolates from Korea were included in the alignment to compare the recent Korean strains with previous endemic Korean PEDV strains. Multiple alignment with other PEDV complete genomes indicated that the reemerging Korean strains possess genome sequences, which are distinct from those of previous Korean field strains (Fig. 1) . doi = 10.1016/j.meegid.2014.06.005 id = cord-262592-0rdiosxd author = Cuevas, José M. title = Human norovirus hyper-mutation revealed by ultra-deep sequencing date = 2016-04-17 keywords = PCR; RNA summary = This revealed the presence of low-frequency sequences carrying large numbers of U-to-C or A-to-G base transitions, suggesting a role for hyper-mutation in NoV diversity. Based on the sequence context of the observed changes, we propose that NoV hypermutation might be driven by ADAR-mediated editing of the viral genomic RNA of either polarity during replication. We used 16 stool samples from patients acutely infected with NoV GII.4 to amplify by RT-PCR a 386-base region encompassing nucleotides 1 to 386 of the VP1 gene (reference sequence: GenBank JX459908; Fig. 1A ). After 48 h incubation, total RNA was extracted from cells, residual DNA was removed with DNAse I, a specific primer annealing to the minus-strand of the VP1 capsid gene was used for reverse transcription, and high-fidelity PCR amplification of a region encompassing positions 19 to 323 of the VP1 gene (305 bases, although only the 266 bases excluding primer regions Fig. 1 . doi = 10.1016/j.meegid.2016.04.017 id = cord-299827-lxyo3z3u author = Di Martino, Barbara title = A novel feline norovirus in diarrheic cats date = 2015-12-29 keywords = ITA summary = In the full-length ORF2, encoding the VP1 capsid protein, the virus was genetically closest to the canine GVI.2 NoV strains C33/Viseu/2007/PRT and FD53/2007/ITA (81.0–84.0% nt and 93.0–94.0% aa identities), suggesting a recombination nature, with the cross-over site being mapped to the ORF1-ORF2 junction. c o m / l o c a t e / m e e g i d Altogether these findings indicate that diverse NoV strains may infect cats, as observed in dogs, and that the feline and canine host may be infected by the same NoV strains, thus constituting an enlarged host reservoir for these animal NoVs. In order to draw a more complete picture of NoVs molecular epidemiology in cats, in this study a collection of fecal specimens from diarrheic and healthy animals was screened using either broadly-reactive primers for caliciviruses and primers specific for NoVs. A total of 105 stool samples from domestic cats aged 2-12 months were collected from April to July 2013 in three different shelters located in South Italy. doi = 10.1016/j.meegid.2015.12.019 id = cord-271897-9oqzsd70 author = Domanska-Blicharz, Katarzyna title = Molecular epidemiology of infectious bronchitis virus in Poland from 1980 to 2017 date = 2020-01-07 keywords = IBV; Poland; polish; strain summary = Additionally, two strains from 1989 and 1997 formed a separate branch of the phylogenetic tree categorized as unique early Polish variants, and one strain was revealed to be the recombinant of these and GI-1 lineage viruses. Irrespective of year of isolation and S1-dependent genotype, the genome sequences of Polish IBV strains showed the presence of six genes and 13 ORFs: 5′UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3′UTR, however their individual genes and putative proteins had different lengths. Genotyping based on phylogenetic analysis of full S1 coding region sequences of 34 Polish IBV strains from the years 1980-2017 grouped (caption on next page) K. Phylogenetic analysis of the full S1 coding region showed that strain 80/ 1989 forms a separate branch on the tree designated as early Polish and was classified as a unique variant of IBV within the GI genotype. doi = 10.1016/j.meegid.2020.104177 id = cord-257584-v38tjof3 author = Fahmi, Muhamad title = Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV date = 2020-03-03 keywords = SARS; protein summary = Two of six Clade 2 nonstructural proteins, NS7b and NS8, were exclusively conserved among 2019-nCoV, BetaCoV_RaTG, and BatSARS-like Cov. NS7b and NS8 have previously been shown to affect immune response signaling in the SARS-CoV experimental model. This was done using a combination of the phylogenetic tree constructed from the genome sequences and the cluster tree developed from the profiles retrieved from the presence and absence of homologs of ten 2019-nCoV proteins. The phylogenetic analysis using complete genome sequences showed that 2019-nCoV was the most closely related to BatCoV RaTG13 and belonged to the Sarbecovirus subgenus of Betacoronavirus, together with SARS coronavirus and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45) with the full support of reliability (Fig. 1) . Two (NS7b and NS8) of five nonstructural proteins were specific for 2019-nCoV and its closely related species, BatCoV RaTG13 and Bat-SARS-like coronavirus (BAT-SL-CoVZXC21 and BAT-SL-CoVZC45). doi = 10.1016/j.meegid.2020.104272 id = cord-311144-tumtzad8 author = Franco-Muñoz, Carlos title = Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America date = 2020-09-17 keywords = Colombia; SARS summary = A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Substitution matrices of nucleotides and amino acids of S and N proteins were generated from a multiple sequence alignment with the reference genome against the 43 assembled Colombian SARS-CoV-2 genomes (Table 1) using the Muscle algorithm (Edgar, 2004) in MEGA X (Kumar et al., 2016) . The analysis of substitution frequencies by country shows that D614G substitution in the S protein was frequent in Argentina, Brazil, Chile, Colombia and Peru, with J o u r n a l P r e -p r o o f Journal Pre-proof 80-100% of the reported sequences ( Fig. 2A) . doi = 10.1016/j.meegid.2020.104557 id = cord-253245-433mg0ke author = Gao, Zhiru title = A systematic review of re-detectable positive virus nucleic acid among COVID-19 patients in recovery phase date = 2020-08-05 keywords = SARS summary = A recent study reported that four medical workers aged 30-36 years who had re-detectable positive (RP) for SARS-CoV-2 within 5-13 days after being cured and discharged, indicating that some of the recovered patients may still be virus carriers, which caused widespread concern (Lan et al., 2020). Although the results of the three nucleic acid tests were negative for the patient, there were viral residue in the lungs, so even if the patient was discharged, we supposed that virus would transfer positive again after a period of time (Yao et al., 2020) . In addition, initial studies reported that the SARS-CoV-2 RNA could be detected in the feces of 81.8% recovered patients (54/66), even in those with negative throat swabs (Ling et al., 2020) . In other words, even if sometimes the virus nucleic acid tested by RT-PCR is positive in the recovery phase of COVID-19, it will not cause a more serious condition, and antiviral therapy may not be required in most patients. doi = 10.1016/j.meegid.2020.104494 id = cord-261547-8tfbhmzo author = Góes, Luiz Gustavo Bentim title = Genetic diversity of bats coronaviruses in the Atlantic Forest hotspot biome, Brazil date = 2016-07-26 keywords = bat summary = In this report, we identified and characterized previously unknown and diverse genetic clusters of bat coronaviruses in the Atlantic Forest Biome, Brazil. Recently, a number of novel bats CoVs have been identified, primarily from African, Asian and European bats (Calisher et al., 2006; Chu et al., 2006; Drexler et al., 2014) , as well as from South American countries including Costa Rica, Panama, Ecuador, Mexico and Brazil (Corman et al., 2013; Goes et al., 2013) . Coronaviruses were detected in 15 bat intestines samples from eight bat species with distinct diet habit, demonstrating a marked potential of CoVs distribution among bat species in AFB that harbours 9% of world''s bat diversity. α-CoV sequences obtained from bats of same genus presented high nucleotide sequence similarity (e.g. Artibeus, Glossophaga, Carollia, Molossus, Myotis and Sturnira) (Fig. 1D and Supplementary table), even with sequences detected in other studies from bats of geographically distant regions. It is indispensable in future to investigate the evolutionary events in genetically diverse bats CoVs using complete genome sequences, and their possible transmission potentials to human being. doi = 10.1016/j.meegid.2016.07.034 id = cord-260644-5moccf8c author = Hashemi, Seyed Ahmad title = Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 date = 2020-11-07 keywords = SARS summary = title: Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2 Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Some researchers evaluated and compared the whole genome sequence of SARS-CoV-2 isolated in various parts of the world and identified some mutations. The high-frequency mutations of the SARS-CoV-2 genome were seen in nsp6, RNA polymerase, helicase, membrane glycoprotein, RNA primase, nucleocapsid phosphoprotein, and spike protein genes (Yin, 2020) . In the first step, we used the sequence of S protein of SARS-CoV-2, published in Gene bank with accession number MT252819.1, for appropriate restriction endonuclease selection and primer design. The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity doi = 10.1016/j.meegid.2020.104625 id = cord-268968-0s6e6y8s author = Kim, You-Jin title = Rapid replacement of human respiratory syncytial virus A with the ON1 genotype having 72 nucleotide duplication in G gene date = 2014-05-10 keywords = HRSV; Korea; ON1 summary = The mean evolutionary rate of G protein was calculated as 3.275 × 10(−3) nucleotide substitution/site/year and several positively selected sites for amino acid substitutions were located in the predicted epitope region. Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication Complete genome sequence of human respiratory syncytial virus genotype A with a 72-nucleotide duplication in the attachment protein G gene Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nucleotide duplication in the G protein gene Genetic analysis of attachment glycoprotein (G) gene in new genotype ON1 of human respiratory syncytial virus detected in Japan doi = 10.1016/j.meegid.2014.05.007 id = cord-297530-7zbvgvk8 author = Kühnert, Denise title = Phylogenetic and epidemic modeling of rapidly evolving infectious diseases date = 2011-08-31 keywords = HIV-1; bayesian; model; population summary = By using Kingman''s coalescent as a prior density on trees, Bayesian inference can be used to simultaneously estimate the phylogeny of the viral sequences and the demographic history of the virus population (Drummond et al., 2002 (Drummond et al., , 2005 , see Box 1). A maximum likelihood based method (the single rate dated tips (SRDT) model; Rambaut, 2000) , estimates ancestral divergence times and overall substitution rate on a fixed tree, assuming a strict molecular clock. While the generalized skyline plot is a good tool for data exploration, and to assist in model selection (e.g., Pybus et al., 2003; Lemey et al., 2004) , it infers demographic history based on a single input tree and therefore does not account for sampling error produced by phylogenetic reconstruction nor for the intrinsic stochasticity of the coalescent process. doi = 10.1016/j.meegid.2011.08.005 id = cord-267136-1abp6oom author = Lan, Yu-Ching title = Phylogenetic analysis and sequence comparisons of structural and non-structural SARS coronavirus proteins in Taiwan date = 2004-12-07 keywords = CUHK; SARS; Taiwan summary = Taiwan experienced a large number of severe acute respiratory syndrome (SARS) viral infections between March and July 2003; by September of that year, 346 SARS cases were confirmed by RT-PCR or serological tests. In order to better understand evolutionary relationships among SARS coronaviruses (SCoVs) from different international regions, we performed phylogenetic comparisons of full-length genomic and protein sequences from 45 human SCoVs (including 12 from Taiwan) and two civet SCoVs. All the Taiwanese SARS-CoV strains which associated with nosocomial infection formed a monophyletic clade within the late phase of the SARS epidemic. To better understand evolutionary relationships between SCoVs isolated in Taiwan and those isolated in other parts of the world, we constructed phylogenetic trees with two different methods using full-length genomic sequences from 45 human (12 Taiwanese) and two civet SCoVs. Tree topologies were consistent for the NJ (Fig. 1a) and Pars (Fig. 1b) methods. Pairwise comparison methods were used to analyze nucleotide sequence variation within the full-length genomes of 20 human SCoVs (7 from early epidemic and 13 from late epidemic) (Fig. 2) . doi = 10.1016/j.meegid.2004.08.005 id = cord-338723-3vm23fgy author = Lee, In-Hee title = A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations date = 2020-08-26 keywords = ACE2; SARS; TMPRSS2 summary = title: A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations Nonetheless, a systematic mutagenesis study on the receptor binding domain of ACE2 is required to understand the difference in host-viral interaction across populations. SARS-CoV-2 is an enveloped and positive single-stranded RNA (ssRNA) virus and initiates human cell entry by binding of spike (S) protein present on the viral envelope to angiotensin converting enzyme 2 (ACE2) receptor on the host cells (Zhou et al., 2020b) . Here we surveyed the genetic variants in functional residues of ACE2, TMPRSS2, CTSB/L (CatB/L), and TLR3/7/8 to investigate the difference in the genetic predisposition to the susceptibly of SARS-CoV-2 infection and the initiation of innate immune response. The list of reported genetic variants in the genes and their allele frequencies (AFs) were ACE2 is highly conserved with few nonsynonymous variants in the interacting domain with the SARS-CoV-2 RBM (Lan et al., 2020) . doi = 10.1016/j.meegid.2020.104507 id = cord-279836-lyvvtwvg author = Li, Huiping title = Molecular detection and genomic characteristics of bovine kobuvirus from dairy calves in China date = 2019-06-24 keywords = China; vp1 summary = In this study, 96 diarrheic and 77 non-diarrheic fecal samples from dairy calves were collected from 14 dairy farms in 4 provinces to investigate the molecular prevalence and genomic characteristics of Bovine Kobuvirus (BKoV) in China. Interestingly, three potential novel VP1 lineages were identified from 15 complete VP1 sequences, and a unique triple nucleotide insertion which can result in an aa insertion, was first observed in the 11/12 VP0 fragments with 660 bp long in this study, compared with known BKoV VP0 sequences. Interestingly, phylogenetic tree based on aa sequences of these genomes showed that CHZ/CHINA was clustered into an independent branch, suggesting the strain may represent a novel BKoV strain. Further phylogenetic analysis based on genomic sequences revealed that CHZ/CHINA clusters on an independent branch, with the three VP0, VP3, VP1 protein aa sequences generating the same result (Fig. 3) , showing that CHZ/CHINA displays a larger genetic distance from the other three genomes and indicating that CHZ/CHINA may represent a novel BKoV strain. doi = 10.1016/j.meegid.2019.103939 id = cord-278973-82n0d1dh author = Li, Zhijie title = Characterization and pathogenicity of a novel mammalian orthoreovirus from wild short-nosed fruit bats date = 2016-05-31 keywords = B/03; MRV; pfu; virus summary = This study describes the isolation, molecular characterization and analysis of pathogenicity of MRV variant B/03 from wild short-nosed fruit bats. BALB/c mice experimentally infected with B/03 virus by intranasal inoculation developed severe respiratory distress with tissue damage and inflammation. MRV isolates were obtained from hosts with or without clinical signs of disease, and the virus can infect a broad range of mammals (Dermody et al., 2013) . In this study, we report the characterization of a novel MRV strain (called "B/03") isolated from healthy, wild shortnosed fruit bats in Guangdong province, China. In this study, one strain of MRV, B/03, was isolated by in vitro cell culture from thirty wild short-nosed fruit bat samples from Shaoguan city of China''s Guangdong province. Based on sequence comparison and phylogenetic analysis, we conclude that the B/03 isolate is a novel type 1 bat orthoreovirus, and it might have originated from gene segment mixing during infection with more than one MRV strain in nature. doi = 10.1016/j.meegid.2016.05.039 id = cord-279495-zxerb7de author = Liu, Xiaoli title = Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome date = 2012-11-21 keywords = IBV; LHLJ/07VII; strain summary = Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41and H120-like strains at the switch site located at the 3′ end of the nucleocapsid (N) genes. Herein, we sequenced the complete genome of four IBV Mass-type strains that showed S1 gene diversity (Liu et al., 2009; Ma et al., 2012; Sun et al., 2011) , and we present evidence for in-field recombination between pathogenic and vaccinal strains. Sequence evidence for RNA recombination in field isolates of avian coronavirus infectious bronchitis virus doi = 10.1016/j.meegid.2012.09.016 id = cord-252441-190jmgcq author = Liu, Yong-sheng title = The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern date = 2011-03-05 keywords = EV71; codon; usage summary = To give a new perspective on the evolutionary characteristics shaping the genetic diversity of enterovirus 71 (EV71) and the effects of natural selection from its host on the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, codon usage bias (CUB) values, effective number of codons (ENCs) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. Although it is known that compositional constraints and translation selection are the more generally accepted mechanisms accounting for codon usage bias (Coleman To give a new perspective on the evolutionary characteristics shaping the genetic diversity of enterovirus 71 (EV71) and the effects of natural selection from its host on the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, codon usage bias (CUB) values, effective number of codons (ENCs) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. doi = 10.1016/j.meegid.2011.02.018 id = cord-263481-w5ytp1q7 author = Lokman, Syed Mohammad title = Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach date = 2020-06-02 keywords = CoV-2; RBD; SARS summary = MERS-CoV uses dipeptidyl peptidase-4 (DPP4) as entry receptor [11] whereas SARS-CoV and SARS-CoV-2 utilize ACE-2 (angiotensin converting enzyme-2) [12] , abundantly available in lung alveolar epithelial cells and enterocytes, suggesting S glycoprotein as a potential drug target to halt the entry of SARS-with remarkable properties like glutamine-rich 42 aa long exclusive molecular signature (DSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIE) in position 983-1024 of polyprotein 1ab (pp1ab) [16] , diversified receptor-binding domain (RBD), unique furin cleavage site (PRRAR↓SV) at S1/S2 boundary in S glycoprotein which could play roles in viral pathogenesis, diagnosis and treatment [17] . There is growing evidence that spike protein, a 1273 amino acid long glycoprotein having multiple domains, possibly plays a major role in SARS-CoV-2 pathogenesis. In this study, we have analyzed 320 genomic sequences of SARS-CoV-2 to identify mutations between the available genomes followed by the amino acid variations in the glycoprotein S to foresee their impact on the viral entry to host cell from structural biology viewpoint. doi = 10.1016/j.meegid.2020.104389 id = cord-339259-4oi7slk9 author = Naguib, Mahmoud M. title = Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination date = 2016-10-26 keywords = IBV; Sudan summary = title: Full genome sequence analysis of a newly emerged QX-like infectious bronchitis virus from Sudan reveals distinct spots of recombination By phylogenetic analysis based on the whole S1-gene according to (Valastro et al., 2016) it appeared that the IBV/Ck/Sudan/AR251-15/2014 is closely related to ITA/90254/ 2005 and the previously reported recombinant strains detected in South Africa (Ck/ZA/3665/11) and Sweden (Ck/SWE/0658946/10) which are clustered together within GI-19 lineage (Fig. 3) . The results showed that the Sudanese isolate was a recombinant virus which probably emerged from at least three different genotypes, including the 4/91 genotype as a major parent and the H120 vaccine strain as well as Italy/90254/2005-like viruses as minor parents (Fig. 4) . Characterization and analysis of the full-length genome of a strain of the european qx-like genotype of infectious bronchitis virus Complete genomic sequence analysis of infectious bronchitis virus ark dpi strain and its evolution by recombination doi = 10.1016/j.meegid.2016.10.017 id = cord-325679-4lfpy84d author = Niu, Ting-Jiang title = Detection and genetic characterization of kobuvirus in cats: The first molecular evidence from Northeast China date = 2018-12-06 keywords = China summary = To investigate the presence and genetic variability of FeKoV in northeast China, 197 fecal samples were collected from 105 cats with obvious diarrhea and 92 asymptomatic cats in Shenyang, Jinzhou, Changchun, Jilin and Harbin regions, Northeast China, and viruses were detected by RT-PCR with universal primers targeting all kobuviruses. By genetic analysis based on partial 3D gene, all kobuvirus-positive samples were more closely related to previous FeKoV strains with high identities of 90.5%–97.8% and 96.6%–100% at the nucleotide and amino acid levels. Additionally, phylogenetic analysis based on the complete VP1 gene indicated that all FeKoV strains identified in this study were placed into a cluster, which separated from other reference strains previously reported, and three identical amino acid substitutions were present at the C-terminal of the VP1 protein for these FeKoV strains. The genetic analysis based on the partial RdRp gene indicated that FeKoV strains shared higher nucleotide (81.2%-82.1%) and amino acid identities (91.4%-92.1%) with CaKoV strains previously reported (Kapoor et al. doi = 10.1016/j.meegid.2018.12.010 id = cord-261914-qfim8nu5 author = Oem, Jae-Ku title = Genetic characteristics and analysis of a novel rotavirus G3P[22] identified in diarrheic feces of Korean rabbit date = 2019-06-04 keywords = RVA; Rab1404 summary = This study aimed to analyze the complete genome sequence, i.e., 11 genome segments of the lapine rotavirus (LRV) identified in the intestine of a dead rabbit in the Republic of Korea (ROK) and to describe the genetic relationships between this lapine isolate [RVA/Rabbit-wt/KOR/Rab1404/2014/G3P[22] (Rab1404)] and other lapine isolates/strains. Additionally, the genome segments VP6 (I2), NSP1 (N2), and NSP5 (H3) of Rab1404 were closely related to those of bovine RVAs. This is the first report describing the complete genome sequence of an LRV detected in the ROK. The objective of this study was to analyze an LRV isolated from the intestine of a dead rabbit in 2014 in the ROK by performing a complete genomic sequence analysis of the 11 genome segments and to characterize the phylogenetic relationships between our isolate and other lapine isolates/strains. doi = 10.1016/j.meegid.2019.06.003 id = cord-331237-t3z1hbox author = Ogawa, Hirohito title = Molecular epidemiology of pathogenic Leptospira spp. in the straw-colored fruit bat (Eidolon helvum) migrating to Zambia from the Democratic Republic of Congo date = 2015-03-16 keywords = Leptospira; Zambia summary = helvum samples and previously reported sequences, revealed that 12 of the fragments grouped with Leptospira borgpetersenii and Leptospira kirschneri; however, the remaining 58 flaB fragments appeared not to be associated with any reported species. Additionally, the 16S ribosomal RNA gene (rrs) amplified from 27 randomly chosen flaB-positive samples was compared with previously reported sequences, including bat-derived Leptospira spp. A nested PCR based on the flagellin B gene (flaB) sequence was used to amplify the extracted DNA samples (n = 529) to detect the flaB gene of pathogenic Leptospira spp. Six flaB fragments (ZFB08-62, ZFB09-25, ZFB09-32, ZFB12-05, ZFB12-107 and ZFB12-110) in the FC5 cluster were related to the corresponding gene sequences, all of which were identical to Leptospira borgpetersenii strains including Jules, De 10, Arborea, Poi, and Veldrat Batavia 46. The phylogenetic analyses of flaB and rrs infer that genes from potentially pathogenic Leptospira spp. doi = 10.1016/j.meegid.2015.03.013 id = cord-302679-wytog9cv author = Panda, Somnath title = Bioinformatics analysis reveals four major hexon variants of human adenovirus type-3 (HAdV-3) as the potential strains for development of vaccine and siRNA-based therapeutics against HAdV-3 respiratory infections date = 2020-06-23 keywords = hexon; variant summary = title: Bioinformatics analysis reveals four major hexon variants of human adenovirus type-3 (HAdV-3) as the potential strains for development of vaccine and siRNA-based therapeutics against HAdV-3 respiratory infections Then, we have identified the conserved locations in HVR encoding regions of the hexon gene and fr om those locations we have designed functional siRNAs. Next, we have also designed immunogenic vaccine peptide epitopes from the hexon protein that can be used to design a vaccine. The variations among the HVR encoding regions of the hexon gene of 3Hv-1 to 3Hv-4 were shown by multi-sequence alignment (MSA), in silico RE analysis Numerous tools are available to design functional siRNAs such as MysiRNA-designer [22] , siDirect [23] and siMAX-siRNA Designer (https://eurofinsgenomics.eu/en/dnarna-oligonucleotides/custom-dna-rna-oligos/simax-sirna/) etc. We have designed functional siRNAs from those conserved regions and immunogenic vaccine peptide epitopes from the hexon protein. doi = 10.1016/j.meegid.2020.104439 id = cord-268480-fd5xi4q1 author = Rojas, Miguel A. title = Identification of two novel Rotavirus A genotypes, G35 and P[50], from Peruvian alpaca faeces date = 2017-09-01 keywords = RVA; vp7 summary = Rotavirus A (RVA) Alp11B was detected from a neonatal Peruvian alpaca presenting with diarrhea, and the Alp11B VP7, VP4, VP6, NSP4, and NSP5 genes were sequenced. Once RVA was detected, the sample was subjected to additional RT-PCR amplifications to identify the VP4, VP7, VP6, NSP4, and NSP5 genotypes using specific primers (Appendix) that were previously published or designed based on RVA sequences available in GenBank. Sequences of Alp11B strain were aligned and compared to that of each corresponding gene of RVA strains obtained from GenBank, by using MegAlign, which are available in the Lasergene software package (DNASTAR, Madison, WI). The nucleotide sequences of the VP4 and VP7 genes from Alp11B were not related to any RVA strain available in GenBank (Fig. 2) . The vicuña strain possesses the unique NSP4-E16 genotype, but the NSP5 gene was not characterized. Infection, Genetics and Evolution 55 (2017) 71-74 E16-H6 with high identity to camelid, bat, and human-like RVA strains. doi = 10.1016/j.meegid.2017.08.019 id = cord-269187-lt0uo7q3 author = Saha, Indrajit title = Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP date = 2020-07-11 keywords = SARS; indian summary = Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. Based on this information, they developed an SNP-based PCR assay to show differentiation between To address the above facts, we have analyzed publicly available 566 Indian complete or near complete SARS-CoV-2 genomes in order to find the mutation points as substitution, deletion J o u r n a l P r e -p r o o f and insertion. In this section, we have discussed the source of data or genomic sequence of virus and methods used in systemic way to accomplish this task of finding mutation points as substitution, deletion, insertion as well as SNPs. The genomic sequences of Indian SARS-CoV-2 virus was collected from Global Initiative on Sharing All Influenza Data (GISAID) 1 in fasta format on 11th June 2020. doi = 10.1016/j.meegid.2020.104457 id = cord-259925-g28sx9qu author = Saleemi, Mansab Ali title = Emergence and molecular mechanisms of SARS-CoV-2 and HIV to target host cells and potential therapeutics date = 2020-10-06 keywords = CD4; HIV; SARS summary = The World Health Organization (WHO) has named the disease caused by the virus as COVID-19 and the virus which is the culprit was renamed from the initial novel respiratory 2019 coronavirus to SARS-CoV-2. To identify the etiological source of a novel human pathogen is a dynamic process that needs comprehensive and extensive scientific validations, such as observed in the Middle East respiratory syndrome (MERS), severe acute respiratory syndrome (SARS), and human immunodeficiency virus (HIV) cases. Up to date, it is unclear how SARS-CoV-2 interacts with the host antiviral immunity, hence lessons can be learned from previous studies of other members of the coronavirus family and also human pathogenic viruses, such as human immunodeficiency viruses and severe acute respiratory syndrome (SARS) CoV known as human CoVs (HCoVs) due to their ability to cause human infections (Andersen et al., 2020) . doi = 10.1016/j.meegid.2020.104583 id = cord-279202-iyteg4h9 author = Shesheer Kumar, Munpally title = Expression of alternate reading frame protein (F1) of hepatitis C virus in Escherichia coli and detection of antibodies for F1 in Indian patients date = 2008-01-05 keywords = HCV summary = title: Expression of alternate reading frame protein (F1) of hepatitis C virus in Escherichia coli and detection of antibodies for F1 in Indian patients Apart from the core (21 kD), a novel hepatitis C virus (HCV) frame shift protein (F1) is synthesized from the initiation codon of the polyprotein sequence followed by ribosomal frame shift into the −2/+1 reading frame. Further, results of western blots, carried out with patients sera titrated with purified core protein, confirmed the presence of antibodies specific to F1. The positive signal observed for F1 in western analysis with HCV infected sera suggests that F1 protein is synthesized in the natural course of HCV infection in Indian patients as well. Functional properties of a 16 kDa protein translated from an alternative open reading frame of the core encoding genomic region of hepatitis C virus doi = 10.1016/j.meegid.2007.12.008 id = cord-269353-wgeuh1i2 author = Tian, Lin title = The adaptation of codon usage of +ssRNA viruses to their hosts date = 2018-06-02 keywords = codon; usage summary = Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. Our results show that NSTVs have a higher degree of matching to their hosts'' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s). As expected, our analysis show that generally NSTVs are more adapted to their hosts'' codon usage pattern and tRNA pools than BSTVs. This may help the virus to use the host transcript machinery more efficiently and, therefore, replicate faster. doi = 10.1016/j.meegid.2018.05.034 id = cord-331503-whw2pq1f author = Torres, Orlando A. title = Role of the IFNG +874T/A polymorphism in Chagas disease in a Colombian population date = 2010-03-30 keywords = Chagas; IFNG summary = The human IFNG IFN-g Chagas disease Single nucleotide polymorphism (SNP) Genetics Association study A B S T R A C T Genetic susceptibility to Trypanosoma cruzi infection and the development of cardiomyopathy is complex, heterogeneous, and likely involves several genes. Here we investigated the association between the interferon-gamma gene (IFNG) +874T/A polymorphism and Chagas disease, focusing on susceptibility and severity. Here we investigated the association between the interferon-gamma gene (IFNG) +874T/A polymorphism and Chagas disease, focusing on susceptibility and severity. Due to this, we selected the +874T/A polymorphism of IFNG to assess the potential association of this SNP in the susceptibility and/or clinical features of Chagas disease in a Colombian population from an endemic area. We found a statistically significant difference in the distribution of the A/A genotype (low production of IFN-g) and the A allele at the IFNG polymorphism between Chagas patient and control groups. doi = 10.1016/j.meegid.2010.03.009 id = cord-269283-jm18lj5t author = Uddin, Md Bashir title = Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective date = 2020-07-01 keywords = COVID-19; China; SARS summary = Bioinformatics analysis, satellite derived imaging data and epidemiological attributes were employed to investigate origin, immunogenic resemblance and global threat of newly pandemic SARS-CoV-2 including Bangladesh perspective. The study also prioritized the temperature comparison through satellite imaging alongside compiling and analyzing the epidemiological outbreak information on the 2019 novel coronavirus based on several open datasets on COVID-19 (SARS-CoV-2) and discussed possible threats to Bangladesh. As the outbreak of the 2019 novel coronavirus (COVID-19 [SARS-CoV-2]) is expanding rapidly, analysis of epidemiological data of COVID-19 is necessary to explore the measures of burden associated with the disease and to simultaneously gather information on determinants and interventions. Moreover, the conservancy study of immunogenic peptides predicted from the SARS-CoV-2 proteins was also compared against other human coronavirus strains (HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1 and MERS-CoV). Cross-checked conservancy analysis of COVID-19 antigenic epitopes with SARS-CoV proteins showed that conservancy when crosschecked with other coronaviruses, including BufCoV-HKU26 of Bangladesh origin, was not significant ( Table 3) . doi = 10.1016/j.meegid.2020.104440 id = cord-318625-hf7fgtnp author = Vashi, Yoya title = Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens date = 2020-05-27 keywords = SARS summary = The present study followed computational approaches to identify Band T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. The potential epitope regions were predicted using the sequence of the S protein of SARS-CoV-2 that showed the least variability (GenBank accession number NC_045512). We identified 18 linear epitopes, predicted by ElliPro (IEDB), which contained regions from 19 of our selected peptides (highlighted in red in Table 2 ). The study could help us to use the predicted peptide as an immunogen for the development of diagnostics and vaccines against SARS-CoV-2. In the present study, peptide segments were identified on S proteins for the development of diagnostics and vaccines against SARS-CoV-2. doi = 10.1016/j.meegid.2020.104382 id = cord-266914-3eatplc2 author = Wang, Yongjin title = Nsp1 proteins of group I and SARS coronaviruses share structural and functional similarities date = 2010-06-02 keywords = IFN; NL63; SARS summary = The group II coronaviruses severe acute respiratory syndrome coronavirus (SARS-CoV) and mouse hepatitis coronavirus (MHV) encode a number of proteins that antagonize host innate immunity. Innate immune signal transduction was stimulated by NDV infection in cells transfected with plasmids-expressing nsp1 from HCoV-229E, HCoV-NL63 or SARS-CoV, or with a control plasmid. Luciferase reporter assays showed that synthesis of the innate immune promoter IFN-band ISG15-driven genes was suppressed by 5-20-folds in HCoV-229E and HCoV-NL63 nsp1-expressing 293 cells (Fig. 4A) . Synthesis of non-immune promoter-driven genes, including for SV40, HSV-TK and CMV promoters, was inhibited to a similar extent by the two group I coronavirus nsp1 proteins (Fig. 4B) . These results indicate that group I coronaviruses have evolved a mechanism strikingly similar to SARS-CoV for antagonizing host cell proliferation and innate immunity using nsp1. Severe acute respiratory syndrome coronavirus nsp1 suppresses host gene expression, including that of type I interferon, in infected cells doi = 10.1016/j.meegid.2010.05.014 id = cord-267168-qjktnnn6 author = Wille, Michelle title = Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs date = 2020-03-20 keywords = Fig; Sweden; USA summary = In this study, Swedish privately-owned dogs with characteristic signs of canine infectious respiratory disease (n = 88) were screened for CRCoV and 13 positive samples (14.7%, 8.4–23.7% [95% confidence interval (CI)]) were further sequenced. To assess recombination, a concatenated sequence was generated including the viruses from which there were sequences from the partial Non-structural protein 2a (NS), and full length HE, S, envelope (E), and M, resulting in 6541 bp for analysis and the genes were placed in genomic order. Assessment of the S, E, M, NS2 and HE genes generated using Sanger and high-throughput sequencing (Table A1 ) demonstrated high genetic similarity of viruses detected in Swedish dogs, despite sampling from numerous clinics across Sweden and an over a period of 3 years. In this study, we aimed to reveal the epidemiology and evolutionary genetics of CRCoV, one of the causative agents of canine infectious respiratory disease (CIRD), in Sweden. doi = 10.1016/j.meegid.2020.104290 id = cord-278465-tjjkz16y author = Wille, Michelle title = Urbanization and the dynamics of RNA viruses in Mallards (Anas platyrhynchos) date = 2017-03-18 keywords = IAV; virus summary = Recent studies have been instrumental in starting to describe dynamics and ecology of AMPV-1 and CoV in wild birds; 9-12% of migrating Mallards have CoV infections, compared to a lower prevalence (2%) of AMPV-1 towards the end of the migratory season in Sweden (Tolf et al., 2013b; Wille et al., 2015) . In context of IAV, and to a lesser degree CoV and APMV-1, an assessment of virus prevalence and diversity in an urban population will further allow us to assess if dynamics in wild birds are reflected in an urban setting. In comparing prevalence [Sept-Dec] between our urban dataset and a wild bird dataset from southern Sweden using the same qPCR methods (Wille et al., 2015) , autumnal prevalence for IAV (p b 0.0010) and CoV (p b 0.0010) is significantly different, where prevalence for both these viruses is lower in urban Mallards (Fig. 2) . doi = 10.1016/j.meegid.2017.03.019 id = cord-263476-ju7xqwa7 author = Xia, Jing title = Phylogenetic and antigenic analysis of avian infectious bronchitis virus in southwestern China, 2012–2016 date = 2016-08-13 keywords = China; IBV summary = The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). To determine the antigenic relatedness between the field IBV isolates and the vaccine viral strains, double-direction viral cross-neutralization (VN) tests were performed in chicken embryo kidney (CEK) cells using constant viral titers and diluted serum. The tested strains came from six different genotypes and included seven IBV field isolates (Sczy3, cK/CH/SCDY/141030, cK/CH/SCLS/140104, cK/CH/CQKX/ 150203, cK/CH/SCYB/140913, cK/CH/SCMY/10I, cK/CH/SCYB/141102) and the three most commonly used vaccine viral strains (H120, M41, and 4/91). Ten IBVs, including seven field strains from different genotype backgrounds and three commonly used vaccine strains (H120, 4/91, and M41), were analyzed and grouped into four serotypes: Massachusetts (Mass hereafter), 793B, Sczy3, and SCYB. doi = 10.1016/j.meegid.2016.08.011 id = cord-276052-gk6n8slx author = Yadav, Pragya title = Isolation of Tioman virus from Pteropus giganteus bat in North-East region of India date = 2016-09-09 keywords = India; Pteropus; bat; virus summary = During the survey for Nipah virus among bats at North-East region of India; Tioman virus (TioV), a new member of the Paramyxoviridae family was isolated from tissues of Pteropus giganteus bats for the first time in India. While investigating NiV in urine samples of giant fruit bats of the Pteropus genus on Tioman Island, Malaysia, in 2001, researchers isolated a novel virus which was placed in the Rubulavirus genus of the Paramyxoviridae family. In order to study susceptibility of different vertebrate cells to TioV, the infectious virus titer was determined by estimating 50% tissue culture infective dose (TCID 50 ) using Reed and Muench method (Reed and Muench, 1938) . Negative contrast electron microscopy of the cell supernatant of Vero CCL-81 infected with virus isolate showed the presence of virus particles with the typical paramyxovirus morphology. TioV isolated from kidney tissue homogenate of bat showed a titer of 10 4.61 /100 μL by TCID 50 in Vero CCL-81 cell line. doi = 10.1016/j.meegid.2016.09.010 id = cord-339120-38rsfs0d author = Yan, Nan title = Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China date = 2019-02-20 keywords = RVA summary = authors: Yan, Nan; Tang, Cheng; Kan, Ruici; Feng, Fan; Yue, Hua. title: Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The sequence closest to the NSP4 gene of RVA/Dog-tc/ CHN/SCCD-A/2017/G9P [23] was that of human strain R479 which was previously shown to be of porcine rotavirus origin (Wang et al., 2010) . On the other hand, the sequence closest to the VP1 gene of SCCD-A was that of strain LL3354 which was reported to be the result of a porcine rotavirus having transmitted to a human, but the phylogenetic tree for the VP1 genes showed that strains SCCD-A and LL3354 clustered together in an independent group that was distinct from any of the previously established lineages (Fig. 1) . doi = 10.1016/j.meegid.2019.02.020 id = cord-333712-sdtxi8xw author = Yu, Ping title = Geographical structure of bat SARS-related coronaviruses date = 2019-02-06 keywords = SARS summary = In 2005, the discovery of novel CoVs related to human SARS-CoVs in Chinese horseshoe bats (genus Rhinolophus), named SARS-related coronaviruses (SARSr-CoVs), provided new clue that bats may be the natural host for SARS-CoV (Lau et al., 2005; Li et al., 2005) . SARS-CoV and SARSr-CoVs belong to lineage B of genus Betacoronavirus in the family Coronaviridae and share the same genomic organization with other coronaviruses, including genes coding for 16 nonstructural proteins (nsp, in ORF1ab domain), the structural proteins like spike protein (S), envelope (E), membrane (M), nucleocapsid (N) and other several genes (Perlman and Netland, 2009; Woo et al., 2009) . Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China doi = 10.1016/j.meegid.2019.02.001 id = cord-293588-7pflfznh author = Zang, Minghui title = Analysis of the codon usage of the ORF2 gene of feline calicivirus date = 2017-06-16 keywords = FCV; ORF2; codon summary = Furthermore, there was a significant correlation between the ENC values and the nucleotide compositions (p b 0.01), which indicates that mutational bias influences the synonymous codon usage pattern of the ORF2 gene of FCV. We found a correlation between the Aroma values and U3 s, G3 s and GC3s (p b 0.05), confirming that natural selection influences the codon usage bias of the FCV ORF2 gene. Thus, natural selection plays a major role in shaping the codon usage bias of ORF2 gene of FCV compared to mutational pressure. Here, we used ENC-Plots (Fig. 1) and PCA (Fig. 3) analysis according to the geographical distribution to investigate the major factors shaping the codon usage bias of the FCV ORF2 gene . Furthermore, analysis of the relationships between nucleotide composition and the codon contents at the third base positions suggested that mutation pressure is one of the factors in shaping the codon usage of FCV ORF2. doi = 10.1016/j.meegid.2017.06.013 id = cord-288687-2dz8bu73 author = Zhai, Bintao title = First detection and molecular identification of Borrelia species in Bactrian camel (Camelus bactrianus) from Northwest China date = 2018-06-26 keywords = Borrelia; China summary = In this study, a total of 138 blood specimens collected from Bactrian camels from Zhangye City in Gansu Province and Yili and Aksu in Xinjiang Province, China, were examined for the presence of Borrelia spp. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the 5S-23S rRNA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the flaB gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. Phylogenetic tree of the OspA gene sequences of Borrelia species obtained in the present study and those deposited in GenBank from different countries; accession numbers are shown after isolate names. doi = 10.1016/j.meegid.2018.06.028 id = cord-299989-p59u6qa0 author = Zhang, Lei title = Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues date = 2020-06-18 keywords = ACE2; SARS summary = title: Comparative analysis of SARS-CoV-2 receptor ACE2 expression in multiple solid tumors and matched non-diseased tissues Here, we analyze a large data set comprising ACE2 mRNA expression for 7592 tissue samples across 22 types of primary solid tumor and 4461 samples across matched 18 non-diseased tissues. Our results unravel eight normal tissues and 10 primary solid tumors, which might be at high risk of SARS-CoV-2 infection. These findings may provide additional insight into the prevention and treatment of SARS-CoV-2 infection, in particular for patients with these 10 vulnerable cancer types. Interestingly, our finding that ACE2 was highly expressed in breast appears to be in contrast to a retrospective study on nine pregnant women with COVID-19 in the third trimester, in which the colostrum from six patients tested negative for SARS-CoV-2 (H. doi = 10.1016/j.meegid.2020.104428 id = cord-253090-kllrqoxi author = dos Passos Cunha, Marielton title = Codon adaptation biases among sylvatic and urban genotypes of Dengue virus type 2 date = 2018-05-21 keywords = CAI summary = Dengue virus (DENV) emerged from the sylvatic environment and colonized urban settings, being sustained in a human-Aedes-human transmission chain, mainly by the bites of females of the anthropophilic species Aedes aegypti. In this context, as previous analyses have suggested (Moncayo et al., 2004) , our findings support the notion that for the sylvatic strains to effectively colonize the urban environment, the virus needs a number of silent, adaptive nucleotide substitutions to optimize the codon usage to invertebrate host cells, while maintaining a compositional base balance suitable for efficient alternate spread among both human and insect hosts. In conclusion, our findings provide a comprehensive assessment of the codon adaptation of DENV-2 in different habitats (i.e. urban and sylvatic settings) and host systems (i.e. Homo sapiens and the mosquito vector Aedes aegypti). In this context, although the virus replicates in both human and mosquitoes, our analysis suggested that DENV-2 codon usage is better adapted to humans than to the main cosmopolitan vector (Ae. aegypti). doi = 10.1016/j.meegid.2018.05.017 id = cord-265329-bsypo08l author = van Dorp, Lucy title = Emergence of genomic diversity and recurrent mutations in SARS-CoV-2 date = 2020-05-05 keywords = CoV-2; SARS; figure; genome summary = Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. The extraordinary availability of genomic data during the COVID-19 pandemic has been made possible thanks to a tremendous effort by hundreds of researchers globally depositing SARS-CoV-2 assemblies (Table S1 ) and the proliferation of close to real time data visualisation and analysis tools including NextStrain (https://nextstrain.org) and CoV-GLUE (http://cov-glue.cvr.gla.ac.uk). In this work we use this data to analyse the genomic diversity that has emerged in the global population of SARS-CoV-2 since the beginning of the COVID-19 pandemic, based on a download of 7710 assemblies. The genomic diversity of the global SARS-CoV-2 population being recapitulated in multiple countries points to extensive worldwide transmission of COVID-19, likely from extremely early on in the pandemic. doi = 10.1016/j.meegid.2020.104351