cord-000315-rfwzj1at	2011	title: Hepatitis G Virus associated aplastic anemia: A recent case from Pakistan One of 93 samples from patients with HA-aplastic anemia has hepatitis G associated aplastic anaemia with positive HGV RNA. Zaidi et al, reported a 19 year male before blood transfusion with positive HGV by RT-PCR and suggested that in the absence of any other clincial manifestions the possible infectious agent may be HGV for hepatitis G virus associated aplast anaemia [8] . In the list of studies of Hepatitis G Virus associated aplastic anaemia before blood transfusion we report a case of 11 years female girls. The ideal case regarding Hepatitis G associated aplastic anaemia are pre blood transfusion. Hepatitis GB virus C genome in the serum of aplastic anaemia patients receiving frequent blood transfusions Hepatitis G Virus associated aplastic anemia: A recent case from Pakistan
cord-000389-9vnthmfn	2011	The aim of this study was to investigate the dynamic fluctuations of the peripheral blood lymphocyte subgroups in patients infected with H1N1 swine-origin influenza A virus (S-OIV). The aim of this study is to analyze the dynamic fluctuations of T cells, B cells, natural killer (NK) cells, and regulatory T cells in patients infected with novel influenza H1N1, as well as serum cytokines and C-reactive protein (CRP). The serum cytokines of patients, specifically IL-2, IL-4, IL-6, IL-10, and IFN-γ, whether the H1N1 infection was severe or moderate, showed no significant changes during the whole monitoring process (data not shown). Our clinical data also showed that the most severe infections occur in individuals younger than 25 years old or in middle-aged patients Figure 1 Analysis of the dynamic changes in the lymphocyte subgroup and C-reactive protein (CRP) in the peripheral blood of patients with Influenza A (H1N1) 2009.
cord-000403-vzbh457k	2011	Twenty-seven nanopeptides derived from the matrix (M) protein of porcine reproductive and respiratory syndrome virus (PRRSV) were screened for their ability to elicit a recall interferon-γ (IFN-γ) response from the splenocytes of BALB/c mice following DNA vaccination and a booster vaccination with recombinant vaccinia virus rWR-PRRSV-M. We screened peptides derived from the PRRSV M protein for their ability to induce interferon (IFN)-γ in splenocytes harvested from BALB/ c mice following DNA vaccination and a booster vaccination with recombinant vaccinia virus expressing M protein. In contrast, control mice vaccinated with pVAX1-only or PBS-only did not show significant increases in M protein-specific antibody titers after the booster vaccination with rWR-PRRSV-M (P > 0.05, Additional file 5, Fig. S5 ). Specific increases in the number of cells producing IFN-γ following stimulation with the peptides "K 93 FITSRCRL" and "F 57 GYMTFVHF" was observed by day 3 after the booster vaccination with rWR-PRRSV-M (Figure 1 and 2) .
cord-000640-t0y0b0gb	2012	Following numerous failed attempts, hantavirus RNA was detected in ethanol-fixed liver tissue from two banana pipistrelles (Neoromicia nanus), captured near Mouyassué village in Côte d''Ivoire, West Africa, in June 2011. Phylogenetic analysis of partial L-segment sequences using maximum-likelihood and Bayesian methods revealed that the newfound hantavirus, designated Mouyassué virus (MOUV), was highly divergent and basal to all other rodentand soricomorph-borne hantaviruses, except for Nova virus in the European common mole (Talpa europaea). After innumerable failed attempts, hantavirus RNA was detected by RT-PCR in ethanol-fixed liver tissues from two of 12 banana pipistrelles (Neoromicia nanus Peters 1852), captured during June 2011 near Mouyassué village (5°22''07"N, 3°05''37"W) in Aboisso District, 130 km from Abidjan, in the extreme southeastern region of Côte d''Ivoire in West Africa ( Figure 1 ). The newfound hantavirus, designated Mouyassué virus (MOUV), exhibited low nucleotide and amino acid sequence similarity of less than 69% to all representative soricomorph-and rodent-associated hantaviruses, except for the 76.3% sequence similarity with Nova virus (NVAV), previously reported in the European common mole (Talpa europaea) [12] .
cord-000988-79fp75u3	2013	Twentyseven virus culture-positive specimens and 169 virus culture-negative specimens were randomly selected and tested for the presence of HAdV using a well established in-house real-time PCR assay [18] following recovery of viral DNA was recovered by homogenization with heat treatment or automated nucleic acid extraction. This internally controlled quantitative real-time PCR assay targets the hexon gene of adenovirus, and is validated for detection Table 1 Nucleotide sequences of primers and probes used in this study The analytical sensitivity (or limit of detection, LoD) of the homogenization with heat treatment or nucleic acid extraction, in combination with the real-time PCR, was determined using 10-fold serial dilutions (in UTM) of a cultured HAdV-C type 6. Virus stock dilutions were quantified using commercial real-time PCR assay, and the LoD for homogenization or nucleic acid extraction-based protocols were shown to be approximately equivalent (Figure 2) .
cord-000990-ci6db90d	2013	BACKGROUND: In this study, we sequenced and phylogenetic analyses of the VP2 genes from twelve canine parvovirus (CPV) strains obtained from eleven domestic dogs and a giant panda (Ailuropoda melanoleuca) in China. Substitution of Gln for Arg at the conserved 370 residue in CPV presents an unusual variation in the new CPV-2a amino acid sequence of the giant panda and is further evidence for the continuing evolution of the virus. Canine parvovirus type 2a/2b having mutation at 297 residue (Ser→Ala) is designated as new CPV-2a/2b [8, 9] , residue 297 is located in a minor antigenic site close to epitope B and substitutions at this position may be responsible for changes in antigenicity of CPV variants [10] . In comparison to prototype new-CPV-2a (AY742953), the samples under this study had amino acid residue variations at Tyr324Ile caused by mutation TAT →ATT at nt 3756-3758 of the VP2 gene.
cord-003855-so8xl199	2019	The bat innate immune response appears to be ''pre-activated'' with higher basal levels of type I interferon expression, in contrast to humans, who are very quick responders to viral infections, but require a lot more dampening of their immune signals afterwards to get back to basal levels. demonstrated that bats'' response to stress in form of viral infections is more targeted and thus potentially more effective by numerous adaptions and modifications of the innate immune system. In the ''Pathogenesis and Prevention of Infection'' session, Rosa Coldbeck-Shackley working with Michael Beard at the University of Adelaide, Australia, and also colleagues at the Hudson Institute, presented findings on the importance of interferon-epsilon (IFN-ɛ) in the innate immune response to ZIKV infection. Also in the ''Pathogenesis and Prevention of Infection'' session, Allison Abendroth (University of Sydney) presented ''Disarming the killer: targeting of natural killer cells by varicella zoster virus''.
cord-010336-xfzf7ath	2020	For in vivo studies, female Tmprss2 −/− (B6.129S1-Tmprss2tm1Tsyk) [12, 14] and C57BL/6 JRj wild type (WT) mice (Janvier, 8-12 weeks old) were infected intranasally with 2 × 10 4 ffu PR8_HA(H2) as described before [12] and changes in body weight and survival were monitored for the next 14 days. Viral replication in lungs of infected (dose of 2 × 10 4 ffu) female Tmprss2 −/− and WT mice (8-12 weeks old) revealed no detectable virus replication in Tmprss2 −/− mice, whereas WT mice showed increased lung titers at day 2 and 4 post infection (dpi) (Fig. 2c) . Since no viral replication and only minor immune responses were detected in the studies described above, we confirmed that mice had indeed been infected with the PR8_HA(H2) virus by determining the presence of H2-specific antibodies at 14 dpi in the serum.
cord-011880-qlutgfu2	2020	In addition, different studies, showed that circulating H9N2 strains have acquired affinity to mammalian like-receptors and gained high virulence and pathogenicity through substitutions in their viral proteins [13, 14] ; the most known substitutions are in the HA protein that promotes virus binding to cellular receptors. While the substitution 627 K that confers high pathogenicity, virulence and increased replication in mice [63] , was not detected in our Algerian viruses, three substitutions 318R, 590S and 661 T, associated with mammalian adaptation, were observed [71, 72] . The PB1 substitutions N105S, K577E/M and 578Q, known to be associated with increased polymerase activity, H9N2 pathogenicity in mice as well as adaptation to mammalians [61, 64, 78] , were not observed in the currently circulating Algerian strains, which however shared 105 N, 577 K and 578 K. Amino acids analysis showed that the Algerians H9N2 strains carried out different molecular markers associated with affinity to human-like receptors and increased virulence.
cord-031316-yvid6qps	2020	Sequences of p72 and p54 amplicon were compared with 25 other p72 and p54 ASFV sequences retrieved from the Gen-Bank database and the phylogenetic analysis revealed that the South Kivu ASF virus strains analyzed clustered with p72 genotype X including strains reported in previous studies in Burundi (AF449463), Kenya (AY261360) and Tanzania (JX403648, AF301546, MF437291) ( Fig. 2a and b) . Sequences of African swine fever virus (ASFV) strains from the South Kivu province, eastern DRC, showing tetrameric repeats of representative genotypes, including a reference sequence of a virus isolated in 1950 in Kenya (Kenya 1950; GenBank accession no.
cord-034467-jh9msz1c	2020	In the present study, we examined the expression of important koala cytokines, immune markers and host restrictions factors to determine their pre-and post-vaccination levels in northern koalas harbouring endogenous KoRV. Genes targeted included nine cytokines (CCL4L, Interleukin Open Access *Correspondence: oolagoke@usc.edu.au Genecology Research Centre, University of the Sunshine Coast, Sunshine Coast, QLD, Australia (IL)-1β, IL-4, IL-6, IL-8, IL-10, IL-17A, IL-18 and Interferon gamma (IFN-γ), four host restriction factors (BST2, ISG15, RSAD2 and TRIM1) and two T-cell markers (CD4 and CD8β). In addition, none of the host restriction factors tested (BST2, ISG15, RSAD2 and TRIM1) had significant changes in their expression either at 4-or 8-weeks post-vaccination when compared to prevaccination levels. In this cohort of KoRV vaccinated and endogenously infected koalas, a small but significant increase in the expression of IFN-γ at both 4-and 8-weeks post-vaccination was observed, compared to pre-vaccination levels. Our study investigated the expression of four host restriction factors in koalas harbouring endogenous KoRV: BST2, ISG15, RSAD2 and TRIM1.
cord-048229-ajlctjeb	2005	To identify the protease(s) responsible, U937 cells were treated with phorbol 12-myristate 13-acetate (PMA), an agent that induces cellular differentiation and results in decreased expression of acid-independent serine proteases, including NE and cathepsin (Cat) G. Experiments described in this report demonstrate that reovirus infection in U937 cells does not require cysteine protease activity and is not blocked in the presence of agents that raise vesicular pH. To examine the effect of the NE inhibitor on reovirus replication in U937 cells, we pre-treated them for 3 h with E64 in the presence or absence of the NE inhibitor, infected them with Lang virions or ISVPs at an MOI of 3, and quantified viral yields at 2 d p.i. A representative experiment is shown in Fig. 4 . To determine if NE-generated SVPs required further proteolytic processing of σ3, L929 cells were pre-treated with E64 to block cysteine protease activity and infected at an MOI of 3 with Lang virions, ISVPs or NE-generated subviral particles (NE-SVPs).
cord-048368-wm4c7rk6	2007	Serological analysis showed wide cross-reactivity of this virus with sera produced to H5N1 HPAI viruses isolated earlier in South-East Asia. Earlier HPAI viruses were investigated in mice [4, 5] and murine models were successively used for reverse genetics made influenza vaccines [6] . Sequence comparison of the NA protein of A/duck/Tuva/01/06 aligned with the NA of N2 subtype of A/Wuhan/359/95 (H3N2) influenza virus showed phenotype potentially sensitive to neuraminidase inhibitors. Despite powerful anti-influenza virus effects of TNF-α in lung tissue, as it was described previously [28] , we consider that elevated production of the cytokines seems to be crucial in the pathogenesis of HPAI infection. Summing up, in our study BALB/c mice infected with HPAI, strain A/duck/Tuva/01/06, appeared to be able to produce the innate immune response, which culminated to the development of shock and subsequent multiple organ failure.
cord-048466-fj9l8che	2008	BACKGROUND: Knowledge about the complete genome constellation of seasonal influenza A viruses from different countries is valuable for monitoring and understanding of the evolution and migration of strains. The influenza virus evades host immunity by accumulation of point mutations (drift) in the major surface glycoproteins, haemagglutinin (HA) and neuraminidase (NA) or by reassortment of segments from different viruses co-infecting the same cell leading to a new stain with a HA (and NA) not seen in the population before (shift). The A/Fujian/411/02(H3N2)-like clinical Danish viruses had several substitutions in HA at sites that might influence the virus'' capability for egg growth [10, 37] . Substitutions at antigenic site B and the predicted N-glycosylation at position 144 in HA antigenic site A together with a stronger NA might have contributed to the increased infectivity of the reassorted Fujian-like viruses of the 2003-2004 season, causing an epidemic in Denmark. Positive selection on the H3 hemagglutinin gene of human influenza virus A
cord-253615-qylm0koe	2010	In-silico analysis of potential glycosylation sites and membrane topology suggest properties similar to SARS-CoV ORF 3a protein ( Figure 1B and Table 1 ). To analyze the expression of ORF 3 protein during viral replication, colon carcinoma cells (CaCo-2) and Rhesus monkey kidney cells (LLC-MK2) cells were infected with hCoV-NL63 and an immunofluorescence assay (IFA) was done after two and four days, respectively. In contrast to virus-infected cells, cells overexpressing ORF 3 protein from plasmid with an N-terminal FLAG epitope showed only a single band in Western blot whose migration was consistent with the hypothetical unglycosylated form ( Figure 5B, left panel) . Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice Severe acute respiratory syndrome coronavirus 3a protein is released in membranous structures from 3a protein-expressing cells and infected cells
cord-254384-mwzz1db5	2011	To assess the seroprevalence of hMPV infection in China, we tested a total of 1,156 serum specimens for the presence of anti-hMPV IgG antibody in children and adults free of acute respiratory illness in Beijing, China by using hMPV nucleocapsid (N) protein as an antigen. To assess the seroprevalence of hMPV infection in China, we used hMPV N protein as an antigen to test serum samples for the presence of anti-hMPV IgG antibody in children and adults free of acute respiratory illness in Beijing, China. Lower seropositive rates and geometric mean titer (GMT) of anti-hMPV IgG were observed in children aged six months to six years when compared to hRSV. To test the specificity of the ELISA methods established in this study, the reactions of mouse sera against influenza virus A (subtypes H1-H16), human coronaviruses (229E, HKU1 and NL63), and polyomavirus JC against hMPV and hRSV N protein were evaluated.
cord-254713-ghcwfcx2	2015	RESULTS: From 351 frugivorous bats, we detected 14 coronaviruses from two endemic bats species, of which 13 viruses were identified from Pteropus rufus and one from Eidolon dupreanum, giving an overall prevalence of 4.5%. Studies which aimed to identify potential reservoirs of emerging human CoVs have revealed that the Betacoronavirus SARS-CoV was closely related to CoVs detected in bats, specifically members of the genus (Rhinolophus), which brought the hypothesis of a spillover of this virus to several animal species (including civet cats and raccoons) sold in Chinese markets as bushmeat for human consumption [9] [10] [11] . A total of 351 bats belonging to 3 endemic bat species of the family Pteropodidae were captured and sampled: Rousettus madagascariensis (n = 179), Pteropus rufus (n = 76) and Eidolon dupreanum (n = 96) ( Table 1) . In the context of this study, we detected 14 coronaviruses forming nine genetically distinct strains in two endemic Malagasy frugivorous bat species.
cord-258935-tatae3hs	2011	title: A baculovirus dual expression system-based vaccine confers complete protection against lethal challenge with H9N2 avian influenza virus in mice To evaluate the potency of the recombinant baculovirus BV-Dual-HA against lethal influenza virus challenge, the immunized mice were challenged with 50 MLD 50 of H9N2 V strain on day 42. Most mice vaccinated with pc-HA, AcMNPV-WT, or PBS had detectable lung virus titers A B Figure 3 Antibody responses in immunized mice with BV-Dual-HA. From these results, it is obvious that immunization with BV-Dual-HA can induce a robust antibody response and confer complete protection against lethal virus challenge in a mouse model, indicating that BV-Dual-HA is potential candidate vaccine that can prevent and control the pandemic spread of the H9N2 influenza virus. Baculovirus induces an innate immune response and confers protection from lethal influenza virus infection in mice A pseudotype baculovirus-mediated vaccine confers protective immunity against lethal challenge with H5N1 avian influenza virus in mice and chickens
cord-261579-f0prnpsu	2006	title: The role of single N-glycans in proteolytic processing and cell surface transport of the Lassa virus glycoprotein GP-C In this report, we investigated the effect of each N-glycan on proteolytic cleavage and cell surface transport by disrupting the consensus sequences of eleven potential N-glycan attachment sites individually. To address this question, we investigated in the present report each potential N-glycosylation site of the Lassa virus glycoprotein concerning N-glycan maturation, cleavage of GP-C and glycoprotein transport to the cell surface. In order to investigate the importance of the individual N-glycosylation sites of Lassa virus GP-C for intracellular trafficking we analysed cell surface expression of the mutated glycoproteins using a biotinylation approach. Taken together, our study suggest that individual N-linked oligosaccharides of the Lassa virus glycoprotein differ greatly in terms of their importance for correct protein folding which seems to be important for activation cleavage by SKI-1/S1P.
cord-261634-vfe1lawl	2020	Currently, there are conflicting reports on the survivability of SARS-CoV-2, with data ranging from 3 to 14 days at room temperature for a single surface type, stainless steel Open Access *Correspondence: Shane.Riddell@csiro.au Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia [5, 11] . At 20 °C, infectious SARS-CoV-2 virus was still detectable after 28 days post inoculation, for all non-porous surfaces tested (glass, polymer note, stainless steel, vinyl and paper notes). The present study has demonstrated that in controlled conditions, SARS-CoV-2 at a starting viral load and in a fluid matrix equivalent to that typically excreted by infected patients, remains viable for at least 28 days when dried onto non-porous surfaces at 20 °C and 50% relative humidity. It is important to note that after 28 days, infectious SARS-CoV-2 was also recovered from stainless steel, vinyl and glass, suggesting survivability on paper or polymer banknotes was not very different from the other non-porous surfaces studied.
cord-262599-19aj551d	2013	This study aimed to assess the integrity and viability of human adenovirus (HAdV) in environmental water and evaluate circulating strains by molecular characterization in three sites of the water supply in Florianópolis, Santa Catarina Island, Brazil: Peri Lagoon water, spring source water, and water from the public water supply system. ICC-RT-qPCR, a very sensitive and rapid technique, was able to detect as low as 1 × 10(2) HAdV genome copies per milliliter of infectious viral particles in the environmental water samples. We suggest that HAdV can be efficiently used as a marker of environmental and drinking water contamination and ICC-RT-qPCR demonstrated greater sensitivity and speed of detection of infectious viral particles compared to PA. In this study, we aimed to assess the integrity and viability of human adenovirus (HAdV) detected in environmental water samples and also to use molecular characterization to evaluate circulating strains.
cord-262904-0b0ljjq1	2020	It is worth mentioning that all 6 identified epitopes were conserved in nearly 3500 SARS-CoV-2 genomes, showing that it is helpful to obtain stable and long-acting epitopes under the condition of high frequency of amino acid mutation, which deserved further study at the experiment level. On this basis, we predicted the linear and conformational B cell epitopes, analyzed the conservation of the epitopes, the adaptability and other evolutionary characteristics of the surface protein, which provided a theoretical basis for the vaccine development and prevention of SARS-CoV-2. With the amino acid sequences of the surface protein of SARS-CoV-2 of NC_045512.2 as templates, we predicted the 3D structure of E and M protein through the online server SWISS-MODEL [10] based on homology modeling method, selected the optimal structure based on the template identity and GMQE value [10] , and the rationality of the structure was evaluated by Ramachandran plot [11] with PDBsum server.
cord-263469-2w26l80a	2009	RESULTS: Class III viral fusion proteins (VFP) encoded by members of the Rhabdoviridae, Herpesviridae and Baculoviridae have an internal fusion domain comprised of beta sheets, other beta sheet domains, an extended alpha helical domain, a membrane proximal stem domain and a carboxyl terminal anchor. Structural models were established for BDV G based on the post-fusion structure of a prototypic class III VFP, vesicular stomatitis virus glycoprotein (VSV G). Members of the Flavivirus genus of the Flaviviridae and the Alphavirus genus of the Togaviridae encode class II viral fusion proteins (class II or β-penetrenes) possessing three domains (I-III) of mostly antiparallel β-sheets, a membrane proximal α-helical stem domain and a carboxyl terminal anchor [24] [25] [26] . The three VFP classes for enveloped virus membrane glycoproteins were established based on structural similarities in the post-fusion configurations.
cord-263976-b9shffb3	2014	One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Therefore, a simplified VIDISCA protocol was developed, which lacks the last amplification round, and evaluated using viruses that were cultured from stool samples of acute flaccid paralysis children, and which had remained unrecognized on both cell culture and enterovirus specific real-time PCR. On the other hand, genetic analysis in ORF2 gene (capsid protein) showed that PAK-NIH-VS908 shared 99.7% nucleotide and 100% amino acid similarities with HAstV type 3 isolate IDH2211 (AB54844), a finding which matches with the results from VIDISCA and we conclude that the astrovirus is a recombinant, with a recombination site between ORF1a and ORF2.
cord-267736-rya9w6sh	2012	The ELISA-array assay is based on a "sandwich" ELISA format and consists of viral antibodies printed directly on 96-well microtiter plates, allowing for direct detection of 5 viruses. The developed ELISA-array proved to have similar specificity and higher sensitivity compared with the conventional ELISAs. This method was validated by different viral cultures and three chicken eggs inoculated with infected patient serum. The results demonstrated that this method combined the advantage of ELISA and protein array (multiplex and ease of use) and has potential for the identification of clinical encephalitis virus. When spotting, different spotting buffers and concentrations of capture monoclonal antibodies were evaluated to optimize the ELISA-array assay. To verify the results tested by ELISA-array, RNA extracted from chicken eggs was applied to a real time-RT-PCR assay using primers and probes targeting TBEV. In this study, we developed a multiplex ELISA-based method in a double-antibody sandwich format for the simultaneous detection of five encephalitis-associated viral pathogens.
cord-268560-pwps783y	2009	In B-cells, Gadd34, and EBNA3C are present in a complex with PP1a using microcystin sepharose affinity purification, Using a lymphoblastoid cell line in which EBNA3C protein levels are conditional on hydroxytamoxifen, surprisingly, we found that (i) EBNA3C maintains phosphorylation of eIF2α at serine 51, and (ii) protects against ER stress induced activation of the unfolded protein response as measured by XBP1 (u) versus XBP1(s) protein expression and N-terminal ATF6 cleavage. Recombinant EBV containing a stop codon in the EBNA3C ORF is able to cause B-cell transformation only when transcomplemented for wildtype EBNA3C either in cis or trans, and LCLs immortal-ized by recombinant EBV containing a conditional EBNA3C gene, undergo growth arrest when EBNA3C expression is turned off [5] [6] [7] EBNA3C co-activates transcription with EBNA2 at the viral LMP-1 promoter, as well as heterologous reporter systems designed to test p300 function.
cord-269277-x5c5ogo7	2013	The pGL3-Bov-EGFP vector containing nt 1-252 was transfected into 293 T, A549, HeLa and WI-38 cell lines to assay the activity of the promoter of HBoV1 in these mammalian cells. Here, the activity of the HBoV1 promoter in cells co-transfected with P1 and pGL3-pCMV-NS1mut vector (no NS1 protein expression) was used as a control. In our recent study, NS1 transcripts from the left-hand of the viral genome were detected in pWHL-1 transfected 293 T cells and other mammalian cells including HeLa, A549, WI-38 cell lines (data not shown), suggesting that this promoter is unique and active in most mammalian cells. For detection of HBoV1 promoter activity, mammalian cell lines including 293 T, A549, HeLa and WI-38 were transfected with the pGL3-Bov-EGFP construct and the pEGFP-N1 control vector in 24-well plates. Key elements of the human bocavirus type 1 (HBoV1) promoter and its trans-activation by NS1 protein
cord-271130-6s79q1c1	2017	title: Putative progressive and abortive feline leukemia virus infection outcomes in captive jaguarundis (Puma yagouaroundi) Thus, the aim of this study was to perform additional serological and molecular tests and monitor the population of jaguarundis at FPZSP for FeLV infection and development of FeLV-related diseases for 5 years (2003) (2004) (2005) (2006) (2007) . Two captive-born male jaguarundis, the geriatric #1 and the mature adult #4, presented serological and molecular FeLV test results similar to the progressive FeLV infection outcome in domestic cats [25] . Moreover, consistent with findings in domestic cats with a progressive FeLV infection, no antibodies to FeLV antigens were detected in jaguarundis #1 and #4. Two captive-born jaguarundis, #2 and #22, presented test results similar to those reported for domestic cats with abortive FeLV infection and seroconversion as the only marker of FeLV exposure [28] .
cord-271868-giea69b5	2009	These viruses have a linear positive-sense ssRNA genome of ~25-30 kb, encoding a large polyprotein that is expressed from the genomic RNA, and several additional proteins expressed from a nested set of 3''-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5'' end of the polyprotein coding sequence, ORF1a, in the +2 reading frame. As with other members of the order Nidovirales, these viruses have a linear positive-sense ssRNA genome encoding a large replicase polyprotein that is expressed from the genomic RNA (ORF1a and, via ribosomal frameshifting, an ORF1a-ORF1b fusion product), and a number of other proteinsincluding the structural proteins -which are translated from a nested set of 3''-coterminal sub-genomic RNAs ( Figure 1A ) [1] [2] [3] [4] [5] [6] .
cord-271948-iq29xqrn	2020	title: Transmitted drug resistance mutations and subtype diversity amongst HIV-1 sero-positive voluntary blood donors in Accra, Ghana BACKGROUND: Detection of HIV-1 transmitted drug resistance (TDR) and subtype diversity (SD) are public health strategies to assess current HIV-1 regimen and ensure effective therapeutic outcomes of antiretroviral therapy (ART) among HIV-1 patients. In this study, drug resistance mutations (DRMs) and SD amongst HIV-1 sero-positive blood donors in Accra, Ghana were characterized. The data obtained would inform the selection of drugs for ART initiation to maximize therapeutic options in drug-naïve HIV-1 patients in Ghana. This study found major drug resistance mutations, E138A and K65R that respectively confer high level resistance to NNRTIs and NRTIs. Although, CRF02_AG was most predominant, the recorded percentage of subtype B and the evolutionary relationship inferred by phylogenetic analysis may suggest possible subtype importation. The data obtained is useful for the selection of drugs for ART initiation to maximize therapeutic outcomes in drug-naïve HIV-1 patients in Ghana.
cord-273122-w9hemznv	2016	
cord-273179-bpnak9ov	2017	METHODS: We used real-time TaqMan-based PCR to detect MWPyV in the feces (n = 174) of children with diarrhea, nasopharyngeal aspirates (n = 887) from children with respiratory infections, and sera (n = 200) from healthy adults, and analyzed its clinical characteristics statistically. Therefore, in this study, we used realtime qPCR and DNA sequencing to investigate the presence of MWPyV in fecal samples from 174 children with diarrhea, nasopharyngeal aspirate (NPA) samples from 887 children with acute respiratory tract infections (ARIs), and sera from 200 healthy adults in China. In brief, the analysis of 1261 clinical samples only detected MWPyV in respiratory and fecal specimens from children, suggesting that the establishment of the primary infection occurs at an early age, and that the gastrointestinal and respiratory tracts are sites of viral persistence.
cord-273711-bxijla09	2012	title: RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells When Vero cells were transfected with shRNA expression vectors (p61/GFP, p70/GFP, p165/GFP and p296/GFP) and then infected with GTPV, GTPV-ORF095-70 was found to be the most effective inhibition site in decreasing cytopathic effect (CPE) induced by GTPV. These results suggest that the siRNA generated by in vitro transcription effectively and specifically inhibit the expression of GTPV ORF095 conserved regions in BHK-21 cells. To investigate whether or not knockout of ORF095 relieves cytopathic effect (CPE) induced by GTPV, Vero cells were transfected by plasmids expressing ORF095 protein-targeted shRNAs (p61/GFP, p70/GFP, p165/GFP and p296/GFP), respectively. Therefore, ORF095 gene is a good target to suppress GTPV replication by RNAi. In conclusion, this study demonstrates that vector-based shRNA methodology can effectively inhibit GTPV replication on Vero cells. RNA interference targeting virion core protein ORF095 inhibits Goatpox virus replication in Vero cells
cord-274375-a11ztdpg	2011	In surprise, only A 3 % has a significant correlation with both principle axes which represent the major trend in codon usage variation, suggesting that nucleotide A is the major factor influencing the synonymous codon usage pattern of HAV genome. Despite the ratio of U 3 % was the highest, the major compositional constraint, which shaping the synonymous codon usage pattern of HAV genome, was from the percent of nucleotide A on the third codon position (Table 4) . This discovery was different from many reports which suggest that C+G compositional constraints were the major factor influencing codon usage bias in virus genome [18, 29, 30] . Mutational pressure and natural selection are generally thought to be the main factors that account for codon usage variation between genes in different Table 3 Summary of correlation analysis between the A, U, C, G contents and A 3 , U 3 , C 3 , G 3 organisms [14] [15] [16] [17] [18] [19] [20] [21] .
cord-276550-1in7m56w	2006	title: S1 gene sequence analysis of a nephropathogenic strain of avian infectious bronchitis virus in Egypt RESULTS: Infectious bronchitis virus (IBV) strain closely related to Massachusetts (Mass) serotype was isolated from broiler chickens suffering from severe renal and respiratory distresses. Protection based criteria were: virus re-isolation attempts from trachea, tracheal and renal histopathology as well as IBV antigens detection by immunofluorescent antibody technique in kidney sections. In the present study, Egypt/F/03 was isolated from 25day-old broiler chickens in Fayoum Governorate, identified by Dot-ELISA, RT-PCR and sequenced to determine its serotype. In this study, an Egyptian IBV strain; Egypt\F/03 was isolated from a tissue pool of kidney and trachea from unvaccinated broiler flock with a history of respiratory and renal disease. Challenge experiments to evaluate cross-protection induced at the trachea and kidney level by vaccine strains and Belgian nephropathogenic isolates of avian infectious bronchitis virus
cord-277547-2vim1wno	2011	In the present study, antiviral activity of four types of bioflavonoid against dengue virus type -2 (DENV-2) in Vero cell was evaluated. Daidzein showed a weak anti-dengue activity with IC(50 )= 142.6 μg mL(-1 )when the DENV-2 infected cells were treated after virus adsorption. Although there was no significant direct virucidal activity against DENV-2 by quercetin, continuous treatment of cells from 5 h before virus infection up to 4 days post-infection exhibited anti-dengue activity with IC 50 = 28.9 μg mL -1 (Figure 3a) . There was no significant change in the antiviral activity of daidzein when cells were treated continuously from 5 h before virus infection up to 4 days post infection comparing to its anti-dengue activity for postadsorption treatment (Figure 1 ). To investigate which of the many flavonoids could affect DENV infection, in the present study, we examined the potential effects of quercetin, naringin, hesperetin and daidzein on dengue virus infection of Vero cells.
cord-278250-dwok857k	2019	We performed metagenomic sequencing of fecal samples to detect the bacterial microbiome and virome composition of healthy one-year-old rhesus monkeys housed at the IMBCAMS (Fig. 1) . We comprehensively analyzed the interactions among the gut virome, bacterial microbiome and metabolomes based on the above results there were noticeable differences in bacterial β-diversity between control and experimental animals, as determined using principal component analysis (PCA), and the results showed good repeatability within a single group (Additional file 2: Figure S2F ). Briefly, the fecal virome composition was noticeably altered after depletion of the bacterial microbiome, and the abundances of many DNA viruses, bacteriophages and RNA viruses in the gut were clearly decreased. As expected, the whole gut bacterial microbiome, including gram-positive and gram-negative bacteria (Additional file 2: Figure S2E ), was depleted after treatment with the antibiotic cocktail, except for Escherichia-Shigella species belonging to Proteobacteria, which were resistant to the cocktail.
cord-278324-eqqvwwh6	2018	BACKGROUND: A serological method to simultaneously detect antibodies against infectious laryngotracheitis virus (ILTV) and infectious bronchitis virus (IBV) is imperative for the differential diagnosis and evaluation of antibodies titers after vaccination. Therefore, it is important to establish a method to simultaneously detect ILTV and IBV antibodies for the differential diagnosis and immune response evaluation after vaccination. In this study, a method employing Luminex xMAP technology to simultaneously detect ILTV and IBV antibodies in serum was established, optimized and used for the differential diagnosis of IBV and ILTV. 2 and 3 demonstrated that xMAP duplex assay for ILTV and IBV has a high specificity since there were no cross-reactions with serum positive for other avian diseases, such as avian influenza virus To compare duplex xMAP assay with ELISA for ILTV/IBV detection, 90 chicken serum samples from a chicken farm in Huizhou, China were used and the results are shown in Table 7 .
cord-279784-o80x8nj7	2019	title: Characterization and pathogenicity of Vero cell-attenuated porcine epidemic diarrhea virus CT strain METHODS: In this study, the highly virulent epidemic virus strain CT was serially passaged in Vero cells for up to 120 generations (P120). Previous studies conducted at Fig. 1 Biological characteristics of porcine epidemic diarrhea virus strains after 10, 64, or 120 passages. A newly isolated Chinese virulent genotype GIIb porcine epidemic diarrhea virus strain: biological characteristics, pathogenicity and immune protective effects as an inactivated vaccine candidate Oral efficacy of Vero cell attenuated porcine epidemic diarrhea virus DR13 strain Attenuation of an original US porcine epidemic diarrhea virus strain PC22A via serial cell culture passage Comparative genomic analysis of classical and variant virulent parental/attenuated strains of porcine epidemic diarrhea virus Preparation and characterization of an attenuated porcine epidemic diarrhea virus strain by serial passaging
cord-282343-cko4curf	2015	
cord-283333-u3r1usfs	2019	However, the genotype diversity and epidemiological information relating to HAdVs among hospitalized children with respiratory tract infections (RTIs) is limited. Therefore, the aim of this study was to evaluate the epidemiological, clinical, and molecular characteristics of HAdV infections occurring among children with RTIs in a Chinese tertiary hospital from April 2017 to March 2018. Herein, we describe (i) the prevalence of HAdVs in hospitalized children with RTIs presenting at Beijing Friendship Hospital during a one-year period; (ii) the clinical spectrum of the HAdV-positive RTI patients; (iii) the viral co-pathogens present in the HAdV infections; and (iv) the genetic diversity of the HAdVs. The clinical characteristics of the RTIs caused by HAdV are very similar to those of influenza, PIV and other respiratory tract pathogens, making it difficult to clinically diagnose this type of infection. This 1-year study documented the prevalence, age distribution, seasonality and molecular epidemiology of HAdV infections among children hospitalized with RTIs at Beiing Friendship Hospital.
cord-283689-dzin12qb	2019	RESULTS: Autophagy was activated by porcine reproductive and respiratory syndrome virus (PRRSV) NSP3, NSP5 and NSP9, which are two transmembrane proteins and an RNA-dependent RNA polymerase, respectively. Based on the data presented in Fig. 2c , immunoblotting and immunofluorescence assay showed that the expression of the p62 protein was increased, indicating that NSP3 and NSP5 of PRRSV induced the formation of autophagosomes. As shown in Fig. 3a , ATG5 puncta were arranged in reticular structures and colocalized with calnexin in the Fig. 1 The distribution of autophagy proteins in PRRSV-infected Marc-145 cells. As shown in the present study, the induction of autophagy by PRRSV NSP3 and NSP5 contributed to the formation of autophagosomes derived from the ER, and the mature autophagosomes were not degraded by fusion with lysosomes.
cord-284608-ba7wq52t	2019	
cord-284630-l9ghggu7	2019	
cord-285253-ik5w4t5e	2011	METHODS: We tested nasal and throat swab specimens obtained from 225 infants with respiratory illness for 11 common respiratory viruses using both a multiplex assay (Respiratory MultiCode-PLx Assay [RMA]) and individual real-time RT-PCR (RT-rtPCR). The RMA assay detected significantly more human metapneumovirus (HMPV) and respiratory syncytial virus (RSV), while RT-rtPCR detected significantly more influenza A. Restricting the analysis to the 11 viruses tested with both methods, at least one virus was detected in 174 (78.3%) samples by RMA and in 163 (73.4%) samples by RT-rtPCR. In the second round using redesigned RT-rtPCR HMPV primers and probes, HMPV was detected in 7 samples, 5 of which were concordant with the results of the first RMA assay. Comparison of the Eragen Multi-Code Respiratory Virus Panel with conventional viral testing and real-time multiplex PCR assays for detection of respiratory viruses
cord-286256-yol03hid	2020	title: Non-optimal effectiveness of convalescent plasma transfusion and hydroxychloroquine in treating COVID-19: a case report BACKGROUND: Convalescent plasma (CP) transfusion was reported to be effective in treating critically ill patients with COVID-19, and hydroxychloroquine could potently inhibit SARS-CoV-2 in vitro. CASE PRESENTATION: Laboratory findings showed high lactic acid level (2.1 mmol/L) and C-reactive protein (CRP, 48.8 mg/L), and low white blood cell count (1.96 × 10(9)/L) in a 65-year-old Chinese man, who was diagnosed with severe COVID-19. The lactic acid and C-reactive protein levels remained high (2.1 mmol/L and 73.23 mg/L, respectively), while the arterial oxyhemoglobin saturation decreased to 86% with a low oxygenation index (OI, 76 mmHg) on day 4 after CP transfusion. Few studies have reported the effectiveness of convalescent plasma (CP) transfusion in treating critically ill patients with COVID-19 [2] [3] [4] . Herein, we administered CP transfusion and hydroxychloroquine to a patient with severe COVID-19, and analyzed their clinical symptoms, oxygenation index (OI), and dynamics of viral load.
cord-286332-cdg4im5h	2017	
cord-286842-04cuk2cn	2005	title: Recombinant Tula hantavirus shows reduced fitness but is able to survive in the presence of a parental virus: analysis of consecutive passages in a cell culture Tula hantavirus carrying recombinant S RNA segment (recTULV) grew in a cell culture to the same titers as the original cell adapted variant but presented no real match to the parental virus. Using the two specific RT-PCR conditions, the presence of V-type and REC-type S RNA was monitored on ten sequential passages of the mixture of TULV02 and RecTULV5 variants (Fig. 2 ). Although relatively short, the observed survival time of the recTULV in the presence of the original variant TUL02 seems to be sufficient for transmission of a recombinant virus, in a hypothetical in vivo situation, from one rodent to another. The data presented in this paper show that the recTULV presents no real match to the original cell adapted variant and that the lower fitness of the recombinant virus can not be increased by pre-passaging in cell culture.
cord-289081-9v04gzhf	2015	In this study we determined the frequency and diversity of RV strains associated with upper and lower respiratory tract infections (URTI, LRTI) in Mexico, and describe the clinical characteristics of the illness associated with different RV species. Most studies have described the presence of RV genotypes in hospitalized patients with severe respiratory illness, and only a few studies have described the prevalence of virus genotypes in URTIs. In this work, we carried out a prospective multicenter study of two children populations having either URTI or LRTI. The phylogenetic trees in Figure 2 depict the wide distribution of 5′-UTR sequences of the RV-A and RV-C Table 1 Frequency of RV infections in children with upper and lower respiratory tract infections strains isolated from URTI and LRTI patients. This study describes the frequency of detection of rhinovirus species in children with upper and lower respiratory tract infections in Mexico and their genetic diversity, determined by sequencing the 5′ UTR region of the viral genome.
cord-289397-a1cuq29o	2011	Lycorine treatment of mice challenged with a lethal dose of EV71 resulted in reduction of mortality, clinical scores and pathological changes in the muscles of mice, which were achieved through inhibition of viral replication. To study the inhibitory mechanism of lycorine against EV71 infection, the synthesis of several typical viral proteins were detected by western blotting in 1.5 hours periods following lycorine treatment, when the effects of inhibition was just appeared ( Figure 3A and 3B) . Consistent with the results of the clinical scores and survival rates, virus replication in the muscle of lycorine-treated mice were inhibited by 10-100 folds at different time points compared to that of the saline control as detected by qRT-PCR and semi-quantitative RT-PCR ( Figure 5A and 5B). The virus replication in muscle tissues of lycorine-treated (0.4 mg/kg) mice was significantly inhibited by more than 100-fold compared to the saline control as detected by qRT-PCR and semiquantitative RT-PCR ( Figure 7A and 7B) .
cord-290798-5ca2e6wm	2016	title: Evaluation of custom multiplex real time RT PCR in comparison to fast track diagnostics respiratory 21 pathogens kit for detection of multiple respiratory viruses Therefore the aim of the present study was to develop a cost effective multiplex real time RT-PCR for the detection of 18 respiratory viruses and compare it with an in-vitro diagnostics approved Fast Track Diagnostic Respiratory Pathogens 21 Kit (FTD). METHODS: Nasopharyngeal aspirates and throat swabs were collected and processed for extraction of nucleic acid using an automated extraction system and multiplex real time RT-PCR was performed using the FTD kit and a custom assay on 356 samples. The present study compares custom real-time multiplex PCR primers and probes for the simultaneous detection of 18 respiratory viruses with an in-vitro diagnostics (IVD) approved fast track diagnostics (FTD) kit.
cord-290976-dhwlr2ui	2013	
cord-291961-usl8z6ep	2015	METHODS: The VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. CONCLUSIONS: The prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Previous studies have indicated that a number of HPyVs are associated with human diseases, such as progressive multifocal leukoencephalopathy (JCPyV), hemorrhagic cystitis (BKPyV), Merkel cell carcinoma (MCPyV), and trichodysplasia spinulosa (TSPyV) [3, 7, 9, [17] [18] [19] . Because initial infections with most HPyVs occur in infancy, the prevalence of HPyV6 in NPAs from children was detected with real-time PCR. The detection rate for HPyV6 by real-time PCR assay was 1.7 % in 887 NPA samples collected from hospitalized children with RTI.
cord-292581-6ipzvryb	2012	BACKGROUND: Altered plasma concentrations of vitamin D and mannose binding lectin (MBL), components of innate immunity, have been shown to be associated with the pathogenesis of viral infections. The objective of the present study was to find out whether plasma concentrations of MBL and vitamin D are different in patients with dengue fever (DF) and dengue hemorrhagic fever (DHF). Therefore, we investigated the levels of plasma vitamin D and MBL in dengue infected patients in the context of disease severity and immune status. When the patients were grouped based on immune status and disease severity, secondary DHF cases had significantly higher concentrations of vitamin D as compared to secondary DF cases (P < 0.050). Analysis of circulating concentrations of MBL in dengue cases and healthy controls revealed no significant difference between the two groups suggesting that the MBL mediated pathway of complement activation might be inhibited or may not be induced during DENV infection.
cord-292794-okh6i4l1	2012	Results demonstrated that there was no detectable virus load in all the vaccine-immunized mice, while empty vector control group showed high lung viral titers ( Figure 4 ). Results indicated that all the mice that had been vaccinated with MHa had a detectable virus level, although showed a reduction in mean viral titers in both challenge groups compared with vector control, the reduction did not reach significance (p = 0.06 for rPan09 group and p = 0.67 for G11 group, Figure 4 ). The present study lays the foundation for universal swine influenza vaccine development, and call for further investigations in which the heterologous immune response should be further enhanced, such as the addition of molecular adjuvants [31, 32] and/or more copies of conserved viral protein encoding genes [33] , and the usage of DNA-prime protein/virus-boost immunization schedule [34, 35] .
cord-293938-40zyv1h8	2016	
cord-295207-0p6x4lwx	2011	The aim of this study was to develop therapeutic peptides targeting glycoprotein B (gB), a major glycoprotein of HCMV that is highly conserved across the Herpesviridae family, that specifically inhibit fusion of the viral envelope with the host cell membrane preventing HCMV entry and infection. Previous studies have suggested that synthetic peptides corresponding to or overlapping with sequences in viral fusion proteins that have positive WWIHS scores can sometimes serve as viral entry inhibitors [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] . For example, Enfurvitide (Fuzeon) is a 36-amino acid peptide that overlaps with a WWIHS score-positive sequence in the transmembrane protein (TM) of HIV-1, and prevents viral fusion and entry of the virus. These results suggest that the HCMV inhibitory peptides identified here may serve as Figure 2 Determination of regions within gB that display a high propensity to interact with the lipid surface of cell membranes by using Wimley-White Interfacial Hydrophobicity Scale (WWIHS).
cord-300434-obvm2en0	2018	BACKGROUND: Small hydrophobic (SH) gene is one of the mostly diverse genomic regions of human respiratory syncytial virus (HRSV). When analysis was restricted to strains with identical HVR2 nucleotide sequences and differing SH protein sequences, 75% of differences observed in the SH ectodomain were located within region coding for amino acids 49–51. In molecular epidemiology studies, HRSV surveillance and genotyping are based on sequences of the second, C-terminal hypervariable region of the G gene (HVR2). Following our previous analysis of HVR2 sequences of strains detected within a limited geographical area (the Zagreb region) and limited time frame (March 2011 to March 2014) [16] , the goal of this study was to investigate whether virus variability and inter-genotype differences observed for HVR2 are also present in the SH gene.
cord-300837-d0a8y5qh	2010	
cord-300908-i80tuhqk	2015	title: Application of recombinant severe fever with thrombocytopenia syndrome virus nucleocapsid protein for the detection of SFTSV-specific human IgG and IgM antibodies by indirect ELISA rSFTSV-N protein based indirect IgG and IgM enzyme linked immunosorbent assay (ELISA) systems were established to detect specific human IgG and IgM antibodies, respectively. Application of the rSFTSV-N protein based indirect IgG ELISA to the 115 serum samples showed results that perfectly matched those of the total antibody sandwich ELISA with a sensitivity and specificity of 100 %. To determine the appropriate dilutions of serum samples for the indirect IgG and IgM ELISAs using the rSFTSV-N protein mentioned above, samples from healthy volunteers and SFTS confirmed patients were diluted two-fold from 1:100 up to 1:1000. To evaluate the usefulness for diagnosis of the rSFTSV-N protein we developed, we established an indirect IgG and IgM ELISA for the laboratory diagnosis of SFTSV infection in humans with the serum samples as clinical specimens.
cord-302170-k2apj469	2015	
cord-303313-b8lesr2g	2007	
cord-303494-tofch4j7	2014	
cord-304058-i8cywew0	2009	
cord-305315-0qt7eth0	2015	title: Porcine epidemic diarrhea virus inhibits dsRNA-induced interferon-β production in porcine intestinal epithelial cells by blockade of the RIG-I-mediated pathway In this study, porcine small intestinal epithelial cells (IECs), the target cells of PEDV, were used as the infection model in vitro to identify the possible molecular mechanisms of PEDV-inhibition IFN-β production. CONCLUSION: Taken together, our data demonstrated for the first time that PEDV infection of its target cell line, IECs, inhibited dsRNA-mediated IFN-β production by blocking the activation of IPS-1 in RIG-I-mediated pathway. PEDV failed to induce IFN-β expression and inhibited poly (I:C)-mediated IFN-β production in IECs Type I IFNs (IFN-α/β) are critical to the host antiviral innate immune response. In summary, the findings of the present study suggested that PEDV-infection in IECs inhibits dsRNA-induced IFN-β induction by interfering with IRF-3 activity associated with RIG-I-mediated signaling pathway.
cord-307364-j86t65qu	2014	In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. CONCLUSIONS: This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses. Here we report the discovery of a novel nidovirus in a collection of ball pythons (Python regius) in upstate New York with pneumonia, tracheitis and esophagitis. Based on the phylogenetic position and the genetic distances between In situ hybridization to a 934 nt fragment of the genomic polyprotein 1ab region was used to assess viral infection and distribution in the lung tissue. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius)
cord-308397-kqftn75t	2014	
cord-310372-qc6941pm	2011	
cord-310536-u30cufg7	2018	
cord-313598-2t40ss6h	2015	
cord-314201-6njwigco	2008	
cord-314954-otc0pc09	2010	In this study, the C-terminus of DEV UL26 protein (designated UL26c), which contains the whole of UL26.5, was expressed, and the recombinant UL26c protein was used to immunize BALB/c mice to generate monoclonal antibodies (mAb). Both western blotting and ELISA showed that 1C8 could react specifically with both chicken embryonic fibroblasts (CEF) infected with DEV ( Figure 1B and Figure 1C ) and the recombinant protein UL26c ( Figure 1D and Figure 1C ). The results of both western blotting and ELISA showed that this peptide defined by mAb 1C8 could react with murine anti-DEV antibody ( Figure 4 ), which demonstrated that the epitope had good reactivity. A series of 17 fragments that spanned the UL26c protein were expressed with a GST tag in this study, and used to screen for the minimal epitope recognized by mAb 1C8 using western blotting and ELISA. The specificity and reactivity of the mAb 1C8 were also determined by western blotting using recombinant UL26c protein and CEF infected by DEV, respectively.
cord-315688-ba5dus2j	2012	title: In vitro inhibition of transmissible gastroenteritis coronavirus replication in swine testicular cells by short hairpin RNAs targeting the ORF 7 gene In the reporter assays, three of four shRNA expression plasmids were able to inhibit significantly the expression of ORF 7 gene and replication of TGEV, as shown by real-time quantitative RT-PCR analysis of viral ORF 7 and N genes and detection of virus titers (TCID(50)/ml). Here, we demonstrate that RNAi targeting of the ORF 7 gene of TGEV, introduced by short hairpin RNAs (shRNAs), is capable of inhibiting virus replication and protecting swine testicular (ST) cells from the destruction induced by TGEV, which may be not only a new anti-TGEV strategy, but also a new approach to the study of its pathogenesis. The present study demonstrated the use of RNAi against TGEV via shRNA-expressing plasmid vector pGPU6-GFP, which significantly reduced viral genomic RNA replication and protected ST cells from TGEV destruction, by targeting ORF 7 gene.
cord-316142-wg1qwmj1	2017	
cord-316234-vtjsfi2c	2017	
cord-317773-jdq1d98i	2011	
cord-318686-we6pveus	2016	
cord-318853-mxyxwkhx	2005	Perhaps more importantly, ineluctable generation of broad phenotypic diversity after viral RNA is translated to protein quasispecies suggests a mechanism of disease that specifically targets, and functionally disrupts, the host cell surface molecules – including hormone, lipid, cell signalling or neurotransmitter receptors – that viruses co-opt for cell entry. Hence, as relative concentrations of wild-type and variant viral proteins vary, alteration of both processivity and fidelity of RNA pol results, permitting viruses to adaptively respond to environmental changes, including immune recognition and reaction to evolving cell receptors. As clear evidence exists for viral disruption of leptin function [106] and virus-associated weight gain in humans [107] and monkeys [108] , is it possible the global epidemics of type II diabetes mellitus, insulin resistance, hyperlipidaemia and obesity now prevalent [109] [110] [111] [112] [113] [114] [115] [116] , are just that; epidemics fundamentally caused by viruses that co-opt insulin or leptin or other associated receptors for cell access and generate protein quasispecies that disrupt receptor function?
cord-319954-lh32rhhe	2013	Immunoblotting of lysates prepared from pCAGGS/M transfected cells with MAbM3F8 (anti-M) revealed the presence of a 28 kDa protein, the expected size of the HMPV M protein ( Figure 1C ). Only pCAGGS/F-cmyc transfected cells immunoprecipitated and immunoblotted with anti-cmyc showed the presence of F proteins species corresponding in size to the monomeric and oligomeric F protein ( Figure 1D ). Similarly lysates immunoprecipitated with anti-FLAG and immunoblotted using anti-cmyc revealed increasing amounts of F145 with increasing DSP concentration, together with a cmyc-tagged protein species >300 kDa ( Figure 2F ) whose molecular mass was consistent with higher oligomeric forms of the F protein. We failed to detect the presence of the M protein in detergent extracts prepared from pCAGGS/M transfected cells that were immunoprecipitated with influenza virus anti-NP (i.e. a non-specific antibody) and immunblotted with anti-M ( Figure 4C ); confirming the specificity of the M protein immunoprecipitation.
cord-320617-ucm7wx8b	2018	
cord-320693-de1lmzl1	2019	
cord-321756-a7eh4dkb	2012	
cord-321814-vt6yio6x	2012	
cord-322024-yrqpq9cf	2013	
cord-322238-8iwljdoi	2010	Loop-mediated isothermal amplification (LAMP) was developed to detect the TGEV by incubation at 60°C for 1 h and the product specificity was confirmed by HphI digestion. By using serial sample dilutions as templates, the detection limit of LAMP was about 10 pg RNA, 10 times more sensitive than that of PCR and could be comparable to the nest-PCR. Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method, which amplifies DNA/RNA with high specificity, sensitivity and rapidity under isothermal condition [5] . As a kind of nucleic acid amplification method, LAMP could not only qualitatively detect the TGEV, but also quantitatively analyze the virus. In conclusion, this study demonstrates that the LAMP method established could detect only the TGEV and no cross-reaction with other viruses, the detection limit was about 10 pg RNA, which was 10 times more sensitive than that of PCR and could be comparable to the nest-PCR.
cord-322738-nvyknvc7	2014	
cord-322937-lakdi3x8	2010	
cord-323009-frej2qmb	2013	
cord-325172-a8ntxnmm	2014	
cord-325555-be78qely	2015	
cord-327013-gc6o8ou3	2020	
cord-329517-3yn80r9h	2009	
cord-329520-dt0jku7v	2010	
cord-329680-ekxsv91t	2019	
cord-330251-dwjijmwz	2010	
cord-330777-xcwppaux	2010	
cord-331542-wy068c6o	2020	
cord-333349-tsfxpaj6	2014	title: Elevated dietary zinc oxide levels do not have a substantial effect on porcine reproductive and respiratory syndrome virus (PPRSV) vaccination and infection The purpose of this study was to determine the influence of dietary zinc oxide supplementation on vaccination and challenge infection with PRRSV. CONCLUSIONS: Our results suggest that higher levels of dietary ZnO do not have the potential to stimulate or modulate systemic immune responses after vaccination and heterologous PRRSV infection to an extent that could improve the clinical and virological outcome. In contrast to Vanhee et al., we chose a single-vaccination approach and challenge-infected the animals with a heterologous type I PRRSV (95,38% sequence identity for the envelope glycoprotein GP5, which bears a major neutralizing epitope) in order test the influence of elevated Zn levels on an suboptimal antigen stimulus and on crossprotection. Elevated dietary zinc oxide levels do not have a substantial effect on porcine reproductive and respiratory syndrome virus (PPRSV) vaccination and infection
cord-333913-roftm446	2009	In an effort to identify novel viruses that may be causal agents of diarrhea, we used high throughput mass sequencing to analyze stool samples collected from patients with acute diarrhea. RESULTS: Sequences with limited similarity to known picornaviruses were detected in a stool sample collected in Australia from a child with acute diarrhea. We also detected klassevirus 1 by RT-PCR in a diarrhea specimen collected from a patient in St. Louis, United States as well as in untreated sewage collected in Barcelona, Spain. Extracted nucleic acid from a stool specimen collected in 1984 from a child with acute diarrhea was subjected to high throughput mass sequencing using 454 pyroseqencing technology. Phylogenetic analysis of the VP3/VP1, P2, and P3 regions of the genome demonstrated that this virus sequence is highly divergent from all previously described picornaviruses (Figure 2A -C).
cord-335865-pibq3iwh	2014	title: Imaging analysis of human metapneumovirus-infected cells provides evidence for the involvement of F-actin and the raft-lipid microdomains in virus morphogenesis METHODS: HMPV-infected LLC-MK2 cells were stained with antibodies that recognised the HMPV fusion protein (F protein), attachment protein (G protein) and matrix protein (M protein), and fluorescent probes that detect GM1 within lipid-raft membranes (CTX-B-AF488) and F-actin (Phalloidin-FITC). Cells co-expressing recombinant HMPV G and F proteins formed virus-like particles and were co-stained with antibodies that recognise the recombinant G and F proteins and phalloidin-FITC and CTX-B-AF594, and the distribution of the G and F proteins, GM1 and F-actin determined. We also observed these co-stained filamentous structures spreading to the non-infected cells, suggesting that F-actin may play a role in virus transmission in the monolayer, in a similar manner to that proposed for RSV [17, 25, 30] . HMPV-infected cells were stained with anti-G and CTX-B-AF488, and examined using confocal microscopy at an optical plane that allowed the virus filaments to be visualized ( Figure 4D ).
cord-336510-qzm9wgde	2005	In a first wave of responses, cytokines, primarily type I interferons (IFN) and tumour necrosis factor are produced and exert a direct antiviral effect and activate the macrophages themselves. Generally the type I IFNs exhibit a huge range of biological effects, such as antiviral and antiproliferative effects, stimulation of immune cells such as T cells, natural killer (NK) cells, monocytes, macrophages, and dendritic cells, increased expression of MHC-I, activation of pro-apoptotic genes and inhibition of anti-apoptotic mechanisms, modulation of cellular differentiation, and inhibition of angiogenesis [171] . Effect of IL-4 and IL-13 on IFN-gamma-induced production of nitric oxide in mouse macrophages infected with herpes simplex virus type 2 Herpes Simplex virus type 1-induced interferon production and activation of natural killer cells in mice NF-kappaB activation is responsible for the synergistic effect of herpes simplex virus type 2 infection on interferon-gamma-induced nitric oxide production in macrophages
cord-336870-nirg3269	2020	
cord-337003-7ygcfzii	2017	
cord-337128-yyz7z0xj	2009	title: Immunohistochemistry for detection of avian infectious bronchitis virus strain M41 in the proventriculus and nervous system of experimentally infected chicken embryos Aim of this study was to investigate by immunohistochemistry (IHC) the tissue tropism of avian infectious bronchitis virus (IBV) strain M41 in experimentally infected chicken embryos. Using IHC, antigens of IBV were detected in nasal epithelium, trachea, lung, spleen, myocardial vasculature, liver, gastrointestinal tract, kidney, skin, sclera of the eye, spinal cord, as well as in brain neurons of the inoculated embryos. IBV antigens were detected in the nasal epithelium, trachea, lung, spleen, myocardium, liver, gizzard, proventriculus, kidney, skin, sclera of the eye, spinal cord, as well as in neurons of the central nervous system in infected embryos (Table 1, Figure 1 ).
cord-337274-1fw0xiin	2010	title: A multiplex reverse transcription-nested polymerase chain reaction for detection and differentiation of wild-type and vaccine strains of canine distemper virus A multiplex reverse transcription-nested polymerase chain reaction (RT-nPCR) method was developed for the detection and differentiation of wild-type and vaccine strains of canine distemper virus (CDV). The multiplex reverse transcription-nested polymerase chain reaction (RT-nPCR) method could be used to effectively detect and differentiate between wild-type CDV-infected dogs from dogs which were vaccinated with CDV vaccine, which would make it useful in clinical diagnosis and epidemiological monitoring. In summary, the multiplex RT-nPCR developed in this study is a highly specific and sensitive assay for the rapid detection and differentiation of wild-type and vaccine strains of CDV. A multiplex reverse transcription-nested polymerase chain reaction for detection and differentiation of wild-type and vaccine strains of canine distemper virus
cord-337636-3yc0ribg	2020	Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps. Swabs were spiked in serial dilutions from 1.2 × 10(6) to 1.2 × 10(1) copies/mL and then placed in 2 mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. RESULTS: HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. CONCLUSION: We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. Using human coronavirus 229E (HCoV-229E) as our model organism, we developed a novel two-step methodology of optimized shaker-mill homogenization parameters that allowed for direct-to-PCR viral detection.
cord-338372-xsg0j92t	2012	While varying luciferase activity after parallel HCVpp inoculation is a phenotype we have seen among Huh7 cell lines from different laboratories (Additional file 1: Figure S3 and [34] ), to functionally test whether these cells express suboptimal levels of any of the known HCV entry factors, we transiently transfected PLC, Hep3B and HepG2-CD81 cells with vectors expressing the four known human HCV receptors and reassessed their permissiveness for HCVpp and HCVcc infection 48 h post-transfection. Notably, we have previously shown that IFN-mediated activation of the innate cellular interferon response inhibits HCV RNA replication and subsequent production of de novo HCV virions ( [45] and data not shown), thus the reduced steady-state HCVcc infection levels observed in Hep3B and HepG2-CD81 cells and the decline of HCV infection observed in PLC cells, despite these cells exhibiting comparable infection initiation permissiveness, may be at least in part a consequence of HCV-induced innate immune signaling in these hepatoma cell lines.
cord-339209-oe8onyr9	2014	The organization of each genome was similar to that described previously for the mesoniviruses (NDiV, CavV, HanaV, NseV and MenoV), featuring a long 5''-untranslated region (5''-UTR) of 359 to 370 nt, six major long open reading frames (ORFs), and a long terminal region of 1780 to 1804 nt preceding the poly[A] tail ( Figure 2 ). To determine the phylogenetic relationships of the newly identified insect viruses, maximum likelihood (ML) phylogenetic trees were constructed based on the amino acid alignments of ORF2a (unprocessed S protein) and a concatenated region of the highly conserved domains within ORF1ab (3CL pro , RdRp and ZnHel1). A Clustal X alignment of the mesonivirus ORF3a proteins and individual structural analyses using SignalP and TMHMM and NetNGlyc (www.expasy.org) indicated that each is a class I transmembrane glycoprotein with a predicted N-termimal signal peptide, an ectodomain containing a conserved set of 6 cysteine residues and a single conserved N-glycosylation site, a transmembrane domain and a C-terminal cytoplasmic domain ( Figure 4A, 4D) .
cord-339744-xrit0w5i	2017	Our previous microarray analysis showed that H9N2 virus infection and inactivated viral particle inoculation increased the expression of interferon-inducible transmembrane protein 1 (IFITM1) in human umbilical vein endothelial cells (HUVECs). In present study, we deeply investigated the expression patterns of IFITM1 and IFITM1-mediated antiviral response induced by H9N2 virus infection and inactivated viral particle inoculation in HUVECs. Epithelial cells that are considered target cells of the influenza virus were selected as a reference control. The results indicated that the cellular interaction between intracellular molecules and viral particles might be involved in the induction of IFITM1 expression in HUVECs. To determine the antiviral activity of IFITM1 protein induced by H9N2 virus infection, HUVECs or BEAS-2Bs were infected with H9N2 virus at MOI of 5 and incubated for 1 h, then cells were transfected with IFITM1 specific siRNA or control siRNA for 36 h.
cord-340046-kgbvld0y	2011	BACKGROUND: Exhaled breath condensate (EBC) sampling has been considered an inventive and novel method for the isolation of respiratory viruses. RESULTS: Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. This observation has created a growing interest in the use of EBC as a new sampling method for the screening of respiratory viruses infecting the upper airways. The aim of this study was to investigate whether the EBC collection method was suited for the efficient condensation of aerosolised virus particles during normal breathing and to explore the isolation of respiratory viruses in the condensate. In this study, 102 EBCs were collected from otherwise healthy volunteers showing respiratory or flu-like symptoms (defined in Table 1 ), using a commercially available condenser (RTube™, Respiratory Research Inc., Charlottesville, Virginia, USA). Collection of exhaled breath condensates is a novel and non-invasive method for obtaining samples of the upper respiratory tract.
cord-340883-zf8jbhdl	2007	title: Using patient-collected clinical samples and sera to detect and quantify the severe acute respiratory syndrome coronavirus (SARS-CoV) Reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect and quantify SARS-CoV in 934 sera and self-collected throat washes and fecal samples from 271 patients with laboratory-confirmed SARS managed at a single institution. The highest SARS-CoV RT-PCR rates (70.4–86.3%) and viral loads (log(10 )4.5–6.1) were seen in fecal samples collected 2–4 weeks after the onset of clinical illness. The aim of this study was to detect and quantify SARS-CoV using RT-PCR in sera and throat washes and stools self-collected by 271 patients with laboratory confirmed SARS managed at a single institution. The use of patient self-collected throat washings may reduce risks to healthcare workers, although lower respiratory tract samples such as sputum, NPAs or bronchoalveolar lavage fluid are likely to have higher viral loads and offer increased likelihood of SARS-CoV detection by RT-PCR.
cord-341168-3gd1w2kn	2006	We have previously shown that A-MLV entry is closely associated with cholesterol-rich microdomains like rafts and caveolae [1] and that A-MLV envelope protein is associated with rafts in infected cells suggesting a possible role of rafts in A-MLV assembly [2] . As rafts are suggested to be pre-caveolae [11] and a large fraction of the A-MLV receptor Pit2 was found associated with cholesterol-rich microdomains [1] , we have here investigated if rafts and caveolae are involved in the early steps of A-MLV binding. As GM1 is a general marker for cholesterol-rich microdomains, we investigated if these regions of preferred A-MLV binding were also enriched in caveolin-1 (cav-1), a major structural protein of caveolae. Using confocal microscopy we found that A-MLV binds preferentially to large GM1-positive membrane regions of NIH3T3 cells, which are most likely rafts. In addition, A-MLV binding to large rafts was independent of plasma membrane cholesterol indicating that the A-MLV receptor Pit2 or other virus interacting proteins were still present in these regions.
cord-341321-paucodwz	2008	We have previously described the identification of several sequence fragments with limited sequence identity to known astroviruses in a stool specimen obtained from a child with acute diarrhea, suggesting that a novel virus was present. Like other astroviruses, the AstV-MLB1 genome was predicted to encode three open reading frames (ORF1a, ORF1b, and ORF2) and contained both 5'' and 3'' non-translated regions (NTR), as well as a poly-A tail. In the less conserved regions II-IV, AstV-MLB1 shared only 5-27% amino acid identity to the known human astroviruses. Complete sequencing and genome analysis of Astrovirus MLB1 revealed that the virus has three open reading 1a 787 28 28 NA 29 29 NA NA 29 9 9 NA 10 22 24 1b 511 54 54 NA 54 54 NA NA 54 36 35 NA 36 47 44 2 756 24 24 24 23 23 24 24 24 15 16 16 11 18 19 frames sharing the same organization as other astroviruses.
cord-342117-r2chpw7y	2010	The antiviral effect of siRNA was evaluated by measurement of cell survival rate using the MTT method and viral RNA was quantitated with real-time RT-PCR. CONCLUSIONS: Our data showed that synthetic siRNA against the DEN-1 membrane glycoprotein precursor gene effectively inhibited DEN-1 viral RNA replication and increased C6/36 cell survival rate. Therefore, in this study, we designed and synthesized 21 nt siRNAs against the DEN-I viral PrM gene, and investigated their inhibition effects of dengue virus replication in transfected C6/36 cells. These data indicate that siRNA against DEN viral genome can effectively inhibit viral RNA replication in the C6/36 cells, protect host cell from viral attack, suggesting its potential role in prevention and treatment of dengue fever. Our data showed that synthetic siRNA against the DEN membrane glycoprotein precursor gene effectively inhibited DEN viral RNA replication and increased C6/36 cell survival rate. Inhibition of viral gene expression and replication in mosquito cells by dsRNA-triggered RNA interference
cord-342157-qjyooq68	2008	In our study, complete genomic sequencing of DENV-3 strains collected from different geographical locations and isolation years were determined and the sequence diversity as well as selection pressure sites in the DENV genome other than within the E gene were also analyzed. RESULTS: Using maximum likelihood and Bayesian approaches, our phylogenetic analysis revealed that the Taiwan''s indigenous DENV-3 isolated from 1994 and 1998 dengue/DHF epidemics and one 1999 sporadic case were of the three different genotypes – I, II, and III, each associated with DENV-3 circulating in Indonesia, Thailand and Sri Lanka, respectively. Compared to the prototype strain H87, several unique amino acid substitutions that serve as unique signature sites for each genotype were found within the full genomic sequences of the selected DENV-3 isolates from Taiwan or other countries and are listed by the order of the gene in Table 3 .
cord-342906-51296y8d	2012	
cord-343893-sophqqne	2007	Feline aminopeptidase N (fAPN) serves as a functional receptor for most group 1 coronaviruses including feline infectious peritonitis virus (FIPV), canine coronavirus, transmissible gastroenteritis virus (TGEV), and human coronavirus 229E (HCoV-229E). Group 1 CoVs -including human coronavirus-229E (HCoV-229E), feline infectious peritonitis virus (FIPV), transmissible gastroenteritis virus (TGEV) and canine coronavirus (CCV) -utilize human, feline, porcine, and canine aminopeptidase N (APN) as functional receptors during virus entry [10] [11] [12] [13] . We also cultured seven strains of IBV, including Arkansas 99, Arkansas_DPI, California 99, Connecticut 46, Holland 52, Iowa 97, and Massachusetts 41 (designated as Ark99, Ark_DPI, CA99, Conn46, H52, Iowa97, and Mass41) as candidates to test for fAPN utilization by group 3 avian CoVs. Surprisingly, expression of fAPN did not increase viral infection in any of the strains tested. To verify the functionality of fAPN as a coronavirus receptor, we first tested its ability to rescue FIPV-1146 and TGEV infection of non-permissive cells, as reported in previous studies [11] .
cord-343908-f3v8wi9h	2008	title: Complete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination An infectious bronchitis virus Arkansas DPI (Ark DPI) virulent strain was sequenced, analyzed and compared with many different IBV strains and coronaviruses. Comparative sequence analysis of Ark DPI with other IBV strains shows striking similarity to the Conn, Gray, JMK, and Ark 99, which were circulating during that time period. The complete genome sequence analysis of Ark DPI strain shows striking similarity to the Conn, Gray, JMK, and Ark 99 IBV strains, which were circulating during that time period [1, [19] [20] [21] . Phylogenetic tree analysis of complete Ark DPI genome sequence with other IBV strains Cloning and sequencing of genes encoding structural proteins of avian infectious bronchitis virus Molecular cloning and sequence comparison of the S1 glycoprotein of the Gray and JMK strains of avian infectious bronchitis virus
cord-346574-u28y1ttw	2012	At present, various laboratory methods are available for the detection and surveillance of PHE-CoV, including virus isolation [1] , hemagglutination/hemagglutination inhibition (HA/HI) tests [13] , immunohistochemistry (IHC) assays [10] , and molecular tools such as nestedpolymerase chain reaction (nested PCR) and reverse transcriptase-polymerase chain reaction (RT-PCR) that enable detection of specific CoV RNA sequences from infected tissues [14, 15] . (1) (2) (3) In this study, an immunochromatographic strip with high sensitivity and specificity was developed for the detection of PHE-CoV, combining monoclonal antibody (MAb) and colloidal gold immunochromatography (GICA), and the resulting product is suitable for the surveillance of PHE-CoV. Thus, a lot of brain tissue samples were collected from deceased piglets with suspected PHE-CoV infection, and using RT-PCR and ELISA as reference test, the relative specificity and sensitivity of the immunochromatographic strip were determined to be 100% and 97.78%, respectively.
cord-347319-lcuma3eh	2011	HCV has two envelop proteins named as E1 and E2 which play an important role in cell entry through two main pathways: direct fusion at the plasma membrane and receptor-mediated endocytosis. To investigate the antiviral effect of LA (Chloroquine and NH(4)Cl) on pH dependent endocytosis, HCV pseudoparticles (HCVpp) of 1a and 3a genotype were produced and used to infect liver cells. For antiviral screening of Chloroquine and NH(4)Cl, liver cells were infected with HCVpp of 3a and 1a genotype in the presence or absence of different concentrations of Chloroquine and NH4Cl and there luciferase activity was determined by using a luminometer. We therefore tested the infectivity of HCVpp after treatment of target cells with different concentrations of Chloroquine and NH 4 Cl. HCVpp of 1a and 3a genotype demonstrated dose-dependent inhibition in the presence of Chloroquine and NH 4 Cl. Chloroquine and NH 4 Cl showed greater than 50% reduction of virus infectivity at 50 μM and 10 mM concentration respectively, suggesting a pH-sensitive route of virus entry (Figure 2a and 2b ).
cord-347569-9fvbshz2	2020	On the other hand, negative control siRNA and untreated groups showed higher viral titer than siRNA treated groups: 4 log 10 TCID50/ml at day 10 p.i and 8 log 10 TCID50/ml at day 18 p.i. Analysis of RCMV ALL-03 infected cells undergoing apoptosis/necrosis upon combination siRNAs treatment were studied using flow cytometry. Taking into consideration as positive treatment control group, commercial drug GCV exhibited better rate of CPE inhibition (Fig. 7) compared to other combination siR-NAs but lesser efficient than dpc + ie2b siRNAs. In order to understand more on the role of each combination siRNAs during RCMV ALL-03 infection, all the four combination siRNAs targeting different regions were analyzed individually with specific primers. During the search of effective treatment for CMV, idea of controlling the disease by means of inhibiting virus replication and gene expression by combinations of two and more siRNAs had been explored in this study.
cord-348204-365z3qxz	2013	
cord-348876-v55piprx	2010	In the present study, we designed a tetra-branched multiple antigenic peptide (MAP)-based vaccine, designated M2e-MAP, which contains the sequence overlapping the highly conserved extracellular domain of matrix protein 2 (M2e) of a HPAI H5N1 virus, and investigated its immune responses and cross-protection against different clades of H5N1 viruses. In the present study, we designed and synthesized a tetra-branched multiple antigenic peptide (MAP) derived from the M2e sequence of H5N1 virus VN/1194 strain, denoted as M2e-MAP, with an aim to develop a M2e-based vaccine for induction of M2e-specific immune responses and cross-protection of the vaccinated animals against lethal challenge of divergent H5N1 virus strains. After receiving the lethal dose (10 LD 50 ) of two H5N1 virus strains, the M2e-MAP vaccinated mice were further evaluated in terms of cross-protective ability by daily observation of the clinical symptoms, including weight loss and survival rate for two weeks, and then histopathological examination following removal of lung tissues.
cord-349287-mwj2qby4	2015	The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20 % of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Since asymptomatic zoonoses have been posited [72] , an absence of antibodies to MERS-CoV among some humans who have regular and close contact with camels may reflect the rarity of actively infected animals at butcheries, a limited transmission risk associated with slaughtering DCs [70] , a pre-existing cross-protective immune status or some other factor(s) resulting in a low risk of disease and concurrent seroconversion developing after exposure in this group. First cases of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in France, investigations and implications for the prevention of human-tohuman transmission
cord-349683-3qdnnwvd	2018	The levels of anti-Ad antibodies in the Ad5-null control group (Ad empty vector, 10 11 VP/animal) were higher than those detected for the animals that received the same-dose (high-dose 10 11 VP/ animal) of Ad-HBV group, which may have resulted from gene inserting of truncated Pol, Core and Env antigen. The neutralization activity of the highest-titers serum samples from every animal in the Ad5-null control group and the three Ad-HBV groups (low, mid, and high doses) were then measured by the Ad vector luciferase-expressing inhibition assay. As shown in Table 3 and Fig. 5 , administration with Ad-HBV significantly improved the IFN-γ and IL-2 expression levels of the livers in the mid-dose, high-dose, and Ad-null control group (p < 0.05), but not in the low-dose group.
cord-351920-igmb2yfe	2016	The aims of the study were to investigate the duration and quantity of BCoV shedding in feces and nasal secretions related to clinical signs, the presence of virus in blood and tissues and to test the hypothesis that seropositive calves are not infectious to naïve in-contact calves three weeks after BCoV infection. In two experimental studies, infected calves were not protected against reinfection with a different BCoV strain three weeks after the first challenge, but did not develop clinical signs [19, 20] . The majority of experimental studies have used BCoV inoculation as challenge procedure, which may influence clinical signs and viral shedding, and thereby the transmission potential compared to natural infection. The present study showed that calves infected with BCoV shed viral RNA for five weeks, and harbored viral RNA in intestinal tissues and lymph nodes even longer.
cord-351942-u9zpyy29	2016	title: Isolation and characterization of adenoviruses infecting endangered golden snub-nosed monkeys (Rhinopithecus roxellana) FINDINGS: We conducted a surveillance of viral infection in endangered golden snub-nosed monkeys (Rhinopithecus roxellana) in the subfamily Colobinae in China, and found that 5.1% of sampled individuals were positive for adenovirus. Golden snub-nosed monkeys (Rhinopithecus roxellana) living in Shennongjia Nature Reserve (SNR) in Hubei, China, are an endangered species belonging to the subfamily Colobinae [14] . For investigating the antibody prevalence against the AdV infection, virus neutralization assay was performed using archived serum samples collected from 8 golden snub-nosed monkeys in SNR [23] . The present isolate from these monkeys is distantly related to known AdV types, and likely represents a novel species in the genus Mastadenovirus. AdVs: Adenoviruses; HAdV: Human mastadenovirus; OWMs: Old World monkeys; SAdV: Simian adenovirus or mastadenovirus; SNR: Shennongjia Nature Reserve; WIV: Wuhan Institute of Virology
cord-352361-jh31omg2	2020	Although several rodents and other small mammals are known as important reservoirs for many viruses, bats (order: Chiroptera) represent the vast majority of identified natural reservoirs of several virus families/species to date [1, 14] . In conclusion, due to the continuous detection of new viruses in bats, the unclear situation regarding additional potential BoDV-1-reservoirs and molecular evidence for co-evolution of bats and bornaviruses, this study was conducted to investigate the potential presence of the most common orthobornaviruses in bats from endemic and non-endemic areas in Germany. Although the bicolored white-toothed shrew has been identified as indigenous reservoir of BoDV-1, other potential reservoirs or animal carriers are still unknown so that further investigations of small mammals including bat species are urgently needed. Distribution of Borna disease virus antigen and RNA in tissues of naturally infected bicolored white-toothed shrews, Crocidura leucodon, supporting their role as reservoir host species
cord-354138-ps3rzjve	2014	However, prevalence of A (H1N1) pdm09 influenza virus infection in cats in northeastern China is unknown. However, prevalence of A (H1N1) pdm09 influenza virus infection in cats in northeastern China is unknown. Therefore, the prevalence of A (H1N1) pdm09 influenza virus infections was performed among cats in northeastern China in this study. Therefore, the prevalence of A (H1N1) pdm09 influenza virus infections was performed among cats in northeastern China in this study. Additionally, in order to have a timely data for pandemic (H1N1) 2009 prevalence in northeastern China, 115 blood samples were retrospectively analyzed from pet dogs and pet cats in Harbin in 2008. Perhaps cats were at a higher probability of infection in northeastern China, due to they exposures in dense populations of humans with high influenza A (H1N1) pdm09 attack rates. Serologic evidence of pandemic influenza virus H1N1 2009 infection in cats in China
cord-355119-sdg9zdc1	2016	In the immune protective efficiency tests, the neutralizing antibody titers in sera, the colostrum and the milk on 7th day after farrowing of the inactivated YC2014 PEDV strain immunized group were significantly higher than the inactivated CV777 immunized group and the inactivated DR13 immunized group (P < 0.05). In the present study, a PEDV strain, YC2014, was isolated from intestinal samples of suckling piglets with acute diarrhea in 2014, the evolutionary characteristics and the immune protective efficiency of YC2014 were also determined. The neutralizing antibody titer in the colostrum and the milk on 7th day after farrowing of the YC2014 PEDV strain immunized group was also significantly higher than the other three groups (P < 0.05, Fig. 4c ). In this study, we successfully isolated the YC2014 PEDV strain from porcine intestinal samples in dead piglets during outbreaks of acute diarrhea. Sequence and phylogenetic analysis of nucleocapsid genes of porcine epidemic diarrhea virus (PEDV) strains in China
cord-355489-tkvfneje	2010	
cord-355906-yeaw9nr8	2015	Recent advances in molecular biology have revealed that the genetic makeup of the three elements of dengue infection (the virus, the vector, and the host) plays a primordial role in the pathogenesis of the disease and could potentially contribute to the DHF progression [19, 24, 35] . Dengue virus serotype-1 antigen was expressed in a vector based on pediatric live-attenuated Schwarz measles vaccine (MV) by using the envelope domain III (EDIII) fused with the ectodomain of the membrane protein (ectoM). The Centers for Disease Control and Prevention (USA) have also developed a live-attenuated vaccine named DENVax, which was found to be highly immunogenic in both children and adults and has currently entered phase I clinical trial in the United States [96, 97] .
cord-356064-q56jnhss	2011	title: Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides In this report the proteome of HEK293 cells infected with Vaccinia Virus strain IHD-W was analyzed by 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS in a bottom-up approach. Derivatization of peptides with 4-sulfophenyl isothiocyanate (SPITC) carried out on ZipTipμ-C18 columns enabled protein identification via the peptides'' primary sequence, providing improved s/n ratios as well as signal intensities of the PSD spectra. The E3L gene product has been identified in HEK 293 cells infected with active VACV IHD-W, which is in correlation to proteome analysis of VACV virions that indicate that the putative double-stranded RNA binding protein (D-1) is not present in the virion but is expressed in the early replication phase. Proteome analysis of vaccinia virus IHD-W-infected HEK 293 cells with 2-dimensional gel electrophoresis and MALDI-PSD-TOF MS of on solid phase support N-terminally sulfonated peptides