cord-001152-v6uc0ijw	2013	Here, we provide evidence for the presence of discrete small RNAs of viral origin that are not associated with the RNA-induced silencing complex (RISC), that are highly expressed and detected by Northern blot analysis, and that accumulate as 21to 28-nucleotide (nt) species during infection. We report that the cellular antiviral endoribonuclease RNase L cleaves the viral genome, producing in turn the small RNAs. Surprisingly, we uncovered the presence of a modification on the 3′-end nucleotide of SINV-derived viral small RNAs (SvsRNAs) that might be at the origin of their stability. The identification of small RNAs from RNA viruses could be seen either as a result of a productive mechanism for the pathogen (as for virus-encoded miRNAs) or as the consequence of a host response to control the infection by degrading viral RNAs. SINV expresses four enzymes that play key functions during the viral replicative cycle.
cord-001223-6sb3ipab	2014	In total, our results provide evidence that the conserved N-linked glycans on the EBOV GP1 core protect GP from antibody neutralization despite the negative impact the glycans have on viral entry efficiency. Since complete deglycosylation of the core domains of GP1 did not negatively impact the expression of GP or the transduction of pseudotyped virions, we systematically combined N-linked glycan mutations in the MLD with our 7G mutant. Pseudovirion entry mediated by GP1⌬muc, GP, the 6G mutant, containing a fully deglycosylated glycan cap, and the GPm8G mutant containing a MLD that was fully deglycosylated for N-linked glycans were abrogated by treating Vero cells with the CatB inhibitor CA-074, which profoundly blocked CatB activity (Fig. S4A ). Our findings that deglycosylation of GP pseudovirions enhances the transduction of Vero cells and peritoneal macrophages provides evidence that the N-glycans on GP1 decrease the efficiency of the entry process.
cord-001340-kqcx7lrq	2014	Genome sequences play a critical role in our understanding of viral evolution, disease epidemiology, surveillance, diagnosis, and countermeasure development and thus represent valuable resources which must be properly documented and curated to ensure future utility. Here, we outline a set of viral genome quality standards, similar in concept to those proposed for large DNA genomes (4) but focused on the particular challenges of and needs for research on small RNA/ DNA viruses, including characterization of the genomic diversity inherent in all viral samples/populations. Therefore, we have used technology-agnostic criteria to define five standard categories designed to encompass the levels of completeness most often encountered in viral sequencing projects. There is a trend toward requiring a complete genome sequence when a description of a novel virus is being published, and we agree that this is a good goal; however, the amount of time and resources required to complete the last 1 to 2% of a viral genome is often cost and time prohibitive for projects sequencing a large number of samples, and in most cases the very ends of the segments are not essential for proper identification and characterization.
cord-001450-7vsdqhi0	2014	title: Bone Marrow Dendritic Cells from Mice with an Altered Microbiota Provide Interleukin 17A-Dependent Protection against Entamoeba histolytica Colitis Bone marrow-derived dendritic cells (BMDCs) from SFB-colonized mice had higher levels of IL-23 production in response to stimulation with trophozoites. It is also quite possible that mediators induced by the intestinal microbiota in the serum might influence the bone marrow in such a way as to prime DCs to provide protection against, or exacerbate, enteropathogen infections (27, 28) . histolytica colitis and that bone marrow dendritic cells (BM-DCs) derived from SFB-colonized mice were able to recapitulate protection in mice that had not been colonized with the bacteria. These data suggest that intestinal colonization with a commensal bacterium can alter bone marrow in such a way as to provide protection against parasite infection. Thus, as SFB increased frequency of intestinal DCs, IL-23, IL-17A expression, and circulating serum SAA, we examined the capacity of bone marrow DCs from SFB-infected mice to produce IL-23 in response to trophozoites.
cord-001527-x8yswoua	2015	title: Reply to "Studies on Influenza Virus Transmission between Ferrets: the Public Health Risks Revisited" Likewise, Yoshihiro Kawaoka described the purpose of his ferret gain-of-transmission studies as "[t]o determine whether H5N1 viruses could be transmitted between humans" (25) , and the original reports of ferret transmission experiments say that pandemic potential is associated with the changes observed. Fouchier asserts that his claims of the likely low human transmissibility and lethality of the ferret-adapted strains should not be interpreted as reducing the likely benefits of the work for public health. In summary, while the possibility that ferret gain-of-transmission strains are attenuated in humans modestly reduces the risk estimate associated with producing and using them, it may nullify and even reverse the utility of such studies for public health. Studies on influenza virus transmission between ferrets; the public health risks revisited
cord-001528-33f94doo	2015	Initial calculations of the potential risks associated with research on influenza virus transmission via respiratory droplets or aerosols between ferrets (1-4) used reports on select agent theft, loss, and release collected by the U.S. Centers for Disease Control and Prevention (CDC) from 2004 to 2010 (7) to calculate the probability of occurrence of LAIs. Although these reports have limitations (1, 4, 7) , they provide the most recent account of LAIs in the United States and probably reflect the current state of the art in biosafety and biosecurity practices better than older studies on laboratory incidents (8, 9) , e.g., as a consequence of the implementation of the U.S. select agent program and best practices developed in biosafety and biosecurity in general over the last decades.
cord-001672-7lh8iqm1	2015	I n a Letter to the Editor of mBio, Professor Ron Fouchier published a calculation (1) in which he finds a very low probability, P 1 , for a laboratory-acquired infection (LAI) for a single lab for a single year. Fouchier uses a simplistic formula, y Ï­ 1/P 1 , to calculate the elapsed time in years for an LAI to escape from his laboratory, y Ï­ 1/(1 Ï« 10 -6 ) Ï­ 1 Ï« 10 6 , that is, the million years stated in his Letter. I suggest attaching little weight to this elapsed time calculation and instead concentrating on risk Ï­ likelihood Ï« consequences, starting with the P 1 probability, specifically: potential pandemic fatalities Ï­ (probability of a community LAI) Ï« (probability that the community LAI leads to a pandemic) Ï« (estimated fatalities in a pandemic). My risk calculation estimates the likelihood of a community LAI for both a single laboratory and n laboratories conducting this research over y years.
cord-002467-b0p1b4g8	2017	Similarly, in wild-type mice infected with NL/09 virus, we P2X7 Receptor in Influenza Immunopathology ® observed a significant reduction in body weight at days 4 to 8 postinfection (P Ͻ 0.05) (Fig. 2C) . Reduced virus titers were observed in the lungs of the P2X7r KO mice compared to the wild-type mice, particularly in the samples collected on day 7 postinfection, although these differences were not statistically significant (P ϭ 0.1) (Fig. 3A) . In this study, we showed that mice lacking the purinergic receptor P2X7 have a better clinical outcome after influenza A virus infection characterized by an increased survival rate with an overall reduced immunopathology of the lungs compared to the wild-type mice. Activation of the purinergic receptor P2X7 signaling by increased levels of extracellular ATP caused by influenza virus infection leads to an exacerbated immune response characterized by increased production of proinflammatory cytokines, induction of apoptosis, increased influx of neutrophils in the airways, and development of lung histopathology.
cord-003092-3owcqt3d	2018	These results utilize a method for identifying genome-wide changes associated with brief adaptation to culture to highlight the notion that even brief exposure to immortalized cells may affect key viral properties and underscore the balance of features of the HN-F complex required for fitness by circulating viruses. Deep genomic sequencing of nine sets of paired clinical samples (primary nasal swabs in viral transport medium) and culture isolates (culture harvest from zero passage virus) led to discovery of a number of HN mutations associated with rapid evolution in culture. To assess the frequency of mutations identified earlier, we also performed deep sequencing of 118 HPIV-3 clinical samples and culture isolates from the University of Washington Virology Laboratory, allowing us to confirm that the alterations associated with brief exposure to culture for viral isolation were almost entirely found in the sequences of culture isolates and found commonly within populations of viruses in those isolates.
cord-003143-n6b0r92e	2018	However, the roles of influenza A virus-derived epitopes in the cross-reactive T-cell responses and heterosubtypic protections are not well understood; understanding those roles is important for preventing and controlling new emerging AIVs. Here, among the members of a healthy population presumed to have previously been infected by pandemic H1N1 (pH1N1), we found that pH1N1-specific T cells showed crossbut biased reactivity to human-infecting AIVs, i.e., H5N1, H6N1, H7N9, and H9N2, which correlates with distinct protections. Thus, to investigate the contribution of different cellular antigens of influenza viruses to biased cross-T-cell reactivities, we compared T-cell responses to H7N9 and pH1N1 among the members of the healthy population using overlapping peptides covering the M1 and NP proteins. Further analysis indicated that these peptides contained previously identified HLA class I-or class II-restricted epitopes (see Fig. S2D and H) and that the immunogenicity can be influenced by the substitutions in different AIVs. Phenotypes of the cross-reactive T-cell.
cord-003609-p0ydzjre	2019	RNA was purified from fractions containing monosomes MAV-1 Degrades PKR during Infection ® and polysomes and then used to generate cDNA, which we assayed for PKR mRNA by qPCR (Fig. 4C) . Thus, the 18-hpi time point is considered an early time point during MAV-1 infection of CMT93 cells, prior to DNA replication, suggesting the involvement of an early viral protein in PKR depletion. We examined PKR protein levels during MAV-1 infection and found that PKR was depleted from the cells as early as 12 hpi (Fig. 7) . While the PKR mRNAs in C57BL/6 MEFs were depleted 33% at 48 hpi and 40% at 72 hpi compared to mock-infected lysates, this was not sufficient to explain the 84% and 94% reductions, respectively, in PKR protein levels at those time points (Fig. 2B ).
cord-004469-m2fwefuy	2020	Here, we show that formulation of Combo5 with adjuvants containing saponin QS21 significantly improves protective efficacy, even though all 7 adjuvants tested generated high antigen-specific IgG antibody titers, including alum. Detailed characterization of Combo5 formulated with SMQ adjuvant, a squalene-in-water emulsion containing a TLR4 agonist and QS21, showed significant differences from the results obtained with alum in IgG subclasses generated following immunization, with an absence of GAS opsonizing antibodies. Groups of humanized plasminogen mice were immunized with Combo5 formulated with alum, Advax-2, Advax-4, SWE, LQ, LMQ, or SMQ adjuvant (Table 1) , while negative-control groups were immunized with phosphate-buffered saline (PBS) plus the corresponding adjuvant. Both Advax-2 and Advax-4 induced high antigen-specific antibody titers; however, the rate of survival of vaccinated mice was not significantly higher than that seen with the PBS-adjuvant control groups. Combo5/SMQ immunization resulted in strong secretion of IL-6 and IL-10 and of Th1-type cytokines IFN-␥ and TNF-␣, suggesting a potential role for Th1 responses in protection against invasive GAS infection following vaccination.
cord-012487-s920s5wb	2020	By comparing substrate and enzyme concentrations of the fatty acid and phospholipid synthesis pathways of Escherichia coli across a 3-fold range of carbon-limited growth rates, we show that the rate of membrane phospholipid synthesis during steady-state growth is determined principally through allosteric control of a single enzyme, PlsB. In order to understand how the model Gram-negative species Escherichia coli coordinates membrane synthesis with growth, we quantified substrates and enzymes of the fatty acid and PL synthesis pathways under both steady-state and dynamic conditions. The trends in substrate, enzyme, and intermediate concentrations observed in ppGpp-limited cultures are consistent with growth regulating PL flux via posttranslational control-not transcriptional control-of PlsB. To test whether regulation of PlsB activity is sufficient to control steady-state PL synthesis, we constructed a simplified differential equation model that describes fatty acid, LPS initiation, and PL biosynthesis ( Fig. 2A ; see also Text S1 and Table S1 ).
cord-252671-uf96jgig	2016	title: The Membrane Protein of Severe Acute Respiratory Syndrome Coronavirus Functions as a Novel Cytosolic Pathogen-Associated Molecular Pattern To Promote Beta Interferon Induction via a Toll-Like-Receptor-Related TRAF3-Independent Mechanism In this study, we demonstrate that delivering the membrane gene of severe acute respiratory syndrome coronavirus (SARS-CoV) into HEK293T, HEK293ET, and immobilized murine bone marrow-derived macrophage (J2-Mφ) cells significantly upregulates beta interferon (IFN-β) production. The result of a dual-luciferase assay using the Renilla luciferase gene as a transfection control demonstrated that the SARS-CoV M gene rather than the S and E genes markedly increased IFN-␤ promoter activity (Fig. 1D) , whereas the valineto-alanine alteration at residue 68 of M protein completely abolished this induction, indicating that the specificity of M gene products played a role in this process. Taken together, our data indicate for the first time that SARS-CoV M protein may function as a novel cytosolic PAMP to activate IFN-␤ induction through an intracellular TLR-related signaling pathway in a TRAF3-independent manner.
cord-256550-72i1x02f	2015	
cord-256970-b8czrq29	2016	We first associated each edge with a relevance depending on the type of its connecting nodes (i.e., protein-glycan) according to the proposed weights (see equations 1 to 3 in the supplemental material) as a function of the lectin binding intensity measured via glycan array screenings. The hierarchical view (see Fig. 1 , 3, and 7) allowed linking of the experimentally determined lectin specificities (i.e., the glycan determinants) with the potential receptors (human or viral glycoproteins) and then linking of these glycoproteins to cell types/tissues and body systems. The LGI network of Candida Als and Epa adhesins N-Als1p has been shown to interact with fucose-containing glycans that are present in blood group antigens and preferentially with antigen H type 2 (22) .
cord-260087-9o9tb28h	2015	R ozo and Gronvall, in "The Reemergent 1977 H1N1 Strain and the Gain-of-Function Debate" (1), confirmed the laboratory origin of the 1977 influenza pandemic and judged it was unintentional, but they concluded that its "relevance to GoF research is greatly diminished if the 1977 epidemic was the result of a vaccine trial or vaccine development gone awry; these are both more plausible explanations than a single laboratory accident." Rozo and Gronvall also stated that, "in 1977, influenza research was performed without modern biosafety regulations and protective equipment, making the lab accident hypothesis much less relevant to the modern GoF debate." However, the current record of containment of high-consequence pathogens is hardly reassuring. Activities at the select agent laboratory at the Tulane National Primate Research Center remain suspended after Burkholderia pseudomallei, the agent of melioidosis, escaped containment and caused multiple primate infections in an outdoor primate facility (5, 6) .
cord-263357-krvei97r	2013	Sequencing and bioinformatic analysis of the viral genomic RNA showed that it is a novel virus not previously detected in any other species and that its closest relatives are two Asian bat coronaviruses. demonstrated how state-of-the-art sequencing technology and bioinformatic analysis can quickly provide critical insight into the viral genome sequence, phylogeny, replication strategy, and potential drug and vaccine targets and generate tools to evaluate the possible epidemic risk associated with this novel human virus. In June 2012, a novel coronavirus, tentatively named HCoV-EMC (for Erasmus Medical Center where the initial genome sequence was done), was isolated in a monkey kidney cell line from a sputum specimen from a 60-year-old man from the Kingdom of Saudi Arabia who died of acute severe pneumonia and renal failure. The genomic analysis suggests that HCoV-EMC may be a zoonotic virus that spilled over to infect the 9 laboratory confirmed patients, either directly or indirectly, from an unknown reservoir, possibly a bat.
cord-264050-6zpw6itb	2017	The demonstration that host-mediated damage can drive cryptococcal disease provides proof of concept that the parabola put forth in the damage-response framework has the flexibility to depict complex and changing outcomes of host-microbe interaction. However, the emergence of Cryptococcus gattii in apparently healthy persons in the Pacific Northwest (7) and the unexpected appearance of immune reconstitution inflammatory syndrome (IRIS)-associated cryptococcosis in patients with HIV/AIDS after initiation of antiretroviral therapy (ART) (8, 9) revealed that the host immune response itself can contribute to the pathogenesis of cryptococcosis. The emergence of IRIS-associated cryptococcosis in the setting of ART initiation provided clear evidence that host damage in patients with cryptococcal disease may be driven by inflammation (12) . Chemokine levels and chemokine receptor expression in the blood and the cerebrospinal fluid of HIV-infected patients with cryptococcal meningitis and cryptococcosis-associated immune reconstitution inflammatory syndrome
cord-273391-vmtfn78x	2020	title: Single-Dose, Intranasal Immunization with Recombinant Parainfluenza Virus 5 Expressing Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Spike Protein Protects Mice from Fatal MERS-CoV Infection In this study, we evaluated parainfluenza virus 5 (PIV5)-based vaccine expressing the MERS-CoV envelope spike protein (PIV5/MERS-S) in a human DPP4 knockin C57BL/6 congenic mouse model (hDPP4 KI). Following a single-dose intranasal immunization, PIV5-MERS-S induced neutralizing antibody and robust T cell responses in hDPP4 KI mice. As shown in Fig. 3B to D, we observed a significant increase in the Immunization with PIV5 Expressing MERS-CoV Spike ® percentage and total number of CD8 ϩ -IFN-␥ ϩ cells in the lungs of PIV5-MERS-Simmunized mice in comparison to those infected with PIV5-GFP virus, consistent with a MERS-S-specific primary CD8 T cell response in the lungs. The finding that PIV5 expressing MERS S protected mice against lethal MERS-CoV challenge at a single low dose of 10 4 PFU suggests its potential use as a vaccine vector for emerging viruses such as SARS-CoV-2.
cord-274396-l611eisi	2020	While the lopinavir-ritonavir-, hydroxychloroquine sulfate-, or emtricitabine-tenofovir-treated group exhibited lower overall clinical scores than the phosphate-buffered saline (PBS)-treated control group, the virus titers in nasal washes, stool specimens, and respiratory tissues were similar between all three antiviral-candidate-treated groups and the PBS-treated control group. Compared to the PBS-treated control group, azathioprine-immunosuppressed ferrets exhibited a longer period of clinical illness, higher virus titers in nasal turbinate, delayed virus clearance, and significantly lower serum neutralization (SN) antibody titers. In order to determine the antiviral efficacies of lopinavir-ritonavir, hydroxychloroquine (HCQ) sulfate, or emtricitabine-tenofovir for treatment of SARS-CoV-2 infection, SARS-CoV-2 antibody-free ferrets (10/group) were inoculated with 10 5.8 50% tissue culture infective doses (TCID 50 )/ml of an NMC-nCoV02 strain through the intranasal (i.n.) route ( Fig. 1 ). Therefore, although clinical symptoms were attenuated in ferret groups treated with antiviral candidates, we also evaluated virus titers in respiratory and gastrointestinal tracts using nasal washes and stool samples, respectively, from SARS-CoV-2-infected ferrets.
cord-274399-cd7cmpoj	2020	This is one of the first published seroprevalence studies from North Carolina and included multicenter, primary care, and emergency care facilities serving a low-density, suburban and rural population since description of the North Carolina state index case introducing the SARS-CoV-2 respiratory pathogen to this population. Asymptomatic infection by SARS-CoV-2 (with no clinical symptoms) was examined using an Emergency Use Authorization (EUA)-approved antibody test (Abbott) for the presence of SARS-CoV-2 IgG. This study identifies a very limited seroprevalence of SARS-CoV-2 among asymptomatic individuals accessing the UNC Health system. This study employed an EUA assay performed in a CLIA-certified laboratory on a venous blood sample, with demonstrated specificity to detect antibodies only to SARS-CoV-2, not to seasonal coronaviruses. Upon arrival for SARS-CoV-2 Seroprevalence in North Carolina ® routine care or scheduled visits for enrollment into the study, patients performed a consent procedure that included reviewing recent COVID-19 clinical history using UNC IRB-approved questionnaires.
cord-274663-zyzgk2z3	2011	Using NGS, we detected small but significant changes in host gene expression affecting T cell function that coincided with the initiation of viral RNA production at 12 h postinfection (hpi). In addition, by using NGS, we observed the dramatic expansion of viral mRNA expression and detected new viral splice events occurring during viral replication and differential expression of noncoding RNA species, including microRNA host genes. In our data set, we observed no change in the expression of the Crm1-encoding gene XPO1, but several members of the Ran signaling pathway were downregulated, suggesting that the overall export of unspliced viral RNA was suppressed (see Fig. S5B in the supplemental material; data not shown for XPO1). The regulation of these and transcription factors specific for other functions (e.g., EGR1, KLF13, and MYC) may explain how HIV initiated replication with minimal disruption to host gene expression at 12 hpi but elicited larger-scale changes later in infection.
cord-278303-lnrgom58	2017	This study represents the first time that whole-genome sequencing has been used to investigate an epidemic on a national scale to identify the likely causative agent and the link to an associated zoonotic infection. This isolation of the population has meant that Icelandic horses have remained free from most common contagious diseases of Equidae, including equine influenza, equine rhinopneumonitis, equine viral arteritis, Rhodococcus equi infection, and strangles (Streptococcus equi subsp. Removal of strains with identical sequences that were recovered from the same animal on the same date produced a data set of 59 ST209 isolates with 434 polymorphic core genome positions (Table S2 ). zooepidemicus recovered from Icelandic horses in this study are also likely to have caused clinical signs of disease. zooepidemicus likely persisted in the horses at the Icelandic Veterinary Institute, accruing nucleotide diversity over time within this isolated population.
cord-279979-3ecnbqom	2017	Phylogenetic analysis showed that PREDICT/PDF-2180 is closely related to MERS-CoV across much of its genome, consistent with a common ancestry; however, the spike protein was highly divergent (46% amino acid identity), suggesting that the two viruses may have different receptor binding properties. Predicting the interactions of virus binding domains with a particular host receptor (for example, the human MERS-CoV receptor DPP4) is possible through the use of structural modeling and the generation of infectious clones. This virus (PREDICT/PDF-2180) shares the same putative S1 subunit recombination that was observed in NeoCoV, allowing us to also consider whether the spike recombination was critical for the emergence of MERS-CoV in humans. Based on the current criteria for species demarcation established by the International Committee for the Taxonomy of Viruses (Ͼ90% amino acid sequence identity in the replicase proteins), PREDICT/PDF-2180 shares sufficient genetic identity to MERS-CoV to be considered a member of the MERS-like Coronavirus species.
cord-280001-y7pvj2l1	2020	If the test is positive though, the result is most likely correct, although stray viral RNA that makes its way into the testing process (for example, as the specimen is being collected or as a result of specimen cross-contamination or testing performed by a laboratory worker who is infected with SARS-CoV-2 [these are just some examples]) could conceivably result in a falsely positive result. Testing patients for SARS-CoV-2 helps identify those who are infected, which is useful for individual patient management, as well as for implementation of mitigation strategies to prevent spread in health care facilities and in the community alike (Fig. 1) . Given that SARS-CoV-2 can infect anyone and result in transmission prior to the onset of symptoms or even possibly without individuals ever developing symptoms, testing asymptomatic patients could even be considered. Finally, serologic testing can possibly be used diagnostically to test viral RNA-negative individuals presenting late in their illness.
cord-281389-sht0yx4a	2020	Examination of a publicly available gene expression data set (Gene Expression Omnibus [GEO] accession number GSE147507) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of A549 human lung cells also showed a significant upregulation of CD47 compared to mock-infected controls (Fig. 1D ). Multiple PBMC subsets showed significantly upregulated CD47 expression in response to Borrelia burgdorferi infection compared to naive cells (Fig. 1E) . Overall, the combined in vivo and in vitro results from multiple pathogen infections in both human and mouse cells indicated that the upregulation of CD47 was a conserved host response possibly related to host sensing mechanisms. Compared to healthy controls, monocytes and DCs from HCV patients demonstrated a sustained upregulation of CD47 at all treatment time points, including the 6-month posttreatment time point ( Fig. 3B (B) CD47 MFI on human total PBMCs from 4 separate donors stimulated with titrated concentrations of R848 from 0.1 g/ml to 10 g/ml, as indicated, for 48 h.
cord-286587-x0wqtlxh	2020	Patients with COVID-19 infection are at risk of acute respiratory disease syndrome (ARDS) and death. Clinical trials are needed to determine whether this drug combination might be used to treat patients with severe COVID-19 infection. We believe that investigators in China and elsewhere should undertake studies of patients with severe COVID-19 infection to determine whether targeting the host response with widely available and inexpensive generic drugs, like ARBs and statins, will improve their chances of survival. Convincing evidence of the effectiveness of this treatment would suggest a syndromic approach to treating patients with other emerging infectious diseases, like Ebola and pandemic influenza, as well as everyday illnesses, like sepsis and pneumonia (19) . Treating the host response to emerging virus diseases: lessons learned from sepsis, pneumonia, influenza and Ebola Treating the host response to Ebola virus disease with generic statins and angiotensin receptor blockers
cord-287487-qeltdch7	2017	Alanine substitution of ExoN catalytic residues [ExoN(-)] in severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and murine hepatitis virus (MHV) disrupts ExoN activity, yielding viable mutant viruses with defective replication, up to 20-fold-decreased fidelity, and increased susceptibility to nucleoside analogues. High-or low-fidelity variants are described for many RNA viruses infecting animals, including the coronaviruses (CoVs) murine hepatitis virus (MHV-A59) and severe acute respiratory syndrome-associated coronavirus (SARS-CoV) (13) (14) (15) (16) (17) , as well as foot-and-mouth disease virus (18) (19) (20) (21) (22) , poliovirus (23) (24) (25) (26) (27) (28) (29) , Chikungunya virus (30, 31) , influenza virus (32) , coxsackievirus B3 (33, 34) , and human enterovirus 71 (35) (36) (37) . The evolved mutations in MHV-ExoN(-) nsp14 and nsp12, which encodes the RdRp, accounted for only part of the increased nucleoside analogue resistance of MHV-ExoN(-) P250, implicating multiple replicase proteins in adaptation for viral fitness.
cord-287892-bnqmwst8	2010	The rotavirus nonstructural protein 4 (NSP4), an endoplasmic reticulum (ER) transmembrane glycoprotein, increases intracellular levels of cytoplasmic Ca(2+) ([Ca(2+)]cyto) through a phospholipase C-independent pathway, which is required for virus replication and morphogenesis. We identified an NSP4 domain (amino acids [aa] 47 to 90) that inserts into membranes and has structural characteristics of viroporins, a class of small hydrophobic viral proteins that disrupt membrane integrity and ion homeostasis to facilitate virus entry, assembly, or release. In epithelial cells, expression of wild-type NSP4 increased the levels of free cytoplasmic Ca(2+) by 3.7-fold, but NSP4 viroporin mutants maintained low levels of [Ca(2+)]cyto, were retained in the ER, and failed to form cytoplasmic vesicular structures, called puncta, which surround viral replication and assembly sites in rotavirus-infected cells. We previously showed that NSP4 forms a novel vesicular compartment concomitantly with increased [Ca 2Ï© ]cyto (45) and that these structures associate with the autophagy protein LC3 and surround viroplasms, cytoplasmic inclusions in rotavirus-infected cells that support virus replication.
cord-289360-h6wvx7gw	2015	journal: mBio Viruses account for up to 20% of all human cancers, and although a large percentage of new human papillomavirus (HPV) and HBV infections can now be prevented by vaccination, many are already infected, and the vaccines are not being used to their full potential. The tremendous reduction in mortality from such diseases as variola, measles, and rubella came about only because the causative viruses were identified, cultivated, attenuated, and made into effective vaccines by biomedical research. While we scientists cannot directly control funding or regulations, we can take charge of some aspects of the research enterprise in a way to ensure that it continues to benefit society. This requires engaging our elected officials both directly and indirectly by continuing to educate them and the public at large about the importance of fundamental research in infectious diseases.
cord-290297-efo9f7c5	2020	In recent studies on COVID-19 patients, secondary bacterial infections were significantly associated with worse outcomes and death despite antimicrobial therapies. In the past, the intensive use of antibiotics during the severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic led to increases in the prevalence of multidrug-resistant bacteria. T he outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), is the greatest pandemic of our generation, with 16 million people infected and 650,000 deaths worldwide so far (1) . In a multicenter study that included 476 COVID-19 patients, secondary bacterial infections were significantly associated with outcome severity (2) . During the first SARS-CoV outbreak in 2003, up to 30% of patients were diagnosed with secondary bacterial infections and coinfection was positively associated with disease severity (5, 6) . Increase in methicillin-resistant Staphylococcus aureus acquisition rate and change in pathogen pattern associated with an outbreak of severe acute respiratory syndrome
cord-292742-mio4przi	2020	KEYWORDS One Health, Panthera leo, Panthera tigris, SARS-CoV-2, in situ hybridization, lion, rRT-PCR, tiger, virus isolation, whole-genome sequencing, zoo, zoonotic infection C oronaviruses are a recognized cause of disease in humans and animals (1) . Subsequent to confirmation of SARS-CoV-2 infection in the animals, an epidemiologic investigation of zoo staff identified 10 zoo keepers and two managers who provided care for and had close (Յ1.8-m) but not direct contact with the tigers or lions between 16 March 2020 (the date on which the zoo was closed to the public due to the pandemic) and 27 March to 3 April 2020 (timeline of disease onset in the animals). Nine complete SARS-CoV-2 genome sequences (from four tigers, three lions, and two keepers) and eight full-length S gene sequences (from seven symptomatic animals and one asymptomatic animal) were generated directly from respiratory and/or fecal samples (Data Sets 3 and 4).
cord-292883-7hvq9qaj	2020	RBD-binding MBCs sampled in the convalescent phase of SARS-CoV-2 infection expressed Abs with relatively low numbers of V gene mutations, suggesting that this component of the response largely reflected naive B cell activation by novel epitopes (20) . Approximately one-third of non-SARS-CoV-2-exposed subjects in the healthy donor cohort had low levels of serum IgG against the S and N proteins of SARS-CoV-2, likely reflecting cross-reactivity with seasonal HCoVs (Fig. 1A) . Since the healthy donor samples in our analysis were collected 6 to 10 years before the emergence of SARS-CoV-2, we considered the possibility that a recently circulating HCoV was responsible for the higher anti-OC43 S IgG titers in the convalescent subjects. In contrast, IgG MBCs reactive to the S proteins of the HCoVs OC43 and 229E and the control proteins H1 and TTd were detected in nearly 50% or more of non-SARS-CoV-2-exposed subjects, consistent with the higher levels of serum IgG against these antigens (Fig. 2E to H) .
cord-295946-p9enjxiq	2020	We assessed various newly generated compounds that target the main protease (M(pro)) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and various previously known compounds reportedly active against SARS-CoV-2, employing RNA quantitative PCR (RNA-qPCR), cytopathicity assays, and immunocytochemistry. When VeroE6 cells were exposed to SARS-CoV-2 WK-521 at a multiplicity of infection (MOI) of 0.05 and cultured in the presence of various concentrations of the two indole chloropyridinyl esters GRL-0820 and GRL-0920, the compounds were found to be highly potent against SARS-CoV-2 WK-521 with 50% effective concentration (EC 50 ) values of 15 Ï® 18 and 2.8 Ï® 0.3 M, respectively, using RNA-qPCR (Table 1) . When VeroE6 TMPRSS2 cells were exposed to SARS-CoV-2 WK-521 and cultured in the presence of various concentrations of lopinavir and nelfinavir, many virus-infected cells were seen at 1 and 10 M and stained in green, indicating that these two compounds had no detectable antiviral activity in the assay.
cord-296028-hqrd1e8p	2015	Ultimately, the purpose of summarizing and critiquing some of the arguments within the GOF/PPP debate is to emphasize the many epistemic and ethical value judgments inherent to RBA and to provide evidence for prior claims that a consensus-building quantitative assessment is unlikely (1). As summarized here, many of the disagreements within the GOF/PPP debate involve epistemic and ethical value judgments that suggest that definitive quantitative risk-benefit analysis is not possible. Risks and benefits of gain-of-function experiments with pathogens of pandemic potential, such as influenza virus: a call for a science-based discussion mBio addresses the pause in gain-offunction (GOF) experiments involving pathogens with pandemic potential (PPP) Conducting risk and benefit analysis on gain-of-function research involving pathogens with pandemic potential An epistemological perspective on the value of gain-of-function experiments involving pathogens with pandemic potential Vagueness and costs of the pause on gain-of-function (GOF) experiments on pathogens with pandemic potential, including influenza virus
cord-297082-2rhoffx2	2020	Membrane-associated RING-CH-type 8 (MARCH8) strongly blocks human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) incorporation into virions by downregulating its cell surface expression, but the mechanism is still unclear. We conclude that MARCH8 has a very broad antiviral activity by prohibiting different viral fusion proteins from glycosylation and proteolytic cleavage in the Golgi, which inhibits their transport from the Golgi to the plasma membrane and incorporation into virions. As a control, serine incorporator 5 (SERINC5) protein In addition, FLAG-tagged furin was expressed with HA-tagged human MARCH8 and GPΔMLD in 293T cells. In addition, when the furin-VN/GP-VC pair was expressed with MARCH8, their colocalization was also detected (Fig. 2C ), confirming that these three molecules form a complex in live cells. MARCH8 proteins from different species strongly increased GP 1 and GP 1 ΔMLD expression in cells but completely blocked their secretions (Fig. 7C, lanes 1 to 8) .
cord-298773-vnmc6nqd	2015	title: Is the Debate and "Pause" on Experiments That Alter Pathogens with Pandemic Potential Influencing Future Plans of Graduate Students and Postdoctoral Fellows? This letter is about the potential impact of the debate and pause on graduate students and postdoctoral fellows and how their future plans may be affected. To gain initial insight into how the debate and research pause have affected trainees, I created an informal survey 2 days before the National Academy of Sciences meeting. These projects involve a subset of "gain of function" experiments designed to create mouse adapted viral strains, generate drug resistant viruses to understand drug mechanisms of action, understand host immunity by analyzing viruses with resistance to certain host immune pathways, and to study factors that influence transmission by the respiratory route (which was made famous by work from the Kawaoka and Fouchier labs in 2012). Third, the debate and research pause are influencing future plans of virology trainees.
cord-303262-grrd6jmt	2020	Morens and colleagues describe in the "early pandemic history" section the story of pathogens emerging around 12,000 years ago at the time of Neolithic agricultural revolution. As such, diseases such as "measles, smallpox, tuberculosis (TB), [and] gastric cancer (caused by Helicobacter pylori)" are cited as consequences of "conditions of intense human-animal proximity and environmental alterations." This assertion of the dating of the origin of these aforementioned pathogens is partially misleading. Both viruses (i.e., those causing measles and smallpox) emerged probably much later, while Mycobacterium tuberculosis and Helicobacter pylori started their association with humans before the agricultural revolution. For smallpox, the exact date of divergence of variola virus (VARV) from a zoonotic strain is more disputed, as molecular data gave an estimation of emergence for the most recent common ancestor between the 16th and the 17th century, while skin lesions seen in the mummy of Ramses V, who died in 1157 BCE, suggested earlier interactions (6) .
cord-303915-14yfs4pa	2013	The construction of a full-length infectious cDNA clone of the MERS-CoV genome in a bacterial artificial chromosome is reported here, providing a reverse genetics system to study the molecular biology of the virus and to develop attenuated viruses as vaccine candidates. The mutant viruses presented growth kinetics similar to those of the wild-type virus, indicating that accessory genes were not essential for MERS-CoV replication in cell cultures. Using this clone, recombinant MERS-CoV (rMERS-CoV) deletion mutants were constructed lacking genes nonessential for virus replication. An infectious cDNA clone was assembled as a BAC under the control of the cytomegalovirus (CMV) immediate-early pro-moter, based on the genome sequence of the MERS-CoV-EMC12 strain (GenBank accession number JX869059) (15) . Based on published data showing that the deletion of CoV E protein resulted in either replication-competent, propagation-defective viruses (24) or attenuated viruses (25, 26, 31) , a cDNA clone with the E gene deleted (pBAC-MERS-⌬E) was constructed from pBAC-MERS FL .
cord-305336-wxiazglk	2014	In the present study, we showed that a plant-pathogenic RNA virus, tobacco ringspot virus (TRSV), could replicate and produce virions in honeybees, Apis mellifera, resulting in infections that were found throughout the entire body. While intracellular life cycle, species-level genetic variation, and pathogenesis of the virus in honeybee hosts remain to be determined, the increasing prevalence of TRSV in conjunction with other bee viruses from spring toward winter in infected colonies was associated with gradual decline of host populations and winter colony collapse, suggesting the negative impact of the virus on colony survival. Conventional RT-PCR was performed on RNA samples extracted from adult bees, Varroa mites, different tissues, and bee bread collected from the same colony for the presence and distribution of TRSV.
cord-305698-fjd0rsrf	2014	title: Vagueness and Costs of the Pause on Gain-of-Function (GOF) Experiments on Pathogens with Pandemic Potential, Including Influenza Virus We have numerous concerns with this third stoppage, including the timing of the announcement relative to the ongoing debate, the vagueness in the wording of the statement, and the potential effects on the fields of influenza virus and coronavirus research. Second, we worry about the meaning of "reasonably anticipated." Obviously this phrase is very subjective, and similar wording in the definition of dual use research of concern (DURC) has already made assessments of what constitutes DURC very problematic for journals and authors (10) . The current pause affects two dozen studies that include experiments to develop rodent models of coronavirus research (11) . Risks and benefits of gain-of-function experiments with pathogens of pandemic potential, such as influenza virus: a call for a science-based discussion Influenza gain-of-function experiments: their role in vaccine virus recommendation and pandemic preparedness
cord-308848-chvvtr0d	2020	While the current clinical trials are not investigating this issue directly, we have focused on the MMR vaccine as it is widely available and has the potential for any or all of the three components to induce the MDSCs. However, based on our data in the animal model of fungal/bacterial sepsis, very strong long-lasting protection is afforded from one administration of the attenuated fungal isolate (7) . Finally, while it is true that we do not know how long the trained innate immunity persists, the randomized clinical trial of MMR versus placebo in health care workers and the nonhuman primate study that will test MMR or BCG in a model of COVID-19 infection will go far to answer these questions. To date, the trained innate response with BCG suggests the immunity is functional for approximately 1 year based on infant vaccinations (8) . Immune protection against lethal fungal-bacterial intra-abdominal infections
cord-324978-9qfhsj3n	2014	The presence of viral nucleic acids in rectal and nasal swabs and a subset of serum and whole blood samples was assayed by reverse transcriptionquantitative PCR (RT-qPCR) with primers targeting the upE and ORF1a genome regions of MERS-CoV (16, 17) . Rectal and nasal swabs collected in parallel with serum samples from the same animals were assayed for MERS-CoV nucleic acids by RT-qPCR. PCR analysis of a random selection of serum and whole blood samples collected from nasal or rectal swab PCR-positive, seropositive, and seronegative DC revealed no evidence of viremia (see Table S1 in the supplemental material). Definitive evidence that DC can be infected with MERS-CoV was obtained when viral sequences were detected in nasal swabs from DC sampled in close proximity to outbreaks of the disease among humans in Qatar (11) and Jeddah, KSA (10) .
cord-326160-mf0vh6iu	2014	Given the public health importance of this virus, we performed a pathogenicity study of the H7N9 virus in the cynomolgus macaque model, focusing on clinical aspects of disease, radiographic, histological, and gene expression profile changes in the upper and lower respiratory tracts, and changes in systemic cytokine and chemokine profiles during infection. To elucidate global host responses specifically associated with sites of virus-induced airway injury in influenza virus A/Anhui/1/2013-infected macaques, we used microarrays to assess transcriptional profiles induced in lung lesions compared to the adjacent lung tissue. We identified ten compounds in IPA (Table 1) , four of which were perturbagens listed in CMap. We identified two compounds that met our criteria in IPA and CMap, rosiglitazone and simvastatin, predicted to have inhibitory effects on pathological host responses associated with lesions in influenza virus A/Anhui/1/2013-infected animals ( Table 1) .
cord-327660-p1b07b4t	2018	The current RdRp tree topology combined with gene gain-loss reconstruction suggests the following evolutionary scenario for branch 1 ( Fig. 2A) : a levivirus-like ancestor that, like the extant members of the Leviviridae, possessed a capsid protein unrelated to SJR-CP (19, 52) gave rise to naked eukaryotic RNA replicons known as "mitoviruses" and "narnaviruses." These replicons consist of a single RdRp gene (Fig. 2B ) and replicate in mitochondria and in the cytosol of the host cells of fungal and invertebrate hosts, respectively (the latter hosts were identified in metaviromic holobiont analyses) (14, 53) . This genome architecture could hint at an ancestral flavivirus genome that was assembled from genes borrowed from preexisting viruses, one of which possessed a divergent "tombus-like virus" RdRp. Although the origins of branch 3 are murky, major trends in its subsequent evolution clearly included lineage-specific gene capture, starting with helicases and CapEs in the ancestors of the major lineages and followed by diverse genes in smaller groups (Fig. 4B) .
cord-330315-upcf15q5	2017	Using electron tomography, we demonstrate that for both MERS-CoV and SARS-CoV coexpression of nsp3 and nsp4 is required and sufficient to induce DMVs. Coexpression of MERS-CoV nsp3 and nsp4 either as individual proteins or as a self-cleaving nsp3-4 precursor resulted in very similar DMVs, and in both setups we observed proliferation of zippered ER that appeared to wrap into nascent DMVs. Moreover, when inactivating nsp3-4 polyprotein cleavage by mutagenesis, we established that cleavage of the nsp3/nsp4 junction is essential for MERS-CoV DMV formation. To study whether the transmembrane nsp''s of MERS-CoV are able to induce DMV formation, we expressed nsp3 and nsp4 from a CAG promoter (43) either by cotransfection of cells with plasmids encoding individual proteins or by transfection with a single plasmid encoding a self-cleaving nsp3-4 polyprotein fragment ( Fig. 1A ; Table S1 ). The observation of maze-like bodies and circular double-membrane profiles, which were interpreted to represent tubular structures, led these authors to conclude that coexpression of SARS-CoV nsp3 and nsp4 was not sufficient for DMV formation.
cord-331361-pd9lt4n2	2015	Furthermore, heparin was able to inhibit the interaction of the viruses with the heparan sulfate and to block cell-mediated trans-infection of henipaviruses. Strikingly, heparin was also active when applied after contact with the virus, and both pretreatment and posttreatment with heparin were effective in inhibiting human PBL-mediated trans-infection of either NiV or HeV (Fig. 2B ). Heparin treatment modestly, but significantly, reduced the percentage of infected cells from both cell lines, indicating that this molecule may also directly inhibit or delay the binding of NiV to its entry receptors EFN-B2 and -B3. Nipah virus (isolate UMMC1; Gen-Bank accession number AY029767) (42), recombinant NiV expressing enhanced green fluorescent protein (45) , and Hendra virus (Australia/ horse/1994) obtained from Porton Down Laboratory, United Kingdom, were prepared on Vero-E6 cells as described previously (46) , and infection virus was used in the INSERM Jean Mérieux BSL4 laboratory in Lyon, France.
cord-334463-nvu5tqxb	2012	We found that drugs, small interfering RNAs (siRNAs), and dominant negative mutants that target factors required for clathrin-mediated endocytosis, including clathrin and dynamin, inhibited both EV7 infection and internalization of virions from the cell surface. We previously (19) observed that, to infect polarized epithelium, CVB3 binds DAF on the cell surface, moves to the tight junction, and then enters the cell by an unusual mechanism that is independent of both dynamin and clathrin but which requires caveolin; contact with CAR in the tight junction leads to an essential conformational change in the CVB3 virion, but disruption of the capsid does not appear to occur until the virus has moved to an unidentified intracellular compartment. We had previously observed that CVB3 infection of Caco-2 cells occurs by a complex process that depends on caveolin but not dynamin-2, appears to be independent of clathrin-mediated endocytosis, and is inhibited by depletion of membrane cholesterol (19) .
cord-335432-9aszklx3	2014	(B) Dual-use research of concern (DURC) is a small subset of DUR involving life sciences research that, based on current understanding, can reasonably be anticipated to provide knowledge, information, products, or technologies that could be directly misapplied, posing a significant threat with broad potential consequences to public health and safety, agricultural crops and other plants, animals, the environment, materiel, or national security. (D) Although spanning all of microbiological research, much of the DURC debate has focused on virology, where selection processes of circulating and synthetically generated agents have been used to enhance transmission. For some, gain of function causes the most concern, although even for the influenza transmission studies, it is simplistic to focus on only one phenotype/ one function as a range or on infectivity changed during selection of mammal-adapted avian influenza viruses. Risks and benefits of gain-of-function experiments with pathogens of pandemic potential, such as influenza virus: a call for a science-based discussion
cord-335938-hscgmis5	2013	The results of these studies demonstrate that a fine balance exists between host coagulation and fibrinolysin pathways regulating pathological disease outcomes, including diffuse alveolar damage and acute lung injury, following infection with highly pathogenic respiratory viruses, such as SARS-CoV. To model system-wide behaviors following SARS-CoV infection, we performed a dose-response study that included biological sampling at multiple time points, transcriptional and proteomic systems biology data, and mathematical modeling algorithms to identify signaling networks associated with progression from severe to lethal disease outcomes. These data demonstrate the successful use of highly refined modeling algorithms to identify and validate novel genes and pathways that play critical roles in SARS-CoV pathogenesis and the development of ALI following virus infection in the lung. Similar changes in the urokinase, coagulation, and fibrinolysin pathway expression signatures are noted following highly pathogenic SARS-CoV and influenza virus infections (see Fig. S5B and S6 in the supplemental material), arguing for a con-served role for these pathways in virus-induced end-stage lung diseases, like ALI and ARDS.
cord-337492-o6sy4zi4	2016	The National Institute of Allergy and Infectious Diseases (NIAID) addressed this gap by creating functional genomics centers dedicated to developing high-throughput approaches to assign gene function. High-throughput functional genomics can lead to new therapeutics and better understanding of the next generation of emerging pathogens by rapidly defining new general mechanisms by which organisms cause disease and replicate in host tissues and by facilitating the rate at which functional data reach the scientific community. Unlike large-scale genome-sequencing or structural-genomics efforts, the functional annotation of uncharacterized genes is not well developed technologically, and therefore, the scientific community cannot rely on a well-defined, mature set of experimental approaches. The NIAID has implemented a program aimed at assigning functions to open reading frames (ORFs) and small noncoding RNAs (ncRNAs) that have been discovered by large-scale sequencing efforts to begin addressing this gap in our understanding of bacterial and viral gene function.
cord-339269-7m53i1h9	2014	smegmatis, and we demonstrate the use of mass spectrometry to show expression of over 75% of the predicted proteins, to identify new genes, to refine the genome annotation, and to estimate protein abundance. Proteomic analysis using mass spectrometry provides evidence for expression of at least 83 Patience proteins, two of which are from cryptic open reading frames (ORFs) embedded within annotated genes. Genome annotation of Patience indicates that all open reading frames and one tRNA gene are transcribed in the same direction ( Fig. 5 ; Table 1 ). A similar scenario is seen within Patience gene 20, where two peptides corresponding to a 171-bp open reading frame on the same strand were identified with high confidence (see Fig. S1B in the supplemental material). Their codon usage profiles (see Fig. S6 in the supplemental material) more closely reflect those of the lower-GC mycobacteriophages such as Patience.
cord-341858-uz7vqq3r	2014	Influenza virus GOF studies have focused on several research areas: in vitro and/or in vivo replication in mammalian cell culture or animal hosts, adaptive mutations conferring changes in host susceptibility, alteration of receptor binding profiles and/or tropism for mammalian airway tissues, enhanced polymerase activity, changes in host antiviral response (e.g., cell signaling pathways), susceptibility to antiviral drugs, and pathogenesis and/or transmissibility in mammalian animal models. In both instances, molecularly based surveillance identified naturally occurring mutations in avian influenza viruses isolated from humans that had been demonstrated by GOF studies to increase transmissibility in the ferret model, prompting the public health actions described below. At the same time that increased case numbers were detected, public sequence database mining by researchers identified viruses from several 2013 human infections that possessed the same mutations shown by GOF studies to alter receptor-binding specificity toward an ␣2,6 preference (K189R and Q222L) and enhanced respiratory droplet transmission of a clade 1 virus in ferrets (N220K with Q222L) (42) .
cord-344227-rdlinzrn	2018	As with the outcome of human infection, intranasal infection of C57BL/6J mice with mouse-adapted SARS-CoV results in high-titer virus replication within the lung, induction of inflammatory cytokines and chemokines, and immune cell infiltration within the lung. Mice deficient in C3 (C3 -/-), the central protein of the complement signaling pathway, were protected from SARS-CoV-induced weight loss and had reduced pathology, improved respiratory function, and lower levels of inflammatory cytokines/chemokines in the lung and periphery. Immunohistochemical staining revealed that SARS-CoV MA15 infection induced complement deposition in the lung (Fig. 4) , similar to that associated with pathogenesis in Ross River virus-infected mice (41) and some influenza virus infections (34) , and it is likely that complement deposition contributes to pulmonary disease and inflammatory cell recruitment.
cord-348131-pkovyjo6	2019	The mRNA level of RNase L did not change upon IFN treatment in RoNi/7 cells, indicating that, similarly to the human RNASEL gene, bat RNASEL is not an ISG ( Fig. 2A) , consistent with the lack of an ISRE in its promoter region (data not shown). Upon infection with SINV, degradation of rRNA, as assessed by Bioanalyzer, was detected in wild-type (WT) and bOAS1-KO and bOAS2-KO cells but not in bOAS3-KO and bRNase L-KO cells (Fig. 6C) , indicating that the activation of RNase L during SINV infection in RoNi/7 cells is dependent on bOAS3 expression, similar to our previous findings in human cells. bOASL2 shares high sequence similarity with mouse OASL2 (see Fig. S2 in the supplemental material), suggesting that Activation of Bat RNase L Depends on OAS3 but Not MAVS ® like the mouse protein, bOASL2 may have catalytic activity.
cord-348669-mizygp4j	2016	title: Characterization of a Pathogenic Full-Length cDNA Clone and Transmission Model for Porcine Epidemic Diarrhea Virus Strain PC22A The infectious-clone-derived PEDV (icPEDV) replicated as efficiently as the parental virus in cell culture and in pigs, resulting in lethal disease in vivo. Importantly, recombinant PEDV was rapidly transmitted to uninoculated pigs via indirect contact, demonstrating virulence and efficient transmission while replicating phenotypes seen in the wild-type virus. While the recombinant icPEDV replicated the clinical phenotypes of parental PC22A in vivo, icPEDV-⌬ORF3-RFP infection resulted in a partial attenuation in pigs based on lower diarrhea scores. Both the parental PEDV PC22A strain and its derivative recombinant cloned virus were genetically stable and fully pathogenic in neonatal gnotobiotic pigs, demonstrating that icPEDV provides not only a strategy that allows for the systematic evaluation of the role of viral genes in pathogenesis, tropism, and virulence but also a translational platform for the development of rationally attenuated live virus vaccines.
cord-350603-ssen3q08	2018	While widely recognized for its utility in influenza virus research, ferrets are used for a variety of infectious and noninfectious disease models due to the anatomical, metabolic, and physiological features they share with humans and their susceptibility to many human pathogens. To resolve this, a group of researchers from around the world are working together to develop validated reagents and assays to improve our understanding of the innate and adaptive immune responses in the ferret. Flow Cytometric and cytokine ELISPOT approaches to characterize the cell-mediated immune response in ferrets following influenza virus Infection Screening monoclonal antibodies for cross-reactivity in the ferret model of influenza infection Infection of ferrets with influenza virus elicits a light chain-biased antibody response against hemagglutinin Ferrets as a novel animal model for studying human respiratory syncytial virus infections in immunocompetent and immunocompromised hosts A neutralizing human monoclonal antibody protects against lethal disease in a new ferret model of acute Nipah virus infection
cord-351482-hzh5tyoo	2011	The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. In total, of 4,473,273 start positions in the genome with at least one uniquely mapped read, we found that about 5% (233,236) gave at least 4 reads of the same length in a sample, resulting in 16,054 nonredundant candidate loci for putative small RNAs. About 1.7% (276/16,054) of the candidate loci (median length, 39 nt) were differentially expressed during SARS-CoV and/or influenza virus infection (see Table S2 and Fig. S4a in the supplemental material); 46 of those candidate loci overlapped with annotated miRNA precursors (miRBase version 16).
cord-352096-cc3dzycl	2020	Regardless of whether or when a vaccine becomes available, antivirals for SARS-CoV-2 will still be needed for several reasons: the unlikelihood that a vaccine will be 100% effective, the incompleteness of vaccine coverage because of both vaccine hesitancy and the numerous logistical challenges to accomplishing prompt large-scale immunization of the majority of the population, the possibility of limited durability of vaccine protection, the need for additional prophylaxis for high-risk subjects and poor vaccine responders, and the future value of effective antiviral treatment for Middle East respiratory syndrome (MERS) and new coronaviruses that will likely emerge from zoonoses. suggest that the purported activity against SARS-CoV-2 of the two HIV protease inhibitors, lopinavir and nelfinavir, is probably attributable to cellular toxicity. Structurebased design of antiviral drug candidates targeting the SARS-CoV-2 main protease AT-527 is a potent in vitro replication inhibitor of SARS-CoV-2, the virus responsible for the COVID-19 pandemic
cord-353612-9ux181xg	2013	Here, we investigated whether HCoV-EMC and SARS-CoV induce similar or distinct host responses after infection of a human lung epithelial cell line. Both viruses induced a similar activation of pattern recognition receptors and the interleukin 17 (IL-17) pathway, but HCoV-EMC specifically down-regulated the expression of several genes within the antigen presentation pathway, including both type I and II major histocompatibility complex (MHC) genes. In addition, several kinase inhibitors (including SB203580, LY294002, and U0126) and a glucocorticoid (dexamethasone) were also predicted to be negative regulators of genes changed similarly after SARS-CoV and HCoV-EMC infection at late times postinfection (see Table S2 in the supplemental material). Importantly, this kinase inhibitor was predicted to regulate genes that were DE similarly by SARS-CoV and HCoV-EMC at late times postinfection (see Table S2 in the supplemental material) and could therefore inhibit both viruses'' replication.
cord-356325-gk5jve0i	2020	Here, we performed repeated analyses at 1-month intervals on 31 convalescent individuals to evaluate how the humoral responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein, including neutralization, evolve over time. Of note, while we observed enhanced infectivity for the D614G variant compared to its WT SARS-CoV-2 S counterpart (see Fig. S2A in the supplemental material), no major differences in neutralization with convalescent plasma were detected at either time point (Fig. S2B) , thus suggesting that the D614G change does not affect the overall conformation of the Spike, in agreement with recent findings (17, 22) . The capacity to neutralize SARS-CoV-2 S WT-or D614G-pseudotyped particles significantly correlated with the presence of RBD-specific IgG, IgM, IgA, and anti-S antibodies (Fig. S3) . Interestingly, we observed a pronounced (20% to 30%) decrease in the proportion of convalescent individuals able to neutralize pseudoparticles bearing SARS-CoV-2 S glycoprotein between 6 and 10 weeks after the onset of symptoms.